hfAIM : a reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms

dc.contributor.authorXie, Qingjun
dc.contributor.authorTzfadia, Oren
dc.contributor.authorLevy, Matan
dc.contributor.authorWeithorn, Efrat
dc.contributor.authorPeled-Zehavi, Hadas
dc.contributor.authorVan Parys, Thomas
dc.contributor.authorVan de Peer, Yves
dc.contributor.authorGalili, Gad
dc.date.accessioned2016-08-08T05:42:48Z
dc.date.issued2016-02
dc.description.abstractMost of the proteins that are specifically turned over by selective autophagy are recognized by the presence of short Atg8 interacting motifs (AIMs) that facilitate their association with the autophagy apparatus. Such AIMs can be identified by bioinformatics methods based on their defined degenerate consensus F/W/Y-X-X-L/I/V sequences in which X represents any amino acid. Achieving reliability and/or fidelity of the prediction of such AIMs on a genome-wide scale represents a major challenge. Here, we present a bioinformatics approach, high fidelity AIM (hfAIM), which uses additional sequence requirements—the presence of acidic amino acids and the absence of positively charged amino acids in certain positions—to reliably identify AIMs in proteins. We demonstrate that the use of the hfAIM method allows for in silico high fidelity prediction of AIMs in AIM-containing proteins (ACPs) on a genome-wide scale in various organisms. Furthermore, by using hfAIM to identify putative AIMs in the Arabidopsis proteome, we illustrate a potential contribution of selective autophagy to various biological processes. More specifically, we identified 9 peroxisomal PEX proteins that contain hfAIM motifs, among which AtPEX1, AtPEX6 and AtPEX10 possess evolutionary-conserved AIMs. Bimolecular fluorescence complementation (BiFC) results verified that AtPEX6 and AtPEX10 indeed interact with Atg8 in planta. In addition, we show that mutations occurring within or nearby hfAIMs in PEX1, PEX6 and PEX10 caused defects in the growth and development of various organisms. Taken together, the above results suggest that the hfAIM tool can be used to effectively perform genome-wide in silico screens of proteins that are potentially regulated by selective autophagy. The hfAIM system is a web tool that can be accessed at link: http://bioinformatics.psb.ugent.be/hfAIM/.en_ZA
dc.description.departmentGeneticsen_ZA
dc.description.embargo2017-02-28
dc.description.librarianhb2016en_ZA
dc.description.sponsorshipThe Israeli Ministry of Agriculture, The Israel Science Foundation (grant No.395/11), and the J & R center for scientific research at the Weizmann Institute of Science.en_ZA
dc.description.urihttp://www.tandfonline.com/loi/kaup20en_ZA
dc.identifier.citationQingjun Xie, Oren Tzfadia, Matan Levy, Efrat Weithorn, Hadas Peled-Zehavi,Thomas Van Parys, Yves Van de Peer & Gad Galili (2016) hfAIM: A reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organisms, Autophagy, 12:5, 876-887, DOI:10.1080/15548627.2016.1147668.en_ZA
dc.identifier.issn1554-8627 (print)
dc.identifier.issn1554-8635 (online)
dc.identifier.other10.1080/15548627.2016.1147668
dc.identifier.urihttp://hdl.handle.net/2263/56237
dc.language.isoenen_ZA
dc.publisherTaylor and Francisen_ZA
dc.rights© 2016 Taylor & Francis. This is an electronic version of an article published in Autophagy, vol. 12, no. 5, pp. 876-887, 2016. doi : 10.1080/15548627.2016.114766. Autophagy is available online at : http://www.tandfonline.com/loi/kaup20.en_ZA
dc.subjectAtg8en_ZA
dc.subjectArabidopsisen_ZA
dc.subjectAutophagyen_ZA
dc.subjectBioinformaticsen_ZA
dc.subjectPexophagyen_ZA
dc.subjectAtg8 interacting motifs (AIMs)en_ZA
dc.subjectHigh fidelity AIM (hfAIM)en_ZA
dc.subjectAIM-containing proteins (ACPs)en_ZA
dc.subjectPeroxin (PEX)en_ZA
dc.titlehfAIM : a reliable bioinformatics approach for in silico genome-wide identification of autophagy-associated Atg8-interacting motifs in various organismsen_ZA
dc.typePostprint Articleen_ZA

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