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PLoS Biol. 2019 Jul 22;17(7):e3000373. doi: 10.1371/journal.pbio.3000373. eCollection 2019 Jul.

N-terminal β-strand underpins biochemical specialization of an ATG8 isoform.

Author information

1
The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom.
2
Department of Biological Chemistry, John Innes Centre, Norwich, United Kingdom.
3
Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
4
Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
5
Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
6
Imperial College London, Department of Life Sciences, London, United Kingdom.

Abstract

Autophagy-related protein 8 (ATG8) is a highly conserved ubiquitin-like protein that modulates autophagy pathways by binding autophagic membranes and a number of proteins, including cargo receptors and core autophagy components. Throughout plant evolution, ATG8 has expanded from a single protein in algae to multiple isoforms in higher plants. However, the degree to which ATG8 isoforms have functionally specialized to bind distinct proteins remains unclear. Here, we describe a comprehensive protein-protein interaction resource, obtained using in planta immunoprecipitation (IP) followed by mass spectrometry (MS), to define the potato ATG8 interactome. We discovered that ATG8 isoforms bind distinct sets of plant proteins with varying degrees of overlap. This prompted us to define the biochemical basis of ATG8 specialization by comparing two potato ATG8 isoforms using both in vivo protein interaction assays and in vitro quantitative binding affinity analyses. These experiments revealed that the N-terminal β-strand-and, in particular, a single amino acid polymorphism-underpins binding specificity to the substrate PexRD54 by shaping the hydrophobic pocket that accommodates this protein's ATG8-interacting motif (AIM). Additional proteomics experiments indicated that the N-terminal β-strand shapes the broader ATG8 interactor profiles, defining interaction specificity with about 80 plant proteins. Our findings are consistent with the view that ATG8 isoforms comprise a layer of specificity in the regulation of selective autophagy pathways in plants.

Conflict of interest statement

The authors have declared that no competing interests exist.

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