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

View ORCID ProfileErin K. Zess, Cassandra Jensen, Neftaly Cruz-Mireles, Juan Carlos De la Concepcion, Jan Sklenar, Richard Imre, Elisabeth Roitinger, Richard Hughes, Khaoula Belhaj, Karl Mechtler, Frank L.H. Menke, Tolga Bozkurt, Mark J. Banfield, Sophien Kamoun, Abbas Maqbool, Yasin F. Dagdas
doi: https://doi.org/10.1101/453563
Erin K. Zess
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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  • ORCID record for Erin K. Zess
Cassandra Jensen
2Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Neftaly Cruz-Mireles
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
2Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Juan Carlos De la Concepcion
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
2Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Jan Sklenar
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Richard Imre
3Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
4Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
5Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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Elisabeth Roitinger
3Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
4Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
5Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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Richard Hughes
2Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Khaoula Belhaj
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Karl Mechtler
3Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
4Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
5Institute of Molecular Biotechnology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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Frank L.H. Menke
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Tolga Bozkurt
6Imperial College London, Department of Life Sciences, London, United Kingdom.
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Mark J. Banfield
2Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Sophien Kamoun
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Abbas Maqbool
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
2Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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Yasin F. Dagdas
1The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
3Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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Abstract

ATG8 is a highly-conserved ubiquitin-like protein that modulates autophagy pathways by binding autophagic membranes and numerous 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 followed by mass spectrometry, 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. Additional proteomics experiments indicated that the N-terminal β-strand shapes the 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.

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Posted October 25, 2018.
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N-terminal β-strand underpins biochemical specialization of an ATG8 isoform
Erin K. Zess, Cassandra Jensen, Neftaly Cruz-Mireles, Juan Carlos De la Concepcion, Jan Sklenar, Richard Imre, Elisabeth Roitinger, Richard Hughes, Khaoula Belhaj, Karl Mechtler, Frank L.H. Menke, Tolga Bozkurt, Mark J. Banfield, Sophien Kamoun, Abbas Maqbool, Yasin F. Dagdas
bioRxiv 453563; doi: https://doi.org/10.1101/453563
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N-terminal β-strand underpins biochemical specialization of an ATG8 isoform
Erin K. Zess, Cassandra Jensen, Neftaly Cruz-Mireles, Juan Carlos De la Concepcion, Jan Sklenar, Richard Imre, Elisabeth Roitinger, Richard Hughes, Khaoula Belhaj, Karl Mechtler, Frank L.H. Menke, Tolga Bozkurt, Mark J. Banfield, Sophien Kamoun, Abbas Maqbool, Yasin F. Dagdas
bioRxiv 453563; doi: https://doi.org/10.1101/453563

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