PXD011484

PXD011484 is an original dataset announced via ProteomeXchange.

Title	Biochemical specialization of an ATG8 isoform in Nicotiana benthamiana
Description	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, particularly a single amino acid polymorphism, underpins binding specificity to the protein PexRD54. This isoleucine to valine substitution perturbed the hydrophobic pocket that accommodates the conserved ATG8 interacting motif of PexRD54. Additional proteomics experiments indicated that the N-terminal β-strand impacts ATG8 interactor profile by defining interaction specificity with about ~100 plant proteins. Our findings are consistent with the view that ATG8 isoforms comprise one layer of specificity in the regulation of selective autophagy pathways in plants.
HostingRepository	PRIDE
AnnounceDate	2019-11-12
AnnouncementXML	Submission_2019-11-12_13:27:10.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD011484
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jan Sklenar
SpeciesList	scientific name: Nicotiana benthamiana; NCBI TaxID: 4100;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2018-10-26 06:53:37	ID requested
⏵ 1	2019-11-12 13:27:12	announced

Zess EK, Jensen C, Cruz-Mireles N, De la Concepcion JC, Sklenar J, Stephani M, Imre R, Roitinger E, Hughes R, Belhaj K, Mechtler K, Menke FLH, Bozkurt T, Banfield MJ, Kamoun S, Maqbool A, Dagdas YF, -strand underpins biochemical specialization of an ATG8 isoform. PLoS Biol, 17(7):e3000373(2019) [pubmed]

submitter keyword: Autophagy, ATG8, PexRD54, Phytophthora infestans, Nicotiana benthamiana

Jan Sklenar
contact affiliation	The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, NR4 7UK, United Kingdom
contact email	jan.sklenar@tsl.ac.uk
lab head
Jan Sklenar
contact affiliation	The Sainsbury Laboratory, Norwich, UK
contact email	jan.sklenar@tsl.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD011484
     1. Label: PRIDE project
     2. Name: Biochemical specialization of an ATG8 isoform in Nicotiana benthamiana