PXD023730

PXD023730 is an original dataset announced via ProteomeXchange.

Title	RNAseq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16
Description	Autophagy is an evolutionary ancient mechanism that sequesters substrates for degradation within autolysosomes. The process is driven by many autophagy-related (ATG) proteins, including the core members ATG9 and ATG16. Here, we applied RNAseq and tandem mass tag (TMT) proteomic approaches to identify differentially expressed genes (DEGs) and proteins (DEPs) in ATG9‾, ATG16‾ and ATG9‾/16‾ strains in comparison to AX2 wild-type cells. In total, we identified 332 (279 up and 53 down), 639 (487 up and 152 down) and 260 (114 up and 146 down) DEGs and 124 (83 up and 41 down), 431 (238 up and 193 down) and 677 (347 up and 330 down) DEPs in ATG9‾, ATG16‾ and ATG9‾/16‾ strains, respectively. Thus, in the single knock-out strains, the number of DEGs was higher than the number of DEPs while in the double knock-out strain the number of DEPs was higher. Comparison of RNAseq and proteomic data further revealed, that only a small proportion of the transcriptional changes were reflected on the protein level. This suggests that most changes in protein abundance were not caused by transcriptional changes but were rather due to changes in protein homeostasis. Gene ontology (GO) analysis revealed an enrichment of DEPs involved in lipid metabolism and oxidative phosphorylation. Furthermore, we found increased expression of the anti-oxidant enzymes glutathione reductase (gsr) and catalase A (catA) in ATG16‾ and ATG9‾/16‾ cells, respectively, indicating adaptation to excess reactive oxygen species (ROS). Our study provides the first combined transcriptome and proteome analysis of ATG9‾, ATG16‾ and ATG9‾/16‾ cells and adds to our knowledge of functions of these proteins.
HostingRepository	PRIDE
AnnounceDate	2021-06-15
AnnouncementXML	Submission_2021-06-14_23:36:26.985.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Qiuhong Xiong
SpeciesList	scientific name: Dictyostelium discoideum (Slime mold); NCBI TaxID: 44689;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-01-21 02:42:48	ID requested
⏵ 1	2021-06-14 23:36:27	announced

Dataset with its publication pending

submitter keyword: Autophagy, ATG9, ATG16, RNAseq, proteome, tandem mass tag (TMT), parallel reaction monitoring (PRM), Dictyostelium discoideum

Qiuhong Xiong
contact affiliation	Shanxi University, Wucheng Road 92, Taiyuan 030006, China
contact email	qxiong@sxu.edu.cn
lab head
Qiuhong Xiong
contact affiliation	Shanxi University
contact email	qxiong@sxu.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD023730
     1. Label: PRIDE project
     2. Name: RNAseq and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16