Universität zu Köln

Xiong, Qiuhong, Song, Ning, Li, Ping, Fischer, Sarah, Konertz, Roman, Wagle, Prerana, Gloeckner, Gernot, Wu, Changxin and Eichinger, Ludwig (2021). RNA(seq) and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16. BMC Genomics, 22 (1). LONDON: BMC. ISSN 1471-2164

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Abstract

Background 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. However, the functions of these two core ATG proteins still need further elucidation. Here, we applied RNA(seq) and tandem mass tag (TMT) proteomic approaches to identify differentially expressed genes (DEGs) and proteins (DEPs) in Dictyostelium discoideum ATG9?, ATG16? and ATG9?/16? strains in comparison to AX2 wild-type cells. Result 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 RNA(seq) and proteomic data further revealed, that only a small proportion of the transcriptional changes were reflected on the protein level. 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). Conclusions Our study provides the first combined transcriptome and proteome analysis of ATG9?, ATG16? and ATG9?/16? cells. Our results suggest, that most changes in protein abundance were not caused by transcriptional changes, but were rather due to changes in protein homeostasis. In particular, knock-out of atg9 and/or atg16 appears to cause dysregulation of lipid metabolism and oxidative phosphorylation.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Xiong, Qiuhong UNSPECIFIED UNSPECIFIED UNSPECIFIED Song, Ning UNSPECIFIED UNSPECIFIED UNSPECIFIED Li, Ping UNSPECIFIED UNSPECIFIED UNSPECIFIED Fischer, Sarah UNSPECIFIED UNSPECIFIED UNSPECIFIED Konertz, Roman UNSPECIFIED UNSPECIFIED UNSPECIFIED Wagle, Prerana UNSPECIFIED UNSPECIFIED UNSPECIFIED Gloeckner, Gernot UNSPECIFIED UNSPECIFIED UNSPECIFIED Wu, Changxin UNSPECIFIED UNSPECIFIED UNSPECIFIED Eichinger, Ludwig UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-572589
DOI:	10.1186/s12864-021-07756-2
Journal or Publication Title:	BMC Genomics
Volume:	22
Number:	1
Date:	2021
Publisher:	BMC
Place of Publication:	LONDON
ISSN:	1471-2164
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language RNA-SEQ; DESATURASE; MUTANTS; DISEASE; GENES Multiple languages Biotechnology & Applied Microbiology; Genetics & Heredity Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/57258