PMID- 34126926 OWN - NLM STAT- MEDLINE DCOM- 20210616 LR - 20211217 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 22 IP - 1 DP - 2021 Jun 15 TI - RNA(seq) and quantitative proteomic analysis of Dictyostelium knock-out cells lacking the core autophagy proteins ATG9 and/or ATG16. PG - 444 LID - 10.1186/s12864-021-07756-2 [doi] LID - 444 AB - 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. FAU - Xiong, Qiuhong AU - Xiong Q AD - Institutes of Biomedical Sciences, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92 Wucheng Road, 030006, Taiyuan, China. qxiong@sxu.edu.cn. FAU - Song, Ning AU - Song N AD - Institutes of Biomedical Sciences, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92 Wucheng Road, 030006, Taiyuan, China. FAU - Li, Ping AU - Li P AD - Institutes of Biomedical Sciences, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92 Wucheng Road, 030006, Taiyuan, China. FAU - Fischer, Sarah AU - Fischer S AD - Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931, Cologne, Germany. FAU - Konertz, Roman AU - Konertz R AD - Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931, Cologne, Germany. FAU - Wagle, Prerana AU - Wagle P AD - Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany. FAU - Glockner, Gernot AU - Glockner G AD - Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931, Cologne, Germany. FAU - Wu, Changxin AU - Wu C AD - Institutes of Biomedical Sciences, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92 Wucheng Road, 030006, Taiyuan, China. cxw20@sxu.edu.cn. FAU - Eichinger, Ludwig AU - Eichinger L AD - Center for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931, Cologne, Germany. Ludwig.eichinger@uni-koeln.de. LA - eng GR - 31801972/National Natural Science Foundation of China/ GR - CRC670, TP01/Deutsche Forschungsgemeinschaft/ PT - Journal Article DEP - 20210615 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 RN - 0 (Protozoan Proteins) RN - 63231-63-0 (RNA) SB - IM EIN - BMC Genomics. 2021 Jul 19;22(1):555. PMID: 34281521 MH - Autophagy/genetics MH - *Dictyostelium/genetics MH - Proteomics MH - Protozoan Proteins/genetics MH - RNA PMC - PMC8204557 OTO - NOTNLM OT - ATG16 OT - ATG9 OT - Autophagy OT - Dictyostelium discoideum OT - RNAseq OT - parallel reaction monitoring (PRM) OT - proteome OT - tandem mass tag (TMT) COIS- The authors declare that they have no competing interests. EDAT- 2021/06/16 06:00 MHDA- 2021/06/17 06:00 PMCR- 2021/06/15 CRDT- 2021/06/15 05:47 PHST- 2021/02/22 00:00 [received] PHST- 2021/05/26 00:00 [accepted] PHST- 2021/06/15 05:47 [entrez] PHST- 2021/06/16 06:00 [pubmed] PHST- 2021/06/17 06:00 [medline] PHST- 2021/06/15 00:00 [pmc-release] AID - 10.1186/s12864-021-07756-2 [pii] AID - 7756 [pii] AID - 10.1186/s12864-021-07756-2 [doi] PST - epublish SO - BMC Genomics. 2021 Jun 15;22(1):444. doi: 10.1186/s12864-021-07756-2.