28518
2020
eng
11
21
article
1
--
2020-06-09
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Comprehensive bioinformatics identifies key microRNA players in ATG7-deficient lung fibroblasts
Background: Deficient autophagy has been recently implicated as a driver of pulmonary fibrosis, yet bioinformatics approaches to study this cellular process are lacking. Autophagy-related 5 and 7 (ATG5/ATG7) are critical elements of macro-autophagy. However, an alternative ATG5/ATG7-independent macro-autophagy pathway was recently discovered, its regulation being unknown. Using a bioinformatics proteome profiling analysis of ATG7-deficient human fibroblasts, we aimed to identify key microRNA (miR) regulators in autophagy. Method: We have generated ATG7-knockout MRC-5 fibroblasts and performed mass spectrometry to generate a large-scale proteomics dataset. We further quantified the interactions between various proteins combining bioinformatics molecular network reconstruction and functional enrichment analysis. The predicted key regulatory miRs were validated via quantitative polymerase chain reaction. Results: The functional enrichment analysis of the 26 deregulated proteins showed decreased cellular trafficking, increased mitophagy and senescence as the major overarching processes in ATG7-deficient lung fibroblasts. The 26 proteins reconstitute a protein interactome of 46 nodes and miR-regulated interactome of 834 nodes. The miR network shows three functional cluster modules around miR-16-5p, miR-17-5p and let-7a-5p related to multiple deregulated proteins. Confirming these results in a biological setting, serially passaged wild-type and autophagy-deficient fibroblasts displayed senescence-dependent expression profiles of miR-16-5p and miR-17-5p. Conclusions: We have developed a bioinformatics proteome profiling approach that successfully identifies biologically relevant miR regulators from a proteomics dataset of the ATG-7-deficient milieu in lung fibroblasts, and thus may be used to elucidate key molecular players in complex fibrotic pathological processes. The approach is not limited to a specific cell-type and disease, thus highlighting its high relevance in proteome and non-coding RNA research.
International Journal of Molecular Sciences
1422-0067
10.3390/ijms21114126
urn:nbn:de:bvb:20-opus-285181
2022-09-05T20:22:40+00:00
sword
swordwue
attachment; filename=deposit.zip
e2e6ec3ebb9fcd314d57c4d77aa6f61c
International Journal of Molecular Sciences (2020) 21:11, 4126. https://doi.org/10.3390/ijms21114126
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Stevan D. Stojanović
Maximilian Fuchs
Jan Fiedler
Ke Xiao
Anna Meinecke
Annette Just
Andreas Pich
Thomas Thum
Meik Kunz
eng
uncontrolled
bioinformatics
eng
uncontrolled
miR
eng
uncontrolled
proteomics
eng
uncontrolled
functional network analysis
eng
uncontrolled
senescence
eng
uncontrolled
lung fibrosis
eng
uncontrolled
autophagy
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Import
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/28518/ijms-21-04126-v2.pdf
14330
2015
eng
e0123341
4
10
article
1
2017-01-25
--
--
The Pro-Apoptotic BH3-Only Protein Bim Interacts with Components of the Translocase of the Outer Mitochondrial Membrane (TOM)
The pro-apoptotic Bcl-2-family protein Bim belongs to the BH3-only proteins known as initiators of apoptosis. Recent data show that Bim is constitutively inserted in the outer mitochondrial membrane via a C-terminal transmembrane anchor from where it can activate the effector of cytochrome c-release, Bax. To identify regulators of Bim-activity, we conducted a search for proteins interacting with Bim at mitochondria. We found an interaction of Bim with Tom70, Tom20 and more weakly with Tom40, all components of the Translocase of the Outer Membrane (TOM). In vitro import assays performed on tryptically digested yeast mitochondria showed reduced Bim insertion into the outer mitochondrial membrane (OMM) indicating that protein receptors may be involved in the import process. However, RNAi against components of TOM (Tom40, Tom70, Tom22 or Tom20) by siRNA, individually or in combination, did not consistently change the amount of Bim on HeLa mitochondria, either at steady state or upon de novo-induction. In support of this, the individual or combined knockdowns of TOM receptors also failed to alter the susceptibility of HeLa cells to Bim-induced apoptosis. In isolated yeast mitochondria, lack of Tom70 or the TOM-components Tom20 or Tom22 alone did not affect the import of Bim into the outer mitochondrial membrane. In yeast, expression of Bim can sensitize the cells to Bax-dependent killing. This sensitization was unaffected by the absence of Tom70 or by an experimental reduction in Tom40. Although thus the physiological role of the Bim-TOM-interaction remains unclear, TOM complex components do not seem to be essential for Bim insertion into the OMM. Nevertheless, this association should be noted and considered when the regulation of Bim in other cells and situations is investigated.
PLoS ONE
10.1371/journal.pone.0123341
urn:nbn:de:bvb:20-opus-143301
PLoS ONE 10(4): e0123341 (2015). DOI: 10.1371/journal.pone.0123341
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Daniel O. Frank
Jörn Dengjel
Florian Wilfling
Vera Kozjak-Pavlovic
Georg Häcker
Arnim Weber
eng
uncontrolled
bax
eng
uncontrolled
preproteins
eng
uncontrolled
phosphorylation
eng
uncontrolled
proteomics
eng
uncontrolled
degradation
eng
uncontrolled
cells
eng
uncontrolled
family
eng
uncontrolled
import
eng
uncontrolled
BH3 domains
eng
uncontrolled
Bcl-2 proteins
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/14330/018_Frank_PLOSE-ONE.PDF