bims-ershed 2023-02-05 papers

Issue of 2023‒02‒05
three papers selected by
Matías Eduardo González Quiroz
Worker’s Hospital

FEBS Lett. 2023 Feb 01.

The Bcl-2 family protein Bid interacts with the ER stress sensor IRE1 to differentially modulate its RNase activity.

Samirul Bashir, Mariam Banday, Ozaira Qadri, Debnath Pal, Arif Bashir, Nazia Hilal, Mohammad Altaf, Khalid Majid Fazili.

IRE1 is a transmembrane signaling protein that activates the unfolded protein response under endoplasmic reticulum stress. IRE1 is endowed with kinase and endoribonuclease activities. The ribonuclease activity of IRE1 can switch substrate specificities to carry out atypical splicing of Xbp1 mRNA or trigger degradation of specific mRNAs. The mechanisms regulating the distinct ribonuclease activities of IRE1 have yet to be fully understood. Here, we report the Bcl-2 family protein Bid as a novel recruit of the IRE1 complex, which directly interacts with the cytoplasmic domain of IRE1. Bid binding to IRE1 leads to a decrease in IRE1 phosphorylation in a way that it can only perform Xbp1 splicing while mRNA degradation activity is repressed. The RNase outputs of IRE1 have been found to regulate the homeostatic-apoptotic switch. This study thus provides insight into IRE1-mediated cell survival.

Keywords: Bid; IRE1; RNase activity; UPRosome; phosphorylation

DOI: https://doi.org/10.1002/1873-3468.14593

bioRxiv. 2023 Jan 17. pii: 2023.01.16.524237. [Epub ahead of print]

Divergent Proteome Reactivity Influences Arm-Selective Activation of Pharmacological Endoplasmic Reticulum Proteostasis Regulators.

Gabriel M Kline, Ryan J Paxman, Chung-Yon Lin, Nicole Madrazo, Julia M Grandjean, Kyunga Lee, Karina Nugroho, Evan T Powers, R Luke Wiseman, Jeffery W Kelly.

Pharmacological activation of the activating transcription factor 6 (ATF6) arm of the Unfolded Protein Response (UPR) has proven useful for ameliorating proteostasis deficiencies in a variety of etiologically diverse diseases. Previous high-throughput screening efforts identified the small molecule AA147 as a potent and selective ATF6 activating compound that operates through a mechanism involving metabolic activation of its 2-amino- p -cresol substructure affording a quinone methide, which then covalently modifies a subset of ER protein disulfide isomerases (PDIs). Intriguingly, another compound identified in this screen, AA132, also contains a 2-amino- p -cresol moiety; however, this compound showed less transcriptional selectivity, instead globally activating all three arms of the UPR. Here, we show that AA132 activates global UPR signaling through a mechanism analogous to that of AA147, involving metabolic activation and covalent PDI modification. Chemoproteomic-enabled analyses show that AA132 covalently modifies PDIs to a greater extent than AA147. Paradoxically, activated AA132 reacts slower with PDIs, indicating it is less reactive than activated AA147. This suggests that the higher labeling of PDIs observed with activated AA132 can be attributed to its lower reactivity, which allows this activated compound to persist longer in the cellular environment prior to quenching by endogenous nucleophiles. Collectively, these results suggest that AA132 globally activates the UPR through increased engagement of ER PDIs. Consistent with this, reducing the cellular concentration of AA132 decreases PDI modifications and allows for selective ATF6 activation. Our results highlight the relationship between metabolically activatable-electrophile stability, ER proteome reactivity, and the transcriptional response observed with the enaminone chemotype of ER proteostasis regulators, enabling continued development of next-generation ATF6 activating compounds.

DOI: https://doi.org/10.1101/2023.01.16.524237

bioRxiv. 2023 Jan 18. pii: 2023.01.17.524444. [Epub ahead of print]

p53 controls choice between apoptotic and non-apoptotic death following DNA damage.

Megan E Honeywell, Marie Sophie Lykke Isidor, Nicholas W Harper, Rachel E Fontana, Peter Cruz-Gordillo, Sydney A Porto, Jessica B Spinelli, David A Guertin, Michael J Lee.

DNA damage can activate apoptotic and non-apoptotic forms of cell death; however, it remains unclear what features dictate which type of cell death is activated. We report that p53 controls the choice between apoptotic and non-apoptotic death following exposure to lethal levels of DNA damage. The canonical response to DNA damage involves p53-dependent activation of cell intrinsic apoptosis, downstream of DNA damage response (DDR) activation. Decades of research suggest that DNA damage does not robustly activate cell death in the absence of p53. In contrast, we find that p53-deficient cells die at high rates following exposure to DNA damage, but exclusively using non-apoptotic types of cell death. Our experimental and computational analyses demonstrate that non-apoptotic death in p53-deficient cells has generally been missed due to use of assays that are either insensitive to cell death, or that specifically measure apoptotic cells. To characterize which subtype of non-apoptotic death is activated by DNA damage in p53-deficient cells, we used functional genetic screening, with an analysis method that enables computational inference of the drug-induced death rate, rather than the relative population size. We find in p53-deficient cells that DNA damage activates a mitochondrial respiration-dependent form of cell death called MPT-driven necrosis. This study reveals how the dual functions of p53 in regulating mitochondrial activity and the DDR combine to facilitate choice between apoptotic and non-apoptotic death following DNA damage.

DOI: https://doi.org/10.1101/2023.01.17.524444