bims-apauto 2022-07-17 papers

Issue of 2022–07–17
seven papers selected by
Su Hyun Lee, Seoul National University

Mol Biol Rep. 2022 Jul 12.

The role of autophagy and apoptosis in early brain injury after subarachnoid hemorrhage: an updated review.

Yue Zhao, Yujie Luo, Yibo Liu, Cameron Lenahan, Qun Wu, Sheng Chen.

Subarachnoid hemorrhage (SAH) is a worldwide devastating type of stroke with high mortality and morbidity. Accumulating evidence show early brain injury (EBI) as the leading cause of mortality after SAH. The pathological processes involved in EBI include decreased cerebral blood flow, increased intracranial pressure, vasospasm, and disruption of the blood-brain barrier. In addition, neuroinflammation, oxidative stress, apoptosis, and autophagy have also been proposed to contribute to EBI. Among the various processes involved in EBI, neuronal apoptosis has been proven to be a key factor contributing to the poor prognosis of SAH patients. Meanwhile, as another important catabolic process maintaining the cellular and tissue homeostasis, autophagy has been shown to be neuroprotective after SAH. Studies have shown that enhancing autophagy reduced apoptosis, whereas inhibiting autophagy aggravate neuronal apoptosis after SAH. The physiological substrates and mechanisms of neuronal autophagy and apoptosis by which defects in neuronal function are largely unknown. In this review, we summarize and discuss the role of autophagy and apoptosis after SAH and contribute to further study for investigation of the means to control the balance between them.

Keywords: Apoptosis; Autophagy; Caspase; Early brain injury; Subarachnoid hemorrhage

DOI: https://doi.org/10.1007/s11033-022-07756-9

Nat Commun. 2022 Jul 15. 13(1): 4126

Trigger factor both holds and folds its client proteins.

Kevin Wu, Thomas C Minshull, Sheena E Radford, Antonio N Calabrese, James C A Bardwell.

ATP-independent chaperones like trigger factor are generally assumed to play passive roles in protein folding by acting as holding chaperones. Here we show that trigger factor plays a more active role. Consistent with a role as an aggregation inhibiting chaperone, we find that trigger factor rapidly binds to partially folded glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and prevents it from non-productive self-association by shielding oligomeric interfaces. In the traditional view of holding chaperone action, trigger factor would then be expected to transfer its client to a chaperone foldase system for complete folding. Unexpectedly, we noticed that GAPDH folds into a monomeric but otherwise rather native-like intermediate state while trigger factor-bound. Upon release from trigger factor, the mostly folded monomeric GAPDH rapidly self-associates into its native tetramer and acquires enzymatic activity without needing additional folding factors. The mechanism we propose here for trigger factor bridges the holding and folding activities of chaperone function.

DOI: https://doi.org/10.1038/s41467-022-31767-6

Trends Cell Biol. 2022 Jul 12. pii: S0962-8924(22)00151-9. [Epub ahead of print]

Autophagosomal components recycling on autolysosomes.

Yufen Wang, Huilin Que, Yueguang Rong.

Autophagy is a multistage, intracellular process. Here, we highlight a recently identified autophagosomal components recycling (ACR) stage and the recycler complex (SNX4-SNX5-SNX17), which mediates recycling of autophagosomal outer membrane proteins on the autolysosome surface immediately following autophagosome-lysosome fusion. This discovery opens numerous research directions into the postfusion fate of autophagosomes.

Keywords: ATG9A; STX17; autophagosomal components recycling; autophagy; lysosome

DOI: https://doi.org/10.1016/j.tcb.2022.06.012

Mol Biol Rep. 2022 Jul 09.

Introduction of long non-coding RNAs to regulate autophagy-associated therapy resistance in cancer.

Yanyan Wang, Zhaoping Liu, Zhenru Xu, Wenjun Shao, Dingyu Hu, Huiying Zhong, Ji Zhang.

Autophagy is a lysosomal degradation pathway that depends on various evolutionarily conserved autophagy-related genes (ATGs). Dysregulation of autophagy plays an important role in the occurrence and development of cancer. Chemotherapy, targeted therapy, radiotherapy, and immunotherapy are important treatment options for cancer, which can significantly improve the survival rate of cancer patients. However, the occurrence of therapy resistance results in therapeutic failure and poor prognosis of cancer. Accumulating studies have found that long non-coding RNAs (lncRNAs) are well known as crucial regulators to control autophagy through regulating ATGs and autophagy-associated signaling pathways, including the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) signaling pathway, ultimately mediating chemoresistance and radioresistance. Taken together, this review systematically summarizes and elucidates the pivotal role of lncRNAs in cancer chemoresistance and radioresistance via regulating autophagy. Understanding the specific mechanism of which may provide autophagy-related therapeutic targets for cancer in the future.

Keywords: Autophagy; Cancer therapy resistance; Long non-coding RNA (lncRNA)

DOI: https://doi.org/10.1007/s11033-022-07669-7

BMC Biol. 2022 Jul 14. 20(1): 162

Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning.

Chao Hou, Yuxuan Li, Mengyao Wang, Hong Wu, Tingting Li.

BACKGROUND: Degrons are short linear motifs, bound by E3 ubiquitin ligase to target protein substrates to be degraded by the ubiquitin-proteasome system. Mutations leading to deregulation of degron functionality disrupt control of protein abundance due to mistargeting of proteins destined for degradation and often result in pathologies. Targeting degrons by small molecules also emerges as an exciting drug design strategy to upregulate the expression of specific proteins. Despite their essential function and disease targetability, reliable identification of degrons remains a conundrum. Here, we developed a deep learning-based model named Degpred that predicts general degrons directly from protein sequences.
RESULTS: We showed that the BERT-based model performed well in predicting degrons singly from protein sequences. Then, we used the deep learning model Degpred to predict degrons proteome-widely. Degpred successfully captured typical degron-related sequence properties and predicted degrons beyond those from motif-based methods which use a handful of E3 motifs to match possible degrons. Furthermore, we calculated E3 motifs using predicted degrons on the substrates in our collected E3-substrate interaction dataset and constructed a regulatory network of protein degradation by assigning predicted degrons to specific E3s with calculated motifs. Critically, we experimentally verified that a predicted SPOP binding degron on CBX6 prompts CBX6 degradation and mediates the interaction with SPOP. We also showed that the protein degradation regulatory system is important in tumorigenesis by surveying degron-related mutations in TCGA.
CONCLUSIONS: Degpred provides an efficient tool to proteome-wide prediction of degrons and binding E3s singly from protein sequences. Degpred successfully captures typical degron-related sequence properties and predicts degrons beyond those from previously used motif-based methods, thus greatly expanding the degron landscape, which should advance the understanding of protein degradation, and allow exploration of uncharacterized alterations of proteins in diseases. To make it easier for readers to access collected and predicted datasets, we integrated these data into the website http://degron.phasep.pro/ .

Keywords: Cancer driver mutation; Deep learning; Degron; E3 Ubiquitin ligase; Protein degradation

DOI: https://doi.org/10.1186/s12915-022-01364-6

Cell Death Dis. 2022 Jul 15. 13(7): 615

Autophagic sequestration of SQSTM1 disrupts the aggresome formation of ubiquitinated proteins during proteasome inhibition.

Chenliang Zhang, Chen Huang, Hongwei Xia, Huanji Xu, Qiulin Tang, Feng Bi.

Aggresome formation is a protective cellular response to counteract proteasome dysfunction by sequestering misfolded proteins and reducing proteotoxic stress. Autophagic degradation of the protein aggregates is considered to be a key compensating mechanism for balancing proteostasis. However, the precise role of autophagy in proteasome inhibition-induced aggresome biogenesis remains unclear. Herein, we demonstrate that in the early stage of proteasome inhibition, the maturation of the autophagosome is suppressed, which facilitates aggresome formation of misfolded proteins. Proteasome inhibition-induced phosphorylation of SQSTM1 T269/S272 inhibits its autophagic receptor activity and promotes aggresome formation of misfolded proteins. Inhibiting SQSTM1 T269/S272 phosphorylation using Doramapimod aggravates proteasome inhibitor-mediated cell damage and tumor suppression. Taken together, our data reveal a negative effect of autophagy on aggresome biogenesis and cell damage upon proteasome inhibition. Our study suggests a novel therapeutic intervention for proteasome inhibitor-mediated tumor treatment.

DOI: https://doi.org/10.1038/s41419-022-05061-8