ASC1/RAS2 Suppresses the Growth Defect on Glycerol Caused by the atp1–2 Mutation in the Yeast Saccharomyces cerevisiae

To better define the regulatory role of the F(1)-ATPase alpha-subunit in the catalytic cycle of the ATP synthase complex, we isolated suppressors of mutations occurring in ATP1, the gene for the alpha-subunit in Saccharomyces cerevisiae. First, two atp1 mutations (atp1-1 and atp1-2) were characterized that prevent the growth of yeast on non-fermentable carbon sources. Both mutants contained full-length F(1)alpha-subunit proteins in mitochondria, but in lower amounts than that in the parental strain. Both mutants exhibited barely measurable F(1)-ATPase activity. The primary mutations in atp1-1 and atp1-2 were identified as Thr(383) --> Ile and Gly(291) --> Asp, respectively. From recent structural data, position 383 lies within the catalytic site. Position 291 is located near the region affecting subunit-subunit interaction with the F(1)beta-subunit. An unlinked suppressor gene, ASC1 (alpha-subunit complementing) of the atp1-2 mutation (Gly(291) --> Asp) restored the growth defect phenotype on glycerol, but did not suppress either atp1-1 or the deletion mutant Deltaatp1. Sequence analysis revealed that ASC1 was allelic with RAS2, a G-protein growth regulator. The introduction of ASC1/RAS2 into the atp1-2 mutant increased the F(1)-ATPase enzyme activity in this mutant when the transformant was grown on glycerol. The possible mechanisms of ASC1/RAS2 suppression of atp1-2 are discussed; we suggest that RAS2 is part of the regulatory circuit involved in the control of F(1)-ATPase subunit levels in mitochondria

p62/SQSTM1-droplet serves as a platform for autophagosome formation and anti-oxidative stress response

Autophagy contributes to the selective degradation of liquid droplets, including the P-Granule, Ape1-complex and p62/SQSTM1-body, although the molecular mechanisms and physiological relevance of selective degradation remain unclear. In this report, we describe the properties of endogenous p62-bodies, the effect of autophagosome biogenesis on these bodies, and the in vivo significance of their turnover. p62-bodies are low-liquidity gels containing ubiquitin and core autophagy-related proteins. Multiple autophagosomes form on the p62-gels, and the interaction of autophagosome-localizing Atg8-proteins with p62 directs autophagosome formation toward the p62-gel. Keap1 also reversibly translocates to the p62-gels in a p62-binding dependent fashion to activate the transcription factor Nrf2. Mice deficient for Atg8-interaction-dependent selective autophagy show that impaired turnover of p62-gels leads to Nrf2 hyperactivation in vivo. These results indicate that p62-gels are not simple substrates for autophagy but serve as platforms for both autophagosome formation and anti-oxidative stress. Liquid-liquid phase separation of p62/SQSTM1 has been previously described, although the significance in vivo remains unclear. Here the authors show p62 droplets contain ubiquitin, autophagy-related proteins and Keap1 to serve as platform of not only autophagosome formation but also Nrf2 activation.Peer reviewe

Biallelic Variants in UBA5 Link Dysfunctional UFM1 Ubiquitin-like Modifier Pathway to Severe Infantile-Onset Encephalopathy

The ubiquitin fold modifier 1 (UFM1) cascade is a recently identified evolutionarily conserved ubiquitin-like modification system whose function and link to human disease have remained largely uncharacterized. By using exome sequencing in Finnish individuals with severe epileptic syndromes, we identified pathogenic compound heterozygous variants in UBAS, encoding an activating enzyme for UFM1, in two unrelated families. Two additional individuals with biallelic UBAS variants were identified from the UK-based Deciphering Developmental Disorders study and one from the Northern Finland Intellectual Disability cohort. The affected individuals (n = 9) presented in early infancy with severe irritability, followed by dystonia and stagnation of development. Furthermore, the majority of individuals display postnatal microcephaly and epilepsy and develop spasticity. The affected individuals were compound heterozygous for a missense substitution, c.1111G>A (p.A1a371Thr; allele frequency of 0.28% in Europeans), and a nonsense variant or c.164G>A that encodes an amino acid substitution p.Arg5SHis, but also affects splicing by facilitating exon 2 skipping, thus also being in effect a loss-of-function allele. Using an in vitro thioester formation assay and cellular analyses, we show that the p.A1a371Thr variant is hypomorphic with attenuated ability to transfer the activated UFM1 to UFC1. Finally, we show that the CNS-specific knockout of Ufml in mice causes neonatal death accompanied by microcephaly and apoptosis in specific neurons, further suggesting that the UFM1 system is essential for CNS development and function. Taken together, our data imply that the combination of a hypomorphic p.A1a371Thr variant in trans with a loss-of-function allele in UBAS underlies a severe infantile-onset encephalopathy.Peer reviewe

p62/SQSTM1-droplet serves as a platform for autophagosome formation and anti-oxidative stress response

Autophagy contributes to the selective degradation of liquid droplets, including the P-Granule, Ape1-complex and p62/SQSTM1-body, although the molecular mechanisms and physiological relevance of selective degradation remain unclear. In this report, we describe the properties of endogenous p62-bodies, the effect of autophagosome biogenesis on these bodies, and the in vivo significance of their turnover. p62-bodies are low-liquidity gels containing ubiquitin and core autophagy-related proteins. Multiple autophagosomes form on the p62-gels, and the interaction of autophagosome-localizing Atg8-proteins with p62 directs autophagosome formation toward the p62-gel. Keap1 also reversibly translocates to the p62-gels in a p62-binding dependent fashion to activate the transcription factor Nrf2. Mice deficient for Atg8-interaction-dependent selective autophagy show that impaired turnover of p62-gels leads to Nrf2 hyperactivation in vivo. These results indicate that p62-gels are not simple substrates for autophagy but serve as platforms for both autophagosome formation and anti-oxidative stress

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Activation of p62/SQSTM1–Keap1–Nuclear Factor Erythroid 2-Related Factor 2 Pathway in Cancer

Autophagy and the Keap1–Nrf2 system are major cellular defense mechanisms against metabolic and oxidative stress. These two systems are linked via phosphorylation of the ubiquitin binding autophagy receptor protein p62/SQSTM1 in the p62–Keap1–Nrf2 pathway. The p62–Keap1–Nrf2 pathway plays a protective role in normal cells; however, recent studies indicate that this pathway induces tumorigenesis of pre-malignant cells, and promotes the growth and drug resistance of tumor cells via metabolic reprogramming mediated by Nrf2 activation. These findings suggest that impairment of autophagy is involved in the acquisition of malignancy and maintenance of tumors, and furthermore, that p62/SQSTM1 could be a potential target for chemotherapy in cancers that harbor excess p62

Considering the mechanism by which droplets of ALS-FTD-associated SQSTM1/p62 mutants cause pathology

Large numbers of point mutations in SQSTM1/p62 have been identified in amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). SQSTM1 interacts with ubiquitinated proteins, undergoing liquid-liquid phase separation, and the resulting SQSTM1-droplets are degraded by macroautophagy/autophagy. SQSTM1 also serves as a multiple signaling hub for processes including selective autophagy and the anti-oxidative stress response. Such diverse functions are modulated by multiple domains and regions throughout the protein. Because mutations in SQSTM1 have been identified throughout its gene, including regions encoding the domains and motifs, the effects of these mutations on disease onset have been thought to be complicated. Recently, we thoroughly investigated how 7 mutations around the LC3-interacting region and KEAP1-interacting region (amino acids 335-356) affected autophagic degradation of SQSTM1, the anti-oxidative stress response, the KEAP1-NFE2L2/Nrf2 pathway, and the dynamics of SQSTM1 droplets. We found that reduced inner fluidity of the droplets is a unique, shared defect among all mutants, suggesting a link between qualitative changes in SQSTM1 liquid droplets and ALS-FTD. In this punctum article, we discuss the mechanism whereby reduced inner fluidity of mutant SQSTM1 droplets causes ALS-FTD pathology

Protein lipidation by a ubiquitin-like system is essential for autophagy

Autophagy is a dynamic membrane phenomenon for bulk protein degradation in the lysosome/vacuole．When cells face starvation conditions, the cytoplasmic components are nonselectively enclosed by a double-membrane structure, autophagosome and delivered to the lysosome/vacuole to be degraded （Fig．1)．Autophagy is ubiquitous in eukaryotes and is essential for survival during starvation and cell differentiation．However,the molecular basis of each process in autophagy is still poorly characterized．Taking advantage of yeast genetics, autophagy defective mutants(apg) have been isolated(Tsukada and Ohsumi,1993),and so far 15 APG genes have been cloned．Apg8 is the first molecule found to be localized to the intermediate structures of the autophagosome,and is necessary for autophagosome formation(Kirisako et al., 1999)．Our recent studies revealed that the carboxy-terminal arginine of newly synthesized Apg8 is removed by Apg4 protease,leaving a glycine residue at the C terminus (Kirisako et al.,2000)．This cleavage reaction is essential for production of tightly bound form of Apg8 to unidentified membrane． Interestingly,the membrane bound form of Apg8 is covalently conjugated to phosphatidylethanolamine （PE） through an amide bond between the C-terminal glycine and the amino group of phosphatidylethanolamine．The biochemical analysis of the mechanism for Apg8-PE conjugation revealed that the Apg8-PE was formed by sequential enzyme reactions,similar to ubiquitination- like system．The C-terminal glycine of processed Apg8 (called as Apg8FG in this thesis)was activated in ATP dependent manner by Apg7 (E1 enzyme),and linked to a cysteine residue of Apg7 via a high-energy thioester bond．Through a transthioester reaction, Apg8FG conjugated with a novel identified E2 enzyme, Apg3．Finally, Apg8FG covalently conjugated with the PE．Notably, Apg7 is a unique E1-like enzyme, activates two different proteins, Apg12 and Apg8, and assigns them to specific E2 enzymes,Apg10 and Apg3, respectively．The reactions of Apg8-PE conjugation system were reconstituted in vitro by purified Apg7,Apg3,Apg8FG,and PE only,under the presence of ATP．These in vitro reconstitution studies demonstrated that the PE content of membrane affects the production of Apg8-PE．Apg8-PE conjugation of the in vitro reconstitution was enhanced by high amounts of Apg7 and Apg3．On the other hand,excessive Apg8FG inhibited their PE conjugation in a cell-free system．Apg8-PE conjugation directly occurs from Apg8-Apg3．However,some specific mechanisms seem to be required for the catalytic reactions in the system of Apg8-PE conjugation．The detailed mechanism of Apg8-PE conjugation step and its intracellular localization in yeast might be elucidated by the in vitro reconstitution study of Apg8-PE．Ubiquitination and Ubiquitination-like system generally mediates a covalent conjugation of modifier to its target protein．However,the target of Apg8 turned out to be a PE．This thesis is the first report that ubiquitination-like system mediates protein lipidation