Vacuolar protein Tag1 and Atg1-Atg13 regulate autophagy termination during persistent starvation in S. cerevisiae.

Under starvation conditions, cells degrade their own components via autophagy in order to provide sufficient nutrients to ensure their survival. However, even if starvation persists, the cell is not completely degraded through autophagy, implying the existence of some kind of termination mechanism. In the yeast Saccharomyces cerevisiae, autophagy is terminated after 10-12 h of nitrogen starvation. In this study, we found that termination is mediated by re-phosphorylation of Atg13 by the Atg1 protein kinase, which is also affected by PP2C phosphatases, and the eventual dispersion of the pre-autophagosomal structure, also known as the phagophore assembly site (PAS). In a genetic screen, we identified an uncharacterized vacuolar membrane protein, Tag1, as a factor responsible for the termination of autophagy. Re-phosphorylation of Atg13 and eventual PAS dispersal were defective in the Δtag1 mutant. The vacuolar luminal domain of Tag1 and autophagic progression are important for the behaviors of Tag1. Together, our findings reveal the mechanism and factors responsible for termination of autophagy in yeast.

Gtr/Ego-independent TORC1 activation is achieved through a glutamine-sensitive interaction with Pib2 on the vacuolar membrane.

TORC1 is a central regulator of cell growth in response to amino acids. The role of the evolutionarily conserved Gtr/Rag pathway in the regulation of TORC1 is well-established. Recent genetic studies suggest that an additional regulatory pathway, depending on the activity of Pib2, plays a role in TORC1 activation independently of the Gtr/Rag pathway. However, the interplay between the Pib2 pathway and the Gtr/Rag pathway remains unclear. In this study, we show that Pib2 and Gtr/Ego form distinct complexes with TORC1 in a mutually exclusive manner, implying dedicated functional relationships between TORC1 and Pib2 or Gtr/Rag in response to specific amino acids. Furthermore, simultaneous depletion of Pib2 and the Gtr/Ego system abolishes TORC1 activity and completely compromises the vacuolar localization of TORC1. Thus, the amino acid-dependent activation of TORC1 is achieved through the Pib2 and Gtr/Ego pathways alone. Finally, we show that glutamine induces a dose-dependent increase in Pib2-TORC1 complex formation, and that glutamine binds directly to the Pib2 complex. These data provide strong preliminary evidence for Pib2 functioning as a putative glutamine sensor in the regulation of TORC1.

Low-dose rectal diclofenac does not prevent post-ERCP pancreatitis in low- or high-risk patients.

BACKGROUND AND AIM: The most common adverse event following an endoscopic retrograde cholangiopancreatography (ERCP) procedure is post-ERCP pancreatitis (PEP). Rectal nonsteroidal anti-inflammatory drug (NSAID) administration has shown promise to reduce the risk of PEP in high-risk patients. However, in contrast to high-risk patients, the role of NSAID administration in patients with low risk remains controversial. METHODS: We performed a prospective, single-center, single-blinded, two-arm parallel group, randomized controlled trial to clarify the efficacy of low dose (50 mg) rectal NSAID administration for preventing PEP in at-risk patients. Patients scheduled to undergo ERCP were randomized into two groups, those with and without rectal administration of diclofenac. Patients in the diclofenac group received 50 mg of rectal diclofenac 30 min before undergoing ERCP. The primary endpoint was rate of PEP. RESULTS: A total of 303 were randomized into the study groups. Four patients declined participation following randomization, and another two were withdrawn. As a result, a total of 147 patients were assigned to the diclofenac group and 150 to the control group. The baseline and procedural characteristics were similar in both groups. The primary endpoint of PEP occurrence was seen in 13 of 297 patients (4.4%), including eight (5.4%) in the diclofenac group and five (3.3%) in the control group (P = 0.286). Additionally, those results were not significantly different when patients were classified as low or high risk. CONCLUSIONS: Prophylactic low-dose rectal diclofenac did not reduce the incidence of PEP following ERCP in patients classified as low or high risk.

Atg9A trafficking through the recycling endosomes is required for autophagosome formation.

Autophagy is an intracellular degradation pathway conserved in eukaryotes. Among core autophagy-related (Atg) proteins, mammalian Atg9A is the sole multi-spanning transmembrane protein, and both of its N- and C-terminal domains are exposed to the cytoplasm. It is known that Atg9A travels through the trans-Golgi network (TGN) and the endosomal system under nutrient-rich conditions, and transiently localizes to the autophagosome upon autophagy induction. However, the significance of Atg9A trafficking for autophagosome formation remains elusive. Here, we identified sorting motifs in the N-terminal cytosolic stretch of Atg9A that interact with the adaptor protein AP-2. Atg9A with mutations in the sorting motifs could not execute autophagy and was abnormally accumulated at the recycling endosomes. The combination of defects in autophagy and Atg9A accumulation in the recycling endosomes was also found upon the knockdown of TRAPPC8, a specific subunit of the TRAPPIII complex. These results show directly that the trafficking of Atg9A through the recycling endosomes is an essential step for autophagosome formation.

Phenanthrene Synthesis by Palladium-Catalyzed Benzannulation with o-Bromobenzyl Alcohols through Multiple Carbon-Carbon Bond Formations.

A palladium-catalyzed benzannulation with o-bromobenzyl alcohols enabled the facile construction of phenanthrene skeletons via the sequential multiple carbon-carbon bond formations. A variety of multisubstituted phenanthrenes were synthesized by the reaction of (Z)-ß-halostyrenes with o-bromobenzyl alcohols as well as by the three-component coupling of alkynes, aryl bromides, and o-bromobenzyl alcohols. The electron-deficient phosphine ligand played an important role to control the sequential oxidative addition of two different organic halides employed, which realized the selective formation of the desired phenanthrenes in good yields. This synthetic protocol was also applicable to the synthesis of the highly fused polycyclic aromatic hydrocarbons such as tetraphenes.

Synthesis of Multisubstituted Triphenylenes and Phenanthrenes by Cascade Reaction of o-Iodobiphenyls or (Z)-ß-Halostyrenes with o-Bromobenzyl Alcohols through Two Sequential C-C Bond Formations Catalyzed by a Palladium Complex.

o-Bromobenzyl alcohol has been developed as a novel annulating reagent, bearing both nucleophilic and electrophilic substituents, for the facile synthesis of polycyclic aromatic hydrocarbons. A palladium/electron-deficient phosphine catalyst efficiently coupled o-iodobiphenyls or (Z)-ß-halostyrenes with o-bromobenzyl alcohols to afford triphenylenes and phenanthrenes, respectively. The present cascade reaction proceeded through deacetonative cross-coupling and sequential intramolecular cyclization. An array of experimental data suggest that the reaction mechanism involves the equilibrium of 1,4-palladium migration.

Pib2 is a cysteine sensor involved in TORC1 activation in Saccharomyces cerevisiae.

Target of rapamycin complex 1 (TORC1) is a master regulator that monitors the availability of various amino acids to promote cell growth in Saccharomyces cerevisiae. It is activated via two distinct upstream pathways: the Gtr pathway, which corresponds to mammalian Rag, and the Pib2 pathway. This study shows that Ser3 was phosphorylated exclusively in a Pib2-dependent manner. Using Ser3 as an indicator of TORC1 activity, together with the established TORC1 substrate Sch9, we investigated which pathways were employed by individual amino acids. Different amino acids exhibited different dependencies on the Gtr and Pib2 pathways. Cysteine was most dependent on the Pib2 pathway and increased the interaction between TORC1 and Pib2 in vivo and in vitro. Moreover, cysteine directly bound to Pib2 via W632 and F635, two critical residues in the T(ail) motif that are necessary to activate TORC1. These results indicate that Pib2 functions as a sensor for cysteine in TORC1 regulation.

[Development and Evaluation about "2nd-wave" COVID-19 Vaccines].

To tackle the pandemic of the novel coronavirus (severe acute respiratory syndrome coronavirus 2; SARS-CoV-2), the international society, including Japan, has been actively promoting vaccination for SARS-CoV-2. To effectively utilize these vaccines, clinical trials have been conducted to evaluate their safety and efficacy. For efficacy evaluation, prevention rate of symptomatic novel coronavirus infections (corona virus disease 2019; COVID-19) between placebo groups and investigational vaccine groups has been the key parameter to evaluate the novel COVID-19 vaccines. This approach is based on a consensus among international regulatory authorities. Compared to several months ago, the public vaccination campaign for COVID-19 has substantially progressed in many countries. This makes it difficult to conduct clinical trials, which have placebo control arms, anywhere in the world because of ethical problems in administering a placebo during a pandemic. Therefore, the new international consensus among regulatory authorities is that immunogenicity bridging studies between the new COVID-19 vaccines that are being developed and approved COVID-19 vaccines may be needed when placebo-controlled studies are no longer feasible. In the future, the number of unvaccinated people worldwide is expected significantly decrease; thus, the issue of how to evaluate additional immunization for those who have completed the initial immunization remains to be addressed. This would require new international convergence. The development of COVID-19 vaccines and their evaluation would have to be updated, considering the social situation and vaccine coverage.

Endoscopic ultrasound-guided fine-needle biopsy for the diagnosis of gastric linitis plastica.

We report two cases of patients with gastric linitis plastica (GLP), in which the histopathological diagnosis was made by endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) using a Franseen-tip needle. Esophagogastroduodenoscopy findings showed mucosal swelling and poor distensibility of the gastric antrum. Abdominal computed tomography findings showed significant thickening of the gastric wall at the antrum. Conventional endoscopic and bite-on-bite biopsy were attempted but resulted in failure to diagnose the lesions. We performed EUS-FNB to obtain histopathological samples from a deeper site, which confirmed the diagnosis. We considered this method safe and effective for the diagnosis of GLP.

Isoflurane induces Art2-Rsp5-dependent endocytosis of Bap2 in yeast.

Although general anesthesia is indispensable during modern surgical procedures, the mechanism by which inhalation anesthetics act on the synaptic membrane at the molecular and cellular level is largely unknown. In this study, we used yeast cells to examine the effect of isoflurane, an inhalation anesthetic, on membrane proteins. Bap2, an amino acid transporter localized on the plasma membrane, was endocytosed when yeast cells were treated with isoflurane. Depletion of RSP5, an E3 ligase, prevented this endocytosis and Bap2 was ubiquitinated in response to isoflurane, indicating an ubiquitin-dependent process. Screening all the Rsp5 binding adaptors showed that Art2 plays a central role in this process. These results suggest that isoflurane affects Bap2 via an Art2-Rsp5-dependent ubiquitination system.

Prescription pattern analysis for antibiotics in working-age workers diagnosed with common cold.

Antimicrobial resistance is a major health concern. A primary cause is the inappropriate use of antimicrobials, particularly by patients with upper respiratory tract infection. However, baseline information for antibiotic use for common cold before being applied the National Action Plan on Antimicrobial Resistance in Japan is lacking. Here, we analyzed the inappropriate use of antibiotics in the working-age workers. We used large claims data from an annual health check-up for at least 5 consecutive years. Among 201,223 participants, we included 18,659 working-age workers who were diagnosed with common cold at a clinic/hospital. We calculated the proportion of patients with common cold who were prescribed antibiotics and analyzed predictive factors associated with antibiotics prescription. Antibiotics were prescribed to 49.2% (n = 9180) of patients diagnosed with common cold. In the logistic regression analysis, the group taking antibiotics was predominantly younger, male, without chronic diseases, and diagnosed at a small hospital/clinic (where the number of beds was 0-19). Cephems accounted for the highest proportion of prescribed antibiotics, with 40-45% of patients being prescribed antibiotics. Our data may be applied to prioritize resources such as medical staff-intervention or education of working-age people without chronic diseases who visit clinics for common cold to avoid the potential inappropriate use of antibiotics and prevent antimicrobial resistance acceleration.

Discrepant Diagnostic Results of Nested Polymerase Chain Reaction-based Genotyping in a Patient with Hepatitis C Virus and Human Immunodeficiency Virus Coinfection.

Accurate genotyping is important to improve the treatment of hepatitis C virus (HCV) infection. We herein report a 44-year-old Japanese man with hemophilia A and coinfection of HCV and human immunodeficiency virus (HIV) who was diagnosed with HCV genotype 4 by direct sequencing. Two genotyping tests based on the nested polymerase chain reaction method that we used misdiagnosed his genotype as 2b and 1b. Although several HCV genotyping tests are available in Japan, it is important to recognize that some cannot detect genotype 4. Care should be taken when genotyping HCV patients who have received non-heated coagulation factor preparations or were infected abroad.

Upf1 potentially serves as a RING-related E3 ubiquitin ligase via its association with Upf3 in yeast.

Three Upf proteins are essential to the nonsense-mediated mRNA decay (NMD) pathway. Although these proteins assemble on polysomes for recognition of aberrant mRNAs containing premature termination codons, the significance of this assembly remains to be elucidated. The Cys- and His-rich repeated N terminus (CH domain) of Upf1 has been implicated in its binding to Upf2. Here, we show that CH domain also plays a RING-related role for Upf1 to exhibit E3 ubiquitin ligase activity in yeast. Despite the sequence divergence from typical E3-RING fingers, the CH domain of yeast Upf1 specifically and directly interacted with the yeast E2 Ubc3. Interestingly, Upf1 served as a substrate for the in vitro self-ubiquitination, and the modification required its association with Upf3 rather than Upf2. Substitution of the coordinated Cys and His residues in the CH domain impaired not only self-ubiquitination of Upf1 but also rapid decay of aberrant mRNAs. These results suggest that Upf1 may serve as an E3 ubiquitin ligase upon its association with Upf3 and play an important role in signaling to the NMD pathway.

Diagnostic Fine-Needle Biopsy of Small Solid Pancreatic Lesions Using a Franseen Needle during Endoscopic Ultrasound Examination.

BACKGROUND AND AIM: During endoscopic ultrasound-guided fine needle aspiration biopsy (EUS-FNB), Franseen needles can help collect sufficient tissue to permit histopathological assessment. However, its efficacy might be limited by the size of the targeted lesion. This study aimed to evaluate the feasibility of histopathological assessment of small solid pancreatic lesions using a 22-gauge Franseen needle during EUS-FNB. METHODS: This retrospective study evaluated data from all patients who underwent EUS-FNB using a Franseen needle for solid pancreatic lesions at the University of Toyama Hospital between June 2018 and April 2020. RESULTS: The study included 159 patients who had 152 malignant lesions and 7 benign lesions. The malignant lesions included pancreatic cancers (n = 134), neuroendocrine neoplasms (n = 15), metastatic tumors (n = 2), and a solid pseudopapillary neoplasm (n = 1). The diagnostic accuracy of EUS-FNB (combining histology and cytology) was 98.7%. However, the histopathological diagnosis was only confirmed for 64.3% of small lesions (<10 mm), relative to 97.2% for larger lesions. Multivariate analysis also revealed that lesion size of <10 mm predicted a less accurate histopathological diagnosis (odds ratio: 6.97, 95% confidence interval: 1.02-47.67; p = 0.041). Further analyses revealed a failed histological diagnosis in 4 patients with lesions of <5 mm in size and accurate diagnoses in 9 out of 10 patients with lesions of 5-10 mm in size. CONCLUSIONS: The diagnostic accuracy for small lesions (<10 mm), especially for lesions of <5 mm, based on histological examination alone, was significantly lower than that for others (>10 mm). Furthermore, multivariate analysis revealed that only lesion size was an independent predictor of histopathological diagnosis accuracy.

Starvation-induced autophagy via calcium-dependent TFEB dephosphorylation is suppressed by Shigyakusan.

Kampo, a system of traditional Japanese therapy utilizing mixtures of herbal medicine, is widely accepted in the Japanese medical system. Kampo originated from traditional Chinese medicine, and was gradually adopted into a Japanese style. Although its effects on a variety of diseases are appreciated, the underlying mechanisms remain mostly unclear. Using a quantitative tf-LC3 system, we conducted a high-throughput screen of 128 kinds of Kampo to evaluate the effects on autophagy. The results revealed a suppressive effect of Shigyakusan/TJ-35 on autophagic activity. TJ-35 specifically suppressed dephosphorylation of ULK1 and TFEB, among several TORC1 substrates, in response to nutrient deprivation. TFEB was dephosphorylated by calcineurin in a Ca2+ dependent manner. Cytosolic Ca2+ concentration was increased in response to nutrient starvation, and TJ-35 suppressed this increase. Thus, TJ-35 prevents the starvation-induced Ca2+ increase, thereby suppressing induction of autophagy.

Caf1 regulates translocation of ribonucleotide reductase by releasing nucleoplasmic Spd1-Suc22 assembly.

Appropriate supply of deoxyribonucleotides by the ribonucleotide reductase (RNR) complex is essential for DNA replication and repair. One recent model for the RNR activation in Schizosaccharomyces pombe is translocation of the regulatory subunit Suc22 from the nucleoplasm to the cytoplasm. The RNR inhibitory protein Spd1, which retains Suc22 in the nucleoplasm, is rapidly degraded upon DNA-replication stress, resulting in release of Suc22 to form the active RNR complex in the cytoplasm. Here, we show that Caf1, a component of the Ccr4-Not complex, is responsible for resistance of the replication stress and control of the Suc22 translocation. Caf1 is required not only for the stress-induced translocation of Suc22 from nucleoplasm to cytoplasm but also for the degradation of nucleoplasmic Spd1. DNA-replication stress appears to allow Caf1 to interact with Suc22, resulting in release of the nucleoplasmic Spd1-Suc22 assembly. Taken together, these results suggest a novel function of Caf1 as a key regulator in the stress-induced RNR activation.

The Saccharomyces cerevisiae spindle pole body (SPB) component Nbp1p is required for SPB membrane insertion and interacts with the integral membrane proteins Ndc1p and Mps2p.

The spindle pole body (SPB) in Saccharomyces cerevisiae functions to nucleate and organize spindle microtubules, and it is embedded in the nuclear envelope throughout the yeast life cycle. However, the mechanism of membrane insertion of the SPB has not been elucidated. Ndc1p is an integral membrane protein that localizes to SPBs, and it is required for insertion of the SPB into the nuclear envelope during SPB duplication. To better understand the function of Ndc1p, we performed a dosage suppressor screen using the ndc1-39 temperature-sensitive allele. We identified an essential SPB component, Nbp1p. NBP1 shows genetic interactions with several SPB genes in addition to NDC1, and two-hybrid analysis revealed that Nbp1p binds to Ndc1p. Furthermore, Nbp1p is in the Mps2p-Bbp1p complex in the SPB. Immunoelectron microscopy confirmed that Nbp1p localizes to the SPB, suggesting a function at this location. Consistent with this hypothesis, nbp1-td (a degron allele) cells fail in SPB duplication upon depletion of Nbp1p. Importantly, these cells exhibit a "dead" SPB phenotype, similar to cells mutant in MPS2, NDC1, or BBP1. These results demonstrate that Nbp1p is a SPB component that acts in SPB duplication at the point of SPB insertion into the nuclear envelope.

Purification and analysis of RIN family-novel Rab5 GEFs.

The small GTPase Rab5 plays important roles in membrane budding and trafficking in the early endocytic pathways, and the activation of this GTPase is mediated by several guanine nucleotide exchange factors (GEFs) at each of the transport steps. The RIN family has been identified as GEFs for Rab5 and shown to possess unique biochemical properties. The RIN family preferentially interacts with an activated form of Rab5, although it enhances guanine nucleotide exchange reaction. Moreover, biochemical analysis indicates that the RIN family functions as a tetramer. In this chapter, we describe the isolation of the recombinant RIN family via expression in Spodoptera frugiperda (Sf9) insect cells and in mammalian cells. In addition, functional analysis is also provided to assess the physiological properties of the RIN family.

Novel role of the small GTPase Rheb: its implication in endocytic pathway independent of the activation of mammalian target of rapamycin.

The Ras-homologous GTPase Rheb that is conserved from yeast to human appears to be involved not only in cell growth but also in nutrient uptake. Recent biochemical analysis revealed that tuberous sclerosis complex (TSC), a GTPase-activating protein (GAP), deactivates Rheb and that phosphatidylinositol 3'-kinase (PI3k)-Akt/PKB kinase pathway activates Rheb through inhibition of the GAP-mediated deactivation. Although mammalian target of rapamycin (mTOR) kinase is implicated in the downstream target of Rheb, the direct effector(s) and exact functions of Rheb have not been fully elucidated. Here we identified that Rheb expression in cultured cells induces the formation of large cytoplasmic vacuoles, which are characterized as late endocytic (late endosome- and lysosome-like) components. The vacuole formation required the GTP form of Rheb, but not the activation of the downstream mTOR kinase. These results suggest that Rheb regulates endocytic trafficking pathway independent of the previously identified mTOR pathway. The physiological roles of the two Rheb-dependent signaling pathways are discussed in terms of nutrient uptake and cell growth or cell cycle progression.

Decapping reaction of mRNA requires Dcp1 in fission yeast: its characterization in different species from yeast to human.

Cleavage of the 5'-cap structure is involved in the major 5'-to-3' and nonsense-mediated mRNA decay pathways, and the protein complex consisting of Dcp1 and Dcp2 has been identified as the species responsible for the decapping reaction in Saccharomyces cerevisiae and human. Although in vitro studies indicate that Dcp2 is catalytically an active component, the role of Dcp1 in the decapping reaction remains to be explored in organisms other than budding yeast. To elucidate the Dcp1-dependent decapping mechanisms, we identified the homologues of S. cerevisiae Dcp1 (ScDcp1) in higher eukaryotes and analyzed their functions in the different species. The phenotypes of slow growth and mRNA stabilization induced by Scdcp1-gene disruption in budding yeast could be suppressed by the Shizosaccharomyces pombe SpDcp1 but not by the human homologue hDcp1. In contrast, the same phenotypes caused by Spdcp1-gene disruption in fission yeast were effectively complemented by hDcp1 and its partial sequence comparable to SpDcp1. These results indicate that not only Dcp2 but also Dcp1 plays an indispensable role in mRNA-decay pathway and that the characteristics of Dcp1-dependent decapping reaction in fission yeast hold an intermediate position in the evolution of mRNA-decay machinery from budding yeast to mammals.