Journal of biochemistry最新文献

Mitochondria are intracellular organelles originating from intracellular symbiotic bacteria that play essential roles in life activities such as energy production, metabolism, Ca2+ storage, signal transduction and cell death. Mitochondria also function as hubs for host defence against harmful stimuli such as infection and inflammation control. However, when cells are exposed to stress, mitochondrial homeostasis is disrupted, and mitochondrial DNA (mtDNA) can leak into the cytoplasm or extracellular space. Leaked mtDNA activates innate immune sensors, causing severe inflammation and contributing to the pathogenesis of human diseases. In this review, we summarize the mechanisms by which mtDNA leaks from the mitochondria and subsequently induces inflammation. We also review the relationship between mtDNA leakage and human diseases.

Cdc42 is a member of the Rho family of small GTPases that controls various cellular responses by interacting with more than 45 effector proteins. Recent advances in genomic analysis reveal that Cdc42 missense variants cause various pathological phenotypes, including severe autoinflammation, suggesting previously unknown involvement of Cdc42 in innate immunity. This review aims to update our understanding of how CDC42 mutations are involved in human diseases, with emphasis on early-onset autoinflammation associated with mutations located at the carboxyl-terminus. Further analysis is required to elucidate the complex inflammatory mechanisms induced by various Cdc42 variants, leading to development of therapies that inhibit inflammatory pathologies.

Zinc finger domains are important interaction modules for binding to nucleic acids, proteins, lipids and small molecules. Many small-sized zinc finger proteins are encoded in bacterial genomes, but most of them have not been functionally annotated. We focused on TTHA0897, ZifS, as a small zinc finger protein from the extremely thermophilic eubacterium Thermus thermophilus HB8. In vivo experiments suggested that the cellular function of ZifS is related to the growth transition of T. thermophilus from the lag to the exponential phase under nutritionally limited conditions. In vitro biochemical experiments, including electrophoretic mobility shift assay and pull-down assay, yielded no clues about molecular functions of ZifS. X-ray crystallographic analysis revealed that the dimeric ZifS globally forms a cylinder-like structure, although ZifS dimer has no overall structural similarity to other known zinc finger proteins. The zinc ion-binding manner of ZifS fitted the characteristics of the zinc ribbon fold, which are mostly found in domains from proteins involved in the transcriptional and translational machinery. The crystal structure of ZifS is the first experimental insight into the molecular structure of this protein family, revealing several conserved features that may be functionally relevant.

Our body is constantly exposed to pathogens and equipped with a highly elaborate immune system to fight against invading pathogens. The first line of defence is the innate immune system. It has evolved to detect conserved microbial molecular patterns, dubbed pathogen-associated molecular patterns (PAMPs), through pattern recognition receptors (PRRs). The binding of PRRs to PAMPs activates intracellular signalling cascades that lead to the expression of proinflammatory cytokines, Type I interferons and other antiviral proteins that all coordinate the elimination of pathogens and infected cells. PRRs can be classified as transmembrane receptors, including Toll-like receptors and some C-type lectin receptors, and as cytosolic receptors including retinoic acid-inducible gene-I-like receptors, nucleotide-binding domain and leucine-rich repeat-containing proteins, and cyclic GMP-AMP synthase. Studies have revealed that innate immune signals, including the ones activated by cytosolic PRRs, are triggered on organelle membranes. Here, we review the recent insights into how organelle membranes and their associated membrane lipids contribute to PRR-mediated innate immune signals.

RNA-targeted small molecule drug discovery is widely recognized as an important modality. However, not enough knowledge on the interaction between RNAs and small molecules is accumulated yet. In the present study, 46 RNAs were designed with various internal loops or hairpin loops based on a 29-mer model RNA. The interaction of designed RNAs and three kinds of small molecules, risdiplam, naphthyridine carbamate dimer (NCD) and ciprofloxacin, were examined by nuclear magnetic resonance (NMR) spectroscopy. The results of interaction experiments were quantitatively analysed and RNAs interacting with the small molecules were selected. Among the three compounds, NCD shows relatively stronger affinity to some of the model RNAs as judged by the NMR spectra, and binding sites of NCD for two RNAs were determined. The measurement condition used in this work, including the annealing free sample preparation as well as the Mg2+ free sodium phosphate buffer, can be the standard for the initial NMR screening in the RNA-targeted small molecule drug discovery.

The 5-year survival rate for pancreatic cancer is extremely low, at ~12%, primarily because most patients present with advanced and unresectable tumours. Chemotherapy regimens, such as gemcitabine (GEM) plus paclitaxel (PTX) and FOLFIRINOX, are standard treatments; however, resistance to these therapies remains a major challenge. Autophagy has been implicated in this resistance. Both the Atg8 and Atg12 conjugation systems are essential for autophagosome maturation, and the ubiquitin-like protein activator Atg7 plays an essential role in these systems. This study investigated the effects of Atg7 knockdown on GEM/PTX sensitivity in GEM/PTX-resistant pancreatic cancer MIAPaCa2 (GP-R) cells. GP-R cells exhibited reduced sensitivity to GEM/PTX, increased expression of autophagy-related factors, and elevated basal autophagy compared to parental cells. Atg7 knockdown in GP-R cells effectively inhibited both basal and GEM/PTX-induced autophagy, significantly increased total and mitochondrial reactive oxygen species (ROS), and led to the induction of apoptotic cell death. These findings suggest that autophagy inhibition via Atg7 knockdown enhances GEM/PTX sensitivity in GP-R cells. In conclusion, targeting Atg7 to inhibit autophagy may be a promising approach to improving the efficacy of GEM/PTX therapy in pancreatic cancer.

The axon initial segment (AIS) is a specialized compartment at the proximal axon, characterized by condensed localization of specific cytoskeletal proteins, including Ankyrin G (AnkG) and βIV-spectrin, which organize voltage-gated ion channels. The location and morphology of the AIS can change in response to neuronal activity; however, the precise mechanisms for the AIS plasticity remain unclear. Previously, we demonstrated that ubiquitin E3 ligase ZNRF1 is localized to presynaptic terminals in cultured hippocampal neurons and may play a role in Ca2+-dependent exocytosis. Here, we show that using ZNRF1 knockout (ZNRF1 KO) mice, ZNRF1-dependent AKT degradation induces AIS shift and increased cell surface localization of voltage-gated sodium channel Nav1.2. We also found that ZNRF1 KO mice exhibit enhanced short-term fear memory and increased contextual fear memory. These findings suggest that ZNRF1 may serve as a novel regulator of AIS localization.

The properties of a FRET-based redox probe Redoxfluor have been improved for its sensitivity and dynamic range. Substitution of the Citrine portion of Redoxfluor with circular permutated (cp) Citrine improved the dynamic range without affecting the redox potential. The cp158 mutant, referred to as Redoxfluor 2, possessed the most extended dynamic range and detected intracellular redox changes in yeast and bacteria, while the original did not. Investigation of the glutathione-redox dependency of the FRET ratio of various cysteine-substituted mutants revealed that Cys230 in the linker between Cerulean and the C-terminal cysteine-rich domain (CRD) and Cys385 in Citrine are essential for glutathione redox sensing. Although neither cysteine residues in CRD is essential for glutathione redox sensing, substitution of the CRD cysteine residues prominently affected the dynamic range of redox sensing and the redox potential titrated with glutathione. One of the CRD cysteine-substituted mutants (C259A) showed a greatly extended dynamic range and a substantially reducing redox potential compared to the original Redoxfluor. Redoxfluor 2 and the C259A mutant are suitable for versatile uses including sensitive detection of aberrant redox states, redox visualization in the more reducing intracellular compartments and high-throughput screening of redox modulators active against pathologically abnormal redox states.

DNA topoisomerase II (Top2) induces DNA double-strand breaks (DSBs) to relieve the torsional stress associated with DNA replication and transcription. Etoposide (ETP), a Top2 poison in clinical use as an anticancer drug, traps Top2 reactive intermediates, resulting in the accumulation of DSBs, coupled with the formation of Top2-DNA protein crosslinks (Top2-DPC) at the ends of DSBs. Proteasome-dependent processing of trapped Top2 is necessary for some cellular responses to ETP-induced DSBs; however, the effect of suppressing Top2 removal on DSB repair is not well understood. In this study, we focused on valosin-containing protein (VCP), a proteasome mediator, to analyse the effect of the suppression of Top2-DPC resolution on the repair of ETP-induced DSBs. ETP-induced activation of DNA-dependent protein kinase (DNA-PK), a non-homologous end-joining (NHEJ) factor, was suppressed by VCP inhibitors, similar to the effects observed in proteasome-inhibited cells. Consistent with this finding, VCP inhibition suppressed repair activity in response to ETP-induced DSBs. Additionally, VCP inhibition delayed the resolution of ETP-induced Top2-DPC. These results suggest that the processing of trapped Top2 via the VCP-proteasome pathway is important for efficient DNA-PK activation and subsequent repair in response to ETP-induced DSBs.