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Biochimica et Biophysica Acta (BBA) - Molecular Cell Research

Elsevier BV

Preprints posted in the last 90 days, ranked by how well they match Biochimica et Biophysica Acta (BBA) - Molecular Cell Research's content profile, based on 29 papers previously published here. The average preprint has a 0.02% match score for this journal, so anything above that is already an above-average fit.

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In vitro characterization of the baker's yeast deubiquitinase Ubp3

Bostelmann-Arp, L.; Khosa, S.; Reiners, J.; Mayor Voeltzke, K.; Smits, S. H. J.; Reichert, A. S.; Schmitt, L.

2026-08-20 biochemistry 10.64898/2026.08.19.745719 medRxiv
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Ubp3 is one of about 20 deubiquitinases (DUBs) in S. cerevisiae. The current view generally assumes that Ubp3 requires its interaction partner Bre5, which is proposed to function as a positive regulator. Accordingly, the Ubp3/Bre5 complex has been implicated in a broad range of cellular processes for example trafficking between ER and Golgi, stress granule formation and selective autophagy. However, the molecular basis of this proposed Bre5-dependent activity remains unclear. To address this at a molecular level, Ubp3, Bre5, and related constructs were heterologously expressed in E. coli, purified to homogeneity, and characterized in vitro. Both proteins contain folded domains as well as extensive intrinsically disordered regions (IDRs). Despite this structural complexity, the Ubp3/Bre5 complex could be isolated following either co-expression in vivo or after in vitro assembly. Unexpectedly, complex formation with Bre5 was not required for the catalytic activity of full length Ubp3. Furthermore, even the isolated catalytic domain of Ubp3 was fully active against two distinct substrates in the absence of Bre5, demonstrating that its deubiquitinating activity is intrinsically independent of Bre5. These findings indicate that the catalytic domain alone is sufficient for substrate cleavage, whereas the extensive IDRs of Ubp3 and its cofactor Bre5 might contribute to substrate recognition or specificity. Overall, this study challenges the prevailing model of Bre5-dependent activation of Ubp3 and provides new insights into the molecular organization of the Ubp3/Bre5 system. More broadly, it highlights the importance of intrinsically disordered regions in regulating deubiquitinase function and cellular signaling networks.

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Respiration-Deficient Cells Require Pyruvate Carboxylase to Suppress Asparagine Auxotrophy

Cui, R.; Ryu, K. W.; Fu, Y.; Bakouny, Z.; Li, D.; Kavlashvili, T.; Sfeir, A.; Thompson, C.

2026-08-13 cell biology 10.64898/2026.08.12.744280 medRxiv
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Mutations in mitochondrial DNA (mtDNA) compromise ETC activity and impair oxidative phosphorylation. Since eukaryotic cells contain multiple copies of mtDNA, the resulting phenotype depends on the proportion of mutant mitochondrial genomes (the heteroplasmy level). Using isogenic cell lines carrying similar mtDNA deletions, a linear decline in cellular respiration was observed as mitochondrial DNA heteroplasmy increased. Despite this, cellular redox imbalance did not change until heteroplasmy exceeded 50%. As heteroplasmy increased past 70%, cells also exhibited an integrated stress response (ISR) and impaired translation was observed. These defects were reversed by either addition of asparagine or overexpression of pyruvate carboxylase (PC). The dependence on exogenous asparagine in other respiration-deficient cells was found to correlate inversely with the PC expression level. For example, patient-derived thyroid tumor cells, harboring high heteroplasmy for a Complex I mtDNA mutation and low levels of PC, exhibited asparagine auxotrophy, and L-asparaginase treatment suppressed tumor growth. Together, these findings demonstrate a role for mitochondrial pyruvate carboxylase in cellular asparagine synthesis under conditions of compromised respiratory activity.

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TIM22 Complex-NADH dehydrogenase crosstalk maintains mitochondrial health by modulating cell death

D\'Silva, P.;Chakraborty, A.;Deb, R.;Saladi, S.

2026-06-20 Cell Biology 10.64898/2026.06.19.733344 medRxiv
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Programmed cell death is essential for organismal development. When dysregulated, it leads to neurodegenerative diseases and cancer. Although apoptotic pathways are well studied, the role of mitochondrial import translocases in regulating cell death remains unclear. Our study reveals a unique apoptotic pathway controlled by the TIM22 complex, an inner mitochondrial membrane translocase. This pathway involves a multiprotein complex formed by Tim22 and Nde1, a part of the respiratory electron transport chain. Under stress, the cytosol-exposed Nde1 isoform, a pro-apoptotic factor, is stabilised by the TIM22 complex, which includes the Tim18 subunit and Tim22s transmembrane segments. Notably, impairing the TIM22 complex and deleting Nde1 suppresses apoptosis and restores mitochondrial health. Beyond its role in import, our study uncovers a moonlighting function of the TIM22 complex in regulating mitochondria-dependent apoptotic cell death.

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Human PHOSPHO2 exhibits Mg2+-dependent phospholipid phosphatase activity

Tsunoda, K. A.; Murakami, C.; Sakai, H.; Sakane, F.

2026-08-03 biochemistry 10.64898/2026.07.31.742009 medRxiv
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Phosphatidic acid (PA) phosphatase (PAP) is an enzyme that plays a major role in lipid signaling by controlling the cellular levels of two lipid secondary messengers: its substrate, PA, and its product, diacylglycerol. Two types of mammalian PAPs have been reported to date. Type 1 PAP (PAP1) is an Mg2+-dependent, N-ethylmaleimide (NEM)-sensitive cytosolic enzyme (EC 3.1.3.4), whereas type 2 PAP (PAP2), also known as phospholipid phosphate (PLPP) (EC 3.1.3.113), is an Mg2+-independent, NEM-insensitive transmembrane protein. PAP2 also hydrolyzes other bioactive lipids such as lyso-PA (LPA), sphingosine-1-phosphate (S1P), and ceramide-1-phosphate (C1P). Here, we purified human phosphatase orphan 2 (PHOSPHO2), a putative cytosolic phosphatase containing a haloacid dehalogenase-like domain, and characterized its enzymological properties in vitro. Purified PHOSPHO2 displays Mg2+-dependent, NEM-sensitive phosphatase activities toward PA, LPA, S1P, C1P, and glycerol-3-phosphate (G3P) in vitro. Moreover, PHOSPHO2 showed substrate selectivity for PA molecular species containing shorter saturated fatty acids such as lauric acid and myristic acid, or polyunsaturated fatty acids such as docosahexaenoic acid and arachidonic acid. The PAP activity of PHOSPHO2, but not its other phosphatase activities, was strongly enhanced in the presence of phosphatidylcholine and phosphatidylethanolamine, major components of the cell membranes. These results indicate that mammalian PHOSPHO2 is a novel cytosolic PLPP that primarily functions as a PAP on cytoplasm-facing membranes.

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Structural and functional insights into yeast Rqc1p, a protein required for thermotolerance with potential nuclear localization

Pereira-Antonio, A. C.; Oliveira, F. G. d. C.; Costa-Lima, M. M.; Coelho, A. F.; Rodrigues, E. M.; Franco, G. R.; de Barros, M. H.; Bleicher, L.; Tahara, E. B.

2026-06-22 biochemistry 10.64898/2026.06.19.733457 medRxiv
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Protein homeostasis - i.e., proteostasis - is the biological process by which the qualitative and quantitative balance of the proteome is conducted, either by preserving functionally relevant proteins or by degrading unnecessary ones. Stress conditions can modulate cellular proteostasis in order to promote cytoprotection and preserve the viability of living organisms. Among the cellular pathways already described that can play an important role in preserving biological functions by modulating proteostasis are the heat shock response and the ribosome quality control pathways. In this work, we show that the Rqc1p protein is necessary for the thermoadaptation of S. cerevisiae to heat shock, as RQC1-deficient yeast is sensitive to elevated temperatures. In silico approaches - such as multiple sequence alignment, structural analysis, and molecular dynamics simulations - confirmed earlier predictions that Rqc1p shares characteristics with the bHLH family of proteins. We also verified, through computational prediction of sub-cellular localization, that S. cerevisiae Rqc1p contains nuclear localization signals, suggesting that this protein can potentially be translocated toward the nucleus, thereby broadening its current range of recognized biological functions in this organism. Also, analysis of yeast transcriptomes subjected to heat shock showed that Rqc1p mRNA levels do not fluctuate in response to heat shock, suggesting that cellular concentrations of Rqc1p are already at optimal levels to elicit a rapid and effective response during thermal stress in S. cerevisiae.

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Infrared light stimulates the mitochondrial large-conductance calcium-activated potassium channel in guinea pig cardiomyocytes.

Lewandowska, J.; Bednarczyk, P.; Kalenik, B.; Kulawiak, B.; Wrzosek, A.; Szewczyk, A.

2026-06-15 biochemistry 10.64898/2026.06.11.731586 medRxiv
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Mitochondrial potassium channels play an important role in regulating cellular metabolism, redox balance, and survival, particularly in excitable tissues such as the heart. Among them, the mitochondrial large-conductance calcium-activated potassium (mitoBKCa) channel has been implicated in cardioprotection during ischemia-reperfusion injury. At the same time, growing evidence indicates that mitochondria act as light responsive organelles, with cytochrome c oxidase (COX) serving as a primary chromophore for red and near-infrared (NIR) light. In this study, we investigated whether 820 nm infrared light modulates mitoBKCa channel activity in mitochondria isolated from guinea pig cardiomyocytes. Using patch-clamp recordings of mitoplasts, we demonstrated that illumination at 820 nm NIR wavelength enhanced mitoBKCa channel activity in a redox-dependent manner. Our findings reveal a previously unrecognized mechanism linking NIR light modulation via COX to the regulation of cardiac mitoBKCa channels as a metabolic sensor. This study identifies the mitoBKCa channel as a novel effector of light-induced mitochondrial signaling and suggests that modulation of cardiac mitochondrial potassium transport by NIR light may contribute to cardioprotective effects. These results provide new insight into the integration of bioenergetic and photoregulatory processes in mitochondria and support the development of non-pharmacological strategies targeting mitochondrial function.

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The mitoribosome-associated factor Mrx9 acts as a negative regulator of the prohibitin/m-AAA complex

Chagas, J. A.; Fontanesi, F.; Barros, M. H.

2026-07-29 molecular biology 10.64898/2026.07.28.741247 medRxiv
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The synthesis of mitochondrial-encoded polypeptides is an essential process, primarily regulated at the posttranscriptional level. In yeast, many regulatory factors have been described as acting in proximity to the mitoribosome to promote efficient translation; however, the precise mechanisms by which these components function remain largely unknown. Here, we expand on findings concerning a previously studied mitoribosome interactor, Mrx9, which is found in large expressosome-like assemblies of mitoribosome clusters. Mrx9 was initially linked to mitochondrial translation and was suggested to be associated with the splicing of COX1 and COB transcripts. Our current data show that Mrx9 is associated with the PHB/m-AAA complex at the polypeptide exit tunnel of the mitoribosome. Overexpression of Mrx9 impairs the proteolytic functions of Yta10 and Yta12 within the prohibitin complex, leading to splicing defects; accumulation of aberrant polypeptides; and a noticeable impairment in the processing of the essential mitoribosomal protein bL32m. These findings support a regulatory role for Mrx9 in the PHB/m-AAA complex by modulating the activities of both Yta10 and Yta12.

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Basal Internalization and Subcellular Localization of XCR1

Li, Q.; Pfersdorf, F.; Salgado-Polo, F.; Gustavsson, M.

2026-06-30 pharmacology and toxicology 10.64898/2026.06.25.734240 medRxiv
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Chemokines orchestrate immune cell trafficking through receptor-mediated signaling and are implicated in inflammatory, autoimmune, and neuropathic disorders. The XCL1-XCR1 axis is of particular interest because XCR1 is selectively expressed on mature conventional type 1 dendritic cells (cDC1s), where it supports communication with activated CD8+ T cells and NK cells and promotes antigen cross-presentation. This selectivity has made XCR1 an attractive target for dendritic cell-based cancer vaccines, while emerging evidence also links XCL1-XCR1 signaling to neuroinflammation and pain. Despite its therapeutic potential, the mechanisms governing XCR1 activation and trafficking remain understudied. Here, we characterize XCR1 expression, membrane trafficking, and basal internalization to define mechanisms that may influence therapeutic targeting. We show that XCR1 undergoes constitutive internalization through a {beta}-arrestin-independent but adaptor protein 2 (AP2)-dependent pathway, distinguishing it from other chemokine receptors with constitutive endocytosis. Furthermore, we identify specific sequence motifs critical for its subcellular localization and intracellular trafficking. These findings provide new mechanistic insights into XCR1 regulation and may inform the development of targeted therapeutics and antigen-delivery strategies in cancer and inflammation.

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Mechanistic characterization of tenuazonic acid-induced cellular stress responses in human esophageal KYSE-510 cells

Grgic, D.; Jobst, M.; Pais, M.; Waesoh, N.; Hager, S.; Del Favero, G.; Marko, D.

2026-07-09 pharmacology and toxicology 10.64898/2026.07.06.736731 medRxiv
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Tenuazonic acid (TeA) is an emerging Alternaria mycotoxin frequently detected in food and feed commodities, raising concerns about its toxicological relevance. Chronic oral exposure to TeA has been reported to induce dysplastic alterations in the esophageal mucosa of mice, while human biomonitoring data indicate an association between TeA exposure and esophageal cancer, although a causal relationship has not yet been established. At a mechanistic level, the effects of TeA in esophageal cells remain poorly characterized. Therefore, this study investigated the impact of TeA on cytotoxicity, oxidative stress, DNA damage, mitochondrial homeostasis, cell-cycle distribution and transcriptomic stress responses in human esophageal KYSE-510 cells. TeA induced a concentration-dependent reduction in metabolic activity and total protein content after 24 h exposure to 0.1-100 M. Significant cytotoxicity was measured starting from 20 M. At sub-cytotoxic concentrations, TeA triggered rapid ROS formation within 5-30 min exposure and induced formamidopyrimidine-DNA glycosylase (FPG) sensitive DNA damage after 1 h exposure (5-7.5 M), indicating oxidative DNA lesions. In addition, TeA altered mitochondrial morphology after 4 h exposure at 7.5 M, manifested by shrinkage of the mitochondrial network area and perinuclear redistribution, while mitochondrial respiration showed only a non-significant tendency towards reduced respiratory capacity. RNA sequencing after 6 h exposure to 10 M TeA revealed oxidative stress-associated transcriptional changes, impaired antioxidant and stress-adaptive responses, and p53-associated stress signaling. Furthermore, TeA induced significant G2/M phase accumulation after 24 h exposure to 1-10 M.

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Differential Nucleotide Inhibition Profile of Mouse and Human UCP1 Expressed in Liver Mitochondria Is Associated with an F88S Mutation

Shabalina, I. G.; Jacobsen, L.; Braz, G. R. F.; Zeng, Z. W.; Naren, Q.; Eriksson, B.; Ali, U.; Li, J.; Ericsson, A.; Cannon, B.; Khandelia, H.; Nedergaard, J.

2026-08-20 biochemistry 10.64898/2026.08.19.745785 medRxiv
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Uncoupling protein 1 (UCP1) mediates thermogenesis in brown adipose tissue. Whether human-UCP1 shares the bioenergetic properties established for rodent UCP1 (innate uncoupling, GDP sensitivity, fatty acid (re)activation) is not known. Therefore, we expressed human and mouse UCP1 in mouse liver, using adeno-associated viral vectors, and characterized their properties in isolated liver mitochondria. Both UCP1s induced marked innate uncoupling, characterized by increased substrate-supported respiration and decreased membrane potential, in the absence of exogenous fatty acids. Mouse-UCP1 in liver retained the classical regulatory properties of native brown-fat UCP1, including potent inhibition by GDP and reactivation by oleate. In contrast, human-UCP1 was only weakly inhibited by GDP but was strongly responsive to fatty acids. However, ATP potently inhibited human-UCP1, with an apparent IC of {approx}0.4 mM compared with {approx}1.4 mM for GDP, and ATP markedly decreased the sensitivity of human-UCP1 to oleate (re)activation. Despite substantial UCP1-mediated uncoupling, oxidative phosphorylation capacity and mitochondrial OXPHOS protein levels were preserved. Molecular dynamics simulations suggested a structural basis for the species difference. GDP formed persistent interactions with F88 in mouse-UCP1, an interaction absent at the corresponding S88 residue in human-UCP1. In-silico substitution of F88 by serine reduced GDP interaction at this site. Thus, human and mouse UCP1 share innate thermogenic activity but differ fundamentally in nucleotide regulation. The F88/S88 difference may contribute to the preferential GDP sensitivity of mouse-UCP1, whereas ATP provides effective nucleotide control of human-UCP1.

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Statin-Induced Mitochondrial Coenzyme Q Deficiency Alters Mitochondrial Redox Homeostasis and Bioenergetic Function in Astrocytes

Wojcicki, K.; Galganski, L.; Budzinska, A.; Figura, G.; Pijanowski, W.; Jarmuszkiewicz, W.

2026-06-10 biochemistry 10.64898/2026.06.10.731318 medRxiv
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Statins, widely used cholesterol-lowering drugs, inhibit the mevalonate pathway and reduce coenzyme Q (CoQ) biosynthesis, potentially impairing mitochondrial function. Because astrocytes are essential for maintaining brain redox homeostasis, statin-induced mitochondrial dysfunction in these cells may contribute to CNS pathology. We examined the effects of a six-day statin exposure on mitochondrial bioenergetics in rat astrocytes, focusing on mitochondrial CoQ (mtCoQ) deficiency. Treatment with 200 nM atorvastatin or simvastatin decreased the total mtCoQ pool (mtCoQ9 + mtCoQ10) by 30-35% and decreased the antioxidant pool mtCoQH2 by 40%, whereas the levels of mitochondrial antioxidant proteins, including superoxide dismutase 2 and uncoupling proteins, remained unchanged. Mitochondria of statin-treated astrocytes showed decreased respiratory activity, membrane potential, and ATP synthesis, and increased mtCoQ reduction leading to increased H2O2 production during the oxidation of complex I (CI) and CII substrates. Statin treatment also altered the organization of the respiratory chain, leading to a downregulation of the CI+CIII2+CIV and CIII2+CIV supercomplexes and decreased protein levels and activity of all respiratory chain complexes. Furthermore, a decrease in cytochrome a + a3 content was accompanied by a reduction in the maximum activity of CIV. CoQ10 supplementation elevated mtCoQ levels, restored respiratory function, and decreased H2O2 production in the mitochondria of statin-treated astrocytes. Prolonged statin exposure alters mtCoQ redox homeostasis and impairs mitochondrial bioenergetic function in astrocytes. CoQ10 supplementation attenuates these changes, supporting its potential role in protecting astrocyte mitochondria from statin-induced dysfunction.

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A lipid acyl code-based Dip2-Pkc1 signalling axis maintains mitochondrial integrity in eukaryotes

Sankaranarayanan, R.; Kumar, S.; Shambhavi, S.; Zehra, A.; Chakraborty, A.; Saleem, S. M. H.; Mohapatra, A.; Pal, B.; Kalivendi, S. V.; Kamat, S. S.

2026-07-21 cell biology 10.64898/2026.07.21.739733 medRxiv
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Organelle membranes employ diverse lipids to relay key signals for efficient coordination of cellular processes. Diacylglycerol (DAG) is a simple yet critical lipid secondary messenger, but the regulatory mechanisms and functional implications for its distribution remain poorly understood. We have recently shown that Protein Kinase C (Pkc1) activation is driven by selective DAGs (C36:0, C36:1), whose levels are governed by Disco-interacting protein 2 (Dip2) (Shambhavi et al., 2025). Here, through genetic, chemical, and lipidomic screens, we show that the absence of Dip2 leads to specific DAG accumulation on the mitochondrial membrane and impacts its morphology, function, and quality control in yeast. Remarkably, the elevated DAGs in{Delta} dip2 promote translocation of Pkc1 to mitochondria via its DAG-binding C1 domain, but not the HR1 domain, suggesting functional partitioning between the regulatory domains. We also show that only specific DAGs, not the bulk DAGs, are required for Pkc1s targeting and inactivating Phospholipase C (Plc1) restores Pkc1 localisation and the associated mitochondrial defects. In addition, we identify that respiratory growth triggers specific DAG (C36:1) accumulation in the mitochondria, thereby promoting Pkc1 recruitment. Furthermore, we establish that the Psi1-Plc1-Dip2 axis is required for survival under respiratory growth conditions. Taken together, our study uncovers a novel, Dip2-mediated, unconventional Pkc1 signalling axis for maintaining mitochondrial homeostasis under nutrient transition and highlights how distinct lipid fingerprints enable precise control over organellar homeostasis.

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Na+-translocating oxaloacetate decarboxylase from Vibrio cholerae: the functional tautomeric form of the substrate and the proton pathways in catalysis

Bertsova, Y. V.; Kvartalov, A. D.; Serebryakova, M. V.; Baykov, A. A.; Bogachev, A. V.

2026-06-10 biochemistry 10.64898/2026.06.08.730933 medRxiv
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Membrane-bound decarboxylases couple carboxylic acid decarboxylation to the transport of Na+ ions out of prokaryotic cells. The molecular mechanism of decarboxylase action is not yet known, which contrasts with the progress achieved in studying other primary ion pumps. Measuring decarboxylase activity is complicated by slow keto-enol tautomerization of the substrates during the assay. We found that HEPES exhibits anomalously high efficiency as a general acid catalyst for C-H bond formation during the enol-to-ketone conversion of oxaloacetate. Accordingly, the addition of HEPES to the assay medium eliminated the contribution of tautomerization rate to measured decarboxylation rate. Using the dependence of oxaloacetate tautomerization rate and equilibrium on solvent properties and pH, we established that only the keto form of oxaloacetate is converted by Vibrio cholerae oxaloacetate decarboxylase. Steady-state kinetic measurements did not reveal cooperativity in oxaloacetate conversion and Na+ binding. The effects of ionophores (CCCP, valinomycin, and ETH157) on proton transport in pyranine-loaded membrane vesicles prepared from V. cholerae cells indicated that the proton required for the conversion of oxaloacetate to pyruvate is taken up from the cytoplasmic side of the membrane. Furthermore, the effects suggested that {Delta}pH generation is caused by secondary electrophoretic proton transport in exchange for Na+.These findings advance our understanding of the molecular mechanism of the decarboxylation-supported Na+ transport in bacteria.

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Identification of a transient receptor potential channel that is regulated by phospholipid asymmetry

Nakanishi, R.; Murakami, A.; Sasaki, E.; Tsuchiya, M.; Suzuki, M.; Shiomi, A.; Nagao, K.; Taguchi, T.; Umeda, M.; Uchida, K.; Hara, Y.

2026-08-10 biochemistry 10.64898/2026.08.08.743638 medRxiv
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AbstractPhospholipid asymmetry is a hallmark of mammalian cell membranes and reflects the selective distribution of distinct phospholipid species between the two leaflets of the lipid bilayer. Although this asymmetry is tightly maintained, the membrane proteins whose functions depend on it remain largely unknown. To perturb phospholipid asymmetry experimentally, we expressed a constitutively active phospholipid scramblase and thereby identified transient receptor potential melastatin 8 (TRPM8) as an ion channel regulated by this membrane property. Activation of TRPM8 by both l-menthol and innocuous cold was markedly suppressed following disruption of phospholipid asymmetry. Likewise, selective depletion of phosphatidylserine (PS), a phospholipid enriched in the cytoplasmic leaflet, using a cytosolically targeted PS decarboxylase attenuated TRPM8 activation, indicating that cytoplasmic PS is required for proper TRPM8 function. Mechanistically, our findings suggest that cytoplasmic PS supports efficient TRPM8 activation by maintaining the biochemical state of the channel. Together, these findings identify TRPM8 as a phospholipid asymmetry-dependent ion channel and establish an experimental strategy for systematically identifying membrane proteins regulated by phospholipid asymmetry. This work provides a foundation for future studies investigating the biological significance of this fundamental membrane property.

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Mitochondrial Signaling: Nitric Oxide Synthesis by Cytochrome c Oxidase and Its Oxygen Sensitivity Are Modulated by Adenine Nucleotides

Castello, P. R.; Ball, K. A.; Poyton, R. O.

2026-08-10 biochemistry 10.64898/2026.08.09.743791 medRxiv
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Nitrite can be reduced to nitric oxide (NO) by several heme- and molybdenum-containing proteins, including mitochondrial cytochrome c oxidase (Cco). This activity, designated Cco/NO, has been implicated in hypoxic signaling, but its regulation and quantitative significance relative to other NO-producing systems remain uncertain. We examined its modulation by adenine nucleotides using detergent-solubilized yeast and mouse brain mitochondria supplied with 1 mM nitrite and an ascorbate/TMPD/cytochrome c electron-donor system. ADP and ATP differentially modulated Cco/NO activity, and ADP extended measurable NO formation across the entire oxygen range tested, up to the assay ceiling of 175 {micro}M O2. Nucleotide regulation was also isoform-dependent: ATP slightly inhibited Va-containing Cco but strongly stimulated Vb-containing Cco under anoxic conditions. Rates normalized to cytochrome aa demonstrate multi-turnover nitrite-reductase capacity under these substrate-driven assay conditions. Both the cellular ADP/ATP ratio and subsequently assayed Cco/NO activity increased transiently following a hypoxic shift. These findings establish metabolic and isoform-dependent gating of the catalytic capacity of Cco/NO; they do not establish its fractional contribution to total cellular NO or its operation at physiological nitrite concentrations in intact, coupled mitochondria. This research was supported by CONICET Grant PIP 706 (research team member P.R.C.) and National Institutes of Health Grant GM30228 to R.O.P.

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Characterization of Vlf1 as a regulator of lipophagy.

Fakih, Z.; Cavarischia-Rega, C.; Glueck, B. R.; Reichert, S.; Dutta, P.; Beresh, O.; Schuldiner, M.; Macek, B.; Rapaport, D.; Dimmer, K. S.

2026-08-11 cell biology 10.64898/2026.08.11.744108 medRxiv
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Lipid droplets (LDs) are unique organelles, surrounded by a phospholipid monolayer. They are present in most eukaryotic cells including the unicellular model organism S. cerevisiae. LDs store neutral lipids which serve as precursors for amphipathic membrane lipids and as an energy reserve. Loss of LDs in S. cerevisiae results in multiple cellular defects impairing lipid homeostasis and the biogenesis and function of other organelles. Here, we find that the expression levels of many proteins in isolated mitochondrial fractions are altered in cells that cannot synthesize neutral lipids and therefore lack LDs. In addition, among several downregulated proteins, we identified the previously uncharacterized Ylr001c (which we name Vlf1 for Vacuolar Lipophagy Factor 1). We show that Vlf1 is glycosylated and, in contrast to some previous reports, is actually localized to the vacuole. Furthermore, we demonstrate that changes in Vlf1 expression alter growth sensitivity to rapamycin, and detected a physical interaction of Vlf1 with Atg15, a lipase involved in autophagy. Additionally, we observe higher levels of autophagy/lipophagy in the absence of Vlf1 and a reduction upon overexpression of the protein. Taken together, the effects on lipohagy by Vlf1 makes it, according to our knowledge, the first vacuolar lipophagy regulator identified in S. cerevisiae.

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Endosomal GPR65 signaling in fibroblast-like synoviocytes promotes inflammatory cytokine release and nociceptive neuron sensitization.

Pattison, L. A.; Dannawi, M.; Smith, E. S. J.

2026-06-22 pharmacology and toxicology 10.64898/2026.06.16.732753 medRxiv
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GPR65 is a proton-sensing G protein-coupled receptor implicated in inflammatory pain. In fibroblast-like synoviocytes (FLS), GPR65 activation promotes the release of proinflammatory cytokines capable of sensitizing sensory neurons. Following stimulation by protons, the synthetic agonist BTB09089, and the glycosphingolipid psychosine GPR65 undergoes internalization; however, the contribution of this trafficking to downstream signaling remains unclear. Using heterologous cell systems, the molecular mechanisms governing GPR65 internalization were first defined. Pharmacological and genetic inhibition of internalization revealed that intracellular trafficking is required for activation of extracellular-signal-related kinase (ERK) in the nucleus and transcriptional responses, indicating a spatially restricted signaling program originating from endosomes. The physiological relevance of this pathway was then examined in primary mouse FLS. Inhibition of endogenous GPR65 internalization reduced the ability of the conditioned media from BTB09089 stimulated FLS to sensitize dorsal root ganglia sensory neurons, thus linking receptor trafficking to pro-nociceptive function. Together these findings identify receptor internalization as a key determinant of nuclear ERK signaling and transcription downstream of GPR65 and demonstrate that endosomal signaling is required for pro-nociceptive activity of GPR65 in FLS. One-sentence summaryEndosomal internalization of GPR65 is required to coordinate gene transcription and proinflammatory cytokine production that drive neuronal sensitization.

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Insulin-degrading enzyme activity is modulated by interaction with pyrroline-5-carboxylate reductase 1

Song, E. S.; Camacho-Navas, C.; Goswami, A.; Nayak, A.; Arizaca Maquera, K. A.; Chen, J.; Stamm, S.; Galperin, E.; Hersh, L. B.; Rodgers, D. W.

2026-07-19 biochemistry 10.64898/2026.07.16.739082 medRxiv
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Insulin-degrading enzyme (IDE, insulysin, insulinase) is a peptidase that hydrolyzes a number of bioactive peptides including insulin and the amyloid beta peptide, making it a promising therapeutic target for diabetes and Alzheimers disease. Aspects of its physiological role are still controversial, however. In an attempt to further define IDEs role in cells, we used co-immunoprecipitation experiments to identify potential IDE interacting proteins. The enzyme pyrroline-5-carboxylate reductase 1 (PYCR1) was found associated with IDE in three different cell lines, and the two proteins colocalize in HeLa cells. Purified PYCR1 activates IDE toward small peptide substrates, suggesting a modulatory role for the interaction in vivo. Modeling suggests that the unstructured N-terminal region of PYCR1 inserts into allosteric sites of IDE, contributing to the observed activation. Deleting this sequence alters, but does eliminate, the interaction between PYCR1 and IDE. Since pyrroline-5-carboxylate reductase 1 is a mitochondrial protein, we posit that their interaction could regulate a previously described mitochondrial pool of IDE, which may serve to degrade mitochondrial targeting sequences or amyloid beta peptide that localizes to that organelle.

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Local and non-local impacts of intra-hexamer interactions on temperature compensation of KaiC

Kondo, K.; Furuike, Y.; Horiuchi, K.; Onoue, Y.; Yamashita, E.; Akiyama, S.

2026-06-15 biochemistry 10.64898/2026.06.12.727564 medRxiv
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A hexameric clock protein KaiC exhibits a 24-hour phosphorylation cycle with a unique property termed temperature compensation. The period is kept constant over physiological temperatures through compensatory coordination of underlying elementary reactions. The temperature-compensated ATPase activity of KaiC is one such key reactions that potentially contribute to maintaining a constant circadian period. We identified four amino acid residues responsible for the temperature compensation in an N-terminal ATPase domain of KaiC. D82 and K172 were located in a primary site, and the ATPase activity of each alanine mutant showed a positive correlation with rising temperature. N62 and E69 constituted a secondary site, where each alanine replacement resulted in a negative correlation with the temperature. The primary site exerts a compensatory regulation over the ATPase cycle locally within the N-terminal domain. The secondary site prevents the ATPase activity from becoming over-compensated by suppressing another compensatory regulation mediated through a non-local interaction with a C-terminal domain of KaiC. Therefore, any imbalance between the local and non-local compensatory regulations in KaiC affects the temperature dependence of its phosphorylation rhythm.

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HIV-1 Tat protects macrophages from killing by the Exoenzyme U from Pseudomonas aeruginosa

Jansen, M.; Rivault, A.; Tellier, A.; Chauveau, L.; Blanc-Potard, A.-B.; Beaumelle, B.

2026-06-18 microbiology 10.64898/2026.06.17.732897 medRxiv
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People living with HIV (PLWH) have a higher risk of developing other diseases, such as bacterial pneumonia. While Pseudomonas aeruginosa (PAE) is a common cause of pneumonia in humans, PLWHs are infrequently infected by PAE. The reasons for this relative resistance of PLWH to PAE are not known. The most virulent PAE strains produce ExoU which is a key effector of PAE cytotoxicity. Upon injection into the target cell cytosol by the type III secretion system, ExoU binds to PI(4,5)P2 on the inner leaflet of the plasma membrane. Its phospholipase activity then induces a loss of plasma membrane integrity, rapidly leading to cell death. HIV-Tat is secreted by HIV-infected cells, leading to nanomolar concentrations of Tat in the sera of PLWH, even under antiretroviral therapy. Circulating Tat can be endocytosed by uninfected cells, translocate to the cytosol and bind to PI(4,5)P2 at the plasma membrane. In uninfected cells only, Tat is palmitoylated, enabling Tat to become resident on PI(4,5)P2. We found that Tat can interfere with the recruitment of ExoU by PI(4,5)P2, thereby protecting macrophages from PAE toxicity. HIV Tat could therefore be involved in the relative protection of PLWH against the most aggressive PAE isolates and their ExoU type III effector. Tat nevertheless enhances the toxicity of ExoU-deficient PAE strains toward macrophages. ImportancePeople living with HIV (PLWH) are at risk of developing bacterial pneumonia. A widespread cause of pneumonia is Pseudomonas aeruginosa (PAE) but, for unknown reasons, PLWHs are infrequently infected by PAE. A key effector of PAE cytotoxicity is ExoU that is injected by PAE into the target cell cytosol, then binds to PI(4,5)P2 on the inner leaflet of the plasma membrane. The potent phospholipase activity of ExoU then induces a loss of plasma membrane integrity, rapidly leading to cell death. HIV-Tat is present in the serum of PLWH. Circulating Tat is endocytosed by cells, translocates to the cytosol and bind to PI(4,5)P2 at the plasma membrane with a very high affinity. This study indicates that Tat interferes with the recruitment of ExoU by PI(4,5)P2, thereby protecting macrophages from ExoU+ PAE. HIV Tat could therefore be involved in the relative protection of PLWH against the most aggressive PAE isolates.