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Journal of Biological Chemistry

Elsevier BV

Preprints posted in the last 30 days, ranked by how well they match Journal of Biological Chemistry's content profile, based on 641 papers previously published here. The average preprint has a 0.14% match score for this journal, so anything above that is already an above-average fit.

1
Cleavage specificity of E. coli YicC endoribonuclease

Barnes, S. A.; Lazarus, M. B.; Bechhofer, D. H.

2026-03-26 molecular biology 10.64898/2026.03.25.714237 medRxiv
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Escherichia coli YicC enzyme is the founding member of a family of endoribonucleases that is encoded in virtually all bacterial species. Previous structural studies revealed that this ribonuclease binds RNA by a novel mechanism in which the hexameric apoprotein presents an open channel that undergoes a large rotation upon RNA binding and clamps down on the RNA. The current study follows up on these findings by examining the cleavage of various oligonucleotide substrates designed to probe recognition elements required for YicC binding and cleavage. A 26-nucleotide RNA oligomer (oligo), with a KD in the low micromolar range, was the standard to which numerous oligos with altered sequence were compared. In vitro RNase assays and fluorescence anisotropy binding measurements indicated that the preferred substrates for YicC were relatively small RNAs that contain some secondary structure. Larger RNAs or highly structured RNAs were less-than-optimal substrates. Similarly, RyhB RNA, a [~]90-nucleotide, iron-responsive RNA of E. coli, which has been described as a target of YicC binding and/or cleavage, was a poor YicC substrate in our assays. These results suggest that the native substrates for YicC-family members are very small RNAs or RNA fragments derived from larger RNAs.

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Protein kinase A regulates phosphorylation of UBE2J1 at serine residue S266 in response to glucagon signalling

O'Callaghan, L. E.; Algoufi, N. D.; Dollken, D. S.; Hashem, A. M.; Fleming, J. V.

2026-04-07 biochemistry 10.64898/2026.04.07.716893 medRxiv
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The ubiquitin conjugating enzyme UBE2J1/Ubc6e localizes to the endoplasmic reticulum where it mediates the ubiquitination and proteasomal degradation of terminally misfolded proteins. Although the protein is known to undergo phosphorylation at serine S184, we have considered modification at an additional site and used a bespoke anti-phospho antibody to confirm phosphorylation also at serine residue S266. Despite the well-described role of UBE2J1 in ER associated degradation (ERAD), we found no evidence for regulation at S266 during Unfolded Protein Response (UPR) induction by thapsigargin. Instead, our studies suggest that phosphorylation occurs independently at the S184 and S266 sites, with mutation at one site failing to disrupt basal phosphorylation at the second. We identified several contexts in which these two phosphorylations were differentially regulated. For example, ER localization, which is important for phosphorylation at S184, was not required for modification at S266, and sensitivity to proteasome inhibitors, which is regarded as a distinguishing feature of the S184 phospho-variant, was unaltered by the S266A mutation. Regarding regulation at S266 on the other hand, we found that pharmacological activation of protein kinase A resulted in rapid phosphorylation, with differential use of phospho-specific antibodies confirming that phosphorylation at S184 was unchanged by this treatment. Hormonal stimulation by glucagon resulted in a similar pattern of UBE2J1 phosphorylation, which occurred exclusively at S266 and could be inhibited by H89. The differential regulation demonstrated in these studies extends our understanding of the UBE2J1 enzyme, and may indicate a role in the integration of energy metabolism with environmental stress conditions.

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Phosphorylation of Ube2J1 at serine S184 is regulated by protein phosphatase 2A.

Dollken, D. S.; Lam, S. Y.; Kaminski, T. K.; Fleming, J. V.

2026-03-30 biochemistry 10.64898/2026.03.30.715004 medRxiv
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The Ube2J1 enzyme that mediates the ubiquitination and proteasomal degradation of misfolded proteins at the ER is phosphorylated at serine S184. Following anisomycin treatment of HEK293T cells, we observed an inverse relationship between phosphorylation and dephosphorylation at this site. This suggested a dynamic interchange between the two forms, and we show that S184 is a target for protein phosphatase 2A. The S184-phosphorylated protein is known to exhibit increased sensitivity to proteasomal degradation, and we found that mutation at K186R increased the ratio of S184-phosphorylated to S184-dephosphorylated protein. Although the K186R mutant retained some sensitivity to proteasomal inhibition, our results show that Ube2J1 steady state expression can be exercised at multiple levels, and can involve dynamic phosphorylation and dephosphorylation at S184.

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Molecular basis of collagen triple helix recognition by VWF A-like domain 2 of collagen VII: Implications for interlaced anchoring fibril formation

Hashimoto, M.; Oki, H.; Kawahara, K.; Fujii, K. K.; Koide, T.

2026-03-18 biochemistry 10.64898/2026.03.16.711976 medRxiv
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Anchoring fibrils formed by collagen VII play a critical role in stabilizing the dermal-epidermal junction. The N-terminal non-collagenous (NC1) domain of collagen VII binds firmly to basement membrane components including collagen IV and has also been reported to interact with mesenchymal fibrillar collagens via its von Willebrand factor A-like domain 2 (A2 domain). To elucidate how collagen VII recognizes fibrillar collagen, we performed yeast two-hybrid screening using a triple-helical random peptide library, which resulted in the identification of a Met-Gly-{Phi} ({Phi}; aromatic amino acid residue) motif. Biochemical analysis with synthetic triple-helical peptides revealed a binding preference of Trp > Phe as the {Phi} residue by the A2 domain despite Trp being absent in native collagens. The crystal structure of the A2 domain in complex with the Nle (Met surrogate)-Gly-Trp-containing peptide revealed a unique mechanism by which two distinct hydrophobic pockets of the A2 domain accommodate the Nle and Trp residues corresponding to the Met-Gly-{Phi} motif, engaging all three chains of the triple helix. Subsequent molecular dynamics simulations demonstrated that the A2 domain recognizes the corresponding native Met-Gly-Phe motif in a similar manner, but with lower affinity, implying a transient interaction with mesenchymal collagens. The findings obtained in this work suggest models in which transient A2-triple helix interaction promotes the recruitment of collagen I and III fibrils into the arc-shaped structure of anchoring fibrils. This also provides a foundation for linking structural understanding to skin fragility diseases caused by collagen VII dysfunction.

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Rational design of a protein-protein interaction inhibitor that activates Protein Tyrosine Phosphatase 1B.

Londhe, A. D.; Rizzo, S.; Rizvi, S. M.; Bergeron, A.; Sagabala, R. S.; Banavali, N. K.; Thevenin, D.; Boivin, B.

2026-03-21 biochemistry 10.64898/2026.03.19.712938 medRxiv
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Reversible inactivation of protein tyrosine phosphatases by reactive oxygen species (ROS) is essential to the phosphorylation of growth factor receptors. An important outcome of the inactivation of protein tyrosine phosphatase 1B (PTP1B) by ROS involves the conformational change of its phosphotyrosine binding loop which adopts a solvent exposed position in its oxidized form. We previously demonstrated that 14-3-3{zeta} binds to the phosphotyrosine binding loop of the oxidized form of PTP1B. Using a rational approach, we developed a unique protein-protein interaction (PPI) inhibitor peptide derived from the phosphotyrosine binding loop of PTP1B designed to disrupt the interaction between PTP1B and the 14-3-3{zeta}-complex. Exploiting this cell-permeable peptide, we showed decreased association between PTP1B and the 14-3-3{zeta}-complex in cells treated with epidermal growth factor (EGF). We also demonstrated that preventing the association of this 14-3-3{zeta}-complex to PTP1B deterred oxidation and inactivation of PTP1B following EGF receptor (EGFR) activation and generation of ROS. Treating cells with our PPI inhibitor decreased EGFR phosphorylation on PTP1B-specific sites. Furthermore, treating EGFR-driven epidermal cancer cells with our PPI inhibitor also significantly inhibited colony formation and cell viability, consitent with increased activation of PTP1B. These data highlight the ability of PTP1B to downregulate critical signaling pathways in cancer when activated using peptide drugs such as our protein-protein interaction inhibitor. We anticipate that preventing or destabilizing the reversible oxidation of other members of the protein tyrosine phosphatase superfamily using PPI inhibitors may offer a foundation for a broad therapeutic approach to rectify dysregulated signaling pathways in vivo. Significance StatementLimited understanding of redox mechanisms regulating PTP catalytic activity is a major knowledge gap that has hampered our efforts to develop activation strategies. In its reversibly oxidized and inactivated form, conformational changes of PTP1B influence its association with regulatory proteins. We demonstrate that designing a cell-permeable peptide based on a loop of PTP1B that becomes exposed during oxidation can block its interaction with the 14-3-3{zeta}-multiprotein complex and activate the phosphatase. Moreover, activating PTP1B using our protein-protein interaction inhibitor peptide decreases the phosphorylation of its substrate EGFR and decreases the effectiveness of cancer cells to form colonies. This study provides important insights into the therapeutic potential of protein-protein interaction inhibitors that regulate the redox cycle of PTPs to reestablish physiological signaling.

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Structural analysis of Helicobacter pylori glutamate racemase in a monoclinic crystal form

Spiliopoulou, M.; Schulz, E. C.

2026-04-03 biochemistry 10.64898/2026.04.02.716094 medRxiv
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Glutamate racemase (MurI) catalyzes the stereochemical interconversion of L-glutamate to D-glutamate, a key element of bacterial peptidoglycan biosynthesis. In this study, we present the crystal structure of Helicobacter pylori glutamate racemase at 1.43 [A] and in monoclinic symmetry, as previously reported models, but different unit-cell parameters. The present model contains a single dimer and retains the previously described head-to-head dimer arrangement. The differences between the models arise from variations in unit-cell parameters, which lead to altered crystal packing interactions rather than changes in the quaternary assembly. The monomeric fold and active-site architecture remain conserved and are consistent with the catalytic features described for bacterial glutamate racemases. This structure provides an updated, high-resolution structural model for H. pylori glutamate racemase and highlights the variability in crystal packing within the same space group.

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Decoding the Structural and Functional Impact of the Leukaemia-Associated A338V Mutation in GPR183

Andersson, L.; Wesolowski, P. A.; Jahrstorfer, L.; De Rosa, A.; Heger, T.; Neuman, V.; Sieradzan, A. K.; Wales, D. J.; Kozielewicz, P.

2026-04-01 pharmacology and toxicology 10.64898/2026.03.30.715362 medRxiv
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G protein-coupled receptors rely on dynamic conformational changes to coordinate G protein activation and recruitment of regulatory transducers such as G protein-coupled receptor kinases and {beta}-arrestins. The chemotactic receptor GPR183 has been implicated in a context-dependent role in hematological malignancies. Here, we investigated the impact of A338V mutation located within the C-terminal tail of GPR183. This mutation is associated with acute myeloid leukaemia. Using bioluminescence resonance energy transfer-based assays in HEK293A cells, we assessed receptor-proximal signaling events. The A338V variant displayed preserved agonist potency and comparable agonist-induced Gi activation relative to wild type, although constitutive activity towards Gi was modestly reduced. In contrast, recruitment of GRK2 and {beta}-arrestin2 was consistently impaired across multiple assay configurations. These differences were not attributable to altered receptor abundance, as the C-tail untagged mutant exhibited increased plasma membrane expression despite reduced regulatory transducer engagement. While intramolecular conformational biosensor measurements revealed subtle differences in global receptor conformation between WT and A338V, extensive molecular dynamics simulations supported the altered conformational sampling of the C-terminal tail in the A338V variant. Together, these data support a model in which the A338V substitution selectively alters C-terminal structural dynamics, impairing GRK2 and {beta}-arrestin2 recruitment while preserving G protein activation.

8
Human TBC1 domain-containing kinase is a class I multidomain pseudokinase

Maurya, S.; Cheek, L. E.; Iavarone, A. T.; Zhu, W.

2026-04-03 biochemistry 10.64898/2026.04.02.716191 medRxiv
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TBCK-related encephalopathy (TBCKE) is a neurodevelopmental disorder associated with biallelic mutations in TBCK. Despite the increasing number of reported cases worldwide, the biochemical and biophysical properties of TBCK remain unclear, hindering molecular understanding of its role in disease. Here, we present the successful expression, purification, and biochemical characterization of full-length human TBCK produced in Spodoptera frugiperda cells. Biochemical and biophysical analyses reveal that the catalytically inactive pseudokinase domain of TBCK lacks nucleotide binding, consistent with the absence of the canonical VAIK, HRD, and DFG motifs required for catalysis. These findings support that TBCK is a class I pseudokinase and provide a foundation for future structural and functional studies to elucidate its biological role.

9
FAM122A inhibition of PP2A-B55 through a bipartite binding mechanism

Benavides-Puy, I.; Vigneron, S.; Kettenbach, A.; Lorca, T.; Nilsson, J.

2026-03-25 cell biology 10.64898/2026.03.24.713894 medRxiv
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FAM122A regulates cell cycle progression through inhibition of the PP2A-B55 phosphoprotein phosphatase. Recent structural work has uncovered helical elements in the N-terminus of FAM122A as binding determinants for PP2A-B55 but whether FAM122A inhibition towards PP2A-B55 is regulated is presently unclear. To address this we performed a systematic analysis of the PP2A-B55 interaction with FAM122A in cells uncovering a novel region in the C-terminus of FAM122A, spanning residues 150-170, required for binding. This C-terminal region and the N-terminal helices are both required for efficient binding to PP2A-B55 suggesting a bipartite binding mechanism. We perform amino acid resolution scans of FAM122A 150-170 uncovering several residues in this region contributing to binding including the conserved Ser158, a reported phosphorylation site. We show that Ser158 is important for PP2A-B55 inhibition in human cells as well as efficient stimulation of mitotic entry in Xenopus laevis egg extracts. In human cells and in Xenopus laevis Ser158 phosphorylation is regulated with increased occupancy correlating with cell cycle stages requiring PP2A-B55 inhibition. Collectively our work uncovers novel aspects of FAM122A interaction with PP2A-B55 and provides a possible mechanism for how the inhibitory activity of FAM122A can be regulated during the cell cycle.

10
c-di-AMP inactivates a K+/H+ antiporter in Bacillus subtilis

Figueiredo-Costa, I. R.; Lorga-Gomes, M. M.; Sousa-Moreira, S. C.; Matas, I. M.; Morais-Cabral, J. H.

2026-03-25 biochemistry 10.64898/2026.03.23.713699 medRxiv
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c-di-AMP is a bacterial second messenger with the crucial role of regulating turgor and osmotic adaptation. Due to the importance of intracellular K+ for osmotic balance, c-di-AMP controls the import and export of K+ by regulating the activity and transcription level of K+ transporters and channels. It has been postulated that c-di-AMP inactivates K+ import and activates K+ export. To gain a full understanding of the properties the K+ machinery in the Gram-positive model organism Bacillus subtilis and in particular, of how the machinery is regulated by c-di-AMP, we characterized the molecular properties of CpaA, a cation/H+ antiporter that has been shown to bind the dinucleotide. We determined the crystal structure of the cytosolic RCK domain with and without c-di-AMP and performed a functional characterization of full-length CpaA using a fluorescence-based flux assay. We found that c-di-AMP binds on the interface of the RCK-C subdomain but only small structural differences are detected between the apo- and holo-structure. We determined that CpaA is more active at high pH and that it slightly favors K+ over Na+ for exchange with H+. Unexpectedly, CpaA is inactivated by c-di-AMP with a K1/2 of inactivation around 1 {micro}M. Our results reinforce the emerging view that regulation of the bacterial K+ machinery by c-di-AMP is more complex than previously thought and that a detailed characterization of the molecular properties of the individual protein components and of how their activity is integrated is necessary for a complete view of the machinery physiological function.

11
In vitro Cleavage Requirements and Specificities of Mycobacterial RNase E

Rapiejko, A. R.; Reddy, M.; Sacchettini, J. C.; Shell, S. S.

2026-04-07 molecular biology 10.64898/2026.04.06.716707 medRxiv
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Regulation of RNA pools allows for adaptation to changing environments and stress, which is especially important in pathogenic bacteria such as Mycobacterium tuberculosis. RNA degradation is a significant contributor to RNA abundance, and Ribonuclease (RNase) E has a rate-limiting role in degradation of a majority of mycobacterial transcripts. However, many open questions remain about the RNA substrate requirements and specificities for efficient cleavage by mycobacterial RNase E. Here, using both Mycolicibacterium smegmatis and M. tuberculosis RNase E, we demonstrate that this enzyme is only active on substrates with a minimum length of approximately 27 nt. Furthermore, we show that mycobacterial RNase E prefers substrates with 5 monophosphates rather than 5 triphosphates, and that the positions of cleavage events within substrates are dictated by both sequence and distance from the RNA ends. Our results also suggest that RNase E may be affected by product inhibition. Finally, we show that M. smegmatis RNase E behaves similarly to M. tuberculosis RNase E, validating the use of this model organism for RNA degradation studies.

12
Structural analyses of Trichomonas vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK)

Chiu, A.; Liu, L.; Seibold, S.; Battaile, K.; Craig, J.; Harmon, E.; Subramanian, S.; Chakafana, G.; Early, J.; Cron, L.; Staker, B.; Myler, P. J.; Lovell, S. J.; Van Voorhis, W.; Asojo, O.

2026-03-28 biochemistry 10.64898/2026.03.28.715000 medRxiv
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Trichomonas vaginalis causes trichomoniasis, the most common non-viral sexually transmitted disease in humans. T. vaginalis pyrophosphate-dependent phosphofructokinase (TvPPi-PFK) is a putative target for rational, structure-based drug discovery, given its absence in mammals and its importance for parasite survival. TvPPi-PFK is a cytosolic enzyme that catalyzes the phosphorylation of fructose-6-phosphate using pyrophosphate (PPi) as the phosphoryl donor. This reversible reaction, catalyzed by TvPPi-PFK, is the first committed step in glycolysis. Its reverse reaction is vital for gluconeogenesis in T. vaginalis. The purification, crystallization, structure determination, and preliminary structure-functional analyses of three crystal structures of TvPPi-PFK are presented. All three structures organize as tetramers with the conserved motifs essential for pyrophosphate binding and PPi-PFK catalytic activity. Comparative analysis with structural neighbors from other organisms demonstrated that despite sharing <29% sequence identity, TvPPi-PFKs protomer shares overall topology with both PPi- and ATP-dependent PFKs. Mass photometry confirmed that TvPPi-PFK formed tetramers under near-physiological conditions. Unexpectedly, TvPPi-PFK crystals dephosphorylate ATP to AMP during soaking. In all three structures, either ATP or AMP is bound at the enzymes dimer interface, typical of ATP-PFKs, but a novel finding for PPi-PFKs. Furthermore, a sugar phosphate binding site was observed in proximity to the ATP-binding site. Thus, the three reported TvPPi-PFK structures validate its established PPi-dependent activity while revealing previously unreported ATP and sugar phosphate binding. This study also lays a foundation for future research into putative ATP-dependent activity of TvPPi-PFK and for evaluating known phosphofructokinase inhibitors as potential therapeutics for trichomoniasis. These findings expand our understanding of PFK superfamily diversity and support the continued exploration of TvPPi-PFK as a drug target for trichomoniasis. SynopsisThe production, crystallization, and three crystal structures of a pyrophosphate-dependent phosphofructokinase from Trichomonas vaginalis (TvPPi-PFK) reveal ATP binding and structural similarity to both ATP-dependent and pyrophosphate-dependent phosphofructokinases. TvPPi-PFK dephosphorylates ATP and has a novel ATP-PFK-like ATP-binding cavity.

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Stathmin-2 Mediates Paracrine Hormone Regulation of Glucagon Through Lysosomal Trafficking in αTC1-6 cells

Chang, N.; Ugulini, S.; Dhanvantari, S.

2026-04-05 cell biology 10.64898/2026.04.02.715646 medRxiv
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The secretion of glucagon from the pancreatic alpha () cell within the islets of Langerhans is physiologically regulated by nutrients (glucose, amino acids, fatty acids), neurotransmitters, and paracrine hormones. Insulin and somatostatin form an intra-islet paracrine network to control glucagon secretion through direct inhibitory effects on cell secretory granule exocytosis. In a potential new cellular pathway for the regulation of glucagon secretion, we have previously identified the neuronal trafficking protein Stathmin-2 (Stmn2) as a negative regulator of glucagon trafficking and secretion by directing glucagon to degradative lysosomes. In this study, we examined if insulin and somatostatin direct glucagon to lysosomes in a Stmn2-dependent manner as part of their paracrine mechanisms. Using the TC1-6 glucagon-secreting cell line and confocal microscopy of both fixed and live cells, we show that insulin and somatostatin direct glucagon, glucagon+LAMP1+ vesicles, and LAMP1-RFP to the intracellular region, away from sites of exocytosis. As visualized in live cells, insulin treatment resulted in the rapid retrograde transport of lysosomes from the cell periphery, and this effect was lost under siRNA-mediated silencing of Stmn2. Somatostatin appeared to enhance the intracellular retention of lysosomes, also in a Stmn2-dependent manner. We determined a possible mechanism for Stmn2 in the regulation of lysosome transport in TC1-6 cells through the Arf-like small GTPase Arl8, indicating that Stmn2 may function in lysosomal positioning along microtubules. We propose that Stmn2-mediated lysosomal transport may be a potential new pathway, in addition to inhibition of secretory granule exocytosis, through which insulin and somatostatin regulate glucagon secretion.

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Dominant α-tubulin mutations rescue tauopathy neurodegenerative phenotypes in C. elegans

Benbow, S.; Saxton, A. D.; Baum, M.; Uhrich, R. L.; Stair, J. G.; Keene, K.; Dahleen, C.; Wordeman, L.; Liachko, N.; Kow, R. L.; C. Kraemer, B.

2026-03-20 neuroscience 10.64898/2026.03.18.712642 medRxiv
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Tau protein, the primary component in neurofibrillary tangles characteristic of Alzheimers Disease and related dementia disorders, normally regulates microtubule growth and stability. While tau dysfunction contributes to the progression of tauopathies, the role of microtubules in disease has remained unclear. Through forward genetic screening in Caenorhabditis elegans tauopathy models, we found multiple tubulin gene mutations that rescue tau-mediated neurodegeneration. Whole animal behavioral and in vitro biochemical assays were employed to characterize mutation-driven effects on neuron function, neurodegeneration, and effects on tubulin and tau proteins as well as microtubule function. Mutant tubulin genes were found to confer different levels of suppression correlating with the level of mutant gene expression. Mutant tubulins did not drastically alter total tau protein levels, tau phosphorylation or aggregation, however tau-induced neurodegeneration was rescued. The suppression of tau toxicity by tubulin gene mutations cannot be explained by changes in tau or tubulin expression, tau phosphorylation, or tau aggregation state. Rather the tubulin mutations appear to act by influencing global microtubule properties. In vitro experiments using C. elegans tubulin in semi-isolated and isolated contexts have indicated changes to microtubule properties without observable changes to tau-tubulin affinity. This work suggests that manipulation of microtubules can rescue tauopathy even when pathological tau species persist, supporting the importance of understanding microtubule contributions to disease progression and investigation into microtubule targeted gene therapy or small molecule approaches for tauopathy intervention.

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Application of D4 Fluorescent Probes for Quantitative and Spatial Analysis of Cholesterol in Cells

de La Chappelle, A.; Boiko, E.; Karakus, C.; Trahin, A.; Aulas, A.; Di Scala, C.

2026-04-04 biochemistry 10.64898/2026.04.01.715848 medRxiv
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Cholesterol is a key component of cellular membranes, regulating membrane organization, fluidity, and signaling. However, cholesterol analysis remains technically challenging, as no single method currently allows both accurate quantification and spatially resolved visualization. Biochemical assays provide accurate quantification but lack spatial resolution, whereas imaging strategies can perturb membrane organization or cholesterol accessibility. Here, we describe optimized protocols using fluorescent D4 probes derived from the cholesterol-binding domain of perfringolysin O (D4-mCherry and D4-GFP) to detect, visualize, and quantify cholesterol in biological samples. We detail procedures for probe production, purification, and application, and establish conditions that ensure robust and reproducible labeling of membrane-accessible cholesterol. By combining fluorescence-based imaging with quantitative analysis, this approach enables the assessment of cholesterol distribution while preserving its native membrane environment. The proposed methodology provides a versatile and reliable framework for studying cholesterol in a wide range of experimental systems.

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A lysyl oxidase (LOX)/bone morphogenetic protein-1 (BMP1) complex to facilitate collagen remodeling

Navarro-Gutierrez, M.; Romero-Albillo, V.; Rivas-Munoz, S.; Rosell-Garcia, T.; Jimenez-Sanchez, R.; Deen, M.; Poller, L. M.; Rodriguez-Pascual, F.

2026-03-30 molecular biology 10.64898/2026.03.27.714679 medRxiv
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Collagen biosynthesis within the extracellular matrix (ECM) relies on finely regulated enzymatic steps to ensure proper collagen maturation and fibrillar assembly. Among these, bone morphogenetic protein-1 (BMP1) and the canonical lysyl oxidase (LOX) act on the collagen telopeptide to promote procollagen processing and oxidative cross-linking, respectively. However, the mechanisms that ensure precise coordination of their activities remain poorly understood. Using NanoBiT assays, we identified and characterized a stable LOX/BMP1 protein complex that assembles intracellularly during trafficking through the ER/Golgi pathway and persists after secretion. Analysis of BMP1 and LOX domains involved in the interaction showed that BMP1 binding requires its CUB2/3 domains, while LOX recognition depends on a conserved, positively charged segment of LOX (residues 259-285) located immediately upstream of its catalytic domain. Formation of the LOX/BMP1 complex did not substantially alter LOX enzymatic activity but markedly enhanced LOX association with collagen type I through the carboxy-telopeptide region, facilitating the assembly of a ternary LOX/BMP1/collagen complex. This pre-assembled complex promoted efficient targeting of LOX to nascent collagen fibrils. Our findings reveal a previously unrecognized layer of regulation in collagen biosynthesis, in which LOX and BMP1 act as a functional unit to ensure precise localization and proper processing of collagen. This mechanism offers new insights into ECM assembly and identifies the LOX/BMP1 interface as a potentially druggable node for anti-fibrotic strategies.

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Site-specific O-glycans influence lacritin structure and multimerization in tears

Chang, V.; Chen, R.; Lian, I.; Mahoney, K. E.; Romano, J.; Laurie, G.; Malaker, S. A.

2026-04-02 biophysics 10.64898/2026.03.30.715376 medRxiv
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Lacritin is an abundantly expressed glycoprotein in tear fluid and plays key roles in immune response, tear secretion, and bacterial killing. These biological functions are tightly regulated through several biochemical mechanisms including multimerization, proteolysis, and alternative splicing, especially within its C-terminal domain. Given its critical role at the ocular surface, lacritin is currently under investigation as a diagnostic biomarker and therapeutic candidate for dry eye disease (DED). However, despite over three decades since its initial discovery, the functional significance of the O-glycans that comprise more than 50% of its molecular weight remain largely unknown. To address this gap, we leveraged mass spectrometry (MS)-based glycoproteomics and molecular dynamics (MD) to explore the structural role of site-specific O-glycans on C-terminal lacritin. In doing do, we identified distinct glycosylation profiles between monomeric and multimeric lacritin, particularly at glycosites located near crosslinking residues (Lys101 and Lys104) that modulate multimer formation. Building on our glycoproteomics data, we performed MD simulations on monomer and multimer glycoforms and revealed that O-glycans participate in intra-glycan-protein interactions, thereby affecting the conformational flexibility of lacritin and the spatial arrangement of Lys101 and Lys104. Finally, we quantified the solvent-accessible surface area (SASA) of Lys101 and Lys104, highlighting that proximal O-glycosylation is predicted to affect the propensity of these residues to participate in crosslinking. Taken together, these findings underscore a central role for lacritin O-glycans in affecting structural topology with implications for its downstream biological activity.

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Molecular and functional characterization of telomeric repeat-containing RNAs in Chinese hamster ovary cells

Domingues-Silva, B.; Azzalin, C. M.

2026-04-02 cell biology 10.64898/2026.04.01.715793 medRxiv
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Mammalian telomeric DNA comprises long tracts of tandem TTAGGG repeats. The same repeats are also found at internal chromosomal regions called interstitial telomeric sequences (ITSs). Telomeres are transcribed into UUAGGG-containing transcripts, named TERRA, which serve multiple functions in maintaining telomere integrity. Complementary RNAs containing C-rich telomeric repeats, named ARIA, have also been identified in few yeast mutants and mammalian cells with dysfunctional telomeres. The molecular features and functions of ARIA remain understudied, mainly due to its low abundance and the lack of suitable cellular systems. Here, we show that Chinese hamster ovary (CHO) cells produce abundant TERRA and ARIA transcripts, predominantly originating from ITSs. Both RNAs are polyadenylated, exhibit relatively short half-lives and form large cellular foci. We also show that ARIA depletion leads to exposure of single-stranded (ss) DNA at ITSs and that ssDNA exposure increases when ITS DNA is damaged. SsDNA formation does not require the DNA damage signaling kinases ATM and ATR, nor the exonucleases DNA2 and EXO1; however, ATM prevents excessive ssDNA accumulation when ARIA function is inhibited. These findings establish CHO cells as a powerful model to dissect telomeric RNA functions and reveal ARIA as a key regulator of telomeric repeat DNA integrity.

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Hydration and hydrolysis define antibiotic resistance conferred by macrolide esterases

Kelly, E. T. R.; Myziuk, I.; Hemmings, M. Z.; Mulla, Z.; Blanchet, J.; Ruzzini, A.; Berghuis, A. M.

2026-03-25 biochemistry 10.64898/2026.03.24.713787 medRxiv
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Macrolides are an antibiotic class widely used in both human and veterinary medicine, and function by interfering with protein synthesis. Regrettably, numerous strategies for evading the antibiotic properties of macrolides have been found in bacteria, including enzyme-mediated inactivation. These mechanisms are now widely disseminated among pathogenic, animal-associated and environmental bacteria making them a One Health issue. Macrolide esterases, which hydrolyze the macrolactones ester bond, confer one such resistance mechanism. Two types of macrolide esterases have thus far been identified, the well-studied erythromycin esterases and the recently discovered Est-type enzymes that belong to the /{beta}-hydrolase superfamily. We present detailed structure-function studies for four diverse Est type esterases: which only share 44-66% sequence identity (EstTSf, EstTSt, EstTBc, and EstXEc). In addition to resistance profiling and substrate specificity studies, we present structures for all four enzymes, including structures for EstTBc and EstXEc in complex with tylosin and tylvalosin macrolides, post hydrolysis. Complementing the data with mutational and kinetic studies allowed for a detailed analysis of the structural basis for macrolide-enzyme interactions. Combined the data suggest that promiscuous binding and imprecise positioning, mediated by a water-cage, dictate substrate specificity for Est-type macrolide resistance enzymes. These insights may prove beneficial for next-generation antibiotic development.

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Phosphorylation of the rod-tail hinge region of cingulin regulates its interaction with nonmuscle myosin-2B

Rouaud, F.; Mutero-Maeda, A.; Borgo, C.; Ruzzene, M.; Citi, S.

2026-04-05 cell biology 10.64898/2026.04.02.716052 medRxiv
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The tight junction (TJ) protein cingulin binds directly to nonmuscle myosin 2B (NM2B) through sequences in its C-terminal rod-tail region and recruits it to tight junctions (TJ) to control membrane cortex mechanics, epithelial morphogenesis and cingulin conformation. However, the minimal sequence required for cingulin-NM2B interaction and how this interaction is regulated is not known. Here we identify a 19-aminoacid sequence at the hinge between the cingulin rod and tail that is required for cingulin-NM2B interaction, and we investigate the role of phosphorylation of Ser residues within this region in regulating this interaction. Immunofluorescence microscopy localization of NM2B in cingulin-KO cells rescued with mutant cingulin constructs shows that phospho-mimetic but not dephospho-mimetic cingulin mutants inhibit NM2B recruitment to junctions and downstream regulation of cingulin conformation and TJ tortuosity, correlating with cingulin-NM2B interaction, as determined by GST pulldown analysis. In contrast, either phospo-or dephospho-mimetic mutants of Ser residues within the cingulin head domain do not affect either NM2B recruitment to TJ, or cingulin conformation and localization in cells, or TJ membrane tortuosity. Finally, Ser residues within the hinge display the consensus sequence for protein kinases CK1 and CK2, and, through in vitro phosphorylation, site mutation analysis and use of inhibitors, we identify a complex interplay between CGN phospho-sites, with a prominent negative role of Ser1162 phosphorylation in the regulation of cingulin-NM2B interaction. In summary, we show that cingulin-NM2B interaction is regulated by cingulin phosphorylation within the hinge and identify a potential role for CK1 and CK2 kinases in cingulin phosphorylation.