bluuebunny/crossref_metadata_2025_split huggingface dataset:
Queuine salvaging in the human parasite Entamoeba histolytica
Authors: Sarid Lotem , Sun Jingjing , Chittrakanwong Jurairat , Trebicz-Geffen Meirav , Dedon Peter C. , Ankri Serge 
Published: June 2022

AbstractQueuosine (Q) is a naturally occurring modified nucleoside that occurs in the first position of transfer RNA anticodons such as Asp, Asn, His, and Tyr. As eukaryotes lack pathways to synthesize queuine, the Q nucleobase, they must obtain it from their diet or gut microbiota. Previously, we described the effects of queuine on the physiology of the eukaryotic parasite Entamoeba histolytica and characterized the enzyme EhTGT responsible for queuine incorporation into tRNA. At present, it is unknown how E. histolytica salvages Q from gut bacteria. We used liquid chromatography–mass spectrometry (LC–MS) and N-acryloyl-3-aminophenylboronic acid (APB) PAGE analysis to demonstrate that E. histolytica trophozoites can salvage queuine from Q or E. coli K12 but not from the modified E. coli QueC strain, which cannot produce queuine. We then examined the role of EhDUF2419, a protein with homology to DNA glycosylase, as queuine salvage enzyme in E. histolytica. We found that glutathione S-transferase (GST)-EhDUF2419 catalyzed the conversion of Q into queuine. Trophozoites silenced for EhDUF2419 expression are impaired in their ability to form Q-tRNA from Q or from E. coli. We also observed that Q partially protects control trophozoites from oxidative stress (OS), but not siEhDUF2419 trophozoites. Overall, our data reveal that EhDUF2419 is central for the salvaging of queuine from bacteria and for the resistance of the parasite to OS.
Abl2 mediates microtubule nucleation and repair via tubulin co-condensation
Authors: Lyu Wanqing , Duan Daisy , Wu Kuanlin , Wu Chunxiang , Xiong Yong , Koleske Anthony J. 
Published: June 2022

SummaryAbl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with microtubules to regulate axon guidance and neuronal morphogenesis. Vertebrate Abl2 binds to microtubules and promotes their plus-end elongation both in vitro and in cells, but the molecular mechanisms by which Abl2 regulates microtubule (MT) dynamics were unclear. We report here that Abl2 regulates MT assembly via condensation and direct interactions with both the MT lattice and tubulin dimers. We find that Abl2 promotes MT nucleation, which is further facilitated by the ability of the Abl2 C-terminal half to undergo phase separation and form co-condensates with tubulin. A naturally occurring tubulin binding-deficient Abl2 splice isoform fails to promote nucleation. Abl2 binds to regions adjacent to MT damage and facilitates their repair via fresh tubulin recruitment and increases MT rescue frequency and lifetime. MT recovery after nocodazole treatment is greatly slowed in Abl2 knockout COS-7 cells compared to wild type cells. We propose a model in which Abl2 locally concentrates tubulin and recruits it to MT tips or to defects in the MT lattice to promote MT repair, rescue, and nucleation.
Retinoic acid control of pax8 during renal specification of Xenopus pronephros involves hox and meis3
Authors: Durant-Vesga Jennifer , Suzuki Nanoka , Ochi Haruki , Le Bouffant Ronan , Eschstruth Alexis , Ogino Hajime , Umbhauer Muriel , Riou Jean-François 
Published: June 2022

AbstractDevelopment of the Xenopus pronephros relies on renal precursors grouped at neurula stage into a specific region of dorso-lateral mesoderm called the kidney field. Formation of the kidney field at early neurula stage is dependent on retinoic (RA) signaling acting upstream of renal master transcriptional regulators such as pax8 or lhx1. Althoughlhx1might be a direct target of RA-mediated transcriptional activation in the kidney field, how RA controls the emergence of the kidney field remains poorly understood. In order to better understand RA control of renal specification of the kidney field, we have performed a transcriptomic profiling of genes affected by RA disruption in lateral mesoderm explants isolated prior to the emergence of the kidney field and cultured at different time points until early neurula stage. Besides genes directly involved in pronephric development (pax8, lhx1, osr2, mecom), hox (hoxa1, a3, b3, b4, c5andd1) and the hox co-factormeis3appear as a prominent group of genes encoding transcription factors (TFs) downstream of RA. Supporting the idea of a role of meis3 in the kidney field, we have observed that meis3 depletion results in a severe inhibition ofpax8expression in the kidney field. Meis3 depletion only marginally affects expression oflhx1andaldh1a2suggesting that meis3 principally acts upstream ofpax8. Further arguing for a role of meis3 and hox in the control of pax8, expression of a combination of meis3, hoxb4 and pbx1 in animal caps inducespax8expression, but not that oflhx1. The same combination of TFs is also able to transactivate a previously identifiedpax8enhancer, Pax8-CNS1. Mutagenesis of potential PBX-Hox binding motifs present in Pax8-CNS1 further allows to identify two of them that are necessary for transactivation. Finally, we have tested deletions of regulatory sequences in reporter assays with a previously characterized transgene encompassing 36.5 kb of theX. tropicalis pax8gene that allows expression of a truncated pax8-GFP fusion protein recapitulating endogenouspax8expression. This transgene includes three conservedpax8enhancers, Pax8-CNS1, Pax8-CNS2 and Pax8-CNS3. Deletion of Pax8-CNS1 alone does not affect reporter expression, but deletion of a 3.5kb region encompassing Pax8-CNS1 and Pax8-CNS2 results in a severe inhibition of reporter expression both in the otic placode and kidney field domains.
Methylation status of VTRNA2-1/nc886 is stable across human populations, monozygotic twin pairs and in majority of somatic tissues
Authors: Marttila Saara , Tamminen Hely , Rajić Sonja , Mishra Pashupati P , Lehtimäki Terho , Raitakari Olli , Kähönen Mika , Kananen Laura , Jylhävä Juulia , Hägg Sara , Delerue Thomas , Peters Annette , Waldenberger Melanie , Kleber Marcus E , März Winfried , Luoto Riitta , Raitanen Jani , Sillanpää Elina , Laakkonen Eija K , Heikkinen Aino , Ollikainen Miina , Raitoharju Emma 
Published: June 2022

AbstractAims and methodsOur aim was to characterise the methylation level of a polymorphically imprinted gene, VTRNA2-1/nc886, in human populations and somatic tissues. We utilised 48 datasets, consisting of >30 different tissues and >30 000 individuals.ResultsWe show that the nc886 methylation status is associated with twin status and ethnic background, but the variation between populations is limited. Monozygotic twin pairs present concordant methylation, while ∼30% of dizygotic twin pairs present discordant methylation in the nc886 locus. The methylation levels of nc886 are uniform across somatic tissues, except in cerebellum and skeletal muscle.ConclusionWe hypothesize that the nc886 imprint is established in the oocyte and that after implantation, the methylation status is stable, excluding a few specific tissues.
Inflammatory mediators act at renal pericytes to elicit contraction of vasa recta and reduce pericyte density along this medullary vascular network
Authors: Lilley Rebecca J. , Taylor Kirsti , Wildman Scott S.P. , Peppiatt-Wildman Claire M. 
Published: June 2022

AbstractRegardless of initiating cause, renal injury promotes a potent pro-inflammatory environment in the outer medulla and a concomitant sustained decrease in medullary blood flow (MBF). This decline in MBF is believed to one of the critical events in the pathogenesis of acute kidney injury (AKI), yet the precise cellular mechanism underlying this are still to be fully elucidated. MBF is regulated by contractile pericyte cells that reside on the descending vasa recta (DVR) capillaries, which are the primary source of blood flow to the medulla. Using the rodent and murine live kidney slice models, we sought to investigate the acute effects of key medullary inflammatory mediators TNF-α, IL-1β, IL-33, IL-18, C3a and C5a on vasa recta pericytes. Live kidney slices taken from both mice and rats and exposed to TNF-α, IL-18, IL-33, and C5a demonstrated a real-time pericyte-mediated constriction of DVR. When pro-inflammatory mediators were applied in the presence of the AT1-R blocker Losartan the inflammatory-mediated constriction that had previously been observed was significantly attenuated. When live kidney slices were exposed to inflammatory mediators for 4-hours, we noted a significantly reduction in the number of NG2+ positive pericytes along vasa recta capillaries in both rodent and murine kidney slices. Data collected in this study, demonstrate that inflammatory mediators can dysregulate pericytes to constrict DVR diameter and reduce the density of pericytes along vasa recta vessels, further diminishing the regulatory capacity of the capillary network. We postulate that preliminary findings here suggest pericytes play a role in AKI.New & NoteworthyHow medullary blood flow (MBF) becomes disproportionately dysregulated following renal injury is poorly understood yet is associated with worse prognostic outcomes following AKI. This study shows in both rats and mice that inflammatory mediators associated with AKI have acute and sustained microvascular actions at pericytes eliciting dysregulation of descending vasa recta (DVR) diameter and their loss from the DVR. This work highlights a possible pathology behind the dysregulation and reduction of MBF observed following AKI.
Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired
Authors: LaSarre Breah , Morlen Ryan , Neumann Gina C. , Harwood Caroline S. , McKinlay James B. 
Published: June 2022

AbstractDenitrification is a form of anaerobic respiration wherein nitrate (NO3-) is sequentially reduced via nitrite (NO2-), nitric oxide, and nitrous oxide (N2O) to dinitrogen gas (N2) by four reductase enzymes. Partial denitrifying bacteria possess only one, or some, of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here we tested the denitrifying capabilities of two purple nonsulfur bacteria,Rhodopseudomonas palustrisCGA0092 andRhodobacter capsulatusSB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO2-to N2and SB1003 reduced N2O to N2. For each bacterium, N2O reduction could be used for both electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in the dark. However, N2O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO3-served as a stable, non-catalyzable molecule that was sufficient to activate N2O reduction. Using a β-galactosidase reporter we found that NO3-acted, at least in part, by stimulating N2O reductase gene expression. In SB1003, NO2-, but not NO3-, activated N2O reduction but NO2-was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use.ImportanceDenitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions.
Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification
Authors: Martin Rebeca San , Das Priyojit , Sanders Jacob T. , Hill Ashtyn , McCord Rachel Patton 
Published: June 2022

AbstractHutchinson-Gilford Progeria Syndrome results from a mutation in Lamin A, and it is characterized by the incorporation of progerin into the nuclear lamina. Progerin expression leads to alterations in genome architecture, nuclear morphology, and epigenetic states, which in turn cause altered phenotypes in all cells of the mesenchymal lineage. Here, we report a comprehensive analysis of the transcriptional status of patient derived HGPS fibroblasts, including nine cell lines not previously reported. We observe that these fibroblasts carry abnormal transcriptional signatures, centering around five main functional hubs: DNA maintenance and epigenetics, bone development and homeostasis, blood vessel maturation and development, fat deposition and lipid management, and processes related to muscle growth. Stratification of patients by age revealed that a cohort of genes related to endochondral ossification and chondrogenic commitment show altered expression patterns in children aged four to seven years old, where this differentiation program starts in earnest, related to the growth of long bones. We further report changes in lamin associated domains and 3D genome organization around a cohort of genes of interest, identified in this study.
MicroProteins miP1b/BBX30 and miP1a/BBX31 form a positive feedback loop with ABI5 to retard seedling establishment
Authors: Singh Deeksha , Datta Sourav 
Published: June 2022

AbstractIn plants the switch to autotrophic growth involves germination followed by post-germination seedling establishment. When environmental conditions are not favorable, the stress hormone Abscisic Acid (ABA) signals plants to postpone seedling establishment by inducing the expression of the transcription factor ABI5. The levels of ABI5 determine the efficiency of the ABA mediated post-germination developmental growth arrest. The molecular mechanisms regulating the stability and activity of ABI5 during the transition to light are less known. We found that two microProteins miP1a/ BBX31 and miP1b/BBX30 alongwith ABI5 inhibit post-germination seedling establishment in a partially interdependent manner. MicroProteins are single-domain proteins that interact with multi-domain proteins to modulate their post-translational activity. miP1a/ BBX31 and miP1b/BBX30 physically interact with ABI5 to stabilize it and promote its binding to promoters of downstream genes in light. ABI5 reciprocally induces the expression ofBBX30andBBX31by directly binding to their promoter. ABI5 and the two microProteins thereby form a positive feedback loop to promote ABA-mediated developmental arrest of seedlings. Our study highlights the functional versatility of microProteins which can act as regulators of crucial developmental transitions in plants as well as other eukaryotes.
Tunnel dynamics of quinone derivatives and its coupling to protein conformational rearrangements in respiratory complex I
Authors: Lasham Jonathan , Haapanen Outi , Zickermann Volker , Sharma Vivek 
Published: June 2022

AbstractRespiratory complex I in mitochondria and bacteria catalyzes the transfer of electrons from NADH to quinone (Q). The free energy available from the reaction is used to pump protons and to establish a membrane proton electrochemical gradient, which drives ATP synthesis. Even though several high-resolution structures of complex I have been resolved, how Q reduction is linked with proton pumping, remains unknown. Here, microsecond long molecular dynamics (MD) simulations were performed on Yarrowia lipolytica complex I structures where Q molecules have been resolved in the ~30 Å long Q tunnel. MD simulations of several different redox/protonation states of Q reveal the coupling between the Q dynamics and the restructuring of conserved loops and ion pairs. Oxidized quinone stabilizes towards the N2 FeS cluster, a binding mode not previously described in Yarrowia lipolytica complex I structures. On the other hand, reduced (and protonated) species tend to diffuse towards the Q binding sites closer to the tunnel entrance. Mechanistic and physiological relevance of these results are discussed.
The cohesin modifier ESCO2 is stable during DNA replication
Authors: Jevitt Allison M. , Rankin Brooke D. , Chen Jingrong , Rankin Susannah 
Published: June 2022

AbstractCohesion between sister chromatids by the cohesin protein complex ensures accurate chromosome segregation and enables recombinational DNA repair. Sister chromatid cohesion is promoted by acetylation of the SMC3 subunit of cohesin by the ESCO2 acetyltransferase, inhibiting cohesin release from chromatin. The interaction of ESCO2 with the DNA replication machinery, in part through PCNA-interacting protein (PIP) motifs in ESCO2, is required for full cohesion establishment. Recent reports have suggested that Cul4-dependent degradation regulates the level of ESCO2 protein during late S/G2 phase of the cell cycle. To follow up on these observations, we have characterized ESCO2 stability in Xenopus egg extracts, a cell-free system that recapitulates cohesion establishment in vitro. We found that ESCO2 was stable during DNA replication in this system. Indeed, further challenging the system by inducing DNA damage signaling or increasing the number of nuclei undergoing DNA replication had no significant impact on the stability of ESCO2. In transgenic somatic cell lines, we did not see evidence of GFP-ESCO2 degradation during S phase of the cell cycle using either flow cytometry or live-cell imaging techniques. We conclude that ESCO2 is stable during DNA replication in both embryonic and somatic cells.
Antibodies to protozoan variable surface antigens induce antigenic variation
Authors: Tenaglia Albano H. , Luján Lucas A. , Ríos Diego N. , Midlej Victor , Iribarren Paula A. , Molina Cecilia R. , Berazategui M. Agustina , Torri Alessandro , Saura Alicia , Peralta Damián O. , Rodríguez-Walker Macarena , Fernández Elmer A. , Petiti Juan P. , Serradell Marianela C. , Gargantini Pablo R. , Alvarez Vanina E. , de Souza Wanderley , Luján Hugo D. 
Published: June 2022

AbstractThe genomes of most protozoa encode families of variant surface antigens, whose mutually exclusive changes in expression allow parasitic microorganisms to evade the host immune response1,2. It is widely assumed that antigenic variation in protozoan parasites is accomplished by the spontaneous appearance within the population of cells expressing antigenic variants that escape antibody-mediated cytotoxicity1,2. Here we show, bothin vitroand in animal infections, that antibodies to Variant-specific Surface Proteins (VSPs) of the intestinal parasiteGiardia lambliaare not cytotoxic, inducing instead VSP clustering into liquid-ordered phase membrane microdomains that trigger a massive release of microvesicles carrying the original VSP and switch in expression to different VSPs by a calcium-dependent mechanism. Surface microvesiculization and antigenic switching are also stimulated whenTrypanosoma bruceiandTetrahymena thermophilaare confronted to antibodies directed to their GPI-anchored variable surface glycoproteins. This novel mechanism of surface antigen clearance throughout its release into microvesicles coupled to the stochastic induction of new phenotypic variants not only changes the current paradigm of spontaneous antigenic switching but also provides a new framework for understanding the course of protozoan infections as a host/parasite adaptive process.
Calcium dependence of both lobes of calmodulin is involved in binding to a cytoplasmic domain of SK channels
Authors: Halling D. Brent , Philpo Ashley E. , Aldrich Richard W. 
Published: June 2022

AbstractKCa2.1-3 Ca2+-activated K+-channels (SK) require calmodulin to gate in response to cellular Ca2+. A model for SK gating proposes that the N-terminal domain (N-lobe) of calmodulin is required for activation, but an immobile C-terminal domain (C-lobe) has constitutive, Ca2+-independent binding. Although structures support a domain-driven hypothesis of SK gate activation by calmodulin, only a partial understanding is possible without measuring both channel activity and protein binding. We measured SK2 (KCa2.2) activity using inside-out patch recordings. Currents from calmodulin-disrupted SK2 channels can be restored with exogenously applied calmodulin. We find that SK2 activity only approaches full activation with full-length calmodulin with both an N- and C-lobe. We measured calmodulin binding to a C-terminal SK peptide (SKp) using both composition-gradient multi-angle light scattering and tryptophan emission spectra. Isolated lobes bind to SKp with high affinity, but isolated lobes do not rescue SK2 activity. Consistent with earlier models, N-lobe binding to SKp is stronger in Ca2+, and C-lobe binding affinity is strong independent of Ca2+. However, a native tryptophan in SKp is sensitive to Ca2+binding to both the N- and C-lobes of calmodulin at Ca2+concentrations that activate SK2, demonstrating that the C-lobe interaction with SKp changes with Ca2+. Our peptide binding data and electrophysiology show that SK gating models need deeper scrutiny. We suggest that the Ca2+-dependent associations of both lobes of calmodulin to SKp are crucial events during gating. Additional investigations are necessary to complete a mechanistic gating model consistent with binding, physiology, and structure.