bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prophase removal of chromosome-associated RNAs facilitates anaphase chromosome segregation
Authors: Sharp Judith A. , Wang Wei , Blower Michael D. 
Published: October 2019

AbstractDuring mitosis, the genome is transformed from a decondensed, transcriptionally active state to a highly condensed, transcriptionally inactive state. Mitotic chromosome reorganization is marked by the general attenuation of transcription on chromosome arms, yet how the cell regulates nuclear and chromatin-associated RNAs after chromosome condensation and nuclear envelope breakdown is unknown. SAF-A/hnRNPU is an abundant nuclear protein with RNA-to-DNA tethering activity, coordinated by two spatially distinct nucleic acid binding domains. Here we show that RNA is evicted from prophase chromosomes through Aurora-B-dependent phosphorylation of the SAF-A DNA-binding domain; failure to execute this pathway leads to accumulation of SAF-A:RNA complexes on mitotic chromosomes and elevated rates of anaphase segregation defects. This work reveals a role for Aurora-B in removing chromatin-associated RNAs during prophase, and demonstrates that Aurora-B dependent relocalization of SAF-A during cell division contributes to the fidelity of chromosome segregation.
A microtranslatome coordinately regulates sodium and potassium currents in the heart
Authors: Eichel Catherine A. , Ríos-Pérez Erick B. , Liu Fang , Jameson Margaret B. , Jones David K. , Knickelbine Jennifer J. , Robertson Gail A. 
Published: October 2019

ABSTRACTCatastrophic arrhythmias and sudden cardiac death can occur with even a small imbalance between inward sodium currents and outward potassium currents, but mechanisms establishing this critical balance are not understood. Here, we show that mRNA transcripts encoding INa and IKr channels (SCN5A and hERG, respectively) are associated in defined complexes during protein translation. Using biochemical, electrophysiological and single-molecule fluorescence localization approaches, we find that roughly half the hERG translational complexes contain SCN5A transcripts. Moreover, the transcripts are regulated in a way that alters functional expression of both channels at the membrane. Association and coordinate regulation of transcripts in discrete “microtranslatomes” represents a new paradigm controlling electrical activity in heart and other excitable tissues.
Biochemical, Biophysical, and Functional Analyses of Two Isoforms of the SnRK2 inhibitor AtSCS
Authors: Tarnowski Krzysztof , Klimecka Maria , Ciesielski Arkadiusz , Goch Grażyna , Kulik Anna , Fedak Halina , Poznański Jarosław , Lichocka Małgorzata , Pierechod Marcin , Engh Richard A. , Dadlez Michał , Dobrowolska Grażyna , Bucholc Maria 
Published: October 2019

ABSTRACTSNF1-related protein kinases 2 (SnRK2s) are key signaling elements that regulate abscisic acid (ABA)-dependent plant development and responses to environmental stresses. Our previous data showed that the SnRK2-interacting Calcium Sensor (SCS) is an inhibitor of SnRK2 activity. InArabidopsis thaliana, the use of alternative transcription start sites located withinAtSCSgene results in two in-frame transcripts and subsequently two proteins, which differ only by the sequence position of the N-terminus. We described the longer AtSCS-A earlier, and now we describe the shorter AtSCS-B and compare both isoforms. The two forms differ significantly in their expression profiles in plant organs and in response to environmental stresses, in calcium binding properties, and conformational dynamics in the presence and absence of Ca2+. The results show that only AtSCS-A has the features of a calcium sensor. Both forms inhibit SnRK2 activity, but differ with respect to calcium dependence, as AtSCS-A requires calcium for inhibition, while AtSCS-B does not. Analysis of Arabidopsis plants stably expressing35S::AtSCS-A-c-mycor35S::AtSCS-B-c-mycin thescs-1knockout mutant revealed thatin plantaboth forms are negative regulators of the SnRK2 activity induced in response to ABA and regulate plant defense against water deficit. Moreover, the data present biochemical, biophysical, and functional properties of EF-hand-like motifs in plant proteins.One sentence SummaryTwo isoforms of SnRK2-interacting calcium sensor are expressed in Arabidopsis; they differ in calcium binding properties, but both of them inhibit SnRK2s and subsequently fine tune ABA signaling.
Identification of chloroplast envelope proteins with critical importance for cold acclimation
Authors: Trentmann Oliver , Mühlhaus Timo , Zimmer David , Sommer Frederik , Schroda Michael , Haferkamp Ilka , Keller Isabel , Pommerrenig Benjamin , Neuhaus H. Ekkehard 
Published: October 2019

AbstractThe ability of plants to cope with cold temperatures relies on their photosynthetic activity. This already demonstrates that the chloroplast is of utmost importance for cold acclimation and acquisition of freezing tolerance. During cold acclimation, the properties of the chloroplast change markedly. To provide the most comprehensive view of the protein repertoire of chloroplast envelope, we analysed this membrane system in Arabidopsis thaliana using MS-based proteomics. Profiling chloroplast envelope membranes was achieved by a cross comparison of protein intensities across plastid and the enriched membrane fraction both under normal and cold conditions. Multivariable logistic regression models the probabilities for the classification problem to address envelop localization. In total, we identified 38 envelope membrane intrinsic or associated proteins exhibiting altered abundance after cold acclimation. These proteins comprise several solute carries, such as the ATP/ADP antiporter NTT2 (substantially increased abundance) or the maltose exporter MEX1 (substantially decreased abundance). Remarkably, analysis of the frost recovery of ntt loss-of-function and mex1 overexpressor mutants confirmed that the comparative proteome is well suited to identify novel key factors involved in cold acclimation and acquisition of freezing tolerance. Moreover, for proteins with known physiological function we propose scenarios explaining their possible role in cold acclimation. Furthermore, spatial proteomics introduces a novel layer of complexity and enabled the identification of proteins differentially localized at the envelope membrane under the changing environmental regime.
Ascorbate deficiency does not limit non-photochemical quenching in Chlamydomonas reinhardtii
Authors: Vidal-Meireles André , Tóth Dávid , Kovács László , Neupert Juliane , Tóth Szilvia Z. 
Published: October 2019

SummaryAscorbate (vitamin C) plays essential roles in development, signaling, hormone biosynthesis, regulation of gene expression, stress resistance and photoprotection. In vascular plants, violaxanthin de-epoxidase (VDE) requires ascorbate (Asc) as reductant, thereby it is required for the energy-dependent component of non-photochemical quenching (NPQ). In order to assess the role of Asc in NPQ in green algae, which are known to contain low amounts of Asc, we searched for an insertional Chlamydomonas reinhardtii mutant affected in the VTC2 gene, essential for Asc biosynthesis. The Crvtc2-1 knockout mutant was viable and, depending on the growth conditions, it contained 10 to 20% Asc relative to its wild type. When Chlamydomonas was grown photomixotrophically at moderate light, the zeaxanthin-dependent component of NPQ emerged upon strong red illumination both in the Crvtc2-1 mutant and in its wild type. Deepoxidation was unaffected by Asc deficiency, demonstrating that the Chlorophycean VDE found in Chlamydomonas does not require Asc as a reductant. The rapidly induced, energy-dependent NPQ component, characteristic of photoautotrophic Chlamydomonas cultures grown at high light, was not limited by Asc deficiency either. On the other hand, a reactive oxygen species-induced photoinhibitory NPQ component was greatly enhanced upon Asc deficiency, both under photomixotrophic and photoautotrophic conditions. These results demonstrate that Asc has distinct roles in NPQ formation in Chlamydomonas than in vascular plants.One-sentence summaryIn Chlamydomonas -in contrast to seed plants-, ascorbate is not required for violaxanthin deepoxidation and energy-dependent non-photochemical quenching but it mitigates photoinhibitory quenching.
A mechanism coordinating root elongation, endodermal differentiation, redox homeostasis and response
Authors: Fu Jing , Liu Jiaming , Gao Xudong , Zhang Xinglin , Bai Juan , Hao Yueling , Cui Hongchang 
Published: October 2019

AbstractRoot growth relies on both cell division and elongation, which occur in the meristem and elongation zones respectively. SCARECROW (SCR) is a GRAS family gene essential for root growth and radial patterning in the Arabidopsis root. Previous studies showed that SCR promotes root growth by suppressing cytokinin response in the meristem, but there is also evidence that SCR expressed beyond the meristem is required as well for root growth. Here we report that SCR promotes root growth by promoting cell elongation through suppression of oxidative stress response and maintenance of redox homeostasis in the elongation zone. In the scr root, a higher level of hydrogen peroxide was detected, which can be attributed to down-regulation of peroxidase gene 3. When stress response was blocked or redox status was ameliorated by the aba2 or upb1 mutation, the scr mutant produced a significantly longer root with longer cells and a larger and mitotically more active meristem, even though the stem cell and radial patterning defects still persisted. We showed that WRKY15, an oxidative responsive gene, was a direct target of SCR down-regulated in the scr mutant, which suggests that SCR has an active role in suppressing oxidative stress response. Since hydrogen peroxide and peroxidases are essential for endodermal differentiation, these results suggest that SCR plays a central role in coordinating cell elongation, endodermal differentiation, redox homeostasis, and oxidative stress response in plant root.One sentence summaryThis study reveals a novel mechanism of root growth regulation, which involves a previously unrecognized role of SCR in regulating cell elongation, endodermal differentiation, and redox homeostasis.
BTB-TAZ domain protein MdBT2 modulates malate accumulation by targeting a bHLH transcription factor for degradation in response to nitrate
Authors: Zhang Quan-Yan , Gu Kai-Di , Cheng Lailiang , Wang Jia-Hui , Yu Jian-Qiang , Wang Xiao-Fei , You Chun-Xiang , Hu Da-Gang , Hao Yu-Jin 
Published: October 2019

AbstractExcessive application of nitrate, an essential macronutrient and a signal regulating diverse physiological processes, decreases malate accumulation in apple fruit, but the underlying mechanism remains poorly understood. Here, we show that an apple BTB/TAZ protein MdBT2 is involved in regulating malate accumulation and vacuolar pH in response to nitrate.In vitroandin vivoassays indicate that MdBT2 interacts directly with and ubiquitinates a bHLH transcription factor, MdCIbHLH1, via the ubiquitin/26S proteasome pathway in response to nitrate. This ubiquitination results in the degradation of MdCIbHLH1 protein and reduces the transcription of MdCIbHLH1-targeted genes involved in malate accumulation and vacuolar acidification includingMdVHA-Aencoding a vacuolar H+-ATPase gene, andMdVHP1encoding a vacuolar H+-pyrophosphatase gene, as well asMdALMT9encoding a aluminum-activated malate transporter gene. A series of transgenic analyses in apple materials including fruits, plantlets and calli demonstrate that MdBT2 controls nitrate-mediated malate accumulation and vacuolar pH at least partially, if not completely, via regulating the MdCIbHLH1 protein level. Taken together, these findings reveal that MdBT2 regulates the stability of MdCIbHLH1 via ubiquitination in response to nitrate, which in succession transcriptionally reduces the expression of malate-associated genes, thereby controlling malate accumulation and vacuolar acidification in apples under high nitrate supply.
The Arp2/3 complex and the formin, Diaphanous, are both required to regulate the size of germline ring canals in the developing egg chamber
Authors: Thestrup Josephine , Tipold Marina , Kindred Alexandra , Stark Kara , Curry Travis , Lewellyn Lindsay 
Published: October 2019

AbstractIntercellular bridges are an essential structural feature found in both germline and somatic cells throughout the animal kingdom. Because of their large size, the germline intercellular bridges, or ring canals, in the developing fruit fly egg chamber are an excellent model to study the formation, stabilization, and expansion of these structures. Within the egg chamber, the germline ring canals connect 15 supporting nurse cells to the developing oocyte, facilitating the transfer of materials required for successful oogenesis. The ring canals are derived from a stalled actomyosin contractile ring; once formed, additional actin and actin-binding proteins are recruited to the ring to support the 20-fold expansion that accompanies oogenesis. These behaviors provide a unique model system to study the actin regulators that control incomplete cytokinesis, intercellular bridge formation, and expansion. By temporally controlling their expression in the germline, we have demonstrated that the Arp2/3 complex and the formin, Diaphanous (Dia), coordinately regulate ring canal size and expansion throughout oogenesis. Dia is required for successful incomplete cytokinesis and the initial stabilization of the germline ring canals. Once the ring canals have formed, the Arp2/3 complex and Dia cooperate to determine ring canal size and maintain their stability. Our data suggest that the nurse cells must maintain a precise balance between the activity of these two nucleators during oogenesis.
Hippocampal hub neurons maintain unique functional properties throughout their lifetime
Authors: Bocchio Marco , Gouny Claire , Angulo-Garcia David , Toulat Tom , Tressard Thomas , Baude Agnès , Cossart Rosa 
Published: October 2019

AbstractThe temporal embryonic origins of cortical GABA neurons are critical for their specialization. In the neonatal hippocampus, GABA cells born the earliest (ebGABAs) operate as ‘hubs’ by orchestrating neuronal dynamics. However, their fate remains largely unknown. To fill this gap, we have examined CA1 ebGABAs using a combination of electrophysiology, neurochemical analysis, optogenetic connectivity mapping as well as ex vivo and in vivo calcium imaging. We show that CA1 ebGABAs not only operate as hubs during development, but also maintain distinct morpho-physiological and connectivity profiles, including a bias for long-range targets and local excitatory inputs. In vivo, ebGABAs signal a variety of network states, including the activation of local CA1 assemblies. Hence, ebGABAs are specified from birth to ensure unique functions throughout their lifetime. In the adult brain, this may take the form of a long-range hub role through the coordination of cell assemblies across distant regions.
The pheromone and pheromone receptor mating-type locus is involved in controlling uniparental mitochondrial inheritance inCryptococcus
Authors: Sun Sheng , Fu Ci , Ianiri Giuseppe , Heitman Joseph 
Published: October 2019

ABSTRACTMitochondria are inherited uniparentally during sexual reproduction in the majority of eukaryotic species studied, including humans, mice, nematodes, as well as many fungal species. Mitochondrial uniparental inheritance (mito-UPI) could be beneficial in that it avoids possible genetic conflicts between organelles with different genetic backgrounds, as recently shown in mice; and it could prevent the spread of selfish genetic elements in the mitochondrial genome. Despite the prevalence of observed mito-UPI, the underlying mechanisms and the genes involved in controlling this non-mendelian inheritance are poorly understood in many species. InCryptococcus neoformans, a human pathogenic basidiomyceteous fungus, mating types (MATα andMATa) are defined by alternate alleles at the singleMATlocus that evolved from fusion of the twoMATloci (P/Rencoding pheromones and pheromone receptors,HDencoding homeodomain transcription factors) that are the ancestral state in the basidiomycota. Mitochondria are inherited uniparentally from theMATaparent inC. neoformansand this requires theSXI1α andSXI2aHD factors encoded byMAT. However, there is evidence additional genes contribute to control of mito-UPI inCryptococcus. Here we show that inCryptococcus amylolentus, a sibling species ofC. neoformanswith unlinkedP/RandHD MATloci, mitochondrial uniparental inheritance is controlled by theP/Rlocus, and is independent of theHDlocus. Consistently, by replacing theMATα alleles of the pheromones (MF) and pheromone receptor (STE3) with theMATaalleles, we show that theseP/Rlocus defining genes indeed affect mito-UPI inC. neoformansduring sexual reproduction. Additionally, we show that during early stages ofC. neoformanssexual reproduction, conjugation tubes are always produced by theMATα cells, resulting in unidirectional migration of theMATα nucleus into theMATacell during zygote formation. This process is controlled by theP/Rlocus and could serve to physically restrict movement ofMATα mitochondria in the zygotes, and thereby contribute to mito-UPI. We propose a model in which both physical and genetic mechanisms function in concert to prevent the coexistence of mitochondria from the two parents in the zygote and subsequently in the meiotic progeny, thus ensuring mito-UPI in pathogenicCryptococcus, as well as in closely related non-pathogenic species. The implications of these findings are discussed in the context of the evolution of mito-UPI in fungi and other more diverse eukaryotes.
A highly homogeneous expansion microscopy polymer composed of tetrahedron-like monomers
Authors: Gao Ruixuan , Yu Chih-Chieh (Jay) , Gao Linyi , Piatkevich Kiryl D , Neve Rachael L , Upadhyayula Srigokul , Boyden Edward S 
Published: October 2019

ABSTRACTExpansion microscopy (ExM) physically magnifies biological specimens to enable nanoscale-resolution imaging on conventional microscopes. Current ExM methods permeate biological specimens with free radical-polymerized polyacrylate hydrogels, whose network structure limits the microscopy resolution enabled by ExM. Here we report that ExM is possible using hydrogels with more homogeneous network structure, assembled via non-radical terminal linking of monomers of tetrahedral shape. As with earlier forms of ExM, such “tetra-gel”-embedded specimens can be iteratively expanded for greater physical magnification. Iterative tetra-gel expansion of herpes simplex virus type 1 (HSV-1) virions by ~10x in linear dimension results in a viral envelope deviation from sphericity of 9.2 nm, rather than the 14.3 nm enabled by free radical-polymerized hydrogels used in earlier versions of ExM. Thus, tetra-gel polymer chemistry may support new forms of ExM imaging that introduce fewer spatial errors than earlier versions, and raise the question of whether single biomolecule precision may be achievable.
Site-specific phosphorylation of histone H1.4 is associated with transcription activation
Authors: Saha Ankita , Seward Christopher , Stubbs Lisa , Mizzen Craig Andrew 
Published: October 2019

ABSTRACTCore histone variants like H2A.X and H3.3 and their modified forms serve specialized roles in chromatin processes that depend on their genomic distributions and their interaction with chromatin components. Similarly, previous evidence from our lab and others suggest that amino acid sequence variant forms of the linker histone family and specific posttranslational modifications on these variants also result in distinct functions. These inferences are contrary to the notion that the H1 family function as redundant repressors. Here, we provide the first genome-wide evidence that when phosphorylated at a specific C-terminal domain site i.e serine 187, the linker histone H1.4 is enriched at active promoters. This is in direct contrast to previous reports that suggest that phosphorylation of H1 leads to their dissociation from chromatin. Using a highly specific pS187H1.4 antibody earlier developed in the lab, we studied the distribution patterns of pS187H1.4 in estradiol-responsive MCF7 cells where we demonstrated the inducible nature of this modification. We also used public MCF7 data to confirm the association of pS187H1.4 with well-known active transcription marks. These data suggest that linker histones and their modified forms have a more nuanced role than previously understood and may even play a role in transcription regulation.
A functional analysis of the Drosophila genehindsight: evidence for positive regulation of EGFR signaling
Authors: Kim Minhee , Du Olivia Y. , Whitney Rachael J. , Wilk Ronit , Hu Jack , Krause Henry M. , Kavaler Joshua , Reed Bruce H. 
Published: October 2019

AbstractWe have investigated the relationship between the function of the genehindsight(hnt), which is the Drosophila homolog ofRas Responsive Element Binding protein-1(RREB-1), and the EGFR signaling pathway. We report thathntmutant embryos are defective in EGFR signaling dependent processes, namely chordotonal organ recruitment and oenocyte specification. We also show the temperature sensitive hypomorphic allelehntpebbledis enhanced by the hypomorphic MAPK allelerolled(rl1). We find thathntoverexpression results in ectopicDPax2expression within the embryonic peripheral nervous system, and we show that this effect is EGFR-dependent. Finally, we show that the canonical U-shaped embryonic lethal phenotype ofhnt,which is associated with premature degeneration of the extraembyonic amnioserosa and a failure in germ band retraction, is rescued by expression of several components of the EGFR signaling pathway (sSpi,Ras85DV12,pntP1) as well as the caspase inhibitorp35. Based on this collection of corroborating evidence, we suggest that an overarching function ofhntinvolves the positive regulation of EGFR signaling.
PINK1 Regulates Dopamine and Lipids at Mitochondria to Maintain Synapses and Neuronal Function
Authors: Bus Christine , Geisler Sven , Feldkaemper Marita , Flores-Romero Hector , Schaedler Anna , Zittlau Katharina , Zarani Maria , Uysal Betül , Casadei Nicolas , Fallier-Becker Petra , Schwarz Lisa , Brouwers Jos F. , Koch Henner , Ugun-Klusek Aslihan , Maruszczak Klaudia , Vogt Weisenhorn Daniela M. , Wurst Wolfgang , Schmidt Benjamin , Martens Gerard , Brügger Britta , Rapaport Doron , Garcia Ana , Macek Boris , Krüger Rejko , Gasser Thomas , Kahle Philipp , Fitzgerald Julia C. 
Published: October 2019

AbstractMitochondrial dysfunction contributes to the pathogenesis of Parkinson’s disease but it is not clear why inherent mitochondrial defects lead specifically to the death of dopaminergic neurons of the mid brain. PINK1 is mitochondrial kinase andPINK1mutations cause early onset Parkinson’s disease.We found that in neuronal progenitors, PINK1 regulates mitochondrial morphology, mitochondrial contact to the endoplasmic reticulum (ER) and the phosphorylation of Miro1. A compensatory metabolic shift towards lipid synthesis provides mitochondria with the components needed for membrane renewal and oxidative phosphorylation, maintaining the mitochondrial network once mature.Cholesterol is increased by loss of PINK1, promoting overall membrane rigidity. This alters the distribution of phosphorylated DAT at synapses and impairs dopamine uptake. PINK1 is required for the phosphorylation of tyrosine hydroxylase at Ser19, dopamine and calcium homeostasis and dopaminergic pacemaking.We suggest a novel mechanism for PINK1 pathogenicity in Parkinson’s disease in addition to but not exclusive of mitophagy. We also provide a basis for potential therapeutics by showing that low doses of the cholesterol depleting drug ß-cyclodextrin reverse PINK1-specific phenotypes.