bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ataxia protein sacsin is required for integrin trafficking and synaptic organization
Authors: Romano Lisa E.L. , Aw Wen Yih , Hixson Kathryn M. , Novoselova Tatiana V. , Havener Tammy M. , Howell Stefanie , Hall Charlotte L , Xing Lei , Beri Josh , Nethisinghe Suran , Perna Laura , Hatimy Abubakar , Chioccioli Altadonna Ginevra , Graves Lee M. , Herring Laura E. , Hickey Anthony J. , Thalassinos Konstantinos , Chapple J. Paul , Wolter Justin M. 
Published: August 2021

AbstractAutosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is caused by mutations in SACS, which manifest as a childhood-onset cerebellar ataxia. Cellular ARSACS phenotypes include mitochondrial dysfunction, intermediate filament (IF) disorganization, and loss of Purkinje neurons. It is unclear how the loss of SACS causes these deficits, or why they manifest as cerebellar ataxia. We employed a multi-omics approach to characterize molecular and cellular deficiencies in SACS knockout (KO) cells. We identified alterations in microtubule structure and dynamics, protein trafficking, and mislocalization of synaptic and focal adhesion proteins. Targeting PTEN, a negative regulator of focal adhesions, rescued several cellular phenotypes in SACS KO cells. We found sacsin interacts with proteins implicated in vesicle transport, including HSP proteins, and interactions between structural and cell adhesion proteins were diminished in SACS KO cells. In all, this study suggests that trafficking and localization of synaptic adhesion proteins is a causal molecular deficiency in ARSACS.
Bacterial glycyl tRNA synthetase offers glimpses of ancestral protein topologies
Authors: Dimas-Torres Jorge-Uriel , Rodríguez-Hernández Annia , Valencia-Sánchez Marco Igor , Campos-Chávez Eduardo , Godínez-López Victoria , Rodríguez-Chamorro Daniel-Eduardo , Grøtli Morten , Fleming Cassandra , Hernández-González Adriana , Arciniega Marcelino , Torres-Larios Alfredo 
Published: August 2021

AbstractAminoacyl tRNA synthetases (aaRSs) are among the proposed proteins present in the Last Universal Common Ancestor (LUCA). There are two types of glycyl tRNA synthetases (GlyRSs), from which the archaeal-eukaryal type is the one suggested to be present in LUCA. Here we solved the crystal structure of a complete bacterial glycyl tRNA synthetase (bacGlyRS) and show that indeed, bacGlyRS carries several structural signals that point it at the origin of all aaRSs. Furthermore, if bacGlyRS is ancestral, it should help to build a reliable Tree of Life (ToL). Given the modular nature of protein evolution, we used only two sub-domain segments with duplicated ancestral topologies, no detected orthologs and an assumed limited horizontal gene transfer (HGT). These motifs correspond to the non-specific RNA binding regions of contemporary bacGlyRS, archaeal CCA-adding enzyme (arch-CCAadd), and eukaryotic rRNA processing enzyme (euk-rRNA). The calculated, rooted bacterial ToL agrees with several phyla relationships unaccounted by the available trees.
Mutations that adapt SARS-CoV-2 to mustelid hosts do not increase fitness in the human airway
Authors: Zhou Jie , Peacock Thomas P. , Brown Jonathan C. , Goldhill Daniel H. , Elrefaey Ahmed M.E. , Penrice-Randal Rebekah , Cowton Vanessa M. , Lorenzo Giuditta De , Furnon Wilhelm , Harvey William T. , Kugathasan Ruthiran , Frise Rebecca , Baillon Laury , Lassaunière Ria , Thakur Nazia , Gallo Giulia , Goldswain Hannah , Donovan-Banfield I’ah , Dong Xiaofeng , Randle Nadine P. , Sweeney Fiachra , Glynn Martha C. , Quantrill Jessica L. , McKay Paul F. , Patel Arvind H. , Palmarini Massimo , Hiscox Julian A. , Bailey Dalan , Barclay Wendy S. 
Published: August 2021

AbstractSARS-CoV-2 has a broad mammalian species tropism infecting humans, cats, dogs and farmed mink. Since the start of the 2019 pandemic several reverse zoonotic outbreaks of SARS-CoV-2 have occurred in mink, one of which reinfected humans and caused a cluster of infections in Denmark. Here we investigate the molecular basis of mink and ferret adaptation and demonstrate the spike mutations Y453F, F486L, and N501T all specifically adapt SARS-CoV-2 to use mustelid ACE2. Furthermore, we risk assess these mutations and conclude mink-adapted viruses are unlikely to pose an increased threat to humans, as Y453F attenuates the virus replication in human cells and all 3 mink-adaptations have minimal antigenic impact. Finally, we show that certain SARS-CoV-2 variants emerging from circulation in humans may naturally have a greater propensity to infect mustelid hosts and therefore these species should continue to be surveyed for reverse zoonotic infections.
Progerin-Expressing Endothelial Cells are Unable to Adapt to Shear Stress
Authors: Danielsson Brooke E. , Peters Hannah C. , Bathula Kranthi , Spear Lindsay M. , Noll Natalie A. , Dahl Kris N. , Conway Daniel E. 
Published: August 2021

AbstractHutchinson-Gilford Progeria Syndrome (HGPS) is a rare premature aging disease caused by a single-point mutation in the lamin A gene, resulting in a truncated and farnesylated form of lamin A. This mutant lamin A protein, known as progerin, accumulates at the periphery of the nuclear lamina, resulting in both an abnormal nuclear morphology and nuclear stiffening. HGPS patients experience rapid onset of atherosclerosis, with death from heart attack or stroke as teenagers. Progerin expression has been shown to cause dysfunction in both vascular smooth muscle cells and endothelial cells (ECs). In this study we examined how progerin-expressing ECs adapt to fluid shear stress, the principal mechanical force from blood flow. We compared the response to shear stress for progerin-expressing, wild-type lamin A overexpressing, and control ECs to physiological levels of fluid shear stress. Additionally, we also knocked down ZMPSTE24 in ECs, which results in increased farnesylation of lamin A and similar phenotypes to HGPS. Our results showed that ECs either expressing progerin or with ZMPSTE24 knockdown were unable to adapt to shear stress, experiencing significant cell loss at a longer duration of exposure to shear stress (3 days). ECs overexpressing wild-type lamin A also exhibited similar impairments in adaptation to shear stress, including similar levels of cell loss. Quantification of nuclear morphology showed that progerin-expressing ECs had similar nuclear abnormalities in both static and shear conditions. Treatment of progerin-expressing cells and ZMPSTE24 KD cells with lonafarnib and methystat, drugs previously shown to improve HGPS nuclear morphology, resulted in improvements in adaptation to shear stress. Additionally, pre-alignment of cells to shear stress prior to progerin-expression prevented cell loss. Our results demonstrate that changes in nuclear lamins can affect the ability of EC to properly adapt to shear stress.
Interferon-γ Increases Sensitivity to Chemotherapy and Provides Immunotherapy Targets in Models of Metastatic Castration-Resistant Prostate Cancer
Authors: Korentzelos Dimitrios , Wells Alan , Clark Amanda M. 
Published: August 2021

ABSTRACTInterferon-γ (IFNγ) is a cytokine with limited evidence of benefit in cancer clinical trials to date. However, it could potentially play a role in potentiating anti-tumor immunity in the immunologically “cold” metastatic castration-resistant prostate cancer (mCRPC) by inducing antigen presentation pathways and concurrently providing targets for immune checkpoint blockade therapy. Moreover, it could additionally increase sensitivity to chemotherapy based on its pleiotropic effects on cell phenotype. Here, we show that IFNγ treatment induced expression of major histocompatibility class-I (MHC-I) genes and PD-L1 in prostate cancer cells in vitro. Furthermore, IFNγ treatment led to a decrease in E-cadherin expression with a consequent increase in sensitivity to chemotherapy in vitro. In an in vivo murine tumor model of spontaneous metastatic prostate cancer, IFNγ systemic pretreatment upregulated the expression of HLA-A and decreased E-cadherin expression in the primary tumor, and more importantly in the metastatic site led to increased apoptosis and limited micrometastases in combination with paclitaxel treatment compared to diffuse metastatic disease in control and monotherapy treatment groups. These findings suggest that IFNγ may be useful in combinatorial regimens to induce sensitivity to immunotherapy and chemotherapy in hepatic metastases of mCRPC.
FKBPL and FKBP8 regulate DLK degradation and neuronal responses to axon injury
Authors: Lee Bohm , Oh Yeonsoo , Cho Eunhye , DiAntonio Aaron , Cavalli Valeria , Shin Jung Eun , Cho Yongcheol 
Published: August 2021

AbstractDLK is a key regulator of axon regeneration and degeneration in response to neuronal injury. To understand the molecular mechanisms controlling the DLK function, we performed yeast two-hybrid screening analysis and identified FKBPL as a DLK-binding protein that bound to the kinase domain and inhibited the kinase enzymatic activity of DLK. FKBPL regulated DLK stability through ubiquitin-dependent DLK degradation. We tested other members in the FKBP protein family and found that FKBP8 also induced DLK degradation as FKBPL did. We found that Lysine 271 residue in the kinase domain of DLK was a major site of ubiquitination and SUMO3-conjugation and responsible for FKBP8-mediated degradation. In vivo overexpression of FKBP8 delayed progression of axon degeneration and neuronal death following axotomy in sciatic and optic nerves, respectively, although axon regeneration efficiency was not enhanced. This research identified FKBPL and FKBP8 as new DLK-interacting proteins that regulated DLK stability by MG-132 or bafilomycin A1-sensitive protein degradation.
Subtype specific responses in hKv7.4 and hKv7.5 channels to polyunsaturated fatty acids
Authors: Frampton Damon J A , Nikesjö Johan , Liin Sara I 
Published: August 2021

AbstractThe KV7.4 and KV7.5 subtypes of voltage-gated potassium channels are expressed in several tissues where they play a role in physiological processes such as sound amplification in the cochlea and adjusting vascular smooth muscle tone. Therefore, the mechanisms that regulate KV7.4 and KV7.5 channel function are of interest. Here, we study the effect of polyunsaturated fatty acids (PUFAs) on human KV7.4 and KV7.5 channels expressed inXenopusoocytes. We report that KV7.5 is activated by PUFAs, which shift the V50of the conductanceversusvoltage (G(V)) curve towards more negative voltages. This response depends on the charge of the head group as an uncharged PUFA analogue has no effect and a positively charged PUFA analogue induces positive V50shifts. In contrast, we find that the KV7.4 channel is inhibited by PUFAs, which shift V50towards more positive voltages. No effect on V50of KV7.4 is observed by an uncharged or a positively charged PUFA analogue. Oocytes co-expressing KV7.4 and KV7.5 display an intermediate response to PUFAs. Altogether, the KV7.5 channel’s response to PUFAs is like that previously observed in KV7.1-7.3 channels, whereas the KV7.4 channel response is opposite, revealing subtype specific responses to PUFAs.
XRN2-mediated regulation of tumor suppressor microRNAs is of critical pathophysiological significance in Humans
Authors: Nalawade Rohit , Chowdhury Tamoghna , Chatterjee Saibal 
Published: August 2021

AbstractMicroRNAs (miRNAs) are critical regulators of diverse developmental and physiological processes, and they themselves get regulated both at the level of biogenesis and turnover. We demonstrate that the ribonuclease XRN2 can degrade the mature forms of certain let-7 family members in multiple human cancer cell lines, without affecting their precursors. XRN2 also affects the accumulation of several other tumor suppressor miRNAs known to play important roles in cancer metabolism. XRN2 depletion results in a reduction in the expression of many oncogenes and diminishes the proliferative and metastatic potential of cancer cellsin vitro. These experimental cancer cells also show reduced capacity to form tumors in mice and regress over time. The clinical relevance of these observations is further verified in tumour transcriptomics data from public RNA-sequencing datasets, whereXRN2mRNA expression is inversely correlated with the levels of a large number of miRNAs, including let-7 members, and highXRN2mRNA levels are associated with poor survival in hepatocellular carcinoma, lung adenocarcinoma, and glioblastoma. We demonstrate that the miRNA is released by an as-yet unidentified proteinaceous ‘miRNA release factor’ from the grasp of Argonaute before its degradation, which is more abundant in the nuclear fraction. Our analyses of the patient-derived transcriptomics data also show that XRN2, via its regulation of let-7, affects multiple pathways in a consistent manner across epithelial and glial cell lineages, and thus, is of critical pathophysiological significance.
Heterotypic Assembly Mechanism Regulates CHIP E3 Ligase Activity
Authors: Das Aniruddha , Thapa Pankaj , Santiago Ulises , Shanmugam Nilesh , Banasiak Katarzyna , Dabrowska Katarzyna , Nolte Hendrik , Szulc Natalia A. , Gathungu Rose M. , Cysewski Dominik , Krüger Marcus , Dadlez Michal , Nowotny Marcin , Camacho Carlos J. , Hoppe Thorsten , Pokrzywa Wojciech 
Published: August 2021

ABSTRACTThe E3 ubiquitin ligases CHIP/CHN-1 and UFD-2 team up to accelerate ubiquitin chain formation. However, it remained largely unclear how the high processivity of this E3 set is achieved. Here we studied the molecular mechanism and function of the CHN-1/UFD-2 complex in Caenorhabditis elegans. Our data show that UFD-2 binding promotes the cooperation between CHN-1 and ubiquitin-conjugating E2 enzymes by stabilizing the CHN-1 U-box dimer. The HSP-1 chaperone outcompetes UFD-2 for CHN-1 binding and promotes the auto-inhibited CHN-1 state by acting on the conserved position of the U-box domain. The interaction with UFD-2 enables CHN-1 to efficiently ubiquitinate S-Adenosylhomocysteinase (AHCY-1), an enzyme crucial for lipid metabolism. Our results define the molecular mechanism underlying the synergistic cooperation of CHN-1 and UFD-2 in substrate ubiquitylation.HIGHLIGHTSE3 ligase UFD-2 stimulates ubiquitylation activity of CHIP/CHN-1UFD-2 binding promotes dimerization of CHIP/CHN-1 U-box domains and utilization of E2 enzymesHSP70/HSP-1 by latching the U-box and TPR domains stabilizes the autoinhibitory state of CHIP/CHN-1, limiting interactions with E2s and UFD-2Assembly with UFD-2 enables CHIP/CHN-1 to regulate lipid metabolism by ubiquitylation of S-Adenosylhomocysteinase
Genetic Characterization and Curation of Diploid A-Genome Wheat Species
Authors: Adhikari Laxman , Raupp John , Wu Shuangye , Wilson Duane , Evers Byron , Koo Dal-Hoe , Singh Narinder , Friebe Bernd , Poland Jesse 
Published: August 2021

AbstractThe A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum. monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.) and T. urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC), using genotyping-by-sequencing (GBS) and identified 13,089 curated SNPs. Genomic analysis detected misclassified and duplicated accessions with most duplicates originated from the same or a nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were duplicates supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that the T. urartu as the closest A-genome diploid to wheat through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, β, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring domestication selection signature (Btr1) on the short arm of chromosome 3Am at ~ 70 Mb. We established A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 80% of allelic variants in the A-genome collection and constitute a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.One-sentence summaryGenotyping of gene bank collections of diploid A-genome relatives of wheat uncovered relatively higher genetic diversity and unique evolutionary relationships which gives insight to the effective use of these germplasm for wheat improvement.
High-Spatiotemporal-Resolution Nanopore Sequencing of SARS-CoV-2 and Host Cell RNAs
Authors: Tombácz Dóra , Dörmő Ákos , Gulyás Gábor , Csabai Zsolt , Prazsák István , Kakuk Balázs , Harangozó Ákos , Jankovics István , Dénes Béla , Boldogkői Zsolt 
Published: August 2021

AbstractRecent studies have disclosed the genome, transcriptome and epigenetic compositions of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the effect of viral infection on gene expression of the host cells. It has been demonstrated that, besides the major canonical transcripts, the viral genome also codes for non-canonical RNA molecules. While the structural characterizations have revealed a detailed transcriptomic architecture of the virus, the kinetic studies provided poor and often misleading results on the dynamics of both the viral and host transcripts due to the low temporal resolution of the infection event and the low virus/cell ratio (MOI=0.1) applied for the infection. In this study, we used direct cDNA and direct RNA nanopore sequencings for the generation of high-coverage, high-temporal-resolution transcriptomic datasets on SARS-CoV-2 and on primate host cells infected with a high virus titer (MOI=5). Sixteen sampling time points ranging from 1 to 96h with a varying time resolution and three biological replicates were used in the experiment for both the infected and the non-infected cells.
Vps54 regulates lifespan and locomotor behavior in adult Drosophila melanogaster
Authors: Wilkinson Emily C. , Starke Emily L. , Barbee Scott A. 
Published: August 2021

ABSTRACTVps54 is an integral subunit of the Golgi-associated retrograde protein (GARP) complex, which is involved in tethering endosome-derived vesicles to the trans-Golgi network (TGN). A destabilizing missense mutation in Vps54 causes the age-progressive motor neuron (MN) degeneration, muscle weakness, and muscle atrophy observed in the wobbler mouse, an established animal model for human MN disease. It is currently unclear how the disruption of Vps54, and thereby the GARP complex, leads to MN and muscle phenotypes. To develop a new tool to address this question, we have created an analogous model in Drosophila by generating novel loss-of-function alleles of the fly Vps54 ortholog (scattered/scat). We find that null scat mutant adults are viable but have a significantly shortened lifespan. Like phenotypes observed in the wobbler mouse, we show that scat mutant adults are male sterile and have significantly reduced body size and muscle area. Moreover, we demonstrate that scat mutant adults have significant age-progressive defects in locomotor function. Interestingly, we see sexually dimorphic effects, with scat mutant adult females exhibiting significantly stronger phenotypes. Finally, we show that scat interacts genetically with rab11 in MNs to control age-progressive muscle atrophy in adults. Together, these data suggest that scat mutant flies share mutant phenotypes with the wobbler mouse and may serve as a new genetic model system to study the cellular and molecular mechanisms underlying MN disease.
Development of a universal nanobody-binding Fab module for fiducial-assisted cryo-EM studies of membrane proteins
Authors: Bloch Joël S. , Mukherjee Somnath , Kowal Julia , Filippova Ekaterina V. , Niederer Martina , Pardon Els , Steyaert Jan , Kossiakoff Anthony A. , Locher Kaspar P. 
Published: August 2021

AbstractWith conformation-specific nanobodies being used for a wide range of structural, biochemical, and cell biological applications, there is a demand for antigen-binding fragments (Fabs) that specifically and tightly bind these nanobodies without disturbing the nanobody-target protein interaction. Here we describe the development of a synthetic Fab (termed NabFab) that binds the scaffold of an alpaca-derived nanobody with picomolar affinity. We demonstrate that upon CDR grafting onto this parent nanobody scaffold, nanobodies recognizing diverse target proteins and derived from llama or camel can cross-react with NabFab without loss of affinity. Using NabFab as a fiducial and size enhancer (50 kDa), we determined the high-resolution cryo-EM structures of nanobody-bound VcNorM and ScaDMT, both small membrane proteins of ~50 kDa. Using an additional anti-Fab nanobody further facillitated reliable initial 3D structure determination from small cryo-EM test datasets. Given that NabFab is of synthetic origin, humanized, and can be conveniently expressed in E. coli in large amounts, it may not only be useful for structural biology, but also for biomedical applications.
Stable antibiotic resistance and rapid human adaptation in livestock-associated MRSA
Authors: Matuszewska Marta , Murray Gemma G. R. , Ba Xiaoliang , Wood Rhiannon , Holmes Mark A. , Weinert Lucy A. 
Published: August 2021

AbstractMobile genetic elements (MGEs) are agents of horizontal gene transfer in bacteria, but can also be vertically inherited by daughter cells. Establishing the dynamics that led to contemporary patterns of MGEs in bacterial genomes is central to predicting the emergence and evolution of novel and resistant pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex (CC) 398 is the dominant MRSA in European livestock and a growing cause of human infections. Previous studies have identified three categories of MGEs whose presence or absence distinguishes livestock-associated CC398 from a closely related and less antibiotic-resistant human-associated population. Here we fully characterise the evolutionary dynamics of these MGEs using a collection of 1,180 CC398 genomes, sampled from livestock and humans, over 27 years. We find that the emergence of livestock-associated CC398 coincided with the acquisition of a Tn916 transposon carrying a tetracycline resistance gene, which has been stably inherited for 57 years. This was followed by the acquisition of a type V SCCmec that carries methicillin, tetracycline and heavy metal resistance genes, which has been maintained for 35 years, with occasional truncations and replacements with type IV SCCmec. In contrast, a class of prophages that carry a human immune evasion gene cluster and that are largely absent from livestock-associated CC398, have been repeatedly gained and lost in both human- and livestock-associated CC398. These contrasting dynamics mean that when livestock-associated MRSA is transmitted to humans, adaptation to the human host outpaces loss of antibiotic resistance. In addition, the stable inheritance of resistance-associated MGEs suggests that the impact of ongoing reductions in antibiotic and zinc oxide use in European farms on livestock-associated MRSA will be slow to be realised.