bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondria serve as axonal shuttle for Cox7c mRNA through mechanism that involves its mitochondrial targeting signal
Authors: Cohen Bar , Golani-Armon Adi , Altman Topaz , Savulescu Anca F. , Mhlanga Musa M. , Perlson Eran , Arava Yoav S. 
Published: May 2021

AbstractLocalized protein synthesis plays a key role in spatiotemporal regulation of the cellular proteome. Neurons, which extend axons over long distances, heavily depend on this process. However, the mechanisms by which axonal mRNAs are transported to protein target sites are not fully understood. Here, we describe a novel role for mitochondria in shuttling a nuclear encoded mRNA along axons. Fractionation analysis and smFISH revealed that the mRNA encoding Cox7c protein is preferentially associated with mitochondria from a neuronal cell line and from primary motor neuron axons. Live cell imaging of MS2-tagged Cox7c or Cryab control mRNA in primary motor neurons further confirmed the preferential colocalization of Cox7c mRNA with mitochondria. More importantly, Cox7c demonstrated substantial cotransport with mitochondria along axons. Intriguingly, the coding region, rather than the 3’UTR, was found to be the key domain for the cotransport. Furthermore, we show that puromycin treatment as well as hindering the synthesis of the mitochondrial targeting signal (MTS) reduced the colocalization. Overall, our results reveal a novel mRNA transport mode which exploits mitochondria as a shuttle and translation of the MTS as a recognition feature. Thus, mitochondria may play a role in spatial regulation of the axonal transcriptome and self-sustain their own proteome at distant neuronal sites.
Epigenetic repression of Wnt receptors in AD: a role for Sirtuin2-induced H4K16ac deacetylation of Frizzled1 and Frizzled7 promoters
Authors: Palomer Ernest , Martin-Flores Núria , Jolly Sarah , Pascual-Vargas Patricia , Benvegnù Stefano , Podpolny Marina , Teo Samuel , Vaher Kadi , Saito Takashi , Saido Takaomi C , Whiting Paul , Salinas Patricia C 
Published: May 2021

ABSTRACTGrowing evidence supports a role for deficient Wnt signalling in Alzheimer′s disease (AD). First, the Wnt antagonist DKK1 is elevated in AD brains and is required for amyloid-β-induced synapse loss. Second, LRP6 Wnt co-receptor is required for synapse integrity and three variants of this receptor are linked to late-onset AD. However, the expression/role of other Wnt signalling components remain poorly explored in AD. Wnt receptors Frizzled1 (Fzd1), Fzd5, Fzd7 and Fzd9 are of interest due to their role in synapse formation/plasticity. Our analyses showed reducedFZD1andFZD7mRNA levels in the hippocampus of human early AD stages and in the hAPPNLGF/NLGFmouse model. This transcriptional downregulation was accompanied by reduced levels of the pro-transcriptional histone mark H4K16ac and a concomitant increase of its deacetylase Sirt2 atFzd1andFzd7promoters in AD.In vitroandin vivoinhibition of Sirt2 rescuedFzd1andFzd7mRNA expression and H4K16ac levels at their promoters. In addition, we showed that Sirt2 recruitment toFzd1andFzd7promoters is dependent on FoxO1 activity in AD, thus acting as a co-repressor. Finally, we found reduced levels of Sirt2 inhibitory phosphorylation in nuclear samples from human early AD stages with a concomitant increased in the Sirt2 phosphatase PP2C. This results in hyperactive nuclear Sirt2 and favoursFzd1andFzd7repression in AD. Collectively, our findings define a novel role for nuclear hyperactivated Sirt2 in repressingFzd1andFzd7expressionviaH4K16ac deacetylation in AD. We propose Sirt2 as an attractive target to ameliorate AD pathology.
Cellulonodin-2 and Lihuanodin: Lasso Peptides with an Aspartimide Post-translational Modification
Authors: Cao Li , Beiser Moshe , Koos Joseph D. , Orlova Margarita , Elashal Hader E. , Schröder Hendrik V. , Link A. James 
Published: May 2021

AbstractLasso peptides are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) defined by their threaded structure. Besides the class-defining isopeptide bond, other post-translational modifications (PTMs) that further tailor lasso peptides have been previously reported. Using genome mining tools, we identified a subset of lasso peptide biosynthetic gene clusters (BGCs) that are colocalized with protein L-isoaspartyl methyltransferase (PIMT) homologs. PIMTs have an important role in protein repair, restoring isoaspartate residues formed from asparagine deamidation to aspartate. Here we report a new function for PIMT enzymes in the post-translational modification of lasso peptides. The PIMTs associated with lasso peptide BGCs first methylate an L-aspartate sidechain found within the ring of the lasso peptide. The methyl ester is then converted into a stable aspartimide moiety, endowing the lasso peptide ring with rigidity relative to its unmodified counterpart. We describe the heterologous expression and structural characterization of two examples of aspartimide-modified lasso peptides from thermophilic Gram-positive bacteria. The lasso peptide cellulonodin-2 is encoded in the genome of actinobacterium Thermobifida cellulosilytica, while lihuanodin is encoded in the genome of firmicute Lihuaxuella thermophila. Additional genome mining revealed PIMT-containing lasso peptide BGCs in 48 organisms. In addition to heterologous expression, we have reconstituted PIMT-mediated aspartimide formation in vitro, showing that lasso peptide-associated PIMTs transfer methyl groups very rapidly as compared to canonical PIMTs. Furthermore, in stark contrast to other characterized lasso peptide PTMs, the methyltransferase functions only on lassoed substrates.Abstract Figure
Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities
Authors: Lin Qiang , Dini-Andreote Francisco , Meador Travis B. , Angel Roey , Meszárošová Lenka , Heděnec Petr , Li Lingjuan , Baldrian Petr , Frouz Jan 
Published: May 2021

AbstractDevelopment of soil microbial communities along ecological succession is crucial for ecosystem recovery and maintenance. However, mechanisms mediating microbial community dynamics and co-occurrence patterns along ecological succession remain unclear. Here, we explored community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Meanwhile, by synthesizing previous studies and ecological theories, we devised two conceptual models that integrate microbial phylogeny with patterns in community dynamics and in taxa co-occurrence. We further tested these models by using empirical data. At early successional stages, bacterial community structures became increasingly phylogenetically clustered with soil age, which was co-determined by the environmental selection from soil vegetation cover and by heterogeneous responses of less phylogenetically similar bacteria to the increasing resource availability along succession. At later successional stages, bacterial community phylogenetic structures displayed progressively lower variability. The fungal community phylogenetic structures varied relatively less and were independent of soil age, soil properties and vegetation cover, which was attributed to the dominance of stochastic processes in community turnover along succession. Network analysis revealed a decrease in bacterial co-occurrence complexity along succession, which aligned with a decrease in average pairwise phylogenetic distances between co-occurring bacteria. These patterns together implied a decrease in potential bacterial cooperation that was probably mediated by increasing resource availability along succession. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic distances between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.
Genetic structure correlates with ethnolinguistic diversity in eastern and southern Africa
Authors: Atkinson Elizabeth G. , Dalvie Shareefa , Pichkar Yakov , Kalungi Allan , Majara Lerato , Stevenson Anne , Abebe Tamrat , Akena Dickens , Alemayehu Melkam , Ashaba Fred K. , Atwoli Lukoye , Baker Mark , Chibnik Lori B. , Creanza Nicole , Daly Mark J. , Fekadu Abebaw , Gelaye Bizu , Gichuru Stella , Injera Wilfred E. , James Roxanne , Kariuki Symon M. , Kigen Gabriel , Koen Nastassja , Koenen Karestan C. , Koenig Zan , Kwobah Edith , Kyebuzibwa Joseph , Musinguzi Henry , Mwema Rehema M. , Neale Benjamin M. , Newman Carter P. , Newton Charles R.J.C. , Ongeri Linnet , Ramachandran Sohini , Ramesar Raj , Shiferaw Welelta , Stein Dan J. , Stroud Rocky E. , Teferra Solomon , Yohannes Mary T. , Zingela Zukiswa , Martin Alicia R. ,   NeuroGAP-Psychosis Study Team
Published: May 2021

SummaryAfrican populations are the most diverse in the world yet are sorely underrepresented in medical genetics research. Here, we examine the structure of African populations using genetic and comprehensive multigenerational ethnolinguistic data from the Neuropsychiatric Genetics of African Populations-Psychosis study (NeuroGAP-Psychosis) consisting of 900 individuals from Ethiopia, Kenya, South Africa, and Uganda. We find that self-reported language classifications meaningfully tag underlying genetic variation that would be missed with consideration of geography alone, highlighting the importance of culture in shaping genetic diversity. Leveraging our uniquely rich multi-generational ethnolinguistic metadata, we track language transmission through the pedigree, observing the disappearance of several languages in our cohort as well as notable shifts in frequency over three generations. We find suggestive evidence for the rate of language transmission in matrilineal groups having been higher than that for patrilineal ones. We highlight both the diversity of variation within the African continent, as well as how within-Africa variation can be informative for broader variant interpretation; many variants appearing rare elsewhere are common in parts of Africa. The work presented here improves the understanding of the spectrum of genetic variation in African populations and highlights the enormous and complex genetic and ethnolinguistic diversity within Africa.
A Modular Platform for Streamlining Automated Cryo-FIB Workflows
Authors: Klumpe Sven , Fung Herman K. H. , Goetz Sara K. , Zagoriy Ievgeniia , Hampoelz Bernhard , Zhang Xiaojie , Erdmann Philipp S. , Baumbach Janina , Müller Christoph W. , Beck Martin , Plitzko Jürgen M. , Mahamid Julia 
Published: May 2021

AbstractLamella micromachining by focused ion beam milling at cryogenic temperature (cryo-FIB) has matured into a preparation method widely used for cellular cryo-electron tomography. Due to the limited ablation rates of low Ga+ ion beam currents required to maintain the structural integrity of vitreous specimens, current preparation protocols are time-consuming and labor intensive. The improved stability of new generation cryo-FIB instruments now enables automated operations. Here, we present an open-source software tool, SerialFIB, for creating automated and customizable cryo-FIB preparation protocols. The software encompasses a graphical user interface for easy execution of routine lamellae preparations, a scripting module compatible with available python packages, and interfaces with 3-dimensional correlative light and electron microscopy (CLEM) tools. The software enables the streamlining of advanced cryo-FIB protocols such as multi-modal imaging, CLEM guided preparation and in situ lamella lift-out procedures. Our software therefore provides a foundation for further development of advanced cryogenic imaging and sample preparation protocols.
A hybridoma-derived monoclonal antibody with high homology to the aberrant myeloma light chain
Authors: Pornnoppadol Ghasidit , Zhang Boya , Desai Alec A. , Berardi Anthony , Remmer Henriette A. , Tessier Peter M. , Greineder Colin F. 
Published: May 2021

AbstractThe identification of antibody variable regions in the heavy (VH) and light (VL) chains from hybridomas is necessary for the production of recombinant, sequence-defined monoclonal antibodies (mAbs) and antibody derivatives. This process has received renewed attention in light of recent reports of hybridomas having unintended specificities due to the production of non-antigen specific heavy and/or light chains for the intended antigen. Here we report a surprising finding and potential pitfall in variable domain sequencing of an anti-human CD63 hybridoma. We amplified multiple VL genes from the hybridoma cDNA, including the well-known aberrant Sp2/0 myeloma VK and a unique, full-length VL. After finding that the unique VL failed to yield a functional antibody, we discovered an additional full-length sequence with surprising similarity (~95% sequence identify) to the non-translated myeloma kappa chain but with a correction of its key frameshift mutation. Expression of the recombinant mAb confirmed that this highly homologous sequence is the antigen-specific light chain. Our results highlight the complexity of PCR-based cloning of antibody genes and strategies useful for identification of correct sequences.
Transcriptional states of retroelement-inserted regions and KRAB zinc finger protein association regulate DNA methylation of retroelements in human male germ cells
Authors: Fukuda Kei , Makino Yoshinori , Kaneko Satoru , Okada Yuki , Ichiyanagi Kenji , Shinkai Yoichi 
Published: May 2021

ABSTRACTDNA methylation, repressive histone modifications, and PIWI-interacting RNAs are essential for controlling retroelement silencing in mammalian germ lines. Dysregulation of retroelement silencing is associated with male sterility. Although retroelement silencing mechanisms have been extensively studied in mouse germ cells, little progress has been made in humans. Here, we show that the Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs) are associated with DNA methylation of retroelements in human primordial germ cells (hPGCs), and hominoid-specific retroelement SINE-VNTR-Alus (SVA) is subjected to transcription-directed de novo DNA methylation during human spermatogenesis. Furthermore, we show that the degree of de novo DNA methylation in SVAs varies among human individuals, which confers a significant inter-individual epigenetic variation in sperm. Collectively, our results provide potential molecular mechanisms for the regulation of retroelements in human male germ cells.
The unfolded protein response of the endoplasmic reticulum supports mitochondrial biogenesis by buffering non-imported proteins
Authors: Knöringer Katharina , Groh Carina , Krämer Lena , Stein Kevin C. , Hansen Katja G. , Herrmann Johannes M. , Frydman Judith , Boos Felix 
Published: May 2021

AbstractAlmost all mitochondrial proteins are synthesized in the cytosol and subsequently targeted to mitochondria. The accumulation of non-imported precursor proteins occurring upon mitochondrial dysfunction can challenge cellular protein homeostasis. Here we show that blocking protein translocation into mitochondria results in the accumulation of mitochondrial membrane proteins at the endoplasmic reticulum, thereby triggering the unfolded protein response (UPRER). Moreover, we find that mitochondrial membrane proteins are also routed to the ER under physiological conditions. The levels of ER-resident mitochondrial precursors is enhanced by import defects as well as metabolic stimuli that increase the expression of mitochondrial proteins. Under such conditions, the UPRER is crucial to maintain protein homeostasis and cellular fitness. We propose the ER serves as a physiological buffer zone for those mitochondrial precursors that can’t be immediately imported into mitochondria while engaging the UPRER to adjust the ER proteostasis capacity to the extent of precursor accumulation.
Cell-free Expression of Proton-Coupled Folate Transporter in the Presence of Nanodiscs
Authors: Do Hoa Quynh , Bassil Carla M. , Andersen Elizabeth I. , Jansen Michaela 
Published: May 2021

AbstractThe Proton-Coupled Folate Transporter (PCFT) is a transmembrane transport protein that controls the absorption of dietary folates in the small intestine. PCFT also mediates uptake of chemotherapeutically used antifolates into tumor cells. PCFT has been identified within lipid rafts observed in phospholipid bilayers of plasma membranes, a micro environment that is altered in tumor cells. The present study aimed at investigating the impact of different lipids within Lipid-protein nanodiscs (LPNs), discoidal lipid structures stabilized by membrane scaffold proteins, to yield soluble PCFT expression in an E. coli lysate-based cell-free transcription/translation system. In the absence of detergents or lipids, we observed PCFT quantitatively as precipitate in this system. We then explored the ability of LPNs to support solubilized PCFT expression when present during in-vitro translation. LPNs consisted of either dimyristoyl phosphatidylcholine (DMPC), palmitoyl-oleoyl phosphatidylcholine (POPC), or dimyristoyl phosphatidylglycerol (DMPG). While POPC did not lead to soluble PCFT expression, both DMPG and DMPC supported PCFT translation directly into LPNs, the latter in a concentration dependent manner. The results obtained through this study provide insights into the lipid preferences of PCFT. Membrane-embedded or solubilized PCFT will enable further studies with diverse biophysical approaches to enhance the understanding of the structure and molecular mechanism of folate transport through PCFT.HighlightsCell free expression of PCFT without any lipids or detergents resulted in quantitative precipitation of in-situ synthesized PCFT.Additives for expression of PCFT in the soluble fraction were identified.
Sequence-based modeling of genome 3D architecture from kilobase to chromosome-scale
Authors: Zhou Jian 
Published: May 2021

AbstractThe structural organization of the genome plays an important role in multiple aspects of genome function. Understanding how genomic sequence influences 3D organization can help elucidate their roles in various processes in healthy and disease states. However, the sequence determinants of genome structure across multiple spatial scales are still not well understood. To learn the complex sequence dependencies of multiscale genome architecture, here we developed a sequence-based deep learning approach, Orca, that predicts genome 3D architecture from kilobase to whole-chromosome scale, covering structures including chromatin compartments and topologically associating domains. Orca also makes both intrachromosomal and interchromosomal predictions and captures the sequence dependencies of diverse types of interactions, from CTCF-mediated to enhancer-promoter interactions and Polycomb-mediated interactions. Orca enables the interpretation of the effects of any structural variant at any size on multiscale genome organization and provides an in silico model to help study the sequence-dependent mechanistic basis of genome architecture. We show that the models accurately recapitulate effects of experimentally studied structural variants at varying sizes (300bp-80Mb) using only sequence. Furthermore, these sequence models enable in silico virtual screen assays to probe the sequence-basis of genome 3D organization at different scales. At the submegabase scale, the models predicted specific transcription factor motifs underlying cell-type-specific genome interactions. At the compartment scale, based on virtual screens of sequence activities, we propose a new model for the sequence basis of chromatin compartments: sequences at active transcription start sites are primarily responsible for establishing the expression-active compartment A, while the inactive compartment B typically requires extended stretches of AT-rich sequences (at least 6-12kb) and can form ‘passively’ without depending on any particular sequence pattern. Orca thus effectively provides an “in silico genome observatory” to predict variant effects on genome structure and probe the sequence-based mechanisms of genome organization.
HPF1 dynamically controls the PARP1/2 balance between initiating and elongating ADP- ribose modifications
Authors: Langelier Marie-France , Billur Ramya , Sverzhinsky Aleksandr , Black Ben E. , Pascal John M. 
Published: May 2021

ABSTRACTUpon detecting DNA strand breaks, PARP1 and PARP2 produce the posttranslational modification poly(ADP-ribose) to orchestrate the cellular response to DNA damage. Histone PARylation factor 1 (HPF1) binds to PARP1/2 to directly regulate their catalytic output. HPF1 is required for the modification of serine residues with ADP-ribose, whereas glutamate/aspartate residues are modified in the absence of HPF1. PARP1 is an abundant nuclear protein, whereas HPF1 is present in much lower amounts, raising the question of whether HPF1 can pervasively modulate PARP1 activity. Here we show biochemically that HPF1 efficiently regulates PARP1/2 catalytic output at the sub-stoichiometric ratios matching their relative cellular abundances. HPF1 rapidly associates and dissociates from multiple PARP1 molecules, initiating ADP-ribose modification of serine residues before modification can initiate on glutamate/aspartate residues. HPF1 accelerates the rate of attaching the first ADP-ribose, such that this initiation event is comparable to the rate of the elongation reaction to form poly(ADP-ribose). This “hit and run” mechanism ensures that HPF1 contributions to the PARP1/2 active site during initiation do not persist and interfere with PAR chain elongation at sites of DNA damage. HPF1 thereby balances initiation and elongation events to regulate PARP1/2 output. Structural analysis of HPF1 in complex with PARP1 provides first insights into the assembly on a DNA strand break, and the HPF1 impact on PARP1 retention on DNA. Our data support the prevalence of the serine-ADP-ribose modification in cells and establish that HPF1 imparts the efficiency of serine-ADP-ribose modification required for an acute response to DNA damage.
A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius)
Authors: Brown Autumn R. , Comai Kaylee , Mannino Dominic , McCullough Haily , Donekal Yamini , Meyers Hunter C. ,   The BIO306W Consortium, Graves Chiron W. , Seidel Hannah S. 
Published: May 2021

AbstractColor morphs in ball pythons (Python regius) provide a unique and largely untapped resource for understanding the genetics of coloration in reptiles. Here we use a community-science approach to investigate the genetics of three color morphs affecting production of the pigment melanin. These morphs—Albino, Lavender Albino, and Ultramel—show a loss of melanin in the skin and eyes, ranging from severe (Albino) to moderate (Lavender Albino) to mild (Ultramel). To identify genetic variants causing each morph, we recruited shed skins of pet ball pythons via social media, extracted DNA from the skins, and searched for putative loss-of-function variants in homologs of genes controlling melanin production in other vertebrates. We report that the Albino morph is associated with missense and non-coding variants in the gene TYR. The Lavender Albino morph is associated with a deletion in the gene OCA2. The Ultramel morph is associated with a missense variant and a putative deletion in the gene TYRP1. Our study is one of the first to identify genetic variants associated with color morphs in ball pythons and shows that pet samples recruited from the community can provide a resource for genetic studies in this species.