bluuebunny/crossref_metadata_2025_split huggingface dataset:
Re-examination of the taxonomic status of the AntarcticPseudomonas syringaeLz4W isolate and proposal to rename it as a novel speciesPseudomonas cryophilasp. nov
Authors: Ray Malay K , Pandiyan Apuratha , Sahu Bhubanananda 
Published: April 2024

AbstractA taxonomic re-evaluation of the Antarctic psychrotrophic bacteriumPseudomonas syringaeLz4W was performed in the light of its available genome sequence and due to a revision in the key phenotypic characteristics that are in conflict with the “syringae” group of Pseudomonads. A 16S rRNA gene sequence based phylogenetic analysis suggested that Lz4WTstrain belongs to “fragi” cluster ofPseudomonasspecies, with closest similarity (99.72%) to the type strainP. deceptionensisM1T. However,in silicoanalysis of the Lz4W genome sequence using SpecI (species identification tools), ANI (average nucleotide identity), and GBDP (Genome Blast Distance phylogeny) methods suggest that Lz4WTstrain cannot be delineated with any of the type strains of “fragi” cluster of species. Based on predictive low DNA-DNA hybridization value (<29.9%) and differences in phenotypic features with the related species we suggest that Lz4WTis a novel species under thePseudomonasgenus, and we propose that the strain be named asPseudomonas cryophilasp. nov. The type strain is Lz4WT(=CFBP 8403T=KCTC 42933T=LMG 29591T=MTCC 673T).
Characterization of novel and essential kinetoplast-associated proteins inTrypanosoma brucei
Authors: Cadena Lawrence Rudy , Svobodová Michaela , Benz Corinna , Rašková Vendula , Chmelová Ľubomíra , Škodová-Sveráková Ingrid , Yurchenko Vyacheslav , Lukeš Julius , Hammond Michael , Durante Ignacio Miguel 
Published: April 2024

ABSTRACTThe kinetoplast is one of the defining features of kinetoplastid protists and represents a unique concentration of mitochondrial DNA. This subcellular structure is a highly complex assembly of thousands of mutually catenated, circular DNA molecules as well as up to one hundred dedicated proteins. These components work in tandem to replicate and segregate the mitochondrial genome during cellular division, additionally coordinating with the basal body and flagellum through the tripartite attachment complex (TAC) superstructure. Here, we screened the MitoTag localization repository and identified a number of previously undescribed hypothetical proteins exhibiting putative signals within the kinetoplast ofTrypanosoma brucei. Through endogenous tagging we verify their association with the kinetoplast or TAC. The essentiality for several of these kinetoplast proteins (KP) was assessed by RNAi knock-downs, revealing that the newly characterized KP56, KP84 and KP86 are indispensable for growth of the procyclic stage. Additionally, KP37, KP56, and KP84 displayed alterations in the abundance of maxicircles or minicircles, while the depletion of KP84 and KP86 resulted in cell cycle alternations. Pulldown assays using the endogenously V5-tagged cell lines identified novel interactors, which were additionally subjected to endogenous tagging for subcellular localization, revealing two additional proteins (KP45 and KP66) with dual localization to the kinetoplast and throughout the mitochondrial lumen. This work represents the most extensive identification of novel KPs to date and provides a methodological pipeline for the characterization of remaining KPs to further understand this intricate molecular structure.
Cell-free assays reveal that the HIV-1 capsid protects reverse transcripts from cGAS
Authors: Scott Tiana M. , Arnold Lydia M. , Powers Jordan A. , McCann Delaney A. , Rowe Ana B. , Christensen Devin E. , Pereira Miguel J. , Zhou Wen , Torrez Rachel M. , Iwasa Janet H. , Kranzusch Philip J. , Sundquist Wesley I. , Johnson Jarrod S. 
Published: April 2024

AbstractRetroviruses can be detected by the innate immune sensor cyclic GMP-AMP synthase (cGAS), which recognizes reverse-transcribed DNA and activates an antiviral response.However, the extent to which HIV-1 shields its genome from cGAS recognition remains unclear. To study this process in mechanistic detail, we reconstituted reverse transcription, genome release, and innate immune sensing of HIV-1 in a cell-free system. We found that wild-type HIV-1 capsids protect viral genomes from cGAS even after completing reverse transcription. Viral DNA could be “deprotected” by thermal stress, capsid mutations, or reduced concentrations of inositol hexakisphosphate (IP6) that destabilize the capsid. Strikingly, the capsid inhibitor lenacapavir also disrupted viral cores and dramatically potentiated cGAS activity, both in vitro and in cellular infections. Our results provide biochemical evidence that the HIV-1 capsid lattice conceals the genome from cGAS and that chemical or physical disruption of the viral core can expose HIV-1 DNA and activate innate immune signaling.
How distributed subcortical integration of reward and threat may inform subsequent approach-avoidance decisions
Authors: Hulsman Anneloes M. , Klaassen Felix H. , de Voogd Lycia D. , Roelofs Karin , Klumpers Floris 
Published: April 2024

ABSTRACTHealthy and successful living involves carefully navigating rewarding and threatening situations by balancing approach and avoidance behaviours. Excessive avoidance to evade potential threats often leads to forfeiting potential rewards. However, little is known about how reward and threat information is integrated neurally to inform approach or avoidance decisions. In this preregistered study, participants (Nbehaviour=31, 17F; NMRI=28, 15F) made approach-avoidance decisions under varying reward (monetary gains) and threat (electrical stimulations) prospects during functional MRI scanning. In contrast to theorizedparallel subcorticalprocessing of reward and threat information before cortical integration, Bayesian Multivariate Multilevel analyses revealed subcortical reward and threatintegrationprior to indicating approach-avoidance decisions. This integration occurred in the ventral striatum, thalamus, and bed nucleus of the stria terminalis (BNST). When reward was low, risk-diminishing avoidance decisions dominated, which was linked to more positive tracking of threat magnitude prior to indicating avoidance than approach decisions across these regions. In contrast, the amygdala exhibited dual sensitivity to reward and threat. While anticipating outcomes of risky approach decisions, we observed positive tracking of threat magnitude within the salience network (dorsal anterior cingulate cortex, thalamus, periaqueductal gray, BNST). Conversely, after risk-diminishing avoidance, characterized by reduced reward prospects, we observed more negative tracking of reward magnitude in the ventromedial prefrontal cortex and ventral striatum. These findings shed light on the temporal dynamics of approach-avoidance decision-making. Importantly, they demonstrate the role of subcortical integration of reward and threat information in balancing approach and avoidance, challenging theories positing predominantly separate subcortical processing prior to cortical integration.
SETDB1 activity is globally directed by H3K14 acetylation via its Triple Tudor Domain
Authors: Chandrasekaran Thyagarajan T. , Choudalakis Michel , Bröhm Alexander , Weirich Sara , Kouroukli Alexandra G , Ammerpohl Ole , Rathert Philipp , Bashtrykov Pavel , Jeltsch Albert 
Published: April 2024

AbstractSETDB1 is a major H3K9 methyltransferase involved in heterochromatin formation and silencing of repeat elements. It contains a unique Triple Tudor Domain (3TD) which specifically binds the dual modification of H3K14ac in the presence of H3K9me1/2/3. Here, we explored the role of the 3TD H3-tail interaction for the H3K9 methylation activity of SETDB1. We generated a binding reduced 3TD mutant and demonstrate in biochemical methylation assays on peptides and recombinant nucleosomes containing H3K14ac analogs, that H3K14 acetylation is crucial for the 3TD mediated recruitment of SETDB1. We also observe this effect in cells where SETDB1 binding and activity is globally correlated with H3K14ac, and KO of the H3K14 acetyltransferase HBO1 causes a drastic reduction in H3K9me3 levels at SETDB1 dependent sites. Further analyses revealed that 3TD particularly important at specific target regions like L1M repeat elements, where SETDB1 KO cannot be efficiently reconstituted by the 3TD mutant of SETDB1. In summary, our data demonstrate that the H3K9me3 and H3K14ac are not antagonistic marks but rather the presence of H3K14ac is required for SETDB1 recruitment via 3TD binding to H3K9me1/2/3-K14ac and establishment of H3K9me3.
Deep sequencing of 16Ixodes ricinusticks unveils insights into their interactions with endosymbionts
Authors: Lesiczka Paulina M. , Azagi Tal , Krawczyk Aleksandra I. , Scott William T. , Dirks Ron P. , Šimo Ladislav , Dobler Gerhard , Nijsse Bart , Schaap Peter J. , Sprong Hein , Koehorst Jasper J. 
Published: April 2024

AbstractBackgroundIxodes ricinusticks act as vectors for numerous pathogens that present substantial health threats. Additionally, they harbour vertically transmitted symbionts, some of which have been linked to diseases. The difficulty of isolating and cultivating these symbionts has hampered our understanding of their biological role, their potential to cause disease, and their modes of transmission. To expand our understanding on the tick symbiontMidichloria mitochondriiand onRickettsia helvetica, which has been linked to disease in humans, we utilized deep sequencing on sixteen individual adult female ticks collected from coastal dune and forested areas in the Netherlands.ResultsBy employing a combination of second and third-generation sequencing techniques, we successfully reconstructed the complete genomes ofM. mitochondriifrom eleven individuals,R. helveticafrom eight individuals and the mitochondrial genome from all ticks. Additionally, we visualised the location ofR. helveticain tick organs and constructed genome-scale metabolic models (GEMs) of both symbionts to study their environmental dependencies.Our analysis revealed a strong cophylogeny between M. mitochondrii and mitochondrial genomes, suggesting frequent maternal transmission. In contrast, the absence of cophylogeny between R. helvetica and the mitochondrial genomes, coupled with its presence in the receptaculum seminis of I. ricinus females, raises the possibility of paternal transmission of R. helvetica. Notably, the genetic diversity of R. helvetica was found to be very low, except for the rickA virulence gene, where the presence of up to thirteen insertions of a33nt-long repeat led to significant variability. However, this variation could not account for the differences in infection prevalence observed across eight distinct locations in the Netherlands.ConclusionsBy employing deep sequencing, it becomes feasible to extract complete genomes and genetic data of symbionts directly from their host organisms. This methodology serves as a robust means to gain fresh insights into their interactions. Our observations, which suggest paternal transmission ofR. helvetica, a relatively unexplored mode of transmission in ticks, require validation through experimental investigations. The genetic variations identified in therickA virulence gene ofR. helveticahave the potential to influence the infectivity and transmission dynamics ofR. helvetica
A key residue of the extracellular gate provides quality control contributing to ABCG substrate specificity
Authors: Xia Jian , Siffert Alexandra , Torres Odalys , Banasiak Joanna , Pakuła Konrad , Ziegler Jörg , Rosahl Sabine , Ferro Noel , Jasiński Michał , Hegedűs Tamás , Geisler Markus M. 
Published: April 2024

AbstractFor G-type ATP-binding cassette (ABC) transporters, a hydrophobic “di-leucine motif” as part of a hydrophobic extracellular gate has been described to separate a large substrate-binding cavity from a smaller upper cavity and proposed to act as a valve controlling drug extrusion.Here, we show that an L704F mutation in the hydrophobic extracellular gate of Arabidopsis ABCG36/PDR8/PEN3 uncouples the export of the auxin precursor indole-3-butyric acid (IBA) from that of the defense compound camalexin (CLX). Molecular dynamics simulations reveal an increase in free energy and pulling forces for CLX at both the entrance and exit sites of ABCG36L704F, respectively, providing a mechanistic rationale for the transport discrimination of CLX. Mutagenesis of L704 to tyrosine allows export of structurally related non-ABCG36 substrates, indole-3-acetic acid (IAA) and indole, suggesting an allosteric communication between the extracellular gate and the central substrate binding pocket.In summary, our work supports the conclusion that L704 is a key residue of the extracellular gate that provides a final quality control contributing to ABCG substrate specificity.
A phage satellite manipulates the viral DNA packaging motor to inhibit phage and promote satellite spread
Authors: Boyd Caroline M. , Seed Kimberley D. 
Published: April 2024

ABSTRACTICP1, a lytic bacteriophage ofVibrio cholerae, is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs’ dependence on ICP1’s DNA replication machinery, and virion components results in inhibition of ICP1’s lifecycle. PLEs’ are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLE’s indiscriminate genome packaging inhibitor. Gpi binds to ICP1’s large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpi’s negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1’spacsite as a backup strategy to ensure genome packaging. PLE’spacsite mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA, and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1’s lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.
Perpetual step-like restructuring of hippocampal circuit dynamics
Authors: Zheng Zheyang (Sam) , Huszár Roman , Hainmueller Thomas , Bartos Marlene , Williams Alex , Buzsáki György 
Published: April 2024

AbstractRepresentation of the environment by hippocampal populations is known to drift even within a familiar environment, which could reflect gradual changes in single cell activity or result from averaging across discrete switches of single neurons. Disambiguating these possibilities is crucial, as they each imply distinct mechanisms. Leveraging change point detection and model comparison, we found that CA1 population vectors decorrelated gradually within a session. In contrast, individual neurons exhibited predominantly step-like emergence and disappearance of place fields or sustained change in within-field firing. The changes were not restricted to particular parts of the maze or trials and did not require apparent behavioral changes. The same place fields emerged, disappeared, and reappeared across days, suggesting that the hippocampus reuses pre-existing assemblies, rather than forming new fieldsde novo. Our results suggest an internally-driven perpetual step-like reorganization of the neuronal assemblies.
Chimeric origin of eukaryotes from Asgard archaea and ancestral giant viruses
Authors: Karki Sangita , Barth Zachary K. , Aylward Frank O. 
Published: April 2024

AbstractThe details surrounding the evolution of complex cells remain some of the most enduring mysteries in biology. Recent evidence has demonstrated that Asgard archaea are the closest cellular relatives of eukaryotes, but several eukaryotic enzymes involved in key cellular processes lack phylogenetic affinity with archaea. In particular, phylogenies of eukaryotic DNA and RNA polymerases often support a 3-domain topology that is not consistent with an archaeal origin. Here we present comprehensive phylogenetic analysis of eukaryotic family B DNA polymerases and multimeric RNA polymerases and show that these core subunits of these enzymes are derived from the ancestors of modern giant viruses (phylumNucleocytoviricota). Specifically, we show that the eukaryotic delta polymerase (Polδ), a key processive polymerase required for genome replication in all eukaryotes, clusters within an ancient viral clade, strongly supporting a viral origin. By contrast, the other eukaryotic processive polymerase (Polε), clusters within an Asgard archaeal clade. Together, these observations provide a strong and direct link between early eukaryotes, Asgard archaea, and giant viruses. Lastly, we provide a comprehensive phylogenetic analysis of eukaryotic multimeric RNA polymerases to confirm that RNA polymerase II, which is responsible for mRNA transcription in eukaryotes, is also derived from the ancestors of modern giant viruses. In total, our results support a model of eukaryogenesis in which complex cells emerged from a genomic chimera of Asgard archaea and an ancient viral lineage.
Asymptomatic neonatal herpes simplex virus infection in mice leads to long-term cognitive impairment
Authors: Dutton A , Patel CD , Taylor SA , Garland CR , Turnbaugh EM , Alers-Velazquez R , Mehrbach J , Nautiyal KM , Leib DA 
Published: April 2024

AbstractNeonatal herpes simplex virus (nHSV) is a devastating infection impacting approximately 14,000 newborns globally each year. Infection is associated with high neurologic morbidity and mortality, making early intervention and treatment critical. Clinical outcomes of symptomatic nHSV infections are well-studied, but little is known about the frequency of, or outcomes following, sub-clinical or asymptomatic nHSV. Given the ubiquitous nature of HSV infection and frequency of asymptomatic shedding in adults, subclinical infections are underreported, yet could contribute to long-term neurological damage. To assess potential neurological morbidity associated with subclinical nHSV infection, we developed a low-dose (100 PFU) HSV infection protocol in neonatal C57BL/6 mice. At this dose, HSV DNA was detected in the brain by PCR but was not associated with acute clinical symptoms. However, months after initial inoculation with 100 PFU of HSV, we observed impaired mouse performance on a range of cognitive and memory performance tasks. Memory impairment was induced by infection with either HSV-1 or HSV-2 wild-type viruses, but not by a viral mutant lacking the autophagy-modulating Beclin-binding domain of the neurovirulence gene γ34.5. Retroviral expression of wild type γ34.5 gene led to behavioral pathology in mice, suggesting that γ34.5 expression may be sufficient to cause cognitive impairment. Maternal immunization and HSV-specific antibody treatment prevented offspring from developing neurological sequelae following nHSV-1 infection. Altogether, these results support the idea that subclinical neonatal infections may lead to cognitive decline in adulthood, with possible profound implications for research on human neurodegenerative disorders such as Alzheimer’s Disease.
Conserved domains and structural motifs that differentiate closely related Rex1 and Rex3 DEDDh Exoribonuclease families are required for their function in yeast
Authors: Daniels Peter W. , Kelly Sophie , Tebbs Iwan J. , Mitchell Phil 
Published: April 2024

AbstractThe DEDD family of exonucleases has expanded through evolution whilst retaining a well conserved catalytic domain. One subgroup of DEDD exoribonucleases with very closely related catalytic domain sequences includes the yeast enzymes Rex1 (RNA exonuclease 1) and Rex3, the metazoan REXO1 (RNA exonuclease 1 homologue) and Rexo5 proteins, and the plant protein Sdn5 (small RNA degrading nuclease). Comparison of Alphafold models for these proteins reveals that Rex1, Rexo5 and Sdn5 are structural homologues, consisting of a central catalytic domain inserted within a discontinuous alkaline phosphatase (AlkP) domain. The core AlkP domain of Rex1-related proteins contains distinct surface insertions in different eukaryotic lineages. Yeast Rex1 contains three loops that are modelled to be directed towards the DEDD domain, one of which forms an extended helical arch that is conserved across fungi and plants but absent in metazoan homologues. We show that the arch and an adjacent loop are required for Rex1-mediated processing of 5S rRNA and tRNA inSaccharomyces cerevisiae. Rex3 structural homologues, including REXO1, contain a KIX domain (CREB kinase-inducible domain (KID) interacting domain) and a cysteine- and histidine-rich domain (CHORD) adjacent to a C-terminal DEDD domain. In contrast to Rex1, Rex3 proteins are found in metazoans and fungi but not in plants or algae. Deletion of the KIX domain within yeast Rex3 blocked its function in RNase MRP processing. Taken together, this work identifies evolutionarily conserved structural hallmarks of Rex1 and Rex3 enzymes and demonstrates that these features are required for Rex1- and Rex3-mediated RNA processing pathwaysin vivo.