bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure and mechanism of the RalGAP tumor suppressor complex
Authors: Rasche René , Klink Björn Udo , Apken Lisa Helene , Michalke Esther , Chen Minghao , Oeckinghaus Andrea , Gatsogiannis Christos , Kümmel Daniel 
Published: November 2024

AbstractThe RalGAP (GTPase activating protein) complexes are negative regulators of the Ral GTPases and thus crucial components that counteract (oncogenic) Ras signaling. However, no structural information on the architecture of this tumor suppressor complex is available hampering a mechanistic understanding of its functionality. Here, we present a cryo-EM structure of RalGAP that reveals an extended 58 nm tetrameric architecture comprising two heterodimers of the RalGAPα and RalGAPβ subunits. We show that the catalytic domain of RalGAPα requires stabilization by a unique domain of RalGAPβ, providing the molecular basis for why RalGAP complexes are obligatory heterodimers. Formation of RalGAP tetramers is not required for activityin vitro, but essential for function of the complexin vivo. Structural analysis of RalGAP subunit variants reported in cancer patients suggests effects on complex formation and thus functional relevance in tumor development, emphasizing the significance of the obtained structural information for medical research.
Genome-wide association studies identify promising QTL for freezing tolerance in winter and early spring as a basis for in-depth genetic analysis and implementation in winter faba bean (Vicia fabaL.) breeding
Authors: Windhorst Alex , Skovbjerg Cathrine Kiel , Angra Deepti , O’Sullivan Donal Martin , Andersen Stig Uggerhøj , Wolfgang Link 
Published: November 2024

AbstractInterest in faba bean as a locally adapted high-protein grain legume crop has increased in Europe over the past decade. Winter faba bean, which can make use of soil moisture from autumn to spring and partially escape summer droughts, exhibit greater yield potential than the spring-type. However, due to insufficient winter hardiness, winterkill is a major constraint that prevents large-scale production of current winter-type cultivars in Central and Northern Europe. Here, we extend the understanding of freezing tolerance, the main component trait of winter hardiness, during winter and against late-frost in early spring and define genomic target regions for marker-assisted selection. Comparative analysis of genome-wide association studies revealed 13 treatment-specific major QTLs with partially pleiotropic effect on four freezing tolerance related traits. In addition, we identified five treatment-unspecific pleiotropic QTLs, including two major freezing tolerance loci on chromosomes 1 and 5. Our results thus indicate both a distinct and common genetic control of tolerance to winter- and late-frost in winter faba bean. In combination with the promising prediction abilities obtained from marker score-based prediction, our work highlights the potential for marker-assisted and genomic selection toward improved freezing tolerance and winter hardiness in winter faba bean breeding programs.
A novel framework for assessing the robustness of genomic animal models applied to a wild marine fish
Authors: Thia Joshua A. , Aguirre J. David , Hereward James , Evans Jennifer , Liggins Libby , Riginos Cynthia , McGuigan Katrina 
Published: November 2024

ABSTRACTHeritable genetic versus non-heritable plastic phenotypic variation determine how selection may shape evolutionary responses. Population genomic studies typically aim to identify associations between loci (SNPs) and phenotypes, missing broader insight into heritable basis of polygenic traits with quantitative genomic approaches.Genomic animal models can facilitate estimates of trait heritability from genomic data but can be challenging to apply to wild organisms. This is because the populations of many wild organisms are large, comprising many distantly related individuals, which makes the sampling close-kin unlikely. This in turn limits the variation of relatedness in a sample, reducing the efficacy of genomic animal models.We developed a novel framework for applying genomic animal models to wild organisms where sampling close-kin may be near impossible. Our framework combines resampling of genetic markers with simulating different levels of heritability to infer the power and reliability of genomic animal models fitted to datasets lacking kin structure.We use our framework to estimate heritability of head shape traits in a wild marine intertidal fish,Bathygobius cocosensis(Bleeker 1854), using ddRAD SNP genotypes and phenotypes measured using geometric morphometric methods. In its eastern Australian range,B. cocosensisis highly abundant, has high effective gene flow, and occupies diverse habitats and microhabitats.Placing our observed genomic animal model results in the context of simulated results, we conclude that two of the head shape traits were heritable (estimatedh2= 0.26 and 0.18). This suggests that head shape phenotypes could evolve through heritable genetic changes inB. cocosensis, although there is likely a large non- heritable component. We also found strong phenotypic differentiation (pairwisePST≤ 0.33) despite very weak genetic differentiation (pairwiseFST< 0.002), suggesting that environmental factors might structure phenotypes amidst processes homogenising genetic variation.Our study addresses key methodological gaps for using quantitative genomic approaches on wild organisms, offering a rare example of partitioned heritable and non-heritable contributions to phenotypic variation in a non-model wild marine fish.This would have been difficult without our new framework to overcome the challenges of a dataset lacking kin structure.
Sumatran orangutan mothers differ in the extent and trajectory of their expression of maternal behaviour
Authors: Revathe T , Mundry Roger , Utami-Atmoko Sri Suci , Umaira Aprilla Tazkia , A. van Noordwijk Maria , Fröhlich Marlen , Bürkner Paul-Christian , Schuppli Caroline 
Published: November 2024

AbstractMothers arguably play a crucial role in the early development and survival of mammalian offspring, and differences in maternal care may affect offspring’s physical and cognitive development. Whereas biological and socioecological factors contribute to differences among mothers, the individual as a source of variation remains understudied. We investigated between-individual variation in the average expression of and plasticity in six maternal behaviours in Sumatran orangutans, using 15 years of mother-offspring behavioural data. We found that mothers differed substantially in the average expression of four maternal behaviours, even after controlling for known predictors of these behaviours, and that not controlling for these confounding effects erroneously leads to larger estimated between-individual behavioural variation. Furthermore, orangutan mothers substantially differed in how they adjusted two maternal behaviours as their offspring aged – i.e., they showed variation in behavioural plasticity. Our study suggests that Sumatran orangutan mothers are constrained in the average expression of maternal behaviours and their plastic responses, potentially resulting in consistent differences among mothers, otherwise called maternal personality. Our findings highlight that individual variation around the population mean in maternal behaviour is more than noise but also that controlling for confounding effects is crucial to avoid the overestimation of individual variation.
RNF20-mediated H2B monoubiquitination protects stalled forks from degradation and promotes fork restart
Authors: Bhattacharya Debanjali , Dwivedi Harsh Kumar , Nagaraju Ganesh 
Published: November 2024

AbstractChromatin modifications play an important role in transcription, DNA replication and repair. Nonetheless, whether histone modifications regulate replication stress responses remains obscure. Here, we show that RNF20 localizes to and promotes H2B monoubiquitination (H2Bub) at replicating sites. Knockdown of RNF20 leads to degradation of stalled forks by MRE11 nuclease, which can be rescued by inhibition of MRE11 and co-depletion of SMARCAL1/HLTF/ZRANB3 fork remodelers. RNF20 facilitates the loading of RAD51 and RAD51C at the stalled fork sites and participates in the same pathway of RAD51/RAD51C-mediated fork protection and restart. Analyses with the RING domain and phosphorylation-deficient mutants of RNF20 showed that its catalytic activity and ATR/ATM-mediated phosphorylation are essential for its role in replication stress responses. Notably, treatment of RNF20-depleted cells with chromatin relaxing agents rescue the fork protection and restart defects. Collectively, our studies uncover the role of RNF20-mediated H2Bub in regulating the chromatin dynamics to safeguard the replicating genomes.
Influence of Contact Map Topology on RNA Structure Prediction
Authors: Faber Christian , Upadhyay Utkarsh , Taubert Oskar , Schug Alexander 
Published: November 2024

AbstractThe available sequence data of RNA molecules have highly increased in the past years. Unfortunately, while computational power is still under exponential growth, the computer prediction quality from sequence to final structure is still inferior to the labour intensive experimental work. Although a reliable end-to-end procedure was already developed for proteins since Alphafold2, while its successor AlphaFold3 can also predict RNA, its confidence in particular for novel sequences and folds appear still limited. Another strategy entails two steps: (i) predicting potential contacts in the form of a contact maps from evolutionary data, and (ii) simulating the molecule with a physical force field while using the contact map as restraint. However, the quality of the structure prediction crucially depends on the quality of the contact map. Until now, only the proportion of true positive contacts was considered as a quality characteristic. We propose to also include the distribution of these contacts, and have done so in our recent studies. We observed that the clustering of contacts, as is common for many AI algorithms, has a negative impact on prediction quality. In contrast, a more distributed topology is beneficial. We have applied these findings from computer experiments to current algorithms and introduced a measure of distribution, the Gaussian score.
Assessing Long-Read Mappers for Viral Genomics
Authors: Baudeau Thomas , Marchet Camille , Salson Mikaël 
Published: November 2024

ABSTRACTLong-read sequencing technologies from Pacific Biosciences and Oxford Nanopore Technologies (ONT) have advanced genomic research, producing reads over 10 kilobases and enabling rapid field-based viral surveillance. This study evaluates eight long-read mapping tools on viral genomic data, including modern and legacy methods. We assessed their performance on ONT reads and their impact on variant calling using bcftools and medaka. Using simulated and real datasets under varying conditions, reflecting different experimental and biological conditions, such as variable read lengths, error rates and the presence of multiple viral variants, we found that the majority of tools had great difficulty in correctly managing read edges. In addition, it was found that with a default setting, the performance of the tools decreased.
The presence of the Pacific Oyster OSHV-1 resistance marker on chromosome 8 does not impact susceptibility to infection by Vibrioaestuarianus
Authors: Surry Liam B. , Sutherland Ben J. G. , Lunda Spencer L. , Loudon Andrew H. , Divilov Konstantin , Langdon Chris J. , Green Timothy J. 
Published: November 2024

AbstractThe Pacific oyster,Crassostrea gigas, is an important species in global aquaculture, but its production is threatened by pathogenic infections such as Ostreid herpesvirus 1 (OsHV-1) andVibrio aestuarianus. A genetic marker for OsHV-1 resistance has been identified on chromosome 8 of the Pacific oyster genome, and selective breeding has been performed to produce OsHV-1-resistant oysters. However, the potential impact of this marker on susceptibility to other pathogens remains unknown. In this study, we assess the effect of the presence and allelic dosage of the OsHV-1 resistance marker on susceptibility toV. aestuarianusinfections in selectively bred oyster families from the Molluscan Broodstock Program of Oregon State University. Sixteen families were produced with various states of the OsHV-1 resistance marker, and a disease challenge withV. aestuarianuswas performed on these families to track mortality in each individual. Challenged oysters were genotyped at the OsHV-1 resistance locus, andVibriosusceptibility was compared among genotype groups within and between families. Additionally, double digest reduced representation sequencing (ddRADseq) was performed on challenged oysters, and a genome-wide association study was conducted for survivorship from theVibrioexposure. Results showed that prior to theVibrioexposure, the OsHV-1 resistance marker was not observed at the expected Mendelian inheritance ratios in families, with a significantly reduced presence of the homozygous alternate genotype in 75% of heterozygote family crosses. Among the 16 families, mortality rates differed significantly following exposure toV. aestuarianus(range: 85.4% to 47.9%), but there was no association found between the chromosome 8 marker and survival to Vibrio infection. No loci were found to be significantly associated to survivorship toVibrioinfection, suggesting Vibrio resistance in these families is not controlled by one or a few loci of large effect.
DOA/CLK2 phosphorylates Fl(2)d/WTAP to enhance m6A mRNA methyltransferase complex activity
Authors: McQuarrie David W. J. , Bian Wei , Soller Matthias 
Published: November 2024

AbstractN6-methyladenosine (m6A) is the most abundant internal modification in messenger RNA (mRNA) providing an essential layer to the control of gene expression important to many biological processes. A megadalton writer complex deposits m6A methyl marks that are then read by YTH domain containing proteins. Deposition of m6A is thought to be regulated by cellular signalling but how remains uncertain. We identified the kinase DOA, a highly conserved homologue of human CLK2 by using the essential role of m6A in theDrosophilaSxl auto-regulation for sex determination and dosage compensation. We show that DOA kinase is required for m6A deposition andSxlalternative splicing. Overexpression of DOA can compensate writer complex insufficiency and rescue lethality of m6A in the context ofSxlmis- splicing, suggesting a key role in regulating activity of the m6A complex. Through genetic interaction experiments, we identify a phospho-site at the end of a conserved helical structure in Fl(2)d as DOA target. CLK2 phosphorylates the same helix in WTAP, the human homologue of Fl(2)d. CLK2 expands regulatory capacity through additional phospho-sites and changing of theDrosophilasite to a phosphomimetic-like glutamine, overall important for m6A directed regulation of dosage compensation genes in human cells.
Role of a TonB-dependent receptor and an oxygenase in iron-dependent copper resistance inCaulobacter crescentus
Authors: Cherry Pauline , Kasmo Hala , Godelaine Mauro , Tilquin Françoise , Dieu Marc , Renard Patsy , Matroule Jean-Yves 
Published: November 2024

AbstractCopper (Cu) is potentially threatening for living organisms owing to its toxicity at high concentrations, requiring the onset of diverse detoxification strategies to maintain fitness. We previously showed that the environmental conditions modulate the response of the oligotrophic alphaproteobacteriumCaulobacter crescentusto Cu excess. In the present study, we investigated the role of the Fe-importing TonB-dependent receptor (TBDR) CciT and its partner, CciO, a 2-oxoglutarate/Fe2+-dependent oxygenase, in Cu resistance. CciT is specifically involved in Cu resistance in both rich and poor media. Using inductively coupled plasma optical emission spectrometry, we found that under Cu stress, the cellular Cu content is reduced by overexpression ofcciT, while Fe content increases. Mutations of the three known Fe-importing TBDRs reveal that CciT is the primary Fe importer in these conditions and the only TBDR required for Cu resistance. In addition, the extracellular Fe concentration is positively correlated with the cellular Fe content and negatively correlated with the cellular Cu content, resulting in the protection of the cells against Cu excess. The operon organization ofcciTandcciOis highly conserved across bacteria, indicating a functional link between the two proteins. Deletion ofcciT,cciO, or both genes leads to similar Cu sensitivity. Catalytic mutations in CciT and CciO also result in Cu sensitivity. While CciO is not required for Cu and Fe transport, its precise function remains unknown. Overall, this study provides new insights into the role of Fe uptake in Cu resistance, emphasizing the critical influence of environmental conditions on bacterial physiology.ImportanceCopper is an essential metal for many living organisms, as it helps to drive crucial chemical reactions. However, when present in excess, copper turns toxic due to its high reactivity with biological molecules. Bacteria may encounter excess copper in various environments, such as polluted soils, agricultural copper treatments, and within the vacuoles of infected macrophages. In this study, we investigated the copper response in the environmental bacteriumCaulobacter crescentus. Our findings reveal that environmental iron levels play a critical role in copper resistance, as increased iron prevents cellular copper accumulation and toxicity. We identified two essential proteins, CciT and CciO, that are involved in iron transport, providing protection against copper excess.
A Novel Actinobacteria-Specific Ribosome Hibernation Factor inMycobacterium tuberculosis
Authors: Majumdar Soneya , Li Yunlong , Manjari Swati R. , Gamper Howard B. , Hou Ya-Ming , Banavali Nilesh K. , Ojha Anil K. , Agrawal Rajendra K. 
Published: November 2024

AbstractMycobacterium tuberculosis(Mtb), the causative agent of tuberculosis (TB), persists within its host for long periods. Treatment of TB requires prolonged administration of antibiotics, some of which target Mtb ribosomes, the protein synthesizing machine of the cell. We determined high-resolution cryo-EM structures of Mtb ribosomes obtained from biofilms under zinc-depleted conditions that are expected to induce ribosome hibernation. In these structures, in addition to finding the Mtb homolog of the hibernation promoting factor Mpy that binds to the decoding center in the small ribosomal subunit, we discovered an actinobacteria-specific protein, previously of unknown function, bound in the nascent polypeptide-exit tunnel (NPET) within the large ribosomal subunit. We refer to this NPET-bound protein as a actinobacteria-specific ribosome tunnelocclusion factor (RTOF). RTOF is found with vacant or E-tRNA-bound 70S ribosomes, but not in actively translating Mtb ribosomes, suggesting that its binding coincides with ribosome hibernation. RTOF makes strong interactions through the entire stretch of NPET extending up to the peptidyl-transferase center (PTC), such that it would block the passage of nascent polypeptide chain. The highly conserved FRRKSG motif of RTOF also interferes with accommodation of the formyl-methionyl moiety of initiator fMet-tRNAfMetin the conformation required for translation initiation. A molar excess of mRNA and initiator fMet-tRNAfMetdisplaces RTOF by triggering a significant alteration to the conformation of FRRKSG motif, which suggests how RTOF-bound hibernating ribosomes can be reactivated under optimal cellular conditions. The presence of RTOF would interfere with the binding of PTC-targeting drugs, such as macrolides, lincosamides, and oxazolidines, thereby maintaining a drug-free pool of hibernating Mtb ribosomes.
Dynamic regulation of the oxidative stress response by the E3 ligase TRIP12
Authors: Ingersoll Andrew J. , McCloud Devlon M. , Hu Jenny Y. , Rape Michael 
Published: November 2024

AbstractThe oxidative stress response is centered on the transcription factor NRF2 and protects cells from reactive oxygen species (ROS). While ROS inhibit the E3 ligase CUL3KEAP1to stabilize NRF2 and elicit antioxidant gene expression, cells recovering from stress must rapidly reactivate CUL3KEAP1to prevent reductive stress and oxeiptosis-dependent cell death. How cells restore efficient NRF2-degradation upon ROS clearance remains poorly understood. Here, we identify TRIP12, an E3 ligase dysregulated in Clark-Baraitser Syndrome and Parkinson’s Disease, as a component of the oxidative stress response. TRIP12 is a ubiquitin chain elongation factor that cooperates with CUL3KEAP1to ensure robust NRF2 degradation. In this manner, TRIP12 accelerates stress response silencing as ROS are being cleared, but limits NRF2 activation during stress. The need for dynamic control of NRF2-degradation therefore comes at the cost of diminished stress signaling, suggesting that TRIP12 inhibition could be used to treat degenerative pathologies characterized by ROS accumulation.
Dynamic whole-body models for infant metabolism
Authors: Zaunseder Elaine , Mohammad Faiz Khan , Mütze Ulrike , Kölker Stefan , Heuveline Vincent , Thiele Ines 
Published: November 2024

1AbstractComprehensive, sex-specific whole-body models (WBMs) accounting for organ-specific metabolism have been developed to allow for the simulation of adult and infant metabolism. These WBMs are evaluated daily, giving insights into metabolic flux changes that occur in one day of an infant’s or adult’s life. However, for medical applications, such as in metabolic diseases and their treatment, an evaluation and concentration predictions on a shorter time scale would be beneficial. Therefore, we developed a dynamic infant-WBM that couples metabolite dynamics in short time frames through physiology-based pharma-cokinetic models with the existing infant whole-body models. We then tailored the dynamic infant-WBM enabling the prediction of isovalerylcarnitine (C5), a clinical biomarker used for the inherited metabolic disease isovaleric aciduria (IVA). Our results show that, as expected, the predicted C5 concentrations exceeded the newborn screening thresholds during the time (36 - 72 hours) newborn screening blood samples are taken in the IVA models but not in models simulating healthy infants. We also demonstrate how the dynamic infant-WBMs can be used to test the effect changes in dietary intake have on the biomarker. Since the dynamic infant-WBMs were parametrised with literature-derived experimental or estimated values, we show how uncertainty quantification can be applied to quantify the parameter uncertainties. We found that the fractional unbound plasma needed to be estimated correctly, as this parameter strongly impacted C5 concentration predictions of the dynamic infant-WBMs. Overall, the dynamic infant-WBMs hold promise for personalised medicine, as it enables personalised biomarker concentration predictions of healthy and diseased infant metabolism in various time intervals.