bluuebunny/crossref_metadata_2025_split huggingface dataset:
The structural repertoire ofFusarium oxysporumf. sp.lycopersicieffectors revealed by experimental and computational studies
Authors: Yu Daniel S. , Outram Megan A. , Smith Ashley , McCombe Carl L. , Khambalkar Pravin B. , Rima Sharmin A. , Sun Xizhe , Ma Lisong , Ericsson Daniel J. , Jones David A. , Williams Simon J. 
Published: December 2021

AbstractPlant pathogens secrete proteins, known as effectors, that function in the apoplast or inside plant cells to promote virulence. Effector recognition by cell-surface or cytosolic receptors results in the activation of defence pathways and plant immunity. Despite their importance, our general understanding of fungal effector function and recognition by immunity receptors remains poor. One complication often associated with effectors is their high sequence diversity and lack of identifiable sequence motifs precluding prediction of structure or function. In recent years, several studies have demonstrated that fungal effectors can be grouped into structural classes, despite significant sequence variation and existence across taxonomic groups. Using protein x-ray crystallography, we identify a new structural class of effectors hidden within the secreted in xylem (SIX) effectors fromFusarium oxysporumf. sp.lycopersici(Fol). The recognised effectors Avr1 (SIX4) and Avr3 (SIX1) represent the founding members of theFoldual-domain (FOLD) effector class, with members containing two distinct domains. Using AlphaFold2, we predicted the full SIX effector repertoire ofFoland show that SIX6 and SIX13 are also FOLD effectors, which we validated experimentally for SIX6. Based on structural prediction and comparisons, we show that FOLD effectors are present within three divisions of fungi and are expanded in pathogens and symbionts. Further structural comparisons demonstrate thatFolsecretes effectors that adopt a limited number of structural folds during infection of tomato. This analysis also revealed a structural relationship between transcriptionally co-regulated effector pairs. We make use of the Avr1 structure to understand its recognition by the I receptor, which leads to disease resistance in tomato. This study represents an important advance in our understanding ofFol-tomato, and by extension plant-fungal interactions, which will assist the development of novel control and engineering strategies to combat plant pathogens.
Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass
Authors: Kersten Sonja , Chang Jiyang , Huber Christian D. , Voichek Yoav , Lanz Christa , Hagmaier Timo , Lang Patricia , Lutz Ulrich , Hirschberg Insa , Lerchl Jens , Porri Aimone , Van de Peer Yves , Schmid Karl , Weigel Detlef , Rabanal Fernando A. 
Published: December 2021

AbstractRepeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.
Proteome-wide cellular thermal shift assay reveals novel crosstalk between brassinosteroid and auxin signaling
Authors: Lu Qing , Zhang Yonghong , Hellner Joakim , Xu Xiangyu , Pauwels Jarne , Giannini Caterina , Ma Qian , Dejonghe Wim , Han Huibin , Van de Cotte Brigitte , Impens Francis , Gevaert Kris , Friml Jiří , De Smet Ive , Molina Daniel Martinez , Russinova Eugenia 
Published: December 2021

AbstractDespite the growing interest in using chemical genetics in plant research, small-molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass-spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or post-translational modifications allows the identification of drug targets, or the study of protein-metabolite and protein-protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal- and the phospho-proteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a novel substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf thus, revealing a novel crosstalk between brassinosteroid and auxin signaling.Significance StatementChemical genetics, which investigates the biological processes using small molecules, is gaining interest in plant research. However, a major challenge is to uncover the mode of action of the small molecule. Here, we applied the cellular thermal shift assay coupled with mass spectrometry (CETSA MS) to intact Arabidopsis cells and showed that bikinin, the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, changed the thermal stability of some of its direct targets and putative GSK3 interacting proteins. In combination with phosphoproteomics, we also revealed that GSK3s phosphorylate the auxin carrier PIN-FORMED1 (PIN1) and regulated its polarity that is required for the vascular patterning in the leaf.
Evolution of miRNA binding sites and regulatory networks in cichlids
Authors: Mehta Tarang K. , Penso-Dolfin Luca , Nash Will , Roy Sushmita , Di-Palma Federica , Haerty Wilfried 
Published: December 2021

AbstractThe divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analysing the selective constraints driving evolution of miRNA and transcription factor (TF) binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA and TF binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared to subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA and TF binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired e.g. clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits.
PHASE: A MATLAB Based Program for the Analysis of Drosophila Phase, Activity and Sleep under Entrainment
Authors: Persons J.L. , Abhilash L. , Lopatkin A.J. , Roelofs A. , Bell E.V. , Fernandez M.P. , Shafer O.T. 
Published: December 2021

AbstractThe problem of entrainment is central to circadian biology. In this regard, Drosophila has been an important model system. Owing to the simplicity of its nervous system and the availability of powerful genetic tools, the system has shed significant light on the molecular and neural underpinnings of entrainment. However, much remains to be learned regarding the molecular and physiological mechanisms underlying this important phenomenon. Under cyclic light/dark conditions, Drosophila melanogaster displays crepuscular patterns of locomotor activity with one peak anticipating dawn and the other anticipating dusk. These peaks are characterized through an estimation of their phase relative to the environmental light cycle and the extent of their anticipation of light transitions. In Drosophila chronobiology, estimations of phases are often subjective, and anticipation indices vary significantly between studies. Though there is increasing interest in building flexible analysis software tools in the field, none incorporates objective measures of Drosophila activity peaks in combination with the analysis of fly activity/sleep in the same program. To this end, we have developed PHASE, a MATLAB-based program that is simple and easy to use and (i) supports the visualization and analysis of activity and sleep under entrainment, (ii) allows analysis of both activity and sleep parameters within user-defined windows within a diurnal cycle, (iii) uses a smoothing filter for the objective identification of peaks of activity (and therefore can be used to quantitatively characterize them), and (iv) offers a series of analyses for the assessment of behavioral anticipation of environmental transitions.
Selection on early survival does not explain germination rate clines in Mimulus cardinalis (Phrymaceae)
Authors: Muir Christopher D. , Van Den Elzen Courtney L. , Angert Amy L. 
Published: December 2021

AbstractPremiseMany traits covary with environmental gradients to form phenotypic clines. While local adaptation to the environment can generate phenotypic clines, other nonadaptive processes may also. If local adaptation causes phenotypic clines, then the direction of genotypic selection on traits should shift from one end of the cline to the other. Traditionally genotypic selection on non-Gaussian traits like germination rate have been hampered because it is challenging to measure their genetic variance.MethodsHere we used quantitative genetics and reciprocal transplants to test whether a previously discovered cline in germination rate showed additional signatures of adaptation in the scarlet monkeyflower (Mimulus cardinalis). We measured genotypic and population level covariation between germination rate and early survival, a component of fitness. We developed a novel discrete log-normal model to estimate genetic variance in germination rate.ResultsContrary to our adaptive hypothesis, we found no evidence that genetic variation in germination rate contributed to variation in early survival. Across populations, southern populations in both gardens germinated earlier and survived more.ConclusionsSouthern populations have higher early survival but this is not caused by faster germination. This pattern is consistent with nonadaptive forces driving the phenotypic cline in germination rate, but future work will need to assess whether there is selection at other life stages. This statistical framework should help expand quantitative genetic analyses for other waiting-time traits.
Selective pressure on membrane proteins drives the evolution of Helicobacter pylori Colombian subpopulations
Authors: Guevara Alix A. , Torres Roberto C. , Castro-Valencia Fabian L. , Suárez John J. , Criollo-Rayo Angel , Bravo Maria Mercedes , Carmona Luis Carvajal , Polanco M. Magdalena Echeverry de , Bohórquez Mabel E. , Torres Javier 
Published: December 2021

AbstractHelicobacter pylori have coevolved with mankind since its origins, adapting to different human groups. In America H. pylori has evolved in several subpopulations specific for regions or even countries. In this study we analyzed the genome of 163 Colombian strains along with 1,113 strains that represent worldwide H. pylori populations to better discern the ancestry and adaption to Colombian people. Population structure was inferred with FineStructure and chromosome painting identifying the proportion of ancestries in Colombian isolates. Phylogenetic relationship was analyzed using the SNPs present in the core genome. Also, a Fst analysis was done to identify the gene variants with the strongest fixation in the identified Colombian subpopulations in relation to their parent population hspSWEurope. Worldwide, population structure analysis allowed the identification of two Colombian subpopulations, the previously described hspSWEuropeColombia and a novel subpopulation named hspColombia. In addition, three subgroups of H. pylori were identified within hspColombia that follow their geographic origin. The Colombian H. pylori subpopulations represent an admixture of European, African and Native indigenous ancestry; although some genomes showed a high proportion of self-identity, suggesting a strong adaption to these mestizo Colombian groups. The Fst analysis identified 82 SNPs significantly fixed in 26 genes of the hspColombia subpopulation that encode mainly for outer membrane proteins and proteins involved in central metabolism. The strongest fixation indices were identified in genes encoding the membrane proteins HofC, HopE, FrpB-4 and Sialidase A. These findings demonstrate that H. pylori has evolved in Colombia to give rise to subpopulations following a geographical structure, evolving to an autochthonous genetic pool, drive by a positive selective pressure especially on genes encoding for outer membrane proteins.
Ecological landscapes guide the assembly of optimal microbial communities
Authors: George Ashish B. , Korolev Kirill S. 
Published: December 2021

AbstractAssembling optimal microbial communities is key for various applications in biofuel production, agriculture, and human health. Finding the optimal community is challenging because the number of possible communities grows exponentially with the number of species, and so an exhaustive search cannot be performed even for a dozen species. A heuristic search that improves community function by adding or removing one species at a time is more practical, but it is unknown whether this strategy can discover an optimal or nearly optimal community. Using consumer-resource models with and without cross-feeding, we investigate how the efficacy of search depends on the distribution of resources, niche overlap, cross-feeding, and other aspects of community ecology. We show that search efficacy is determined by the ruggedness of the appropriately-defined ecological landscape. We identify specific ruggedness measures that are both predictive of search performance and robust to noise and low sampling density. The feasibility of our approach is demonstrated using experimental data from a soil microbial community. Overall, our results establish the conditions necessary for the success of the heuristic search and provide concrete design principles for building high-performing microbial consortia.Author summaryResearch shows that microbial communities comprised of specific species combinations can cure disease, improve agricultural output, or synthesize valuable chemicals. But finding the species combinations that generate high-performing communities is challenging because there are too many species combinations to test exhaustively. So, scientists use heuristic strategies that test only a few species combinations to search for high-performing communities. However, these heuristic strategies often fail to find the best species combinations, and we still do not understand when they fail. Here, we develop a framework to analyze these heuristic strategies, building on the concept of fitness landscapes studied in evolution and computer science. We apply this framework to data from simulated microbial community models to identify biological properties that affect the success of heuristic search strategies, such as the extent to which microbes compete for the same metabolites. Further, we establish statistical measures of the landscape structure that can help estimate search success from preliminary data. We validate our findings using experimental data from communities of soil microbes. Together, our results develop a conceptual framework to analyze and develop heuristic search strategies and identify guiding principles to help scientists choose species and environmental conditions that make finding high-performing microbial communities easier.
Animal soil food web complexity triggers shifts in microbial communities, including PAH degraders, but without clear effects on phenanthrene phytoremediation
Authors: Correa-Garcia Sara , Corelli Vincenzo , Tremblay Julien , Dozois Jessica Ann , Mukula Eugenie , Séguin Armand , Yergeau Etienne 
Published: December 2021

AbstractThe aim of this study was to determine whether the complexity of the animal soil food web (SFWC) is a significant factor influencing the soil microbial communities, the productivity of the willow, and the degradation rates of 100 mg kg-1 phenanthrene contamination. The SFWC treatment had eight levels: just the microbial community (BF), or the BF with nematodes (N), springtails (C), earthworms (E), CE, CN, EN, CEN. After eight weeks of growth, the height and biomass of willows were significantly affected by the SFWC, whereas the amount of phenanthrene degraded was not affected, reaching over 95% in all pots. SFWC affected the structure and the composition of the bacterial, archaeal and fungal communities, with significant effects of SFWC on the relative abundance of fungal genera such as Sphaerosporella, a known willow symbiont during phytoremediation, and bacterial phyla such as Actinobacteriota, containing many PAH degraders. These SFWC effects on microbial communities were not clearly reflected in the community structure and abundance of PAH degraders, even though some degraders related to the Actinobacteriota and the diversity of Gram-negative degraders were affected by the SFWC treatments. Overall, our results suggest that, under our experimental conditions, SFWC does not affect significantly willow phytoremediation outcomes.ImportancePolycyclic aromatic hydrocarbons (PAH) pose a threat to soil ecosystems. Phytoremediation is a green technology that can help restore ecosystems’ health affected by PAH contamination. Past research on phytoremediation of PAH has focused on the roles of plant and microbes in contaminant fates. However, soil environments usually harbor large faunal communities that interact with both the plant and the microbial communities, potentially altering the phytoremediation process. We hypothesized that soil food web complexity (SFWC), represented by increasing levels of soil fauna, influences PAH degradation through interactions with the plant and the microbes. In this study, we demonstrated that SFWC increases the plant biomass and changes the composition of the microbial community, especially the fungal structure. In our pot experiment, more complex levels of SFWC did not contribute to higher degradation rates, but the increased plant biomass and the higher relative abundance of fungal genera associated with lower plant stress could indirectly contribute to better phytoremediation outcomes. Our results highlight the importance of considering the contributions of soil fauna to the success of phytoremediation.
Integrated Analyses of Growth Differentiation Factor-15 Concentration and Cardiometabolic Diseases in Humans
Authors: Lemmelä Susanna , Wigmore Eleanor M. , Benner Christian , Havulinna Aki , Ong Rachel M. Y. , Kempf Tibor , Wollert Kai C. , Blankenberg Stefan , Zeller Tanja , Peters James E. , Salomaa Veikko , Fritsch Maria , March Ruth , Palotie Aarno , Daly Mark , Butterworth Adam S. , Kinnunen Mervi , Paul Dirk S. , Matakidou Athena 
Published: December 2021

AbstractGrowth differentiation factor 15 (GDF15) is a stress response cytokine that is elevated in several cardiometabolic diseases and has attracted interest as a potential therapeutic target. To further explore the association of GDF15 with human disease, we conducted a broad study into the phenotypic and genetic correlates of GDF15 concentration in up to 14,099 individuals. Assessment of 772 traits across 6,610 participants in FINRISK identified associations of GDF15 concentration with a range of phenotypes including all-cause mortality, cardiometabolic disease, respiratory diseases and psychiatric disorders as well as inflammatory markers. A meta-analysis of genome-wide association studies (GWAS) of GDF15 concentration across 3 different assay platforms (n=14,099) confirmed significant heterogeneity due to a common missense variant rs1058587 in GDF15, potentially due to epitope-binding artefacts. After conditioning on rs1058587, statistical fine-mapping identified 4 independent putative causal signals at the locus. Mendelian randomisation (MR) analysis did not find evidence of a causal relationship between GDF15 concentration and cardiometabolic traits. Using reverse MR, we identified a potential causal association of body mass index on GDF15 (IVW pFDR=0.0072). Taken together, our data do not support a role for elevated GDF15 concentrations as a causal factor in human cardiometabolic disease but support its role as a biomarker of metabolic stress.