bluuebunny/crossref_metadata_2025 huggingface dataset:
Elemental profiling and genome-wide association mapping reveal genomic variants modulating ionomic composition inPopulus trichocarpaleaves
Authors: Ployet Raphael , Feng Kai , Zhang Jin , Baxter Ivan , Glasgow David C. , Chen Jin-Gui , Tuskan Gerald A. , Tschaplinski Timothy J. , Weston David J. , Martin Madhavi Z. , Muchero Wellington
Published: May 2024

The ionome represents elemental composition in plant tissues and can be an indicator of nutrient status as well as overall plant performance. Thus, identifying genetic determinants governing elemental uptake and storage is an important goal in plant breeding and engineering. In this study, we coupled high-throughput ionome characterization with high-resolution genome-wide association studies (GWAS) to uncover genetic loci that modulate ionomic composition in leaves of 584 black cottonwood poplar (Populus trichocarpa) genotypes. Congruence of alternate ionomic profiling platforms, i.e., inductively coupled plasma-mass spectrometry (ICP-MS), neutron activation analysis (NAA) and laser-induced breakdown spectroscopy (LIBS), was performed on leaf samples from a subset of the population. Significant agreement was observed across the three platforms with some notable exceptions for individual elements. Subsequently, we used the ICP-MS platform to profile the 584 genotypes focusing on 20 elements. GWAS performed using a set of high-density (>8.2 million) single nucleotide polymorphisms (SNP), identified multiple loci significantly associated with variations in these mineral elements. The potential causal genes for variations in the ionome were significantly enriched in genes whose homologs were previously associated to ion homeostasis in other species. Notably, a polymorphic copy of the high-affinity molybdenum transporter MOT1 was found directly associated to molybdenum content in leaf tissues. The results of the GWAS also provided evidence of physiological and genetic interactions between mineral elements in poplar. The new candidate genes predicted to play a key role in cross-homeostasis of multiple elements are new targets for engineering a variety of traits of interest in tree species.
Involvement of Pf-like phages in resistance to phage infection in clinical isolates of P. aeruginosa from cystic fibrosis patients
Authors: Blasco Lucia , Barrio-Pujante Antonio , Lopez-Causape Carla , Arman Lucia , Bleriot Ines , Pacios Olga , Fernandez-Garcia Laura , Ortiz-Cartagena Concha , Ibarguren-Quiles Clara , Canton Rafael , Oliver Antonio , Tomas Maria
Published: May 2024

Pseudomonas aeruginosa is a bacterial pathogen that is a major cause of lung infections in cystic fibrosis (CF) and other patients. Isolates of P. aeruginosa from CF patients commonly carry filamentous phages (Pf phages), a type of temperate phage known to be related to biofilm production and antibiotic sequestration. In this study, 12 new Pf-like phages were identified in a collection of clinical isolates of P. aeruginosa from CF patients. Analysis of the phage genomes revealed different anti-phage defence systems, described here for first time in these types of phages. Finally, relationships between resistance to phage infection and the presence of Pf-like phages and also between each defence system and resistance were observed.
Evolutionary rate covariation is pervasive between glycosylation pathways and points to potential disease modifiers
Authors: Thorpe Holly J , Partha Raghavendran , Little Jordan , Clark Nathan L , Chow Clement Y
Published: May 2024

Mutations in glycosylation pathways, such as N-linked glycosylation, O-linked glycosylation, and GPI anchor synthesis, lead to Congenital Disorders of Glycosylation (CDG). CDGs typically present with seizures, hypotonia, and developmental delay but display large clinical variability with symptoms affecting every system in the body. This variability suggests modifier genes might influence the phenotypes. Because of the similar physiology and clinical symptoms, there are likely common genetic modifiers between CDGs. Here, we use evolution as a tool to identify common modifiers between CDG and glycosylation genes. Protein glycosylation is evolutionarily conserved from yeast to mammals. Evolutionary rate covariation (ERC) identifies proteins with similar evolutionary rates that indicate shared biological functions and pathways. Using ERC, we identified strong evolutionary rate signatures between proteins in the same and different glycosylation pathways. Genome-wide analysis of proteins showing significant ERC with GPI anchor synthesis proteins revealed strong signatures with ncRNA modification proteins and DNA repair proteins. We also identified strong patterns of ERC based on cellular sub-localization of the GPI anchor synthesis enzymes. Functional testing of the highest scoring candidates validated genetic interactions and identified novel genetic modifiers of CDG genes. ERC analysis of disease genes and biological pathways allows for rapid prioritization of potential genetic modifiers, which can provide a better understanding of disease pathophysiology and novel therapeutic targets.
Novel PotentialCannabisPathogen: Discovery of Tobacco necrosis virus A in a Diseased ColombianCannabis sativaPlant
Authors: Lopez-Jimenez Juliana , Palacio-Torres Herman D. , Alzate Juan F.
Published: May 2024

ABSTRACT

Plant viral infections pose a significant threat to global crop productivity. Despite their profound impact on agriculture, plant viruses have been relatively understudied, primarily due to technological limitations associated with classical molecular methods. However, the advent of NGS RNA-seq analysis has revolutionized virus characterization in environmental settings, overcoming previous limitations and providing a powerful tool for studying plant viruses.

In an RNA-seq experiment conducted on a diseased ColombianCannabis sativahemp plant, we identified a linear single-stranded RNA (ssRNA) genome belonging to Tobacco Necrosis Virus A (TNVA), a common cause of necrotic lesions in plants such as tobacco and tulipa. The affectedCannabis sativahemp plant exhibited severe symptoms, including alterations in pigmentation, leaf morphology such as chlorosis, necrotic tissue formation, and surface wear on the leaves. The complete genome sequence of theCannabis sativaTNVA was 3,656 nucleotides long, containing five putative ORFs, and was classified in the family Tombusviridae, genus Alphanecrovirus, and belonging to the Necro-like clade based on RdRp protein phylogenetic analysis. Our analysis revealed a well-conserved RdRp protein among the Alphanecroviruses, with 89% of the amino acid residues in the peptide being entirely conserved. In contrast, the coat protein exhibited significantly higher variability, with only 49.3% of the residues being 100% conserved. Regarding the viral genome expression ofCannabis sativaTNVA, we observed that the virus was highly abundant in the leaves of the diseased plant, ranking among the topmost abundant transcripts, occupying the percentile position of 3.06%. Overall, our study generated the first reference genome of TNVA virus in the tropical region and reported the first case of this virus infecting aCannabis sativaplant.
Controlling the frequency dynamics of homing gene drives for intermediate outcomes
Authors: Camm Benjamin J. , Fournier-Level Alexandre
Published: May 2024

Gene drives have enormous potential for solving biological issues by forcing the spread of desired alleles through populations. However, to safeguard from the potentially irreversible consequences on natural populations, gene drives with intermediate outcomes that neither fixate nor get removed from the population are of outstanding interest.

To elucidate the conditions leading to intermediate gene drive frequency, a stochastic, individual allele-focused gene drive model accessible was developed to simulate the diffusion of a homing gene drive in a population. The frequencies of multiple alleles at a locus targeted by a gene drive were tracked under various scenarios. These explored the effect of gene drive conversion efficiency, strength and frequency of resistance alleles, presence and strength of a fitness cost for the gene drive, its dominance and the level of inbreeding.

Four outcomes were consistently observed: Fixation, Loss, Temporary and Equilibrium. The latter two are defined by the frequency of the gene drive peaking then crashing or plateauing, respectively. No single variable determined the outcome of a drive, instead requiring a combination of variables. The difference between the conversion efficiency and resistance level differentiated the Temporary and Equilibrium outcomes. The frequency dynamics of the gene drive within outcomes varied extensively, with different variables driving this dynamics between outcomes.

These simulation results highlight the possibility of fine-tuning gene drive outcomes and compensating through biotechnological design constraint imposed by population features. To that end, we provide a web application implementing our model which will guide the safer design of gene drives able to achieve a range of controllable outcome tailored to population management needs.
Changes in Cerebrospinal Fluid Proteins across the Spectrum of Untreated and Treated Chronic HIV-1 Infection
Authors: Hu Zicheng , Cinque Paola , Dravid Ameet , Hagberg Lars , Yilmaz Aylin , Zetterberg Henrik , Fuchs Dietmar , Gostner Johanna , Blennow Kaj , Spudich Serena S. , Kincer Laura , Zhou Shuntai , Joseph Sarah , Swanstrom Ronald , Price Richard W. , Gisslén Magnus
Published: May 2024

Using theOlink Explore 1536platform, we measured 1,463 unique proteins in 303 cerebrospinal fluid (CSF) specimens from four clinical centers that included uninfected controls and 12 groups of people living with HIV-1 infection representing the spectrum of progressive untreated and treated chronic infection.

We present three initial analyses of these measurements: an overview of the CSF protein features of the sample; correlations of the CSF proteins with CSF HIV-1 RNA and neurofilament light chain protein (NfL) concentrations; and comparison of the CSF proteins in HIV-associated dementia (HAD) and neurosymptomatic CSF escape (NSE). These reveal a complex but coherent picture of CSF protein changes that includes highest concentrations of many proteins during CNS injury in theHADandNSEgroups and variable protein changes across the course of neuroasymptomatic systemic HIV-1 progression, including two common patterns, designated aslymphoidandmyeloidpatterns, related to the principal involvement of their underlying inflammatory cell lineages. Antiretroviral therapy reduced CSF protein perturbations, though not always to control levels.

The dataset of these CSF protein measurements, along with background clinical information, is posted online. Extended studies of this unique dataset will provide more detailed characterization of the dynamic impact of HIV-1 infection on the CSF proteome across the spectrum of HIV-1 infection, and further the mechanistic understanding of HIV-1-related CNS pathobiology.
Synchronization between chloroplastic and cytosolic protein synthesis for photosynthesis complex assembly
Authors: Fujita Tomoya , Wakigawa Taisei , Kawamoto Naohiro , Kurihara Yukio , Hirose Yuu , Hirayama Takashi , Toh Hirotaka , Kuriyama Tomoko , Hashimoto Atsushi , Matsuura-Suzuki Eriko , Mochida Keiichi , Yoshida Minoru , Matsui Minami , Iwasaki Shintaro
Published: May 2024

Through symbiosis, subunits of chloroplastic complexes are encoded in distinct genomes in the nucleus and organelles. For plant cells to maintain the stoichiometry of subunits and respond to environmental cues, orchestration of the nuclear and organellar gene expression systems is an essential task. However, the mechanism maintaining chloroplastic complexes remains largely enigmatic. Here, we simultaneously assessed the translatomes of the chloroplast and the cytoplasm via ribosome profiling and revealed the differential mechanisms employed by these two systems to cope with acute light/dark transitions: in chloroplasts, translational regulation is employed, whereas in the cytoplasm, control of the mRNA abundance is employed. This strategy is widely conserved in land plants (Arabidopsisand the grass plantBrachypodium) and green algae (Chlamydomonas). The translational control in chloroplasts may be established on the basis of organelle symbiosis; the primitive chloroplast in Glaucophyta (Cyanophora) was found to have already acquired translational control, whereas cyanobacteria (Synechocystis) employ control of the mRNA abundance. Moreover, treatment with photosynthetic electron transport inhibitors indicated that reduced plastoquinones may trigger translational activation in chloroplasts. Our work reveals an early origin of coordination of chloroplast and nuclear/cytoplasmic gene expression upon light exposure.
Docking interactions determine substrate specificity of members of a widespread family of protein phosphatases
Authors: Caban-Penix Suhaily , Ho Kristin , Yang Wendy , Baral Rishika , Bradshaw Niels
Published: May 2024

How protein phosphatases achieve specificity for their substrates is a major outstanding question. PPM family serine/threonine phosphatases are widespread in bacteria and eukaryotes, where they dephosphorylate target proteins with a high degree of specificity. In bacteria, PPM phosphatases control diverse transcriptional responses by dephosphorylating anti-anti-sigma factors of the STAS domain family, exemplified byB. subtilisphosphatases SpoIIE, which controls cell-fate during endospore formation, and RsbU, which initiates the General Stress Response. Using a combination of forward genetics, biochemical reconstitution, and AlphaFold2 structure prediction, we identified a conserved, tripartite substrate docking interface comprised of three variable loops on the surface of the PPM phosphatase domain that recognize the three-dimensional structure of the substrate protein. Non-conserved amino acids in these loops facilitate the accommodation of the cognate substrate and prevent dephosphorylation of the non-cognate substrate. Together, single-amino acid substitutions in these three elements cause an over five-hundred fold change in specificity. Our data additionally suggest that substrate-docking interactions regulate phosphatase specificity through a conserved allosteric switch element that controls the catalytic efficiency of the phosphatase by positioning the metal cofactor and substrate. We hypothesize that this is a generalizable mechanistic model for PPM family phosphatase substrate specificity. Importantly, the substrate docking interface with the phosphatase is only partially overlapping with the much more extensive interface with the upstream kinase, suggesting the possibility that kinase and phosphatase specificity evolved independently.
Skeletal Muscle Mitochondrial Dysfunction Mediated byPseudomonas aeruginosaQuorum Sensing Transcription Factor MvfR: Reversing Effects with Anti-MvfR and Mitochondrial-Targeted Compounds
Authors: Aggarwal Shifu , Singh Vijay , Chakraborty Arijit , Cha Sujin , Dimitriou Alexandra , de Crescenzo Claire , Izikson Olivia , Yu Lucy , Plebani Roberto , Tzika A. Aria , Rahme Laurence G
Published: May 2024

Sepsis and chronic infections withPseudomonas aeruginosa,a leading “ESKAPE” bacterial pathogen, are associated with increased morbidity and mortality and skeletal muscle atrophy. The actions of this pathogen on skeletal muscle remain poorly understood. In skeletal muscle, mitochondria serve as a crucial energy source, which may be perturbed by infection. Here, using the well-established backburn and infection model of murineP. aeruginosainfection, we deciphered the systemic impact of the quorum sensing (QS) transcription factor MvfR by interrogating five days post-infection its effect on mitochondrial-related functions in the gastrocnemius skeletal muscle and the outcome of the pharmacological inhibition of MvfR function and that of the mitochondrial-targeted peptide, Szeto-Schiller 31 (SS-31). Our findings show that the MvfR perturbs ATP generation, oxidative phosphorylation (OXPHOS), and antioxidant response, elevates the production of reactive oxygen species, and promotes oxidative damage of mitochondrial DNA in the gastrocnemius muscle of infected mice. These impairments in mitochondrial-related functions were corroborated by the alteration of key mitochondrial proteins involved in electron transport, mitochondrial biogenesis, dynamics and quality control, and mitochondrial uncoupling. Pharmacological inhibition of MvfR using the potent anti-MvfR lead, D88, we developed, or the mitochondrial-targeted peptide SS-31 rescued the MvfR- mediated alterations observed in mice infected with the wild-type strain PA14. Our study provides insights into the actions of MvfR in orchestrating mitochondrial dysfunction in the skeletal murine muscle, and it presents novel therapeutic approaches for optimizing clinical outcomes in affected patients.
Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation
Authors: Verdejo-Torres Odette , Klein David C. , Novoa-Aponte Lorena , Carrazco-Carrillo Jaime , Bonilla-Pinto Denzel , Rivera Antonio , Fitisemanu Fa’alataitaua , Jiménez-González Martha L. , Flinn Lyra , Pezacki Aidan T. , Lanzirotti Antonio , Ortiz-Frade Luis Antonio , Chang Christopher J. , Navea Juan G. , Blaby-Haas Crysten , Hainer Sarah J. , Padilla-Benavides Teresita
Published: May 2024

Copper (Cu) is an essential trace element required for respiration, neurotransmitter synthesis, oxidative stress response, and transcriptional regulation. Imbalance in Cu homeostasis can lead to several pathological conditions, affecting neuronal, cognitive, and muscular development. Mechanistically, Cu and Cu-binding proteins (Cu-BPs) have an important but underappreciated role in transcription regulation in mammalian cells. In this context, our lab investigates the contributions of novel Cu-BPs in skeletal muscle differentiation using murine primary myoblasts. Through an unbiased synchrotron X-ray fluorescence-mass spectrometry (XRF/MS) metalloproteomic approach, we identified the murine cysteine rich intestinal protein 2 (mCrip2) in a sample that showed enriched Cu signal, which was isolated from differentiating primary myoblasts derived from mouse satellite cells. Immunolocalization analyses showed that mCrip2 is abundant in both nuclear and cytosolic fractions. Thus, we hypothesized that mCrip2 might have differential roles depending on its cellular localization in the skeletal muscle lineage. mCrip2 is a LIM-family protein with 4 conserved Zn2+-binding sites. Homology and phylogenetic analyses showed that mammalian Crip2 possesses histidine residues near two of the Zn2+-binding sites (CX2C-HX2C) which are potentially implicated in Cu+-binding and competition with Zn2+. Biochemical characterization of recombinant human hsCRIP2 revealed a high Cu+-binding affinity for two and four Cu+ions and limited redox potential. Functional characterization using CRISPR/Cas9-mediated deletion ofmCrip2in primary myoblasts did not impact proliferation, but impaired myogenesis by decreasing the expression of differentiation markers, possibly attributed to Cu accumulation. Transcriptome analyses of proliferating and differentiatingmCrip2KO myoblasts showed alterations in mRNA processing, protein translation, ribosome synthesis, and chromatin organization. CUT&RUN analyses showed that mCrip2 associates with a select set of gene promoters, includingMyoD1andmetallothioneins, acting as a novel Cu-responsive or Cu-regulating protein. Our work demonstrates novel regulatory functions of mCrip2 that mediate skeletal muscle differentiation, presenting new features of the Cu-network in myoblasts.
Adaptation to skin mycobiota promotes antibiotic tolerance inStaphylococcus aureus
Authors: Kowalski Caitlin H. , Lawhorn Susannah , Smith T. Jarrod , Corrigan Rebecca M. , Barber Matthew F.
Published: May 2024

The microbiota can promote host health by inhibiting pathogen colonization, yet how host-resident fungi, or the mycobiota, contribute to this process remains unclear. The human skin mycobiota is uniquely stable compared to other body sites and dominated by yeasts of the genusMalassezia. We observe that colonization of human skin byMalassezia sympodialissignificantly reduces subsequent colonization by the prominent bacterial pathogenStaphylococcus aureus.M. sympodialissecreted products possess potent bactericidal activity againstS. aureusand are sufficient to impairS. aureusskin colonization. This bactericidal activity requires an acidic environment and is exacerbated by free fatty acids, demonstrating a unique synergy with host-derived epidermal defenses. Leveraging experimental evolution to pinpoint mechanisms ofS. aureusadaptation in response to the skin mycobiota, we identified multiple mutations in the stringent response regulator Rel that promote survival againstM. sympodialis. Similar Rel alleles have been reported inS. aureusclinical isolates, and natural Rel variants are sufficient for tolerance toM. sympodialisantagonism. Partial stringent response activation underlies tolerance to clinical antibiotics, with both laboratory-evolved and natural Rel variants conferring multidrug tolerance. These findings demonstrate the ability of the mycobiota to mediate pathogen colonization resistance, identify new mechanisms of bacterial adaptation in response to fungal antagonism, and reveal the potential for microbiota-driven evolution to shape pathogen antibiotic susceptibility.

Highlights

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M. sympodialisreduces colonization of human skin byS. aureus

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Bactericidal activity ofM. sympodialisis exacerbated by features of the skin niche

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S. aureusRel variants are sufficient for tolerance toMalasseziaantagonism

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Evolved tolerance to yeast antagonism coincides withS. aureusmultidrug tolerance
Structural basis of Spliced Leader RNA recognition by theTrypanosoma bruceicap-binding complex
Authors: Bernhard Harald , Petržílková Hana , Popelářová Barbora , Ziemkiewicz Kamil , Bartosik Karolina , Warmiński Marcin , Tengo Laura , Gröger Henri , Dolce Luciano G. , Micura Ronald , Jemielity Jacek , Kowalinski Eva
Published: May 2024

Kinetoplastids are a clade of eukaryotic protozoans that include human parasitic pathogens like trypanosomes and Leishmania species. In these organisms, protein-coding genes are transcribed as polycistronic pre-mRNAs, which need to be processed by the coupled action of trans-splicing and polyadenylation to yield monogenic mature mRNAs. During trans-splicing, a universal RNA sequence, the spliced leader RNA (SL RNA) mini-exon, is added to the 5’-end of each mRNA. The 5’-end of this mini-exon carries a hypermethylated cap structure and is bound by a trypanosomatid-specific cap-binding complex (CBC). The function of three of the kinetoplastid CBC subunits is unknown, but an essential role in cap binding and trans-splicing has been suggested. Here, we report cryo-EM structures that reveal the molecular architecture of theTrypanosoma bruceiCBC (TbCBC) complex. We find thatTbCBC interacts with two distinct features of the SL RNA. TheTbCBP20 subunit interacts with the m7G cap whileTbCBP66 recognizes double-stranded portions of the SL RNA. Our findings pave the way for future research on mRNA maturation in kinetoplastids. Moreover, the observed structural similarities and differences betweenTbCBC and the mammalian cap-binding complex will be crucial for considering the potential ofTbCBC as a target for anti-trypanosomatid drug development.

Highlights

Cryo-EM reveals the molecular architecture of the tetramericTrypanosoma bruceicap-binding complex (TbCBC).

TbCBP110 is the kinetoplastid homolog of mammalian CBP80 and forms the scaffold forTbCBP20.

TbCBC has a bilobal architecture withTbCBP30 bridging the flexibly attachedTbCBP66 subunit and theTbCBP20-TbCBP110 core complex.

TbCBC recognizes the m7G RNA cap independent of the other trypanosomatid-specific cap4 methylations.

TheTbCBP66 subunit contains a binding site for dsRNA, augmenting the affinity ofTbCBC for the SL RNA.
Control of 3ʹ splice site selection by the yeast splicing factor Fyv6
Authors: Senn Katherine A. , Lipinski Karli A. , Zeps Natalie J. , Griffin Amory F. , Wilkinson Max E. , Hoskins Aaron A.
Published: May 2024

Pre-mRNA splicing is catalyzed in two steps: 5ʹ splice site (SS) cleavage and exon ligation. A number of proteins transiently associate with spliceosomes to specifically impact these steps (1stand 2ndstep factors). We recently identified Fyv6 (FAM192A in humans) as a 2ndstep factor inS. cerevisiae; however, we did not determine how widespread Fyv6’s impact is on the transcriptome. To answer this question, we have used RNA-seq to analyze changes in splicing. These results show that loss of Fyv6 results in activation of non-consensus, branch point (BP) proximal 3ʹ SS transcriptome-wide. To identify the molecular basis of these observations, we determined a high-resolution cryo-EM structure of a yeast product complex spliceosome containing Fyv6 at 2.3 Å. The structure reveals that Fyv6 is the only 2ndstep factor that contacts the Prp22 ATPase and that Fyv6 binding is mutually exclusive with that of the 1ststep factor Yju2. We then use this structure to dissect Fyv6 functional domains and interpret results of a genetic screen forfyv61suppressor mutations. The combined transcriptomic, structural, and genetic studies allow us to propose a model in which Yju2/Fyv6 exchange facilitates exon ligation and Fyv6 promotes usage of consensus, BP distal 3ʹ SS.
Proteogenomic reconstruction of organ-specific metabolic networks in an environmental sentinel species, the amphipodGammarus fossarum
Authors: Koenig Natacha , Baa-Puyoulet Patrice , Lafont Amélie , Lorenzo-Colina Isis , Navratil Vincent , Leprêtre Maxime , Sugier Kevin , Delorme Nicolas , Garnero Laura , Queau Hervé , Gaillard Jean-Charles , Kielbasa Mélodie , Ayciriex Sophie , Calevro Federica , Chaumot Arnaud , Charles Hubert , Armengaud Jean , Geffard Olivier , Esposti Davide Degli
Published: May 2024

Metabolic pathways are targets of environmental contaminants underlying a large variability of toxic effects throughout biodiversity. However, the systematic reconstruction of metabolic pathways remains limited in environmental sentinel species due to the lack of available genomic data in many taxa of animal diversity. In order to improve the knowledge of the metabolism of sentinel species, in this study we used a multi-omics approach to reconstruct the most comprehensive map of metabolic pathways for a crustacean model in biomonitoring, the amphipodGammarus fossarum.

We revisited the assembly of RNA-seq data byde novoapproaches drastically reducing RNA contaminants and transcript redundancy. We also acquired extensive mass spectrometry shotgun proteomic data on several organs fromG. fossarummales and females to identify organ-specific metabolic profiles.

TheG. fossarummetabolic pathway reconstruction (available through the metabolic database GamfoCyc) was performed by adapting the genomic tool CycADS and we identified 377 pathways representing 7,630 annotated enzymes, 2,610 enzymatic reactions and the expression of 858 enzymes was experimentally validated by proteomics. Our analysis shows organ-specific metabolic profiles, such as an elevated abundance in enzymes involved in ATP biosynthesis and fatty acid beta-oxidation indicative of the high-energy requirement of the gills, or the key anabolic and detoxification role of the hepatopancreatic caeca, as exemplified by the specific expression of the retinoid biosynthetic pathways and glutathione synthesis.

In conclusion, the multi-omics data integration performed in this study provides new resources to investigate metabolic processes in crustacean amphipods and their role in mediating the effects of environmental contaminant exposures in sentinel species.
Transit amplifying cells balance growth and differentiation in above-ground meristems
Authors: Joossens Jessica , Herwegh Denia , Laureyns Reinout , Pevernagie Julie , Hautegem Tom Van , Pollaris Lotte , Bhattacharya Samik , Korfhage Christian , Depuydt Thomas , Demuynck Kirin , Vandepoele Klaas , Saeys Yvan , Whipple Clinton , Strable Josh , Nelissen Hilde
Published: May 2024

In both animals and plants, stem cell niches balance between cell-renewal and the generation of progeny cells that differentiate into specialized tissues. The multipotent and highly proliferative transit amplifying cells (TACs) integrate signals from stem cells and their differentiating progeny cells. Here we used spatial transcriptomics mapped to individual cells to illustrate the localization of TACs in maize meristems based on transcriptional gradients. Through genetic interactions and fluctuations in the transcriptional gradients we show that the multiplicative cell divisions are independently controlled from the TAC cell divisions. The dynamic nature of transcriptional variation in response to cell state or environment, together with the potential to improve yield by their modulation highlights the importance of finetuned modulation of networks rather than constitutive perturbations for crop improvement.
Exploring sex-specific neuroendocrine influences on the sensorimotor-association axis in single individuals
Authors: Serio Bianca , Yilmaz Deniz , Pritschet Laura , Grotzinger Hannah , Jacobs Emily G. , Eickhoff Simon B. , Valk Sofie L.
Published: May 2024

Human neuroimaging studies consistently show multimodal patterns of variability along a key principle of macroscale cortical organization - the sensorimotor-association (S-A) axis. However, little is known about day-to-day fluctuations in functional activity along this axis within an individual, including sex-specific neuroendocrine factors contributing to such transient changes. We leveraged data from two densely sampled healthy young adults, one female and one male, to investigate intra-individual daily variability along the S-A axis, which we computed as our measure of functional cortical organization by reducing the dimensionality of functional connectivity matrices. Daily variability was greatest in temporal limbic and ventral prefrontal regions in both participants, and was more strongly pronounced in the male subject. Next, we probed local- and system-level effects of steroid hormones and self-reported perceived stress on functional organization. Our findings revealed modest effects that differed between participants, hinting at subtle -potentially sex-specific- associations between neuroendocrine fluctuations and intra-individual variability along the S-A axis. In sum, our study points to neuroendocrine factors as possible modulators of intra-individual variability in functional brain organization, highlighting the need for further research in larger samples.
Superhydrophobic Sand Mulch and Date Palm Biochar Dramatically Boost Growth ofMoringa oleiferain Sandy Soil: Insights into Evapotranspiration Budgeting and Metabolomic Profiling
Authors: Odokonyero Kennedy , Vernooij Bob , Albar Batool , Exposito Lisa Oki , Alsamdani Aishah , Haider Amin Akhter Ghulam , Musskopf Nayara Vivian Huve , Gallo Adair , Kharbatia Najeh , Mishra Himanshu
Published: May 2024

In response to the challenge of nutrient-deficient sandy soils and water scarcity due to excessive evaporative water loss in arid regions, we developed and tested two complementary soil amendment technologies: Superhydrophobic sand (SHS) mulch and an enriched date palm biochar. In a greenhouse pot experiment, we investigated the stand-alone and synergistic effects of SHS mulch (10 mm-thickness) and biochar (2% w/w) onMoringa oleiferaplants under normal (N,100% field capacity) and reduced (R, 50% ofN) irrigation scenarios. UnderNandR, SHS mulch reduced evaporation by 71% and 64%, respectively; while SHS+biochar reduced evaporation by 61% and 47%, respectively, in comparison with the control (p< 0.05). Total transpiration significantly increased in SHS plants by 311% and 385% underNandR, respectively. Compared with the control, transpiration increased in biochar-amended plants by 103% and 110%; whereas, its combination with SHS increased transpiration by 288% and 301% underNandR, respectively (p< 0.05). Irrespective of the irrigation regimes, we found superior effects of SHS, biochar, and their combination on plant height (62–140%), trunk diameter (52–91%), leaf area index (57–145%), leaf chlorophyll content index (11–19%), stomatal conductance (51–175%), as well as shoot (390–1271%) and root (52–142%) biomass, in comparison with the controls. Metabolomics analysis showed significantly higher relative abundance of amino acids, sugars, fatty acids, and organic acids in the leaves of control plants relative to other treatments, as a response to water or nutrient stress induced by excessive water loss through evaporation. Next, we found a higher concentration of D-Mannose, D-Fructose, glucose, and malic acid in plants grown with SHS or biochar treatment underNandRirrigation, attributed to increased water/nutrient-use efficiency and carbon assimilation because of higher photosynthesis rates than in the control plants. Our results show that, our complementary technologies could address the challenge of water loss via evaporation from soil and maximize soil nutrient retention for improving plant growth in arid regions. This could underscore the success and sustainability of irrigated agriculture and greening efforts in arid lands.
Genome-guided, field-deployable loop-mediated isothermal amplification (LAMP) assay for specific detection ofDickeya dadantii
Authors: Montesinos Stefania , Tyagi Garima , Feng Zhuokun , Hampson Ella , Adhikari Achyut , Minaai Michael , Wong Landon , Haubner Meagan , Dobhal Shefali , Arizala Dario , Andreason Sharon A. , Mollov Dimitre , Ochoa-Corona Francisco , Bingham Jon-Paul , Odani Jenee , Jenkins Daniel , Ma Li Maria , Fletcher Jacqueline , Stack James P. , Arif Mohammad
Published: May 2024

Potatoes, among the most economically significant crops worldwide, are susceptible to various plant pathogens that significantly impact their propagation, production, storage, and distribution. Soft rot disease, caused primarily byDickeyaandPectobacterium, results in substantial economic losses to the agricultural industry annually. In this study, we developed a rapid, reliable, and field-deployable loop-mediated isothermal amplification (LAMP) assay for detectingD. dadantii, a common soft rot causing bacteria. TheD. dadantii-specific LAMP primers were designed targeting a highly conserved genomic region withinD. dadantii, the TetR/AcrR family transcriptional regulator CDS and its flanking sequences. This assay was thoroughly validated with the members of inclusivity (nine strains ofD. dadantii) and exclusivity panels (85 strains, including allDickeyaspecies, related taxa, and host DNA), detecting no false positives or negatives. The limit of detection (LOD) was established by performing assays with 10-fold serially diluted pure gDNA ofD. dadantiiand gDNA spiked with host crude extract; the assay detected the target pathogen down to 1 pg (188 copies) without being adversely affected by the host crude extract. The developed LAMP assay specifically detected the target pathogen in infected plant materials. Additional multi-operator blind and multi-instrument tests were conducted to assess the assay’s robustness and applicability, consistently yielding accurate results without false positives or negatives. These findings demonstrate the assay’s potential utility for biosecurity, routine diagnostics, and epidemiological studies.
A large attachment organelle mediates interaction between a novel Nanobdellota archaeon YN1 and its host
Authors: Johnson Matthew D , Sakai Hiroyuki , Paul Bindusmita , Nunorura Takuro , Dalvi Somavally , Mudaliyar Manasi , Shepherd Doulin , Shimizu Michiru , Udupa Shubha , Ohkuma Moriya , Kurosawa Norio , Ghosal Debnath
Published: May 2024

DPANN archaea are an enigmatic superphylum that are difficult to isolate and culture in the laboratory due to their specific culture conditions and apparent ectosymbiotic lifestyle. Here we successfully isolated and cultivated a co-culture system of a novel Nanobdellota archaeon YN1 and its host Sulfurisphaera ohwakuensis YN1HA. We characterised the co-culture system by complementary methods, including metagenomics and metabolic pathway analysis, fluorescence microscopy, and high-resolution electron cryo-tomography (CryoET). We show that YN1 is deficient in essential metabolic processes and requires host resources to proliferate. CryoET imaging revealed an enormous attachment organelle present in the YN1 envelope that forms a direct interaction with the host cytoplasm, bridging the two cells. Together our results unravelled the molecular and structural basis of ectosymbiotic relationship between YN1 and YNHA. This research broadens our understanding of DPANN biology and the versatile nature of their ectosymbiotic relationships.
Deletion of an sRNA primes development in a multicellular bacterium
Authors: Fortezza Marco La , Verwilt Jasper , Cossey Sarah , Eisner Sabrina , Velicer Gregory J. , Yu Yuen-Tsu N.
Published: May 2024

ABSTRACT

Small non-coding RNAs (sRNAs) are essential in regulating gene expression during many biological processes. The myxobacteria genepxrencodes an sRNA known to block fruiting-body development, an aggregative multicellular process triggered by starvation. Deletion ofpxrallowsMyxococcus xanthuscells to develop in the presence of nutrients. However, potential Pxr binding targets and most genes regulated by Pxr remain unknown. Here, we found that the absence ofpxrexpression dramatically alters the temporal dynamics of development, thus suggesting an important new role of this sRNA in myxobacterial ecology. We transcriptionally profiled vegetative cells ofM. xanthusstrains possessing vs lackingpxrand found that over half of the genes impacted bypxrdeletion during growth are linked to development, including known and potentially novel critical regulators. Many other genes are associated with general metabolic processes, which Pxr regulates positively. Our study discovers new phenotypic effects of Pxr regulation of likely ecological importance, identifies the suite of genes this sRNA controls during vegetative growth, reveals a previously unknown developmental regulator and provides new insights into the early molecular regulation of myxobacterial development.
A fully phased, chromosome-scale genome of sugar beet line FC309 enables the discovery of Fusarium Yellows resistance QTL
Authors: Todd Olivia , Simpson Sheron , Scheffler Brian , Dorn Kevin
Published: May 2024

Sugar beet (Beta vulgaris L.) is a global source for table sugar and animal fodder. Here we report a highly contiguous and haplotype phased genome assembly and annotation for sugar beet line FC309. Both assembled haplomes for FC309 represent the largest and most contiguous assembled beet genomes reported to date, as well as gene annotations sets that capture over 1500 additional protein-coding loci compared to prior beet genome annotations. These new genomic resources were used to identify novel quantitative trait loci (QTL) for Fusarium Yellows resistance from the FC309 genetic background using an F2 mapping-by-sequencing approach. The highest QTL signals were detected on Chromosome 3, spanning approximately 10 Mbp in both haplomes. A parallel transcriptome profiling experiment identified candidate genes within the Chromosome 3 QTL with plausible roles in disease response, including NBS-LRR genes with expression trends suggestive of their role as causal resistance genes. Collectively, the genomic resources for FC309 presented here be foundational tool for comparative genomics, m mapping other traits in the FC309 background, and as a reference genome for other beet studies due to its contiguity, completeness, and high-quality gene annotations.
The role of Med15 sequence features in transcription factor interactions
Authors: Cooper David G. , Liu Shulin , Grunkemeyer Emma , Fassler Jan S.
Published: May 2024

Med15 is a general transcriptional regulator and subunit within the tail module of the RNA Pol II Mediator complex. TheS. cerevisiaeMed15 protein has a well-structured N-terminal KIX domain, three Activator Binding Domains (ABDs), several naturally variable polyglutamine (poly-Q) tracts (Q1, Q2, Q3) embedded in an intrinsically disordered central region, and a C-terminal Mediator Association Domain (MAD). We investigated how the presence of ABDs and changes in length and composition of poly-Q tracts influences Med15 activity and function using phenotypic, gene expression, transcription factor interaction and phase separation assays of truncation, deletion, and synthetic alleles. We found that individual Med15 activities were influenced by the number of activator binding domains (ABDs) and adjacent polyglutamine tract composition. Robust Med15 activity required at least the Q1 tract and the length of that tract modulated activity in a context-dependent manner. We found that loss of Msn2-dependent transcriptional activation due to Med15 Q1 tract variation correlated well with a reduction in Msn2:Med15 interaction strength, but that interaction strength did not always mirror the propensity for phase separation. We also observed that distant glutamine tracts and Med15 phosphorylation affected the activities of the KIX domain, suggesting that intramolecular interactions may affect some Med15-transcription factor interactions. Further, two-hybrid based interaction studies revealed intramolecular interactions between the N-terminal KIX domain and the Q1R domain of Med15.

Author Summary

Glutamine tracts are relatively uncommon, but are a feature of many transcriptional regulators including the Med15 subunit of the Mediator Complex which is a large protein complex that plays an important role in gene expression in eukaryotic organisms including yeast and animals. Strains lacking Med15 are compromised in their ability to grow on many kinds of media, under stress conditions, and in fermentation, reflecting its importance in gene expression. Naturally occurring yeast strains specialized for growth in specific environments (e.g., wine, beer, clinical) vary in their glutamine tract lengths, suggesting that the length of glutamine tracts may influence Med15 function in a manner that is adaptive for a specific environment. In this study, we intentionally manipulated the length of the glutamine tracts in Med15 and found that these changes have subtle effects on Med15 interactions with transcription factors, target gene expression and growth. Taken together, our data suggests that glutamine tracts do not themselves mediate critical interactions with partner proteins, but instead may influence the shape of the Med15 protein, thus indirectly affecting the nature of these interactions.
Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction
Authors: Kumar Ramasamy P. , Matos Jason O. , Black Brandon Y. , Ellenburg William H. , Chen Jiahua , Patterson MacKenzie , Gehtman Jacob A. , Theobald Douglas L. , Krauss Isaac J. , Oprian Daniel D.
Published: May 2024

In a continuing effort to understand reaction mechanisms of terpene synthases catalyzing initial anti-Markovnikov cyclization reactions, we solved the X-ray crystal structure of (+)-caryolan-1-ol synthase (CS) fromStreptomyces griseus, with and without an inactive analog of the FPP substrate, 2-fluorofarnesyl diphosphate (2FFPP), bound in the active site of the enzyme. The CS-2FFPP complex was solved to 2.65 Å resolution and showed the ligand in a linear, elongated orientation, incapable of undergoing the initial cyclization event to form a bond between carbons C1 and C11. Intriguingly, the apo CS structure (2.2 Å) also had electron density in the active site, in this case density that was well fit with a curled-up tetraethylene glycol molecule presumably recruited from the crystallization medium. The density was also well fit by a molecule of farnesene suggesting that the structure may mimic an intermediate along the reaction coordinate. The curled-up conformation of tetraethylene glycol was accompanied by dramatic rotamer shifts among active-site residues. Most notably, W56 was observed to undergo a 90° rotation between the 2FFPP complex and apo-enzyme structures, suggesting that it contributes to steric interactions that help curl the tetraethylene glycol molecule in the active site, and by extension perhaps also a derivative of the FPP substrate in the normal course of the cyclization reaction. In support of this proposal, the CS W56L variant lost the ability to cyclize the FPP substrate and produced only the linear terpene products farnesol and α- and β-farnesene.
Loss of Intracellular Fibroblast Growth Factor 14 (iFGF14)Increasesthe Excitability of Mature Hippocampal and Cortical Pyramidal Neurons
Authors: Ransdell Joseph L. , Carrasquillo Yarimar , Bosch Marie K. , Mellor Rebecca L. , Ornitz David M. , Nerbonne Jeanne M.
Published: May 2024

Mutations inFGF14, which encodes intracellular fibroblast growth factor 14 (iFGF14), have been linked to spinocerebellar ataxia type 27 (SCA27), a multisystem disorder associated with progressive deficits in motor coordination and cognitive function. Mice (Fgf14-/-) lacking iFGF14 display similar phenotypes, and we have previously shown that the deficits in motor coordination reflectreducedexcitability of cerebellar Purkinje neurons, owing to the loss of iFGF14-mediated regulation of the voltage-dependence of inactivation of the fast transient component of the voltage-gated Na+(Nav) current, INaT. Here, we present the results of experiments designed to test the hypothesis that loss of iFGF14 also attenuates the intrinsic excitability of mature hippocampal and cortical pyramidal neurons. Current-clamp recordings from adult mouse hippocampal CA1 pyramidal neurons in acutein vitroslices, however, revealed that repetitive firing rates werehigherinFgf14-/-, than in wild type (WT), cells. In addition, the waveforms of individual action potentials were altered inFgf14-/-hippocampal CA1 pyramidal neurons, and the loss of iFGF14 reduced the time delay between the initiation of axonal and somal action potentials. Voltage-clamp recordings revealed that the loss of iFGF14 altered the voltage-dependence of activation, but not inactivation, of INaTin CA1 pyramidal neurons. Similar effects of the loss of iFGF14 on firing properties were evident in current-clamp recordings from layer 5 visual cortical pyramidal neurons. Additional experiments demonstrated that the loss of iFGF14does notalter the distribution of anti-Nav1.6 or anti-ankyrin G immunofluorescence labeling intensity along the axon initial segments (AIS) of mature hippocampal CA1 or layer 5 visual cortical pyramidal neuronsin situ. Taken together, the results demonstrate that, in contrast with results reported for neonatal (rat) hippocampal pyramidal neurons in dissociated cell culture, the loss of iFGF14 doesnotdisrupt AIS architecture or Nav1.6 localization/distribution along the AIS of mature hippocampal (or cortical) pyramidal neuronsin situ.