bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACTSepsis 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

ABSTRACTCopper (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

SummaryThe 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-M. sympodialisreduces colonization of human skin byS. aureus-Bactericidal activity ofM. sympodialisis exacerbated by features of the skin niche-S. aureusRel variants are sufficient for tolerance toMalasseziaantagonism-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

AbstractKinetoplastids 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.HighlightsCryo-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

ABSTRACTPre-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

AbstractMetabolic 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

AbstractIn 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.
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

AbstractIn 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

ABSTRACTPotatoes, 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.
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

ABSTRACTSmall 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.
The role of Med15 sequence features in transcription factor interactions
Authors: Cooper David G. , Liu Shulin , Grunkemeyer Emma , Fassler Jan S. 
Published: May 2024

AbstractMed15 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 SummaryGlutamine 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.