bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methane and ethane production rates by methyl-coenzyme M reductase in cell extracts from different methanogens
Authors: Nguyen V. P. Thinh , Keller Sebastian , Scheller Silvan 
Published: January 2024

AbstractThe enzyme methyl-coenzyme M reductase (Mcr) is responsible for most of the biologically produced methane. Mcr catalyzes the reversible conversion of methyl-coenzyme M and coenzyme B to methane and the corresponding heterodisulfide CoM-S-S-CoB as the last step in all methanogens. In anaerobic methanotrophs, it catalyzes the same reaction to proceed in the reverse direction.While Mcr has been historically considered as an enzyme exclusive to the one-carbon metabolism, recent studies have demonstrated that homologs of Mcr have evolved to catalyze the first step of the archaeal anaerobic oxidation of medium and long-chain alkanes to their corresponding alkyl-coenzyme M thioethers.While ample metagenomic studies and data related to Mcr is available, in vitro experiments are limited, because purifying Mcr in its active nickel-I form is challenging. Fully active enzyme has only been reported forMethanothermobacter marburgensisisoenzyme I, from which most of the enzyme studies have been performed.To get an overview of the substrate scope of different Mcr variants, we tested cell-free lysates from the methanogensMethanosarcina mazei, Methanosarcina acetivorans, Methanococcus maripaludis, Methanothermococcus okinawensis, andM. marburgensisfor their rates to convert methyl- and ethyl-coenzyme M to methane and to ethane, respectively.Cell extracts fromM. mazeishowed an ethane production rate of ca. 8% relative to methane production at 37 °C, and about 14% at 49 °C in an assay relying on titanium (III) citrate and cobalamin to regenerate coenzyme B from the CoM-S-S-CoB heterodisulfide.For cell extracts ofM. marburgensis, we found an ethane-to-methane production rate of 8%, which is substantially higher than the reported value of ca. 0.3% for the ratio of their maximal catalytic rate for purified isoenzyme I. SinceM. marburgensisis known to express two isoenzymes depending on the growth conditions, we hypothesize that isoenzyme II is substantially more promiscuous towards ethane formation than the well-described isoenzyme I.Which it is still challenging to obtain accurate kinetic parameters of the Mcr-catalyzed reaction, our experiments demonstrate that Mcr activity can be quickly and conveniently studiedviacell-free lysates, and that substrate promiscuity towards ethane formation is generally larger than anticipated.
Electrostatic Trade-Off between Mesophilic Stability and Adaptation in Halophilic Proteins
Authors: Herrero Pablo , Pejenaute Alba , Millet Oscar , Ortega Gabriel 
Published: January 2024

AbstractExtremophile organisms have adapted to extreme physicochemical conditions. Halophilic organisms, in particular, survive at very high salt concentrations. To achieve this, they have engineered the surface of their proteins to increase the number of short, polar and acidic amino acids, while decreasing large, hydrophobic and basic residues. While these adaptations initially decrease the thermodynamic stability in the absence of salt, they grant halophilic proteins remarkable stability in environments with extremely high salt concentrations, where non-adapted proteins unfold and aggregate. The molecular mechanisms by which halophilic proteins achieve this, however, are not yet clear. Here, we test the hypothesis that the halophilic amino acid composition destabilizes the surface of the protein, but in exchange improves the stability in the presence of salts. To do that, we have measured the folding thermodynamics of various protein variants with different degrees of halophilicity in the absence and presence of different salts, and at different pH values to tune the ionization state of the acidic amino acids. Our results show that, although electrostatic interactions decrease the stability of halophilic proteins, in exchange they induce a significant salt-induced stabilization and improve solubility. Besides electrostatic interactions, we also show that other general contributions, such as hydrophobic effect and preferential exclusion, are important. Overall, our findings suggest a trade-off between folding thermodynamics and halophilic adaptation to optimize the stability of halophilic proteins in hypersaline environments.Significance statementThis work explores how extreme halophiles adapt their proteins for survival in hypersaline environments. By engineering the protein surface, evolution has selected proteins adapted to high salt concentrations. Our findings suggest a delicate balance between protein stability and haloadaptation modulated in part by electrostatic interactions, furthering our understanding of life adaptation to extreme environments.
Signaling events at TMEM doorways provide potential targets for inhibiting breast cancer dissemination
Authors: Surve Chinmay R. , Duran Camille L. , Ye Xianjun , Chen Xiaoming , Lin Yu , Harney Allison S. , Wang Yarong , Sharma Ved P. , Stanley E. Richard , Cox Dianne , McAuliffe John C. , Entenberg David , Oktay Maja H. , Condeelis John S. 
Published: January 2024

AbstractTumor cell intravasation is essential for metastatic dissemination, but its exact mechanism is incompletely understood. We have previously shown that in breast cancer, the direct and stable association of a tumor cell expressing Mena, a Tie2hi/VEGFhimacrophage, and a vascular endothelial cell, creates an intravasation portal, called a “tumor microenvironment of metastasis” (TMEM) doorway, for tumor cell intravasation, leading to dissemination to distant sites. The density of TMEM doorways, also called TMEM doorway score, is a clinically validated prognostic marker of distant metastasis in breast cancer patients. Although we know that tumor cells utilize TMEM doorway-associated transient vascular openings to intravasate, the precise signaling mechanisms involved in TMEM doorway function are only partially understood. Using two mouse models of breast cancer and anin vitroassay of intravasation, we report that CSF-1 secreted by the TMEM doorway tumor cell stimulates local secretion of VEGF-A from the Tie2hiTMEM doorway macrophage, leading to the dissociation of endothelial junctions between TMEM doorway associated endothelial cells, supporting tumor cell intravasation. Acute blockade of CSF-1R signaling decreases macrophage VEGF-A secretion as well as TMEM doorway-associated vascular opening, tumor cell trans-endothelial migration, and dissemination. These new insights into signaling events regulating TMEM doorway function should be explored further as treatment strategies for metastatic disease.
Evaluation of the effects of ripening-related genes on fruit metabolites and the associated regulatory mechanisms in tomato
Authors: Jia Huimin , Xu Yaping , Deng Yuanwen , Xie Yinhuan , Gao Zhongshan , Lang Zhaobo , Niu Qingfeng 
Published: January 2024

AbstractFruit ripening, which is a complex process involving dynamic changes to metabolites, is controlled by multiple factors, including transcription factors (TFs). Several TFs are reportedly essential regulators of tomato fruit ripening. To evaluate the effects of specific TFs on metabolite accumulation during fruit ripening, CRISPR/Cas9-mediated mutagenesis was combined with metabolome and transcriptome analyses to explore regulatory mechanisms. Specifically, we generated various genetically engineered tomato lines that differed regarding metabolite contents and fruit colors. The metabolite and transcript profiles indicated that the selected TFs have distinct functions that control fruit metabolite contents, especially carotenoids and sugars. Our findings may provide new insights into the regulatory mechanisms governing tomato fruit ripening. Moreover, a mutation toELONGATED HYPOCOTYL5(HY5) increased the tomato fruit fructose and glucose contents by approximately 20% (relative to the wild-type levels). Ourin vitroassay showed that HY5 can bind directly to the G-boxcis-element in theSWEET12cpromoter to activate expression, thereby modulating sugar transport. Our findings have clarified the mechanism regulating fruit metabolic networks, while also providing the theoretical basis for breeding horticultural crops that produce fruit with diverse flavors and colors.g
Ultrasound-Driven Programmable Artificial Muscles
Authors: Shi Zhan , Zhang Zhiyuan , Ahmed Daniel 
Published: January 2024

ABSTRACTDespite their promise for technological and medical innovations, the advancement of artificial muscles faces challenges in dynamic programmability, wireless control, scalability, and responsiveness. Ultrasound offers a promising yet underutilized solution, providing effective and robust actuation. We introduce an innovative design paradigm for soft artificial muscles, utilizing tens of thousands of resonant microbubbles for targeted activation, enabling a wide range of programmable motions. We developed a comprehensive theoretical model and conducted various applications: from actuating soft grippers and powering centimeter-scale biomimetic stingraybots for propulsion to demonstrating the multimodal shape transformation of a functional surface and equipping static objects with transformative robotic skins for mobility. Our approach is marked by its compactness, high force intensity, rapid responsiveness, and lightweightness. The customizable, scalable design of our artificial muscles offers both immediate and long-term impact on robotics, wearable technology, haptics, prosthetic development, and the development of avant-garde biomedical devices like soft surgical tools.One-Sentence SummaryWe introduced a first-of-its-kind, programmable artificial muscle using ultrasound-activated microbubbles, providing a compact, responsive, and scalable solution.
Hierarchical Ordination, A unifying framework for drivers of community processes
Authors: O’Hara R.B. , van der Veen B. 
Published: January 2024

AbstractOrdination methods have been used by community ecologists to describe and explore the communities they sample by reducing this variation down to a small number of dimensions. More recently, Joint Species Distribution Models have been developed to model and predict the distributions of several species simultaneously. Contemporary models for the data for both of these problems are essentially the same, called Generalised Linear Latent Variable Models (GLLVMs). Based on this we suggest some avenues of cross-fertilisation between the two areas of research. We also describe some of the extensions to GLLVMs, and from this suggest the development of Hierarchical Ordination, as a way of efficiently modelling communities of species in space.
Inferring strain-level mutational drivers of phage-bacteria interaction phenotypes arising during coevolutionary dynamics
Authors: Lucia-Sanz Adriana , Peng Shengyun , Leung Chung Yin (Joey) , Gupta Animesh , Meyer Justin R. , Weitz Joshua S. 
Published: January 2024

AbstractThe enormous diversity of bacteriophages and their bacterial hosts presents a significant challenge to predict which phages infect a focal set of bacteria. Infection is largely determined by complementary – and largely uncharacterized – genetics of adsorption, injection, cell take-over and lysis. Here we present a machine learning approach to predict phage-bacteria interactions trained on genome sequences of and phenotypic interactions amongst 51Escherichia colistrains and 45 phageλstrains that coevolved in laboratory conditions for 37 days. Leveraging multiple inference strategies and withouta prioriknowledge of driver mutations, this framework predicts both who infects whom and the quantitative levels of infections across a suite of 2,295 potential interactions. We found that the most effective approach inferred interaction phenotypes from independent contributions from phage and bacteria mutations, accurately predicting 86% of interactions while reducing the relative error in the estimated strength of the infection phenotype by 40%. Feature selection revealed key phageλandE. colimutations that have a significant influence on the outcome of phage-bacteria interactions, corroborating sites previously known to affect phageλinfections, as well as identifying mutations in genes of unknown function not previously shown to influence bacterial resistance. The method’s success in recapitulating strain-level infection outcomes arising during coevolutionary dynamics may also help inform generalized approaches for imputing genetic drivers of interaction phenotypes in complex communities of phage and bacteria.
Approaching pathogenicClostridiafrom a One Health perspective
Authors: Cersosimo Laura M. , Worley Jay N. , Bry Lynn 
Published: January 2024

AbstractSpore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. These behaviors require a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs, and as commensals or infecting pathogens in human and veterinary populations. Among anaerobic spore-formers, genomic resources for pathogens includingC.botulinum,C.difficile, andC.perfringensenable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI’s Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
A mouse model to study glutathione limitationin vivo
Authors: Timson Rebecca C. , Khan Artem , Uygur Beste , Saad Marwa , Yeh Hsi-Wen , DelGaudio Nicole , Weber Ross , Alwaseem Hanan , Gao Jing , Yang Chingwen , Birsoy Kıvanç 
Published: January 2024

AbstractGlutathione (GSH) is a highly abundant tripeptide thiol that performs diverse protective and biosynthetic functions in cells. While changes in GSH availability are linked to many diseases, including cancer and neurodegenerative disorders, determining the function of GSH in physiology and disease has been challenging due to its tight regulation. To address this, we generated cell and mouse models that express a bifunctional glutathione-synthesizing enzyme fromStreptococcus Thermophilus(GshF). GshF expression allows efficient production of GSH in the cytosol and mitochondria and prevents cell death in response to GSH depletion, but not ferroptosis, indicating that GSH is not a limiting factor under lipid peroxidation. CRISPR screens using engineered enzymes revealed metabolic liabilities under compartmentalized GSH depletion. Finally, GshF expression in mice is embryonically lethal but sustains postnatal viability when restricted to adulthood. Overall, our work identifies a conditional mouse model to investigate the role of GSH availability in physiology and disease.
Genome-wide patterns of non-coding sequence variation in the major fungal pathogenAspergillus fumigatus
Authors: Brown Alec , Steenwyk Jacob L. , Rokas Antonis 
Published: January 2024

AbstractA. fumigatusis a deadly fungal pathogen, responsible for >400,000 infections/year and high mortality rates.A. fumigatusstrains exhibit variation in infection-relevant traits, including in their virulence. However, mostA. fumigatusprotein-coding genes, including those that modulate its virulence, are shared betweenA. fumigatusstrains and closely related non-pathogenic relatives. We hypothesized thatA. fumigatusgenes exhibit substantial genetic variation in the non-coding regions immediately upstream to the start codons of genes, which could reflect differences in gene regulation between strains. To begin testing this hypothesis, we identified 5,812 single-copy orthologs across the genomes of 263A. fumigatusstrains.A. fumigatusnon-coding regions showed higher levels of sequence variation compared to their corresponding protein-coding regions. Specifically, we found that 1,274 non-coding regions exhibited <75% nucleotide sequence similarity (compared to 928 protein-coding regions) and 3,721 non-coding regions exhibited between 75% and 99% similarity (compared to 2,482 protein-coding regions) across strains. Only 817 non-coding regions exhibited ≥99% sequence similarity compared to 2,402 protein-coding regions. By examining 2,482 genes whose protein-coding sequence identity scores ranged between 75% and 99%, we identified 478 total genes with signatures of positive selection only in their non-coding regions and 65 total genes with signatures only in their protein-coding regions. 28 of the 478 non-coding regions and 5 of the 65 protein-coding regions under selection are associated with genes known to modulateA. fumigatusvirulence. Non-coding region variation betweenA. fumigatusstrains included single nucleotide polymorphisms and insertions or deletions of at least a few nucleotides. These results show that non-coding regions ofA. fumigatusgenes harbor greater sequence variation than protein-coding regions, raising the hypothesis that this variation may contribute toA. fumigatusphenotypic heterogeneity.
Mapping the tRNA Modification Landscape ofBartonella henselaeHouston I andBartonella quintanaToulouse
Authors: Quaiyum Samia , Sun Jingjing , Marchand Virginie , Sun Guangxin , Reed Colbie J. , Motorin Yuri , Dedon Peter C. , Minnick Michael F. , de Crécy-Lagard Valérie 
Published: January 2024

AbstractTransfer RNA (tRNA) modifications play a crucial role in maintaining translational fidelity and efficiency, and they may function as regulatory elements in stress response and virulence. Despite their pivotal roles, a comprehensive mapping of tRNA modifications and their associated synthesis genes is still limited, with a predominant focus on free-living bacteria. In this study, we employed a multidisciplinary approach, incorporating comparative genomics, mass spectrometry, and next-generation sequencing, to predict the set of tRNA modification genes responsible for tRNA maturation in two intracellular pathogens—Bartonella henselaeHouston I andBartonella quintanaToulouse, which are causative agents of cat-scratch disease and trench fever, respectively. This analysis presented challenges, particularly because of host RNA contamination, which served as a potential source of error. However, our approach predicted 26 genes responsible for synthesizing 23 distinct tRNA modifications inB. henselaeand 22 genes associated with 23 modifications inB. quintana. Notably, akin to other intracellular and symbiotic bacteria, bothBartonellaspecies have undergone substantial reductions in tRNA modification genes, mostly by simplifying the hypermodifications present at positions 34 and 37.B. quintanaexhibited the additional loss of four modifications and these were linked to examples of gene decay, providing snapshots of reductive evolution.
Nature AND Nurture: Enabling formate-dependent growth inMethanosarcina acetivorans
Authors: Bao Jichen , Somvanshi Tejas , Tian Yufang , Laird Maxime , Garcia Pierre Simon , Schöne Christian , Rother Michael , Borrel Guillaume , Scheller Silvan 
Published: January 2024

AbstractMethanogenic archaea are crucial in global carbon cycling as around 1 Gt of the potent greenhouse gas, methane, is produced annually. Major contributors belong to the order Methanosarcinales, which contain some of the most versatile methanogens that are capable of acetotrophic, methylotrophic and CO2-reducing methanogenesis. The genetically tractable model methanogen,Methanosarcina acetivorans, by its nature shows versatility in substrate utilization and energy conservation pathways but cannot utilize formate. In this study, we expanded the primary metabolism ofM. acetivoransto include formate-dependent methanogenesis. By introducing an exogenous formate dehydrogenase, the two metabolically engineeredM. acetivoransstrains acquired the capacity for formate-dependent methanogenesis pathways with one capable of formate-dependent methyl-reduction and the other capable of formate-dependent CO2-reduction. Through nurturing the strain capable of CO2-reduction with adaptive laboratory evolution, we were able to enable growth and methanogenesis ofM. acetivoranssolely on formate, a metabolism only reported in methanogens without cytochromes which are limited by their versatility.M. acetivoransalso showed acetogenic potential where the formate-dependent CO2-reducing strain was able to divert ≈ 10% of carbon to acetate instead of methane. Our results show that even thoughM. acetivoranslacks energy converting hydrogenase and cannot use H2, it has yet-uncharacterized capacity to obtain reduced ferredoxins from oxidizing formate. Our work encourages reevaluation of our understanding of formate utilization in Methanosarcinales. By enabling formate-dependent methanogenesis, we have expanded the substrate spectrum of a versatile model methanogen with cytochromes to include formate as well.
Interactors of sacsin’s DNAJ domain identify function in organellar transport and membrane composition relevant to ARSACS pathogenesis
Authors: Paré Alexandre M. , Cheng-Boivin Zacharie , Dabbaghizadeh Afrooz , Minotti Sandra , Durham Heather D. , Gentil Benoit J. 
Published: January 2024

AbstractAutosomal Recessive Spastic Ataxia of the Charlevoix Saguenay (ARSACS) is caused by loss of function mutations in theSACSgene encoding sacsin, a 520kDa protein with multiple functional domains. The goal of this study was to identify client proteins interacting with the J domain, a cochaperone domain interacting with Hsp70 chaperones, to gain insights into sacsin’s function and its disruption in experimental models of ARSACS. Pull downs from mouse brain identified Rabs and Rab-associated proteins including Rab1b, ARF5 and endophilin B2, involved in organelle trafficking. In cell and mouse models of ARSACS, higher molecular weight species of Rab1b were identified on SDS-PAGE in addition to the normal 25kDa band and Rab1was retained in the soma along with membranous organelles (i.e., ER, Golgi and ATG9 autophagic vesicles). These changes were reversed by expression of the DNAJ domain or the Ubl domain of sacsin and occurred independent of the formation of abnormal bundles of intermediate filaments, a key feature of ARSACS. Although Rab1b was associated with both Golgi and ER in bothSacs+/+andSacs-/-cells, expression of the DNAJ domain or the Ubl domain of sacsin increased Rab1b association with ER and restored normal electrophoretic mobility. Finally, subcellular distribution of another membrane protein, neuroplastin, a key receptor for synapse formation and plasticity, also was impaired, pointing to a general problem in Rab-dependent membrane trafficking in the absence of sacsin.