bluuebunny/crossref_metadata_2025_split huggingface dataset:
Edge-strand of BepA interacts with immature LptD on the β-barrel assembly machine to direct it to on- and off-pathways
Authors: Miyazaki Ryoji , Watanabe Tetsuro , Yoshitani Kohei , Akiyama Yoshinori 
Published: March 2021

AbstractThe outer membrane (OM) of gram-negative bacteria functions as a selective permeability barrier.Escherichia coliperiplasmic Zn-metallopeptidase BepA contributes to the maintenance of OM integrity through its involvement in the biogenesis and degradation of LptD, a β-barrel protein component of the lipopolysaccharide translocon. BepA either promotes the maturation of LptD when it is on the normal assembly pathway (on-pathway) or degrades it when its assembly is compromised (off-pathway). BepA performs these functions probably on the β-barrel assembly machinery (BAM) complex. However, how BepA recognizes and directs an immature LptD to different pathways remains unclear. Here, we explored the interactions among BepA, LptD, and the BAM complex. We found that the interaction of the BepA edge-strand located adjacent to the active site with LptD was crucial not only for proteolysis but also, unexpectedly, for assembly promotion of LptD. Site-directed crosslinking analyses indicated that the unstructured N-terminal half of the β-barrel-forming domain of an immature LptD contacts with the BepA edge-strand. Furthermore, the C-terminal region of the β-barrel-forming domain of the BepA-bound LptD intermediate interacted with a “seam” strand of BamA, suggesting that BepA recognized LptD assembling on the BAM complex. Our findings provide important insights into the functional mechanism of BepA.
Unconventional Translation Initiation Factor EIF2A is required for Drosophila spermatogenesis
Authors: Lowe David D. , Montell Denise J. 
Published: March 2021

AbstractThe eukaryotic initiation factor EIF2A is an unconventional translation factor required for initiation of protein synthesis from non-AUG codons from a variety of transcripts, including oncogenes and stress related genes in mammalian cells. Its function in multicellular organisms has not been reported. Here, we identify and characterize mutant alleles of the CG7414 gene, which encodes the Drosophila EIF2A ortholog. We identified that CG7414 undergoes sex-specific splicing that regulates its male-specific expression. We characterized a Mi{Mic} transposon insertion that disrupts the coding regions of all predicted isoforms and is a genetic null allele, and a PBac transposon insertion into an intron, which is a hypomorph. The Mi{Mic} allele is homozygous lethal, while the viable progeny from the hypomorphic PiggyBac allele are male sterile and female fertile. In dEIF2A mutant flies, sperm failed to individualize due to defects in F-actin cones and failure to form and maintain cystic bulges, ultimately leading to sterility. These results demonstrate that EIF2A is essential in a multicellular organism, both for normal development and spermatogenesis, and provide an entree into the elucidation of the role of EIF2A and unconventional translation in vivo.
The opportunistic intracellular bacterial pathogenRhodococcus equielicits type I interferons by engaging cytosolic DNA sensing in macrophages
Authors: Vail Krystal J , da Silveira Bibiana Petri , Bell Samantha L , Bordin Angela I , Cohen Noah D , Patrick Krisitn L , Watson Robert O 
Published: March 2021

ABSTRACTRhodococcus equiis a major cause of foal pneumonia and an opportunistic pathogen in immunocompromised humans. While alveolar macrophages constitute the primary replicative niche forR. equi, little is known about how intracellularR. equiis sensed by macrophages. Here, we discovered that that in addition to previously characterized pro-inflammatory cytokines (e.g., Tnfa, Il6, Il1b), macrophages infected withR. equiinduce a robust type I IFN response, includingIfnband interferon-stimulated genes (ISGs), similar to the evolutionarily related pathogen,Mycobacterium tuberculosis. Follow up studies using a combination of mammalian and bacterial genetics, demonstrated that induction of this type I IFN expression program is largely dependent on the cGAS/STING/TBK1 axis of the cytosolic DNA surveillance pathway, suggesting thatR. equiperturbs the phagosomal membrane and causes DNA release into the cytosol following phagocytosis. Consistent with this we found that a population of ~12% ofR. equiphagosomes recruited the galectin-3, −8 and −9 danger receptors. Interesting, neither phagosomal damage nor induction of type I IFN required theR. equi’s virulence-associated plasmid. Importantly,R. equiinfection of both mice and foals stimulated ISG expression, in organs (mice) and circulating monocytes (foals). By demonstrating thatR. equiactivates cytosolic DNA sensing in macrophages and elicits type I IFN responses in animal models, our work provides novel insights into howR. equiengages the innate immune system and furthers our understanding how this zoonotic pathogen causes inflammation and disease.IMPORTANCERhodococcus equiis a facultative intracellular bacterial pathogen of horses and other domestic animals, as well as an opportunistic pathogen of immunocompromised and rarely immunocompetent humans. In human patients,Rhodococcuspneumonia bears some pathological similarities to pulmonary tuberculosis, and poses a risk for misdiagnosis. In horses,R. equiinfection has a major detrimental impact on the equine breeding industry due to a lack of an efficacious vaccine and its ubiquitous distribution in soil. Given the prevalence of subclinical infection and high false positive rate in current screening methods, there exists a critical need to identify factors contributing to positive patient outcomes. Our research identifies innate immune sensing events and immune transcriptional signatures that may lead to biomarkers for clinical disease, more accurate screening methods, and insight into susceptibility to infection.
H2S Prodrug, SG-1002, Protects Against Myocardial Oxidative Damage and Hypertrophy via Induction of Cystathionine β-Synthase and Antioxidant Proteins
Authors: Islam Rahib K. , Donnelly Erinn , Hossain Fokhrul , Gardner Jason D. , Islam Kazi N. 
Published: March 2021

AbstractEndogenously produced hydrogen sulfide (H2S) is critical for cardiovascular homeostasis. Therapeutic strategies aimed at increasing H2S levels have proven cardioprotective in models of acute myocardial infarction (MI) and heart failure (HF). The present study was undertaken to investigate the effects of a novel H2S prodrug, SG-1002, on stress induced hypertrophic signaling in murine HL-1 cardiac muscle cells. Treatment of HL-1 cells with SG-1002 under serum starvation without or with H2O2increased the levels of H2S, H2S producing enzyme, cystathionine β-synthase (CBS) as well as antioxidant protein levels, such as super oxide dismutase1 (SOD1) and catalase and decreased oxidative stress. SG-1002 also decreased the expression of hypertrophic/HF protein markers such as atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) in stressed HL-1 cells. Treatment with SG-1002 caused a significant induction of cell viability and a marked reduction of cellular cytotoxicity in HL-1 cells under serum starvation incubated or with H2O2. Experimental results of this study suggest that SG-1002 attenuates myocardial cellular oxidative damage and/or hypertrophic signaling via increasing H2S levels or H2S producing enzyme, CBS and antioxidant proteins.
Asymmetric structures and conformational plasticity of the uncleaved full-length human immunodeficiency virus (HIV-1) envelope glycoprotein trimer
Authors: Zhang Shijian , Wang Kunyu , Wang Wei Li , Nguyen Hanh T. , Chen Shuobing , Lu Maolin , Go Eden P. , Ding Haitao , Steinbock Robert T. , Desaire Heather , Kappes John C. , Sodroski Joseph , Mao Youdong 
Published: March 2021

ABSTRACTThe functional human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer [(gp120/gp41)3] is produced by cleavage of a conformationally flexible gp160 precursor. Gp160 cleavage or the binding of BMS-806, an entry inhibitor, stabilizes the pre-triggered, “closed” (State-1) conformation recognized by rarely elicited broadly neutralizing antibodies. Poorly neutralizing antibodies (pNAbs) elicited at high titers during natural infection recognize more “open” Env conformations (States 2 and 3) induced by binding the receptor, CD4. We found that BMS-806 treatment and crosslinking decreased the exposure of pNAb epitopes on cell-surface gp160; however, after detergent solubilization, crosslinked and BMS-806-treated gp160 sampled non-State-1 conformations that could be recognized by pNAbs. Cryo-electron microscopy of the purified BMS-806-bound gp160 revealed two hitherto unknown asymmetric trimer conformations, providing insights into the allosteric coupling between trimer opening and structural variation in the gp41 HR1Nregion. The individual protomer structures in the asymmetric gp160 trimers resemble those of other genetically modified or antibody-bound cleaved HIV-1 Env trimers, which have been suggested to assume State-2-like conformations. Asymmetry of the uncleaved Env potentially exposes surfaces of the trimer to pNAbs. To evaluate the effect of stabilizing a State-1-like conformation of the membrane Env precursor, we treated cells expressing wild-type HIV-1 Env with BMS-806. BMS-806 treatment decreased both gp160 cleavage and the addition of complex glycans, implying that gp160 conformational flexibility contributes to the efficiency of these processes. Selective pressure to maintain flexibility in the precursor of functional Env allows the uncleaved Env to sample asymmetric conformations that potentially skew host antibody responses toward pNAbs.IMPORTANCEThe envelope glycoprotein (Env) trimers on the surface of human immunodeficiency virus (HIV-1) mediate the entry of the virus into host cells and serve as targets for neutralizing antibodies. The functional Env trimer is produced by cleavage of the gp160 precursor in the infected cell. We found that the HIV-1 Env precursor is highly plastic, allowing it to assume different asymmetric shapes. This conformational plasticity is potentially important for Env cleavage and proper modification by sugars. Having a flexible, asymmetric Env precursor that can misdirect host antibody responses without compromising virus infectivity would be an advantage to a persistent virus like HIV-1.
The ArabidopsisWRR4AandWRR4Bparalogous NLR proteins both confer recognition of multipleAlbugo candidaeffectors
Authors: Redkar Amey , Cevik Volkan , Bailey Kate , Furzer Oliver J. , Fairhead Sebastian , Borhan M. Hossein , Holub Eric B. , Jones Jonathan D.G. 
Published: March 2021

SummaryThe oomyceteAlbugo candidacauses white blister rust, an important disease of Brassica crops. Distinct races ofA. candidaare defined by their specificity for infecting different host species.TheWhite Rust Resistance 4(WRR4) locus in Col-0 accession ofArabidopsis thalianacontains three genes that encode TIR-NLR resistance proteins. The Col-0 alleles ofWRR4AandWRR4Bconfer resistance to at least fourA. candidaraces (2, 7 and 9 fromB. juncea, B. rapaandB. oleracea, respectively, and Race 4 fromCapsella bursa-pastoris). Resistance mediated by both paralogs can be overcome by Col-0-virulent isolates of Race 4.After comparing repertoires of candidate effectors in resisted and resistance-breaking strains, we used transient co-expression in tobacco orArabidopsisto identify effectors recognized byWRR4AandWRR4B. A library of CCG effectors from fourA. candidaraces was screened forWRR4A-orWRR4B-dependent elicitation of hypersensitive response (HR). These CCG genes were validated for WRR-dependent HR by bombardment assays in wild type Col-0,wrr4Aorwrr4Bmutants.Our analysis revealed eightWRR4A-recognized CCGs and fourWRR4B-recognized CCGs. Remarkably, the N-terminal region of 100 amino acids after the secretion signal is sufficient forWRR4Arecognition of these eight recognized effectors. This multiple recognition capacity potentially explains the broad-spectrum resistance to manyA. candidaraces conferred byWRR4paralogs.
Revisiting the evolutionary history of pigs via de novo mutation rate estimation by deep genome sequencing on a three-generation pedigree
Authors: Zhang Mingpeng , Yang Qiang , Ai Huashui , Huang Lusheng 
Published: March 2021

AbstractThe mutation rate used in the previous analyses of pig evolution and demographics was cursory and brought potential bias in inferring its history. Herein, we estimated de novo mutation rate of pigs using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and validation. The estimated mutation rate was 3.6 × 10−9per generation, corresponding to 1.2 × 10−9per site per year. Using this mutation rate, we re-investigated the evolutionary history of pigs. Our estimates agreed to the divergence time of ~10 kiloyears ago (Kya) between European wild and domesticated pigs, consistent with the domestication time of European pigs based on archaeological evidence. However, other divergence events inferred here were not as ancient as previously described. Our estimates suggested that: Sus speciation occurred ~1.36 Million years ago (Mya); European pigs split up with Asian ones only ~219 Kya; South and North Chinese wild pig split ~25 Kya. Meanwhile, our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao plain, North China, approximately 20 Kya, supporting the possibly independent domestication in North China along the middle Yellow River. We also found the maximum effective population size of pigs was ~6 times larger than the previous estimate. Notably by simulation, we confirmed an archaic migration from other Sus species originating ~ 2 Mya to European pigs during pigs’ western colonization, which possibly interfered with the previous demographic inference. Our findings advance the understanding of pig evolutionary history.
Astrocyte-neuron interplay is critical for Alzheimer’s disease pathogenesis and is rescued by TRPA1 channel blockade
Authors: Paumier Adrien , Boisseau Sylvie , Pernet-Gallay Karin , Buisson Alain , Albrieux Mireille 
Published: March 2021

AbstractBackgroundThe sequence of cellular dysfunctions in preclinical Alzheimer’s disease must be understood if we are to plot new therapeutic routes. Hippocampal neuronal hyperactivity is one of the earliest events occurring during the preclinical stages of Alzheimer’s disease in both humans and mouse models. The most common hypothesis describes amyloid β accumulation as the triggering factor of the disease but the effects of such accumulation and the cascade of events leading to cognitive decline remain unclear. In mice, we previously showed that amyloid β-dependent TRPA1 channel activation triggers hippocampal astrocyte hyperactivity, subsequently inducing hyperactivity in nearby neurons. In this work, we investigated the potential protection brought by an early chronic pharmacological inhibition of TRPA1 channel on Alzheimer’s disease progression.MethodsWe administered a specific inhibitor of TRPA1 channel (HC030031) intraperitoneally from the onset of amyloid β overproduction in the APP/PS1-21 mouse model of Alzheimer’s disease. We characterized short-, medium-, and long-term effects of this chronic pharmacological TRPA1 blockade on Alzheimer’s disease progression at functional (astrocytic and neuronal activity), structural, biochemical, and behavioural levels.ResultsOur results revealed that the first observable disruptions in the Alzheimer’s disease transgenic mouse model used correspond to aberrant hippocampal astrocyte and neuron hyperactivity. We showed that chronic TRPA1 blockade normalizes astrocytic activity, avoids perisynaptic astrocytic process withdrawal, prevents neuronal dysfunction, preserves structural synaptic integrity and strengthens the glial plaque barrier. These protective effects preserved spatial working-memory in this Alzheimer’s disease mouse model.ConclusionThe toxic effect of amyloid β on astrocytes triggered by TRPA1 channel activation is pivotal to Alzheimer’s disease progression. TRPA1 blockade prevent irreversible neuronal dysfunction, making this channel a potential therapeutic target to promote neuroprotection.
Sexually dimorphic placental responses to maternal SARS-CoV-2 infection
Authors: Bordt Evan A , Shook Lydia L , Atyeo Caroline , Pullen Krista M , De Guzman Rose M , Meinsohn Marie-Charlotte , Chauvin Maeva , Fischinger Stephanie , Yockey Laura J. , James Kaitlyn , Lima Rosiane , Yonker Lael M , Fasano Alessio , Brigida Sara , Bebell Lisa M , Roberts Drucilla J , Pépin David , Huh Jun R , Bilbo Staci D , Li Jonathan Z , Kaimal Anjali , Schust Danny , Gray Kathryn J , Lauffenburger Douglas , Alter Galit , Edlow Andrea G 
Published: March 2021

ABSTRACTThere is a persistent male bias in the prevalence and severity of COVID-19 disease. Underlying mechanisms accounting for this sex difference remain incompletely understood. Interferon responses have been implicated as a modulator of disease in adults, and play a key role in the placental anti-viral response. Moreover, the interferon response has been shown to alter Fc-receptor expression, and therefore may impact placental antibody transfer. Here we examined the intersection of viral-induced placental interferon responses, maternal-fetal antibody transfer, and fetal sex. Placental interferon stimulated genes (ISGs), Fc-receptor expression, and SARS-CoV-2 antibody transfer were interrogated in 68 pregnancies. Sexually dimorphic placental expression of ISGs, interleukin-10, and Fc receptors was observed following maternal SARS-CoV-2 infection, with upregulation in males. Reduced maternal SARS-CoV-2-specific antibody titers and impaired placental antibody transfer were noted in pregnancies with a male fetus. These results demonstrate fetal sex-specific maternal and placental adaptive and innate immune responses to SARS-CoV-2.
Reciprocal allostery arising from a bi-enzyme assembly controls aromatic amino acid biosynthesis inPrevotella nigrescens
Authors: Bai Yu , Parker Emily J. 
Published: March 2021

ABSTRACTModular protein assembly has been widely reported as a mechanism for constructing allosteric machinery. Recently, a distinctive allosteric system has been identified in a bi-enzyme assembly comprising a 3-deoxy-d-arabinoheptulosonate-7-phosphate synthase (DAH7PS) and chorismate mutase (CM). These enzymes catalyze the first and branch point reactions of aromatic amino acid biosynthesis in the bacteriumPrevotella nigrescens(PniDAH7PS), respectively. The interactions between these two distinct catalytic domains support functional inter-reliance within this bifunctional enzyme. The binding of prephenate, the product of CM-catalyzed reaction, to the CM domain is associated with a striking rearrangement of overall protein conformation that alters the interdomain interactions and allosterically inhibits the DAH7PS activity. In this study, we observed allosteric activation of CM activity in the presence of all DAH7PS substrates. Using small angle X-ray scattering (SAXS) experiments we show that changes in overall protein conformations and dynamics are associated with the presence of different DAH7PS substrates and the allosteric inhibitor prephenate. Furthermore, we have identified an extended interhelix loop located in CM domain, loopC320-F333, as a crucial segment for the interdomain structural and catalytic communications. Our results suggest that the dual function enzymePniDAH7PS contains a reciprocal allosteric system between the two enzymatic moieties, as a result of this bidirectional interdomain communication. This arrangement allows for a complex feedback and feedforward system for control of pathway flux by connecting the initiation and branch point of aromatic amino acid biosynthesis.
The small acid-soluble proteins ofClostridioides difficileare important for UV resistance and serve as a check point for sporulation
Authors: Nerber Hailee N. , Sorg Joseph A. 
Published: March 2021

AbstractClostridioides difficileis a nosocomial pathogen which causes severe diarrhea and colonic inflammation.C. difficilecauses disease in susceptible patients when endospores germinate into the toxin-producing vegetative form. The action of these toxins results in diarrhea and the spread of spores into the hospital and healthcare environments. Thus, the destruction of spores is imperative to prevent disease transmission between patients. However, spores are resilient and survive extreme temperatures, chemical exposure, and UV treatment. This makes their elimination from the environment difficult and perpetuates their spread between patients. In the model spore-forming organism,Bacillus subtilis,the small acid-soluble proteins (SASPs) contribute to these resistances. The SASPs are a family of small proteins found in all endospore-forming organisms,C. difficileincluded. Although these proteins have high sequence similarity between organisms, the role(s) of the proteins differ. Here, we investigated the role of the main α/β SASPs, SspA and SspB, and two annotated SASPs, CDR20291_1130 and CDR20291_3080, in protectingC. difficilespores from environmental insults. We found that SspA is necessary for conferring spore UV resistance, SspB minorly contributes, and the annotated SASPs do not contribute to UV resistance. In addition, none of these SASPs contribute to the resistance of tested chemicals. Surprisingly, the combined deletion ofsspAandsspBprevented spore formation. Overall, our data indicate that UV resistance ofC. difficilespores is dependent on SspA and that SspA and SspB regulate / serve as a checkpoint for spore formation, a previously unreported function of SASPs.ImportanceC. difficileinfections remain problematic and elimination of spores within an environment is essential to limit person-to-person spread. A deeper understanding of how spores resist cleaning efforts could lead to better strategies to eradicate the spores in a contaminated environment. The small acid-soluble proteins (SASPs), found in all endospore-forming organisms, are one mechanism that allows for spore resilience. Here, we find thatC. difficileSspA and SspB protect against UV light. Unexpectedly, these SASPs also regulate spore formation, a role not described for any SASP to date.