bluuebunny/crossref_metadata_2025 huggingface dataset:
Enterococcus montenegrensis sp. nov., isolated from artisanal Montenegrin dry sausage
Authors: Daza-Prieto Beatriz , Raicevic Nadja , Cabal Adriana , Hyden Patrick , Mösenbacher Tobias , Ladstätter Johann , Richter Susanne , Stöger Anna , Joao Cardoso Maria , Chakeri Ali , Hasenberger Petra , Stadlbauer Silke , Mach Robert L. , Martinovic Aleksandra , Ruppitsch Werner
Published: January 2024

A novel, Gram-positive, facultative anaerobe, coccoid and non-motile bacterium, designated as CoE-012-22T was isolated from dried beef sausage (the original name in Montenegro is Govedji Kulen) manufactured in the municipality of Rozaje (Montenegro) in 2021. Cells of this strain were oxidase- and catalase-negative. Growth occurred at 4–50 °C, at pH 5.0–8.0 and with 0–6.5 % (w/v) NaCl in diverse growth media. MALDI-TOF analysis identified the strain as

Enterococcus canintestini

(log score 2). Phylogenetic analysis of the 16S rRNA gene and whole genome sequences assigned the strain to the genus

Enterococcus

. The closest relatives were

E. canintestini

DSM 21207T and

E. dispar

ATCC 51266T with 16S rRNA gene sequence pairwise similarities of 99.34 and 98.59 %, respectively. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between isolate CoE-012-22T and other enterococci species were below the thresholds for species delineation thresholds (95.0 % ANI; 70.0 % dDDH) with maximum identities of 84.13 % (ANIb), 86.43 % (ANIm) and 28.4 % (dDDH) to

E. saigonensis

JCM 31193T and 70.97 % (ANIb), 88.99 % (ANIm) and 32.4 % (dDDH) to

E. malodoratus

ATCC 43197T. Two unknown

Enterococcus

isolates,

Enterococcus

sp. MJM12 and

Enterococcus

SMC-9, showed identities of 99.87 and 99.94 % (16S rRNA), 98.57 and 98.65 % (ANIb), 98.93 and 99.02 % (ANIm), and 89.8 and 90.0 % (dDDH) to strain CoE-012-22T and can therefore be regarded as the same species. Based on the characterization results, strain CoE-012-22T was considered to represent a novel species, for which the name Enterococcus montenegrensis sp. nov. is proposed. The type strain is CoE-012-22T (=DSM 115843T=NCIMB 15468T).
Insights from comparative plastid genomics of colorless facultative pathogensPrototheca(Chlorophyta): Unveiling membrane transport and organelle division as key functions
Authors: Maciszewski Kacper , Wilga Gabriela , Jagielski Tomasz , Bakuła Zofia , Gawor Jan , Gromadka Robert , Karnkowska Anna
Published: January 2024

Plastids are usually involved in photosynthesis, but the secondary loss of this function is a widespread phenomenon in various lineages of algae and plants. In addition to the loss of genes associated with photosynthesis, the plastid genomes of colorless algae are frequently reduced further. To understand the pathways of reductive evolution associated with the loss of photosynthesis, it is necessary to study a number of closely related strains.Prototheca, a chlorophytean genus of facultative pathogens, provides an excellent opportunity to study this process with its well-sampled array of diverse colorless strains.

We have sequenced the plastid genomes of 13Protothecastrains and reconstructed a comprehensive phylogeny that reveals evolutionary patterns within the genus and among its closest relatives. Our robust phylogenomic analysis revealed three independent losses of photosynthesis among theProtothecastrains and considerable coding content variability in their ptDNA. Despite this diversity, allProtothecastrains retain the same key plastid functions. These include processes related to gene expression, as well as crucial roles in fatty acid and cysteine biosynthesis, membrane transport, and organelle division. While the retention of vestigial genomes in colorless plastids is typically associated with the biosynthesis of secondary metabolites, the remarkable conservation of plastid membrane transport and organellar division systems in the nonphotosynthetic generaProtothecaandHelicosporidiumprovides an additional constraint against the loss of ptDNA in this lineage. Furthermore, these genes can potentially serve as targets for therapeutic intervention, indicating their importance beyond the evolutionary context.
Colistin resistance genes inEscherichia coliisolated from patients with urinary tract infections
Authors: Al Momani Waleed M. , Ata Nour , Maslat Ahmed O.
Published: January 2024

Introduction

Antimicrobial resistance is alarmingly high because it happens in humans, environment, and animal sectors from a “One Health” viewpoint. Due to the fact, thatEscherichia coli (E. coli)is broadly disseminated in all sectors, the food web and the environment may have a role in carrying colistin resistance genes from animals to humans. The rise of plasmid-mediated mobile colistin resistance (MCR) genes threatens colistin efficacy, which is the last line to remedy Gram-negative infections multidrug resistance (MDR).

Objectives

The current study aimed to investigate development of colistin resistance (MCR1-5) genes betweenE. coliisolated from patients with urinary tract infections (UTI) in Jordan.

Methods

E. coli(n=132) isolated were collected from urine specimens.E. coliisolated from human UTI patients were examined for genes resistance to colistinMCR(1-5). All isolates were investigated against 20 antimicrobials utilizing the standard disk diffusion method. For analysis of colistin resistance, the broth microdilution technique was employed. In addition, theMCR(1-5) genes were detected by multiplex PCR assay.

Results

Out of 132 isolates, one isolate was colistin-resistant, having a minimum inhibitory concentration of 8 μg/mL and possessing theMCR-1 gene. A total of 132E. coliisolates showed high resistance against penicillin, amoxicillin, cephalexin, nalidixic acid, tetracycline, and cefepime in the percentages of 100%, 79.55%, 75.76%, 62.88%, 58.33%, and 53.79%, respectively. However, resistance was lowest towards fosfomycin (6.06%), florfenicol (10.61%), and chloramphenicol (15.91%). Significant differences were observed betweenE. coliisolated from pediatrics and those isolated from adults.

Conclusion

This is the first report on the presence of the plasmid-codedMCR-1 gene recovered fromE. colifrom a patient with UTIs in Jordan. That is threatening as colistin is the last line used for infections induced by MDR gram-negative bacteria. There is a crucial need for control and harsh utilization of antibiotics to control and prevent the emergence and prevalence of colistin resistance genes.

E. coliisolated from human UTI patients were examined for genes resistance to colistinMCR(1-5). This is the first report on the presence of the plasmid-codedMCR-1 gene recovered fromE. colifrom a patient with UTIs in Jordan. That is threatening as colistin is the last line used for infections induced by MDR gram-negative bacteria. There is a crucial need for control and harsh utilization of antibiotics to control and prevent the emergence and prevalence of colistin resistance genes. A total of 132E. coliisolates showed high resistance against penicillin, amoxicillin, cephalexin, nalidixic acid, tetracycline, and cefepime in the percentages of 100%, 79.55%, 75.76%, 62.88%, 58.33%, and 53.79%, respectively
Sunpheno: a deep neural network for phenological classification of sunflower images
Authors: Bengoa Luoni Sofia A. , Ricci Riccardo , Corzo Melanie A. , Hoxha Genc , Melgani Farid , Fernandez Paula C.
Published: January 2024

Leaf senescence is a complex mechanism governed by multiple genetic and environmental variables that affect crop yield. It is the last stage of leaf development and is characterized by an active decline in the photosynthetic rate, nutrient recycling, and cell death. Leaf senescence begins in the lower leaves, and photoassimilates are translocated to the younger tissues. During early anthesis, leaf senescence becomes crucial for grain filling, because photoassimilates are translocated to the seeds. Therefore, a correct sync between leaf senescence and phenological stages is necessary to obtain the required yields. Furthermore, genotypes with early senescence were correlated with poor yield and low seed quality. Like all the crops growing in the field, studying phenology and its correlation with the senescence process is a laborious task where most of the parameters depend on highly trained people who conduct sampling and measurements. Several high-throughput phenotyping techniques have been developed in recent years. In this study, we evaluated the performance of five deep machine-learning methods for the evaluation of the phenological stages of sunflowers using images taken with cell phones in the field. From the analysis, we found that the method based on the pre-trained network resnet50 outperformed the other methods, both in terms of accuracy and velocity. Finally, the model generated, Sunpheno, was used to evaluate the phenological stages of two contrasting lines, B481_6 and R453, during senescence. We observed clear differences in phenological stages, confirming the results obtained in previous studies.
Geographic, ecological, and temporal patterns of seabird mortality during the 2022 HPAI H5N1 outbreak on the island of Newfoundland
Authors: McPhail Gretchen M. , Collins Sydney M. , Burt Tori V. , Careen Noah G. , Doiron Parker B. , Avery-Gomm Stephanie , Barychka Tatsiana , English Matthew D. , Giacinti Jolene A. , Jones Megan E.B. , Provencher Jennifer F. , Soos Catherine , Ward Christopher R.E. , Duffy Steven , Wilhelm Sabina I. , Wight Jordan , Rahman Ishraq , Hargan Kathryn E. , Lang Andrew S. , Montevecchi William A.
Published: January 2024

Highly pathogenic avian influenza (HPAI) H5N1 caused mass seabird mortality across the North Atlantic in 2022. Following outbreaks in Europe, the first case in North America was detected on the island of Newfoundland (NFLD), Canada in November 2021, before spreading through all North American flyways. During the following breeding season, NFLD experienced the second-highest number of seabird mortalities in Canadian provinces. Surveys and citizen reports identified 13543 seabird mortalities from April to September 2022. Many carcasses occurred on the west coast of NFLD in May and June 2022. Reported mortalities peaked in July along the southeastern coast. In August and September, mortalities were concentrated along the northeastern coast. With the exception of two colony surveys, reported mortalities decreased in September. Most mortality was found among Northern Gannet (6622), Common Murre (5992), Atlantic Puffin (282), and Black-legged Kittiwake (217). Using comprehensive knowledge of seabird ecology, we formulated exploratory hypotheses regarding traits that could contribute to mortality. Species differences in mortality were most strongly associated with nesting density, timing of breeding, and at-sea overlap with allospecifics from other colonies. Unprecedented seabird mortality and ongoing transmission within the circulating avian influenza viruses highlight the need for continued monitoring and development of conservation strategies.
Mobile-CRISPRi as a powerful tool for modulatingVibriogene expression
Authors: Geyman Logan , Tanner Madeline , Rosario-Melendez Natalia , Peters Jason , Mandel Mark J. , van Kessel Julia C.
Published: January 2024

CRISPRi (Clustered Regularly Interspaced Palindromic Repeats interference) is a gene knockdown method that uses a deactivated Cas9 protein (dCas9) that binds a specific gene target locus dictated by an encoded guide RNA (sgRNA) to block transcription. Mobile-CRISPRi is a suite of modular vectors that enable CRISPRi knockdowns in diverse bacteria by integrating IPTG-inducibledcas9andsgRNAgenes into the genome using Tn7transposition. Here, we show that the Mobile-CRISPRi system functions robustly and specifically in multipleVibriospecies:Vibrio cholerae, Vibrio fischeri, Vibrio vulnificus, Vibrio parahaemolyticus, andVibrio campbellii. We demonstrate efficacy by targeting both essential and non-essential genes that function to produce defined, measurable phenotypes: bioluminescence, quorum sensing, cell division, and growth arrest. We anticipate that Mobile-CRISPRi will be used inVibriospecies to systematically probe gene function and essentiality in various behaviors and native environments.
Multiomics analysis revealsB.MO1 as a distinctBabesiaspecies and provides insights into its evolution and virulence
Authors: Singh Pallavi , Vydyam Pratap , Fang Tiffany , Estrada Karel , Gonzalez Luis Miguel , Grande Ricardo , Kumar Madelyn , Chakravarty Sakshar , Berry Vincent , Ranwez Vincent , Carcy Bernard , Depoix Delphine , Sánchez Sergio , Cornillot Emmanuel , Abel Steven , Ciampossin Loic , Lenz Todd , Harb Omar , Sanchez-Flores Alejandro , Montero Estrella , Le Roch Karine G. , Lonardi Stefano , Ben Mamoun Choukri
Published: January 2024

Babesiosis, caused by protozoan parasites of the genusBabesia, is an emerging tick-borne disease of significance for both human and animal health.Babesiaparasites infect erythrocytes of vertebrate hosts where they develop and multiply rapidly to cause the pathological symptoms associated with the disease. The identification of variousBabesiaspecies underscores the ongoing risk of new zoonotic pathogens capable of infecting humans, a concern amplified by anthropogenic activities and environmental shifts impacting the distribution and transmission dynamics of parasites, their vectors, and reservoir hosts. One such species,BabesiaMO1, previously implicated in severe cases of human babesiosis in the midwestern United States, was initially considered closely related toB. divergens, the predominant agent of human babesiosis in Europe. Yet, uncertainties persist regarding whether these pathogens represent distinct variants of the same species or are entirely separate species. We show that although bothB.MO1 andB. divergensshare similar genome sizes, comprising three nuclear chromosomes, one linear mitochondrial chromosome, and one circular apicoplast chromosome, major differences exist in terms of genomic sequence divergence, gene functions, transcription profiles, replication rates and susceptibility to antiparasitic drugs. Furthermore, both pathogens have evolved distinct classes of multigene families, crucial for their pathogenicity and adaptation to specific mammalian hosts. Leveraging genomic information forB.MO1,B. divergens, and other members of the Babesiidae family within Apicomplexa provides valuable insights into the evolution, diversity, and virulence of these parasites. This knowledge serves as a critical tool in preemptively addressing the emergence and rapid transmission of more virulent strains.
Catabolic pathway acquisition by soil pseudomonads readily enables growth with salicyl alcohol but does not affect colonization ofPopulusroots
Authors: Christel Stephan , Carrell Alyssa A. , Burdick Leah H. , Villalobos Solis Manuel I. , Abraham Paul E. , Jawdy Sara S. , Chaves Julie E. , Engle Nancy L. , Berhane Timkhite-Kulu , Yao Tao , Chen Jin-Gui , Muchero Wellington , Tschaplinski Timothy J. , Cregger Melissa A. , Michener Joshua K.
Published: January 2024

Horizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally reproduced one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol into soil isolates from thePseudomonasgenus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferred by HGT but is selectively neutral under environmentally-relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting, because the selective benefits are small and negative frequency-dependent.
EvoAug-TF: Extending evolution-inspired data augmentations for genomic deep learning to TensorFlow
Authors: Yu Yiyang , Muthukumar Shivani , Koo Peter K
Published: January 2024

Deep neural networks (DNNs) have been widely applied to predict the molecular functions of regulatory regions in the non-coding genome. DNNs are data hungry and thus require many training examples to fit data well. However, functional genomics experiments typically generate limited amounts of data, constrained by the activity levels of the molecular function under study inside the cell. Recently, EvoAug was introduced to train a genomic DNN with evolution-inspired augmentations. EvoAug-trained DNNs have demonstrated improved generalization and interpretability with attribution analysis. However, EvoAug only supports PyTorch-based models, which limits its applications to a broad class of genomic DNNs based in TensorFlow. Here, we extend EvoAug’s functionality to TensorFlow in a new package we call EvoAug-TF. Through a systematic benchmark, we find that EvoAug-TF yields comparable performance with the original EvoAug package.

Availability

EvoAug-TF is freely available for users and is distributed under an open-source MIT license. Researchers can access the open-source code on GitHub (https://github.com/p-koo/evoaug-tf). The pre-compiled package is provided via PyPI (https://pypi.org/project/evoaug-tf) with in-depth documentation on ReadTheDocs (https://evoaug-tf.readthedocs.io). The scripts for reproducing the results are available at (https://github.com/p-koo/evoaug-tf_analysis).
Exposure of gut bacterial isolates to the anthelminthic drugs, ivermectin and moxidectin, leads to antibiotic-like phenotypes of growth inhibition and adaptation
Authors: Dommann Julian , Keiser Jennifer , Garneau Julian , Gandelin Alison , Casanova Carlo , Keller Peter M. , Sayasone Somphou , Vonaesch Pascale , Schneeberger Pierre H. H.
Published: January 2024

Due to their broad-spectrum activities, ivermectin and moxidectin are widely used anthelminthics in veterinary and human medicine. However, ivermectin has recently been shown to perturbate gut-microbial growth. Given the macrolide-like structure of both ivermectin and moxidectin, there is a need to characterize the antibiotic spectrum of these anthelminthic drugs and their potential implications in the development of cross-resistance to macrolides and other families of antibiotics. Here, we incubated 59 bacterial isolates representing different clades frequently found in the gut with ivermectin and moxidectin at different concentrations for 16-72h. Further, we challenged 10 bacterial isolates with repeated and gradually increasing concentrations of these two anthelminthics and subsequently characterized their sensitivity to different antibiotics as well as ascending anthelminthic concentrations. We found, that antibacterial activity of the two anthelminthics is comparable to a selection of tested antibiotics, as observed by potency and dose dependence. Bacterial anthelminthic challengingin vitroresulted in decreased anthelminthic sensitivity. Further, adaptation to anthelminthics is associated with decreased antibiotic sensitivity towards three macrolides, a lincosamide, a fluoroquinolone, a tetracycline and two carbapenems. The observed change in bacterial sensitivity profiles is associated with - and likely caused by - repeated anthelminthic exposure. Hence, current and future large-scale administration of ivermectin and moxidectin, respectively, for the control of helminths and malaria raises serious concerns - and hence potential off-target effects should be carefully monitored.
Characterization of a novel humanized heavy chain antibody targeting endogenous retroviruses with anti-lymphoma activity
Authors: Spriano Filippo , Cascione Luciano , Sgrignani Jacopo , Bendik Nikolai , Napoli Sara , Sartori Giulio , Cannas Eleonora , Gong Tao , Arribas Alberto J. , Pizzi Marco , Rossi Davide , Robbiani Davide F. , Cavalli Andrea , Bertoni Francesco
Published: January 2024

Lymphomas continue to pose therapeutic challenges, with a considerable portion of patients facing refractory disease. This study focuses on Diffuse Large B-cell Lymphoma (DLBCL), the most prevalent lymphoma type. Within the human genome, transposable elements (TEs), particularly Human Endogenous Retroviruses (HERVs), constitute a significant yet understudied portion. Among HERVs, the HERV-K family, specifically HERV-K113 and HERV-K115, has intact open reading frames. Epigenetic regulation tightly controls HERV expression, and aberrant expression has been observed in various cancers, including lymphomas.

This research investigates the potential of HERV-K as a therapeutic target in DLBCL. The study encompasses comprehensive methods, including RNA extraction, PCR detection, flow cytometry, immunoblotting, peptide prediction, phage display, surface plasmon resonance, ELISA, antibody-dependent cell-mediated cytotoxicity, internalization assays, and bioinformatic analysis. Results reveal the presence and expression of HERVs in lymphoma patients and cell lines, with the HERV-K envelope protein identified as a crucial contributor to lymphoma cell growth. Moreover, the study identifies immunogenic regions of HERV-K, leading to the development of a humanized camelid nanobody (FF-01) with potential therapeutic applications. Furthermore, bioinformatic analysis differentiates DLBCL subgroups based on TE expression, providing insights into prognostic variations. Patients with high HERV-K113 expression show activation of pathways related to antiviral responses, suggesting a viral mimicry state.

In conclusion, the study highlights the clinical relevance of HERVs in lymphomas, proposing them as novel therapeutic targets. The newly developed nanobody FF-01 demonstrates anti-lymphoma activity through antibody-dependent cellular cytotoxicity and internalization. This research opens avenues for exploring endogenous retroviruses as targets for immunotherapy in lymphomas, showcasing the potential of FF-01 as a promising candidate for further investigation.
A Bacteriophage Cocktail TargetingYersinia pestisProvides Strong Post-Exposure Protection in a Rat Pneumonic Plague Model
Authors: Kilgore Paul B. , Sha Jian , Hendrix Emily K. , Neil Blake H. , Lawrence William S. , Peel Jennifer E. , Hittle Lauren , Woolston Joelle , Sulakvelidze Alexander , Schwartz Jennifer A. , Chopra Ashok K.
Published: January 2024

Yersinia pestis, one of the deadliest bacterial pathogens ever known, is responsible for three plague pandemics and several epidemics, with over 200 million deaths during recorded history. Due to high genomic plasticity,Y. pestisis amenable to genetic mutations as well as genetic engineering that can lead to the emergence or intentional development of pan-drug resistant strains. The dissemination of suchY. pestisstrains could be catastrophic, with public health consequences far more daunting than those caused by the recent COVID-19 pandemic. Thus, there is an urgent need to develop novel, safe, and effective treatment approaches for managingY. pestisinfections. This includes infections by antigenically distinct strains for which vaccines, none FDA approved yet, may not be effective, and those that cannot be controlled by approved antibiotics. Lytic bacteriophages provide one such alternative approach. In this study, we examined post-exposure efficacy of a bacteriophage cocktail, YPP-401, to combat pneumonic plague caused byY. pestisCO92. YPP-401 is a four-phage preparation with a 100% lytic activity against a panel of 68 genetically diverseY. pestisstrains. Using a pneumonic plague aerosol challenge model in gender-balanced Brown Norway rats, YPP-401 demonstrated ∼88% protection when delivered 18 hours post-exposure for each of two administration routes (i.e., intraperitoneal and intranasal) in a dose-dependent manner. Our studies suggest that YPP-401 could provide an innovative, safe, and effective approach for managingY. pestisinfections, including those caused by naturally occurring or intentionally developed strains that cannot be managed by vaccines in development and antibiotics.
Multiple Pathways Impact Swarming Motility ofPseudomonas fluorescensPf0-1
Authors: Pastora Alexander B. , Rzasa Kara M. , O’Toole George A.
Published: January 2024

Swarming motility in pseudomonads typically requires both a functional flagellum and production/secretion of a biosurfactant. Published work has shown that the wild-typePseudomonas fluorescensPf0-1 is swarming-deficient due to a point mutation in thegacAgene, which until recently, was thought to inactivate rather than attenuate the Gac/Rsm pathway. As a result, little is known about the underlying mechanisms that regulate swarming motility byP. fluorescensPf0-1. Here, we demonstrate that a ΔrsmAΔrsmEΔrsmImutant, which phenotypically mimics Gac/Rsm pathway overstimulation, is proficient at swarming motility. RsmA and RsmE appear to play a key role in this regulation. Transposon mutagenesis of the ΔrsmAΔrsmEΔrsmImutant identified multiple factors that impact swarming motility, including pathways involved in flagellar synthesis and biosurfactant production/secretion. We find that loss of genes linked to biosurfactant Gacamide A biosynthesis or secretion impact swarming motility, as does loss of the alternative sigma factor FliA, which results in a defect in flagellar function. Collectively, these findings provide evidence thatP. fluorescensPf0-1 can swarm if the Gac/Rsm pathway is activated, highlight the regulatory complexity of swarming motility in this strain, and demonstrate that the cyclic lipopeptide Gacamide A is utilized as a biosurfactant for swarming motility.

Importance

Swarming motility is a coordinated process that allows communities of bacteria to collectively move across a surface. ForP. fluorescensPf0-1, this phenotype is notably absent in the parental strain and to date little is known about the regulation of swarming in this strain. Here, we identify RsmA and RsmE as key repressors of swarming motility via modulating the levels of biosurfactant production/secretion. Via transposon mutagenesis and subsequent genetic analyses, we further identify potential regulatory mechanisms of swarming motility and link Gacamide A biosynthesis and transport machinery to swarming motility.
TheBacillus subtiliscell envelope stress-inducibleytpABoperon modulates membrane properties and contributes to bacitracin resistance
Authors: Willdigg Jessica R. , Patel Yesha , Arquilevich Briana E. , Subramanian Chitra , Frank Matthew W. , Rock Charles O. , Helmann John D.
Published: January 2024

Antibiotics that inhibit peptidoglycan synthesis trigger the activation of both specific and general protective responses. σMresponds to diverse antibiotics that inhibit cell wall synthesis. Here, we demonstrate that cell wall inhibiting drugs, such as bacitracin and cefuroxime, induce the σM-dependentytpABoperon. YtpA is a predicted hydrolase previously proposed to generate the putative lysophospholipid antibiotic bacilysocin (lysophosphatidylglycerol), and YtpB is the branchpoint enzyme for the synthesis of membrane-localized C35terpenoids. Using targeted lipidomics we reveal that YtpA is not required for the production of lysophosphatidylglycerol. Nevertheless,ytpAwas critical for growth in a mutant strain defective for homeoviscous adaptation due to a lack of genes for the synthesis of branched chain fatty acids and the Des phospholipid desaturase. Consistently, overexpression ofytpAincreased membrane fluidity as monitored by fluorescence anisotropy. TheytpAgene contributes to bacitracin resistance in mutants additionally lacking thebceABorbcrCgenes, which directly mediate bacitracin resistance. These epistatic interactions support a model in which σM-dependent induction of theytpABoperon helps cells tolerate bacitracin stress, either by facilitating the flipping of the undecaprenyl-phosphate carrier lipid or by impacting the assembly or function of membrane-associated complexes proteins involved in cell wall homeostasis.

Importance

Peptidoglycan synthesis inhibitors include some of our most important antibiotics. InBacillus subtilis, peptidoglycan synthesis inhibitors induce the σMregulon, which is critical for intrinsic antibiotic resistance. The σM-dependentytpABoperon encodes a predicted hydrolase (YtpA) and the enzyme that initiates the synthesis of C35terpenoids (YtpB). Our results suggest that YtpA is critical in cells defective in homeoviscous adaptation. Further, we find that YtpA functions cooperatively with the BceAB and BcrC proteins in conferring intrinsic resistance to bacitracin, a peptide antibiotic that binds tightly to the UPP lipid carrier that sustains peptidoglycan synthesis.
Neisseria gonorrhoeaescavenges host sialic acid for Siglec-mediated, complement-independent suppression of neutrophil activation
Authors: Cardenas Amaris J , Thomas Keena S. , Broden Mary W. , Ferraro Noel J. , John Constance M. , Pires Marcos M. , Jarvis Gary A. , Criss Alison K.
Published: January 2024

Gonorrhea, caused by the bacteriumNeisseria gonorrhoeae(Gc), is characterized by neutrophil influx to infection sites. Gc has developed mechanisms to resist killing by neutrophils that include modifications to its surface lipooligosaccharide (LOS). One such LOS modification is sialylation: Gc sialylates its terminal LOS sugars with cytidine-5’-monophosphate-N-acetylneuraminic acid (CMP-NANA) scavenged from the host using LOS sialyltransferase (Lst), since Gc cannot make its own sialic acid. Sialylation enables sensitive strains of Gc to resist complement-mediated killing in a serum-dependent manner. However, little is known about the contribution of sialylation to complement-independent, direct Gc-neutrophil interactions. In the absence of complement, we found sialylated Gc expressing opacity-associated (Opa) proteins decreased the oxidative burst and granule exocytosis from primary human neutrophils. In addition, sialylated Opa+ Gc survived better than vehicle treated or ΔlstGc when challenged with neutrophils. However, Gc sialylation did not significantly affect Opa-dependent association with or internalization of Gc by neutrophils. Previous studies have implicated sialic acid-binding immunoglobulin-type lectins (Siglecs) in modulating neutrophil interactions with sialylated Gc. Blocking neutrophil Siglecs with antibodies that bind to their extracellular domains eliminated the ability of sialylated Opa+ Gc to suppress oxidative burst and resist neutrophil killing. These findings highlight a new role for sialylation in Gc evasion of human innate immunity, with implications for the development of vaccines and therapeutics for gonorrhea.

IMPORTANCE

Neisseria gonorrhoeae,the bacterium that causes gonorrhea, is an urgent global health concern due to increasing infection rates, widespread antibiotic resistance, and its ability to thwart protective immune responses. The mechanisms by which Gc subvert protective immune responses remain poorly characterized. One wayN. gonorrhoeaeevades human immunity is by adding sialic acid that is scavenged from the host onto its lipooligosaccharide, using the sialyltransferase Lst. Here, we found that sialylation enhancesN. gonorrhoeaesurvival from neutrophil assault and inhibits neutrophil activation, independently of the complement system. Our results implicate bacterial binding of sialic acid-binding lectins (Siglecs) on the neutrophil surface, which dampen neutrophil antimicrobial responses. This work identifies a new role for sialylation in protectingN. gonorrhoeaefrom cellular innate immunity, which can be targeted to enhance the human immune response in gonorrhea.
Neutralizing gut-derived lipopolysaccharide as a novel therapeutic strategy for severe leptospirosis
Authors: Xie Xufeng , Chen Xi , Zhang Shilei , Liu Jiuxi , Zhang Wenlong , Cao Yongguo
Published: January 2024

Leptospirosis is an emerging infectious disease caused by pathogenicLeptospiraspp. Humans and some mammals can develop severe forms of leptospirosis accompanied by a dysregulated inflammatory response, which often results in death. The gut microbiota has been increasingly recognized as a vital element in systemic health. However, the precise role of the gut microbiota in severe leptospirosis is still unknown. Here, we aimed to explore the function and potential mechanisms of the gut microbiota in a hamster model of severe leptospirosis. Our study showed that leptospires were able to multiply in the intestine, cause pathological injury, and induce intestinal and systemic inflammatory responses. 16S rRNA gene sequencing analysis revealed thatLeptospirainfection changed the composition of the gut microbiota of hamsters with an expansion of Proteobacteria. In addition, gut barrier permeability was increased after infection, as reflected by a decrease in the expression of tight junctions. Translocated Proteobacteria were found in the intestinal epithelium of moribund hamsters, as determined by fluorescence in situ hybridization, with elevated LPS levels in the serum. Moreover, gut microbiota depletion reduced the survival time, increased the leptospiral load, and promoted the expression of proinflammatory cytokines afterLeptospirainfection. Intriguingly, fecal filtration and serum from moribund hamsters both increased the transcription ofTNF-α,IL-1β,IL-10, andTLR4in macrophages compared with those from uninfected hamsters. These stimulating activities were inhibited by LPS neutralization using polymyxin B. Based on our findings, we identified an LPS neutralization therapy that significantly improved the survival rates in severe leptospirosis when used in combination with antibiotic therapy or polyclonal antibody therapy. In conclusion, our study not only uncovers the role of the gut microbiota in severe leptospirosis but also provides a therapeutic strategy for severe leptospirosis.
Analysis of dietary vitamin C intake levels and the risk of hyperuricemia and gout based on cross-sectional studies and bi-directional Mendelian randomisation
Authors: Peng Zi-Ning , Wang Xing-Qiang , Deng Qian , Yan Wei-Tian , Zhao Wei-Qing , Pu Yong-Bin , Liu Nian , Gu Ling-Li , Peng Jiang-Yun
Published: January 2024

Background

Vitamin C, a common antioxidant, may be useful for treating hyperuricemia and gout. The aim of this study was to investigate the risk association between dietary vitamin C intake and hyperuricemia/gout and to test for causality using the bi-directional Mendelian randomisation method.

Methods

Cross-sectional studies were selected from the National Health and Nutrition Examination Survey from 2007–2018 to assess the association between dietary vitamin C intake and the risk of hyperuricemia/gout, according to multivariate logistic regression modelling. Bi-directional Mendelian randomisation studies were conducted using genetic data from large-scale genome-wide association surveys of supplemental vitamin C, pharmacological vitamin C, and ascorbic acid intake and hyperuricemia/gout; these aimed to infer causal relationships between vitamin C and hyperuricemia/gout. Inverse variance weighting was used as the primary method of Mendelian randomisation analysis. A series of sensitivity analyses were used to assess multiplicity.

Results

The cross-sectional study included 17.52% and 82.48% patients with and without hyperuricemia, respectively, as well as 2.67% and 97.33% patients with and without gout, respectively. In the model correcting for all covariates, the association between vitamin C intake and the risk of hyperuricemia/gout was stable, and the risk of hyperuricemia was generally lower in patients who consumed >111.75 mg vitamin C than in other patients when comparing three models with different moderators. Restricted cubic spline scores indicated that vitamin C intake recommendations of 75–525 mg and 75–225 mg were effective for targeting hyperuricemia and gout, respectively. In inverse variance weighting in the Mendelian randomisation analysis, the amount of vitamin C absorbed was negatively associated with hyperuricemia (OR = 0.985, 95% CI = 0.973–0.997, p = 0.015), and supplemental vitamin C was negatively associated with gout (OR = 0.857, 95% CI = 0.797–0.921, p < 0.001); sensitivity analysis yielded consistent results. Reverse Mendelian randomisation analysis showed that vitamin C had no reverse causal relationship with hyperuricemia and gout.

Conclusion

We hypothesise that a dietary vitamin C intake of 75–525 mg or 75–225 mg may reduce the risk of hyperuricemia and gout, respectively. Further research with larger samples is required to confirm this.
Leveraging co-evolutionary insights and AI-based structural modeling to unravel receptor-peptide ligand-binding mechanisms
Authors: Snoeck Simon , Lee Hyun Kyung , Schmid Marc W. , Bender Kyle W. , Neeracher Matthias J. , Fernández-Fernández Alvaro D. , Santiago Julia , Zipfel Cyril
Published: January 2024

Secreted signaling peptides are central regulators of growth, development, and stress responses, but specific steps in the evolution of these peptides and their receptors are not well understood. In addition, the molecular mechanisms of peptide-receptor binding are only known for a few examples, primarily owing to the limited availability of structural capabilities to few laboratories worldwide. Plants have evolved a multitude of secreted signaling peptides and corresponding transmembrane receptors. Stress-responsive SERINE RICH ENDOGENOUS PEPTIDES (SCOOPs) were recently identified. Bioactive SCOOPs are proteolytically processed by subtilases and are perceived by the leucine-rich repeat receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) in the model plantArabidopsis thaliana. How SCOOPs and MIK2 have (co-)evolved, and how SCOOPs bind to MIK2 are however still unknown. Usingin silicoanalysis of 350 plant genomes and subsequent functional testing, we revealed the conservation of MIK2 as SCOOP receptor within the plant order Brassicales. We then leveraged AlphaFold-Multimer and comparative genomics to identify two conserved putative SCOOP-MIK2 binding pockets across Brassicales MIK2 homologues predicted to interact with the ‘SxS’ motif of otherwise sequence-divergent SCOOPs. Notably, mutagenesis of both predicted binding pockets compromised SCOOP binding to MIK2, SCOOP-induced complex formation between MIK2 and its co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1), and SCOOP-induced reactive oxygen species production; thus, confirming ourin silicopredictions. Collectively, in addition to revealing the elusive SCOOP-MIK2 binding mechanisms, our analytic pipeline combining phylogenomics, AI-based structural predictions, and experimental biochemical and physiological validation provides a blueprint for the elucidation of peptide ligand-receptor perception mechanisms.

Significance statement

This study presents a rapid and inexpensive alternative to classical structure-based approaches for resolving ligand-receptor binding mechanisms. It relies on a multilayered bioinformatic approach that leverages genomic data across diverse species in combination with AI-based structural modeling to identify true ligand and receptor homologues, and subsequently predict their binding mechanisms.In silicofindings were validated by multiple experimental approaches, which investigated the effect of amino acid changes in the proposed binding pockets on ligand-binding, complex formation with a co-receptor essential for downstream signaling, and activation of downstream signaling. Our analysis combining evolutionary insights,in silicomodeling and functional validation provides a framework for structure-function analysis of other peptide-receptor pairs, which could be easily implemented by most laboratories.
Localising elements in single-particle reconstructions by REEL-EM: Reconstructed Electron Energy-Loss - Elemental Mapping
Authors: Pfeil-Gardiner Olivia , Rosa Higor Vinícius Dias , Riedel Dietmar , Chen Yu Seby , Lörks Dominique , Kükelhan Pirmin , Linck Martin , Müller Heiko , Van Petegem Filip , Murphy Bonnie J.
Published: January 2024

For structures determined by single particle cryo-EM, no technique currently exists for mapping elements to defined locations, leading to errors in the assignment of metals and other ions, cofactors, substrates, inhibitors, and lipids that play essential roles in activity and regulation. Elemental mapping in the electron microscope is well established for dose-tolerant samples but is challenging for biological samples, especially in a cryo-preserved state. Here, we combine electron energy-loss spectroscopy (EELS) with single-particle image processing to allow elemental mapping in cryo-preserved macromolecular complexes. Proof-of-principle data show that our method, REEL-EM, allows 3D reconstruction of EELS data, such that a high total electron dose is accumulated across many copies of a complex. Working with two test samples, we demonstrate that we can reliably localise abundant elements. We discuss the current limitations of the method and potential future developments.
Environmental controls of dark CO2 fixation in wetland microbiomes
Authors: Grüterich Luise , Woodhouse Jason Nicholas , Mueller Peter , Tiemann Amos , Ruscheweyh Hans-Jo-achim , Sunagawa Shinichi , Grossart Hans-Peter , Streit Wolfgang R.
Published: January 2024

Rising atmospheric concentration of CO2is a major concern to society due to its global warming potential. In soils, CO2fixing microorganisms are preventing a part of the CO2from entering the atmosphere. Yet, the pathways behind dark CO2fixation are rarely studiedin situ. Here we examined the environmental controls on the abundance and expression of key genes involved in microbial CO2fixation in estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic and metatranscriptomic analyses confirmed that wetland microbiota harbor all six known CO2fixation pathways and that these pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reductive tricarboxylic acid cycle (rTCA) and the Calvin cycle were favored by low salinity and O2rich niches high in organic matter, while the transcription of the key genes for the Wood-Ljungdahl pathway (WLP) and dicarboxylate/4-hydroxybutyrate cycle (DC/4-HB cycle) were favored by low O2niches poor in organic matter. Taxonomic assignment of transcripts implied that dark CO2fixation was mainly linked to few bacterial phyla, namely, Desulfobacterota, Gemmatimonadota, Methylomirabilota, Nitrospirota and Pseudomonadota.
Eukaryotic genomic data uncover an extensive host range of mirusviruses
Authors: Zhao Hongda , Meng Lingjie , Hikida Hiroyuki , Ogata Hiroyuki
Published: January 2024

A recent marine metagenomic study has revealed the existence of a novel group of viruses designated mirusviruses, which are proposed to form an evolutionary link between two realms of double-stranded DNA viruses,VaridnaviriaandDuplodnaviria. Metagenomic data suggest that mirusviruses infect microeukaryotes in the photic layer of the ocean, but their host range remains largely unknown. In this study, we investigated the presence of mirusvirus marker genes in publicly available 1,901 eukaryotic genome assemblies, mainly derived from unicellular eukaryotes, to identify potential hosts of mirusviruses. Mirusvirus marker sequences were identified in 1,348 assemblies spanning 284 genera across eight supergroups of eukaryotes. The habitats of the putative mirusvirus hosts included not only marine but also other diverse environments. Among the major capsid protein (MCP) signals in the genome assemblies, we identified 85 sequences that showed high sequence and structural similarities to reference mirusvirus MCPs. A phylogenetic analysis of these sequences revealed their distant evolutionary relationships with the seven previously reported mirusvirus clades. Most of the scaffolds with these MCP sequences encoded multiple mirusvirus homologs, underscoring the impact of mirusviral infection on the evolution of the host genome. We also identified three circular mirusviral genomes within the genomic data of the oil producing thraustochytridSchizochytriumsp. and the endolithic green algaOstreobium quekettii. Overall, mirusviruses probably infect a wide spectrum of eukaryotes and are more diverse than previously reported.

Highlights

Mirusvirus signals detected in genomic data from eight eukaryotic supergroups.

Habits of putative mirusvirus hosts not limited to marine environments.

Major capsid sequences from these assemblies show new mirusviral lineages.

Three circular mirusvirus genomes were identified.
N-acetylglucosamine supplementation fails to bypass the critical acetylation of glucosamine-6-phosphate required forToxoplasma gondiireplication and invasion
Authors: Alberione María Pía , González-Ruiz Víctor , Rudaz Serge , Soldati-Favre Dominique , Izquierdo Luis , Kloehn Joachim
Published: January 2024

The cell surface ofToxoplasma gondiiis rich in glycoconjugates which hold diverse and vital functions in the lytic cycle of this obligate intracellular parasite. Additionally, the cyst wall of bradyzoites, that shields the persistent form responsible for chronic infection from the immune system, is heavily glycosylated. Formation of glycoconjugates relies on activated sugar nucleotides, such as uridine diphosphateN-acetylglucosamine (UDP- GlcNAc). The Glucosamine-phosphate-N-acetyltransferase (GNA1) generatesN- acetylglucosamine-6-phosphate critical to produce UDP-GlcNAc. Here, we demonstrate that downregulation ofT. gondiiGNA1 results in a severe reduction of UDP-GlcNAc and a concomitant drop in glycosylphosphatidylinositol (GPI), leading to impairment of the parasite’s ability to invade and replicate in the host cell. Surprisingly, attempts to rescue this defect through exogenous GlcNAc supplementation fail to completely restore these essential functions. In depth metabolomic analyses elucidate diverse causes underlying the failed rescue: utilization of GlcNAc is inefficient under glucose-replete conditions and fails to restore UDP-GlcNAc levels in GNA1-depleted parasites. In contrast, GlcNAc- supplementation under glucose-deplete conditions fully restores UDP-GlcNAc levels but fails to rescue the defects associated with GNA1 depletion. Our results underscore the essentiality of GlcN6P acetylation in governingT. gondiireplication and invasion and highlight the potential of the evolutionary divergent GNA1 in Apicomplexa as a target for the development of much-needed new therapeutic strategies.