scholarly journals Dynamic pneumococcal genetic adaptations support bacterial growth and inflammation during coinfection with influenza

2019 ◽  
Author(s):  
Amanda P. Smith ◽  
Lindey C. Lane ◽  
Tim van Opijnen ◽  
Stacie Woolard ◽  
Robert Carter ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Single Gene ◽  
Bacterial Species ◽  
Protein Translation ◽  
Morbidity And Mortality ◽  
Lung Pathology ◽  
Genome Wide ◽  
A Genome ◽  
Bacterial Coinfection ◽  
Bacterial Genes

AbstractStreptococcus pneumoniae(pneumococcus) is one of the primary bacterial pathogens that complicates influenza virus infections. These secondary infections increase influenza-associated morbidity and mortality through a number of immunological and viral-mediated mechanisms. However, little is known about how specific bacterial genes contribute to post-influenza pathogenicity. Thus, we used genome-wide transposon mutagenesis (Tn-Seq) to reveal bacterial genes conferring improved fitness in influenza infected hosts. The majority of the 32 identified genes are involved in bacterial metabolism, including nucleotide biosynthesis, amino acid biosynthesis, protein translation, and membrane transport. We investigated five of the genes in detail: SPD1414, SPD2047 (cbiO1), SPD0058 (purD), SPD1098, and SPD0822 (proB). Single-gene deletion mutants showed slight growth attenuationsin vitroandin vivo, but still grew to high titers in both naïve and influenza-infected murine hosts. Despite high bacterial loads in the lung and sustained bacteremia, mortality was significantly reduced or delayed with each of the knockouts. Reductions in pulmonary neutrophils, inflammatory macrophages, and select proinflammatory cytokines and chemokines were observed at discrete times after coinfection with these bacterial mutants. Immunohistochemical staining also revealed altered neutrophil phenotype and distribution in the lungs of animals coinfected with knockouts. These studies demonstrate a critical role for specific bacterial genes in driving virulence and immune function during influenza-associated bacterial pneumonia.Author SummaryStreptococcus pneumoniae(pneumococcus) is a common coinfecting pathogen that increases morbidity and mortality during influenza epidemics and pandemics. It is known that the strain, dose, and timing of bacterial coinfection influence the likelihood of severe pneumonia, but the specific bacterial genes that contribute to bacterial pathogenicity during influenza coinfection remain unknown. Using a genome-wide analysis, we identified the pneumococcal genes that exacerbate disease during influenza-bacterial coinfection. Most of these have a role in metabolism. To better understand their contribution to this lethal disease, we generated 5 mutants that lacked a single gene. The strains grew to high titers in the lungs and blood of both healthy and influenza-infected animals yet mortality was significantly reduced. In influenza-infected animals, there was also significantly lower inflammatory immune responses, and lung pathology. These important pneumococcal adaptations largely facilitate lethality during influenza-pneumococcal coinfection. Investigating whether similar metabolic adaptations are conserved among bacterial species that complicate influenza could yield broadly effective therapies that abrogate lethal post-influenza bacterial infections.

scholarly journals Whole-exome sequencing associates novel CSMD1 gene mutations with familial Parkinson disease

2017 ◽  
Vol 3 (5) ◽  
pp. e177 ◽  
Author(s):  
Javier Ruiz-Martínez ◽  
Luis J. Azcona ◽  
Alberto Bergareche ◽  
Jose F. Martí-Massó ◽  
Coro Paisán-Ruiz
Keyword(s):  
Parkinson Disease ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Genome Wide Association Study ◽  
Single Gene ◽  
Gene Mutations ◽  
Complement Control Protein ◽  
Genome Wide ◽  
Whole Exome ◽  
A Genome

Objective:Despite the enormous advancements made in deciphering the genetic architecture of Parkinson disease (PD), the majority of PD is idiopathic, with single gene mutations explaining only a small proportion of the cases.Methods:In this study, we clinically evaluated 2 unrelated Spanish families diagnosed with PD, in which known PD genes were previously excluded, and performed whole-exome sequencing analyses in affected individuals for disease gene identification.Results:Patients were diagnosed with typical PD without relevant distinctive symptoms. Two different novel mutations were identified in the CSMD1 gene. The CSMD1 gene, which encodes a complement control protein that is known to participate in the complement activation and inflammation in the developing CNS, was previously shown to be associated with the risk of PD in a genome-wide association study.Conclusions:We conclude that the CSMD1 mutations identified in this study might be responsible for the PD phenotype observed in our examined patients. This, along with previous reported studies, may suggest the complement pathway as an important therapeutic target for PD and other neurodegenerative diseases.

scholarly journals Energetic Evolution of Cellular Transportomes

2017 ◽  
Author(s):  
Behrooz Darbani ◽  
Douglas B. Kell ◽  
Irina Borodina
Keyword(s):  
Ion Channels ◽  
Bacterial Species ◽  
Living Cells ◽  
Energetic Efficiency ◽  
Cellular Functions ◽  
Transporter Proteins ◽  
Genome Wide Analysis ◽  
Solute Carriers ◽  
Genome Wide ◽  
A Genome

ABSTRACTTransporter proteins mediate the translocation of substances across the membranes of living cells. We performed a genome-wide analysis of the compositional reshaping of cellular transporters (the transportome) across the kingdoms of bacteria, archaea, and eukarya. We show that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. This change has likely been important in the development of tissues performing energetically costly cellular functions. The transportome analysis also indicated seven bacterial species, includingNeorickettsia risticiiandNeorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, due to the restricted presence therein of clear homologues of modern mitochondrial solute carriers.

scholarly journals sPepFinder expedites genome-wide identification of small proteins in bacteria

2020 ◽  
Author(s):  
Lei Li ◽  
Yanjie Chao
Keyword(s):  
De Novo ◽  
Bacterial Species ◽  
Computational Prediction ◽  
Ribosome Profiling ◽  
Support Vector ◽  
Initiation Rate ◽  
E Coli ◽  
Small Proteins ◽  
Genome Wide ◽  
A Genome

ABSTRACTSmall proteins shorter than 50 amino acids have been long overlooked. A number of small proteins have been identified in several model bacteria using experimental approaches and assigned important functions in diverse cellular processes. The recent development of ribosome profiling technologies has allowed a genome-wide identification of small proteins and small ORFs (smORFs), but our incomplete understanding of small proteins hinders de novo computational prediction of smORFs in non-model bacterial species. Here, we have identified several sequence features for smORFs by a systematic analysis of all the known small proteins in E. coli, among which the translation initiation rate is the strongest determinant. By integrating these features into a support vector machine learning model, we have developed a novel sPepFinder algorithm that can predict conserved smORFs in bacterial genomes with a high accuracy of 92.8%. De novo prediction in E. coli has revealed several novel smORFs with evidence of translation supported by ribosome profiling. Further application of sPepFinder in 549 bacterial species has led to the identification of > 100,000 novel smORFs, many of which are conserved at the amino acid and nucleotide levels under purifying selection. Overall, we have established sPepFinder as a valuable tool to identify novel smORFs in both model and non-model bacterial organisms, and provided a large resource of small proteins for functional characterizations.

scholarly journals A CRISPR-based genome-wide screen for adipogenesis reveals new insights into mitotic expansion and lipogenesis

2020 ◽  
Author(s):  
Keren I. Hilgendorf ◽  
Carl T. Johnson ◽  
Kyuho Han ◽  
Atefeh Rabiee ◽  
Janos Demeter ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Cell Model ◽  
Protein Translation ◽  
Screening Strategy ◽  
Protein Abundance ◽  
Cellular Mechanisms ◽  
Ubiquitin Pathway ◽  
Genome Wide ◽  
A Genome ◽  
Green Fluorescent

SummaryIn response to excess nutrients, white adipose tissue expands by both generating new adipocytes and by upregulating lipogenesis in existing adipocytes. Here, we performed a genome-wide functional genomics screen to identify regulators of adipogenesis in the mouse 3T3-L1 cell model. The pooled screening strategy utilized FACS to isolate populations based on lipid content by gating for fluorescence intensity of the lipophilic, green fluorescent BODIPY 493/503 dye. Additionally, this approach categorized if genes functioned during mitotic expansion or lipogenesis. Cellular mechanisms regulating the rates of protein translation and protein stability were found to be critical for adipogenesis and lipogenesis. These mechanisms were further supported by proteomic analyses, which demonstrated that many changes in protein abundance during 3T3-L1 adipogenesis were not driven by transcription. Within these themes, we illustrate that hypusination is critical for translating adipogenic inducers of mitotic expansion and that the neddylation/ubiquitin pathway modulates insulin sensitivity to regulate lipogenesis.

scholarly journals A genome-wide CRISPR/Cas9 screen to identify phagocytosis modulators in monocytic THP-1 cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Benjamin Lindner ◽  
Eva Martin ◽  
Monika Steininger ◽  
Aleksandra Bundalo ◽  
Martin Lenter ◽  
...  
Keyword(s):  
Translational Control ◽  
Molecular Mechanisms ◽  
Gene Knockout ◽  
Single Gene ◽  
Microbial Pathogens ◽  
Protein Accumulation ◽  
Cellular Mechanisms ◽  
Developmental Defects ◽  
Genome Wide ◽  
A Genome

AbstractPhagocytosis of microbial pathogens, dying or dead cells, and cell debris is essential to maintain tissue homeostasis. Impairment of these processes is associated with autoimmunity, developmental defects and toxic protein accumulation. However, the underlying molecular mechanisms of phagocytosis remain incompletely understood. Here, we performed a genome-wide CRISPR knockout screen to systematically identify regulators involved in phagocytosis of Staphylococcus (S.) aureus by human monocytic THP-1 cells. The screen identified 75 hits including known regulators of phagocytosis, e.g. members of the actin cytoskeleton regulation Arp2/3 and WAVE complexes, as well as genes previously not associated with phagocytosis. These novel genes are involved in translational control (EIF5A and DHPS) and the UDP glycosylation pathway (SLC35A2, SLC35A3, UGCG and UXS1) and were further validated by single gene knockout experiments. Whereas the knockout of EIF5A and DHPS impaired phagocytosis, knocking out SLC35A2, SLC35A3, UGCG and UXS1 resulted in increased phagocytosis. In addition to S. aureus phagocytosis, the above described genes also modulate phagocytosis of Escherichia coli and yeast-derived zymosan A. In summary, we identified both known and unknown genetic regulators of phagocytosis, the latter providing a valuable resource for future studies dissecting the underlying molecular and cellular mechanisms and their role in human disease.

scholarly journals Panton–Valentine leucocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial GWAS

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Bernadette C Young ◽  
Sarah G Earle ◽  
Sona Soeng ◽  
Poda Sar ◽  
Varun Kumar ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Strong Relationship ◽  
Nasal Carriage ◽  
Tropical Regions ◽  
Genome Wide ◽  
A Genome ◽  
Bacterial Genetic ◽  
Bacterial Genes

Pyomyositis is a severe bacterial infection of skeletal muscle, commonly affecting children in tropical regions, predominantly caused by Staphylococcus aureus. To understand the contribution of bacterial genomic factors to pyomyositis, we conducted a genome-wide association study of S. aureus cultured from 101 children with pyomyositis and 417 children with asymptomatic nasal carriage attending the Angkor Hospital for Children, Cambodia. We found a strong relationship between bacterial genetic variation and pyomyositis, with estimated heritability 63.8% (95% CI 49.2–78.4%). The presence of the Panton–Valentine leucocidin (PVL) locus increased the odds of pyomyositis 130-fold (p=10-17.9). The signal of association mapped both to the PVL-coding sequence and to the sequence immediately upstream. Together these regions explained over 99.9% of heritability (95% CI 93.5–100%). Our results establish staphylococcal pyomyositis, like tetanus and diphtheria, as critically dependent on a single toxin and demonstrate the potential for association studies to identify specific bacterial genes promoting severe human disease.

scholarly journals Targeted control of toxin production by a mobile genetic element in Streptococcus pneumoniae

2020 ◽  
Author(s):  
Emily Stevens ◽  
Daniel J. Morse ◽  
Dora Bonini ◽  
Seána Duggan ◽  
Tarcisio Brignoli ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Nuclease Activity ◽  
Toxin Production ◽  
Helicase Domain ◽  
Human Pathogen ◽  
Genome Wide ◽  
A Genome ◽  
Invasive Diseases ◽  
Transcriptional Landscape ◽  
Integrative And Conjugative Element

Introductory ParagraphStreptococcus pneumoniae is a major human pathogen that can cause severe invasive diseases such as pneumonia, septicaemia and meningitis1–3. Young children are at a particularly high risk, with an estimated 800,000 deaths worldwide in those under five attributable to invasive pneumococcal disease each year1–3. The cytolytic toxin pneumolysin (Ply) is a primary virulence factor for this bacterium, however, despite its importance to both the colonisation and pathogenic capabilities of this pathogen, the regulation of its expression is not well defined4–7. Using a genome-wide association approach we identified over a hundred potential affectors of Ply activity, including the Integrative and Conjugative Element (ICE) ICESp23FST818. This regulatory effect is mediated through the activity of a novel modular protein, ZomB, which has an N-terminal UvrD-like helicase domain followed by two Cas4-like nuclease domains. The ZomB protein has potent ATP-dependent nuclease activity and binds specifically to the DNA containing a BOX repeat region that forms part of the ply operon. We hypothesise that with over 100 BOX regions across the pneumococcal genome, the acquisition of the zomB gene on ICESp23FST81 has the potential to re-wire the transcriptional landscape of this major human pathogen.

scholarly journals Genome-wide association mapping of Sclerotinia sclerotiorum resistance in soybean using whole-genome resequencing data

2019 ◽  
Author(s):  
Chiheb Boudhrioua ◽  
Maxime Bastien ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Association Mapping ◽  
Sclerotinia Sclerotiorum ◽  
Single Gene ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Whole Genome ◽  
Sclerotinia Stem Rot ◽  
Genome Wide ◽  
A Genome ◽  
The Impact

Abstract Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is an important cause of yield loss in soybean. Although many papers have reported different loci contributing to partial resistance, few of these were proved to reproduce the same phenotypic impact in different populations. In this study, we identified a major quantitative trait loci (QTL) associated with resistance to SSR progression on the main stem by using a genome-wide association mapping (GWAM). A population of 127 soybean accessions was genotyped with 1.5M SNPs derived from genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS) ensuring an extensive genome coverage and phenotyped for SSR resistance. SNP-trait association led to discovery of a new QTL on chromosome 1 (Chr01) where resistant lines had shorter lesions on the stem by 29 mm . A single gene (Glyma.01g048000) resided in the same LD block as the peak SNP, but it is of unknown function. The impact of this QTL was even more significant in the descendants of a cross between two lines carrying contrasted alleles for Chr01. Individuals carrying the resistance allele developed lesions almost 50% shorter than those bearing the sensitivity allele. These results suggest that this region harbors a promising resistance QTL to SSR that can be used in soybean breeding program.

scholarly journals Screening of clustered regulatory elements reveals functional cooperating dependencies in Leukemia

2019 ◽  
Author(s):  
Salima Benbarche ◽  
Cécile K Lopez ◽  
Eralda Salataj ◽  
Cécile Thirant ◽  
Marie-Charlotte Laiguillon ◽  
...  
Keyword(s):  
Cell Growth ◽  
Cancer Cell ◽  
Tyrosine Kinases ◽  
Massively Parallel Sequencing ◽  
Single Gene ◽  
Functional Characterization ◽  
Leukemia Cell ◽  
Regulatory Elements ◽  
Genome Wide ◽  
A Genome

In the recent years, massively parallel sequencing approaches identified hundreds of mutated genes in cancer(1) providing an unprecedented amount of information about mechanisms of cancer cell maintenance and progression. However, while (it is widely accepted that) transformation processes result from oncogenic cooperation between deregulated genes and pathways, the functional characterization of candidate key players is mostly performed at the single gene level which is generally inadequate to identify these oncogene circuitries. In addition, studies aimed at depicting oncogenic cooperation involve the generation of challenging mouse models or the deployment of tedious screening pipelines. Genome wide mapping of epigenomic modifications on histone tails or binding of factors such as MED1 and BRD4 allowed identification of clusters of regulatory elements, also termed Super-Enhancers (SE)(2). Functional annotation of these regions revealed their high relevance during normal tissue development and cancer ontogeny(3). An interesting paradigm of the tumorigenic function of these SE regions comes from ETO2-GLIS2-driven acute megakaryoblastic leukemia (AMKL) in which the fusion protein ETO2-GLIS2 is sufficient to promote an aberrant transcriptional network by the rewiring of SE regions(4). We thus hypothesized that important regulatory regions could control simultaneously expression of genes cooperating in functional modules to promote cancer development. In an effort to identify such modules, we deployed a genome-wide CRISPRi-based screening approach and nominated SE regions that are functionally linked to leukemia maintenance. In particular, we pinpointed a novel SE region regulating the expression of both tyrosine kinases KIT and PDGFRA. Whereas the inhibition of each kinase alone affected modestly cancer cell growth, combined inhibition of both receptors synergizes to impair leukemia cell growth and survival. Our results demonstrate that genome-wide screening of regulatory DNA elements can identify co-regulated genes collaborating to promote cancer and could open new avenues to the concept of combined gene inhibition upon single hit targeting.

scholarly journals Protoplast fusion in Bacillus species produces frequent, unbiased, genome-wide homologous recombination

2020 ◽  
Author(s):  
Leah H. Burdick ◽  
Jared C. Streich ◽  
Delyana P. Vasileva ◽  
Dawn M. Klingeman ◽  
Hari B. Chhetri ◽  
...  
Keyword(s):  
Protoplast Fusion ◽  
Bacterial Species ◽  
Gc Content ◽  
Genetic Distances ◽  
Genomic Variation ◽  
Bacillus Species ◽  
Large Species ◽  
Natural Systems ◽  
Genome Wide ◽  
A Genome

ABSTRACTIn eukaryotes, fine-scale maps of meiotic recombination events have greatly advanced our understanding of the factors that affect genomic variation patterns and evolution of traits. However, in bacteria that lack natural systems for sexual reproduction, unbiased characterization of recombination landscapes has remained challenging due to variable rates of genetic exchange and influence of natural selection. Here, to overcome these limitations and to gain a genome-wide view on recombination, we crossed Bacillus strains with different genetic distances using protoplast fusion. The offspring displayed complex inheritance patterns with one of the parents consistently contributing the major part of the chromosome backbone and multiple unselected fragments originating from the second parent. Computational analyses suggested that this bias is due to the action of restriction-modification systems whereas genome features like GC content and local nucleotide identity did not affect distribution of recombination events around the chromosome. Furthermore, we found that the intensity of recombination is uniform across the genome without concentration into hotspots. Unexpectedly, our results revealed that large species-level genetic distance did not affect key recombination parameters. Our study provides a new insight into the dynamics of recombination in bacteria and a platform for studying recombination patterns in diverse bacterial species.

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