scholarly journals First Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene

2021 ◽  
Vol 12 ◽  
Author(s):  
Prasad Thomas ◽  
Mostafa Y. Abdel-Glil ◽  
Anbazhagan Subbaiyan ◽  
Anne Busch ◽  
Inga Eichhorn ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genome Structure ◽  
Genetic Material ◽  
Etiologic Agent ◽  
Gas Gangrene ◽  
Clostridium Septicum ◽  
16S Rrna Analysis ◽  
The Core ◽  
Conserved Gene ◽  
Clostridium Chauvoei

Clostridium septicum is a Gram-positive, toxin-producing, and spore-forming bacterium that is recognized, together with C. perfringens, as the most important etiologic agent of progressive gas gangrene. Clostridium septicum infections are almost always fatal in humans and animals. Despite its clinical and agricultural relevance, there is currently limited knowledge of the diversity and genome structure of C. septicum. This study presents the complete genome sequence of C. septicum DSM 7534T type strain as well as the first comparative analysis of five C. septicum genomes. The taxonomy of C. septicum, as revealed by 16S rRNA analysis as well as by genomic wide indices such as protein-based phylogeny, average nucleotide identity, and digital DNA–DNA hybridization indicates a stable clade. The composition and presence of prophages, CRISPR elements and accessory genetic material was variable in the investigated genomes. This is in contrast to the limited genetic variability described for the phylogenetically and phenotypically related species Clostridium chauvoei. The restriction-modification (RM) systems between two C. septicum genomes were heterogeneous for the RM types they encoded. C. septicum has an open pangenome with 2,311 genes representing the core genes and 1,429 accessory genes. The core genome SNP divergence between genome pairs varied up to 4,886 pairwise SNPs. A vast arsenal of potential virulence genes was detected in the genomes studied. Sequence analysis of these genes revealed that sialidase, hemolysin, and collagenase genes are conserved compared to the α-toxin and hyaluronidase genes. In addition, a conserved gene found in all C. septicum genomes was predicted to encode a leucocidin homolog (beta-channel forming cytolysin) similar (71.10% protein identity) to Clostridium chauvoei toxin A (CctA), which is a potent toxin. In conclusion, our results provide first, valuable insights into strain relatedness and genomic plasticity of C. septicum and contribute to our understanding of the virulence mechanisms of this important human and animal pathogen.

scholarly journals Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes

F1000Research ◽  
2013 ◽  
Vol 2 ◽  
pp. 63 ◽  
Author(s):  
Michel A Marin ◽  
Ana Carolina P Vicente
Keyword(s):  
Core Genome ◽  
Position Effect ◽  
Genome Structure ◽  
Enrichment Analysis ◽  
Gene Clusters ◽  
Gene Cassette ◽  
Etiologic Agent ◽  
Functional Genes ◽  
The Core ◽  
Core Genes

Background: Vibrio cholerae, the etiologic agent of cholera, is indigenous to aquatic environments. The V. cholerae genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. The flexible nature of the SI that results from gene cassette capture, deletion and rearrangement is thought to make it a hotspot of V. cholerae diversity, but beyond the basic structure it is not clear if there is a core genome in the SI and if so how it is structured. The aim of this study was to explore the core genome structure and the differences in gene content among strains of V. cholerae.Methods: From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae repeats. Analysis of the pangenome, including cluster analysis of functional genes, pangenome profile analysis, genetic variation analysis of functional genes, strain evolution analysis and function enrichment analysis of gene clusters, was performed using a pangenome analysis pipeline in addition to the R scripts, splitsTree4 and genoPlotR.Results and conclusions: Here, we reveal the genetic architecture of the V. cholerae SI. It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The V. cholerae SI has an open pangenome, which means that V. cholerae may be able to import new gene cassettes to SI. The set of dispensable SI genes is influenced by the niche and type species. The core genes are distributed along the SI, apparently without a position effect.

scholarly journals Sudden death due to gas gangrene caused by Clostridium septicum in goats

2018 ◽  
Vol 14 (1) ◽  
Author(s):  
Abdullah Gazioglu ◽  
Burcu Karagülle ◽  
Hayati Yüksel ◽  
M. Nuri Açık ◽  
Hakan Keçeci ◽  
...  
Keyword(s):  
Sudden Death ◽  
Gas Gangrene ◽  
Clostridium Septicum

scholarly journals Reovirus core proteins λ1 and σ2 promote stability of disassembly intermediates and influence early replication events

2020 ◽  
Author(s):  
Stephanie Gummersheimer ◽  
Pranav Danthi
Keyword(s):  
Conformational Changes ◽  
Genetic Material ◽  
Point Mutations ◽  
Host Cells ◽  
Capsid Proteins ◽  
Endosomal Membrane ◽  
The Core ◽  
Core Proteins ◽  
Early Replication ◽  
Outer Capsid

ABSTRACTThe capsids of mammalian reovirus contain two concentric protein shells, the core and the outer capsid. The outer capsid is comprised of µ1-σ3 heterohexamers which surround the core. The core is comprised of λ1 decamers held in place by σ2. After entry into the endosome, σ3 is proteolytically degraded and µ1 is cleaved and exposed to form ISVPs. ISVPs undergo further conformational changes to form ISVP*s, resulting in the release of µ1 peptides which facilitate the penetration of the endosomal membrane to release transcriptionally active core particles into the cytoplasm. Previous work has identified regions or specific residues within reovirus outer capsid that impact the efficiency of cell entry. We examined the functions of the core proteins λ1 and σ2. We generated a reovirus T3D reassortant that carries strain T1L derived σ2 and λ1 proteins (T3D/T1L L3S2). This virus displays a lower ISVP stability and therefore converts to ISVP*s more readily. To identify the basis for lability of T3D/T1L L3S2, we screened for hyper-stable mutants of T3D/T1L L3S2 and identified three point mutations in µ1 that stabilize ISVPs. Two of these mutations are located in the C-terminal ϕ region of µ1, which has not previously been implicated in controlling ISVP stability. Independent from compromised ISVP stability, we also found that T3D/T1L L3S2 launches replication more efficiently and produces higher yields in infected cells. In addition to identifying a new role for the core proteins in disassembly events, these data highlight that core proteins may influence multiple stages of infection.IMPORTANCEProtein shells of viruses (capsids) have evolved to undergo specific changes to ensure the timely delivery of genetic material to host cells. The 2-layer capsid of reovirus provides a model system to study the interactions between capsid proteins and the changes they undergo during entry. We tested a virus in which the core proteins were derived from a different strain than the outer capsid. We found that this mismatched virus was less stable and completed conformational changes required for entry prematurely. Capsid stability was restored by introduction of specific changes to the outer capsid, indicating that an optimal fit between inner and outer shells maintains capsid function. Separate from this property, mismatch between these protein layers also impacted the capacity of virus to initiate infection and produce progeny. This study reveals new insights into the roles of capsid proteins and their multiple functions during viral replication.

scholarly journals Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248054
Author(s):  
Jaqueline Raquel de Almeida ◽  
Diego Mauricio Riaño Pachón ◽  
Livia Maria Franceschini ◽  
Isaneli Batista dos Santos ◽  
Jessica Aparecida Ferrarezi ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Transmembrane Protein ◽  
Genome Structure ◽  
Rust Fungi ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
The Core ◽  
Mtdna Sequence ◽  
Austropuccinia Psidii

Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.

Verfassungsablösung

2021 ◽  
Author(s):  
Friederike Eggert
Keyword(s):  
Comparative Analysis ◽  
Constitutional Theory ◽  
The Core ◽  
The People ◽  
Legal Understanding

In her work, the author examines the question of how democratic constitutional states can give themselves new constitutions. On the basis of a comparative analysis of constitutional practice, the author develops constitutional replacement as a sui generis institute of constitutional theory. The core of the question is in which constitutional cases and under which legal and theoretical conditions the replacement of the current constitution would be permissible. The author justifies constitutional replacement based on a democratic-legal understanding of the pouvoir constituant, the "constitution-replacing power". In this concept, the constituent sovereignty of the people becomes a right of the people to replace its constitution.

THE COMPARATIVE ANALYSIS OF SOMATIC PHRASEOLOGICAL UNITS WITH КЬИЛ / ГОЛОВА / HEAD IN THE LEZGIN, RUSSIAN AND ENGLISH LANGUAGES

2020 ◽  
Vol 76 (4) ◽  
pp. 24-29
Author(s):  
FATIMA B. VERDIKHANOVA ◽  
◽  
GULNARA SH. PAVLOVA ◽  
Keyword(s):  
Comparative Analysis ◽  
Contrastive Analysis ◽  
Core Component ◽  
The Core ◽  
Semantic Fields

The object of the contrastive analysis in this article is the group of Lezgin, Russian and English phraseological (somatic) units with the component кьил/голова/head. The analysis aims at identifying the universal and specific issues in their contentits characteristic semantic fields, correlation of the general phraseological value with the core component, structural and grammatical features. In the process of the study we have used the method of comparative analysis of Lezgin, Russian and English phraseological units selected by us from foreign and domestic lexicographic sources. As the result of the analysis we have found that there was a similarity in structure, imagery and stylistic coloration of phraseological units. The peculiar characteristics of the studied languages in phraseological units were carried out. This work can serve as a material for further research in the field of phraseology whether the question of education plays an important role in the life of society.

scholarly journals Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Agronomy ◽  
2018 ◽  
Vol 8 (9) ◽  
pp. 159 ◽  
Author(s):  
Xiaojun Nie ◽  
Xian Zhao ◽  
Sue Wang ◽  
Ting Zhang ◽  
Chong Li ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Panicum Virgatum ◽  
Genome Structure ◽  
Structural Features ◽  
Panicum Miliaceum ◽  
Genomic Knowledge ◽  
Broomcorn Millet ◽  
Evolutionary Studies ◽  
Cp Genome

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated cereals worldwide, holding significant agricultural, historical, and evolutionary importance. However, our genomic knowledge of it is rather limited at present, hampering further genetic and evolutionary studies. Here, we sequenced and assembled the chloroplast genome (cp) of broomcorn millet and compared it with five other Panicoideae species. Results showed that the cp genome of broomcorn millet was 139,826 bp in size, with a typical quadripartite structure. In total, 108 genes were annotated and 18 genes were duplicated in the IR (inverted region) region, which was similar to other Panicoideae species. Comparative analysis showed a rather conserved genome structure between them, with three common regions. Furthermore, RNA editing, codon usage, and expansion of the IR, as well as simple sequence repeat (SSR) elements, were systematically investigated and 13 potential DNA markers were developed for Panicoideae species identification. Finally, phylogenetic analysis implied that broomcorn millet was a sister species to Panicum virgatum within the tribe Paniceae, and supported a monophyly of the Panicoideae. This study has reported for the first time the genome organization, gene content, and structural features of the chloroplast genome of broomcorn millet, which provides valuable information for genetic and evolutionary studies in the genus Panicum and beyond.

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