scholarly journals Genomic Variations in the Structural Proteins of SARS-CoV-2 and Their Deleterious Impact on Pathogenesis: A Comparative Genomics Approach

2021 ◽  
Vol 11 ◽  
Author(s):  
Taj Mohammad ◽  
Arunabh Choudhury ◽  
Insan Habib ◽  
Purva Asrani ◽  
Yash Mathur ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Therapeutic Strategies ◽  
Surface Glycoprotein ◽  
Structural Proteins ◽  
Therapeutic Approaches ◽  
Structural Variations ◽  
Main Protease ◽  
Functional Consequences ◽  
Comparative Genomics Analysis ◽  
Global Threat

A continual rise in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection causing coronavirus disease (COVID-19) has become a global threat. The main problem comes when SARS-CoV-2 gets mutated with the rising infection and becomes more lethal for humankind than ever. Mutations in the structural proteins of SARS-CoV-2, i.e., the spike surface glycoprotein (S), envelope (E), membrane (M) and nucleocapsid (N), and replication machinery enzymes, i.e., main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) creating more complexities towards pathogenesis and the available COVID-19 therapeutic strategies. This study analyzes how a minimal variation in these enzymes, especially in S protein at the genomic/proteomic level, affects pathogenesis. The structural variations are discussed in light of the failure of small molecule development in COVID-19 therapeutic strategies. We have performed in-depth sequence- and structure-based analyses of these proteins to get deeper insights into the mechanism of pathogenesis, structure-function relationships, and development of modern therapeutic approaches. Structural and functional consequences of the selected mutations on these proteins and their association with SARS-CoV-2 virulency and human health are discussed in detail in the light of our comparative genomics analysis.

scholarly journals Neurobiochemical Cross-talk Between COVID-19 and Alzheimer’s Disease

2020 ◽  
Author(s):  
Mohammad Azizur Rahman ◽  
Kamrul Islam ◽  
Saidur Rahman ◽  
Md Alamin
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Inflammatory Markers ◽  
Interleukin 1 ◽  
Therapeutic Strategies ◽  
Therapeutic Approaches ◽  
Angiotensin Converting Enzyme 2 ◽  
Apoe4 Allele ◽  
The Common ◽  
Global Threat

Abstract COVID-19, the global threat to humanity, shares etiological cofactors with multiple diseases including Alzheimer’s disease (AD). Understanding the common links between COVID-19 and AD would harness strategizing therapeutic approaches against both. Considering the urgency of formulating COVID-19 medication, its AD association and manifestations have been reviewed here, putting emphasis on memory and learning disruption. COVID-19 and AD share common links with respect to angiotensin-converting enzyme 2 (ACE2) receptors and pro-inflammatory markers such as interleukin-1 (IL-1), IL-6, cytoskeleton-associated protein 4 (CKAP4), galectin-9 (GAL-9 or Gal-9), and APOE4 allele. Common etiological factors and common manifestations described in this review would aid in developing therapeutic strategies for both COVID-19 and AD and thus impact on eradicating the ongoing global threat. Thus, people suffering from COVID-19 or who have come round of it as well as people at risk of developing AD or already suffering from AD, would be benefitted.

scholarly journals Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity

2021 ◽  
Vol 7 (5) ◽  
pp. 337
Author(s):  
Daniel Peterson ◽  
Tang Li ◽  
Ana M. Calvo ◽  
Yanbin Yin
Keyword(s):  
Comparative Genomics ◽  
Orthologous Gene ◽  
Gene Clusters ◽  
Phytopathogenic Fungi ◽  
Secreted Proteins ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Signal Peptides ◽  
Comparative Genomics Analysis

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

Phylogenetic relationships of ascomycetes and basidiomycetes based on comparative genomics analysis

2017 ◽  
Vol 39 (12) ◽  
pp. 1307-1316 ◽  
Author(s):  
Xunbiao Liu ◽  
Qianqian Zhang ◽  
Xinyao Xia ◽  
Xiuyuan Liu ◽  
Lei Ge ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Phylogenetic Relationships ◽  
Comparative Genomics Analysis

scholarly journals Comparative Genomics Analysis of Two Different Virulent Bovine Pasteurella multocida Isolates

2016 ◽  
Vol 2016 ◽  
pp. 1-14 ◽  
Author(s):  
Huihui Du ◽  
Rendong Fang ◽  
Tingting Pan ◽  
Tian Li ◽  
Nengzhang Li ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Pasteurella Multocida ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Insertion Sequences ◽  
Capsular Type ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Comparative Genomics Analysis

The Pasteurella multocida capsular type A isolates can cause pneumonia and bovine respiratory disease (BRD). In this study, comparative genomics analysis was carried out to identify the virulence genes in two different virulent P. multocida capsular type A isolates (high virulent PmCQ2 and low virulent PmCQ6). The draft genome sequence of PmCQ2 is 2.32 Mbp and contains 2,002 protein-coding genes, 9 insertion sequence (IS) elements, and 1 prophage region. The draft genome sequence of PmCQ6 is 2.29 Mbp and contains 1,970 protein-coding genes, 2 IS elements, and 3 prophage regions. The genome alignment analysis revealed that the genome similarity between PmCQ2 and PmCQ6 is 99% with high colinearity. To identify the candidate genes responsible for virulence, the PmCQ2 and PmCQ6 were compared together with that of the published genomes of high virulent Pm36950 and PmHN06 and avirulent Pm3480 and Pm70 (capsular type F). Five genes and two insertion sequences are identified in high virulent strains but not in low virulent or avirulent strains. These results indicated that these genes or insertion sequences might be responsible for the virulence of P. multocida, providing prospective candidates for further studies on the pathogenesis and the host-pathogen interactions of P. multocida.

scholarly journals First Report and Comparative Genomics Analysis of a blaOXA-244–Harbouring Escherichia coli Isolate Recovered in American Continent

2019 ◽  
Author(s):  
Deisy J Abril ◽  
Ingrid Gisell Bustos Moya ◽  
Ricaurte Alejandro Marquez-Ortiz ◽  
Diego Fernando Josa Montero ◽  
Zayda Lorena Corredor Rozo ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Comparative Genomics ◽  
Genomic Island ◽  
Genomic Analysis ◽  
American Continent ◽  
Incompatibility Group ◽  
Coli Isolate ◽  
First Report ◽  
E Coli ◽  
Comparative Genomics Analysis

The carbapenemase OXA-244 is a derivate of OXA-48, and its detection is very difficult in laboratories. Here we report the identification and genomic analysis of an Escherichia coli isolate (28Eco12) harbouring the blaOXA-244 gene identified in Colombia, South America. The 28Eco12 isolate was identified during a retrospective study and it was recovered from a patient treated in Colombia. The complete nucleotide sequence was established using the PacBio platform. A comparative genomics analysis with other blaOXA-244–harbouring Escherichia coli strains was performed. The 28Eco12 isolate belonged to sequence type (ST) 38 and its genome was composed of two molecules, a chromosome of 5,343,367 bp and a plasmid of 92,027 bp, which belonged to the incompatibility group IncY and did not harbour resistance genes. The blaOXA-244 gene was chromosomally-encoded and mobilized by an ISR1-related Tn6237 composite transposon. Notably, this transposon was inserted and located within a new genomic island. For our knowledge this is the first report of a blaOXA-244–harbouring Escherichia coli isolate in American continent.Our results suggest that the introduction of the OXA-244-producing E. coli isolate was through clonal expansion of the ST38 pandemic clone. Other isolates producing OXA-244 could be circulating silently on the American continent.

scholarly journals Comparative genomics analysis of Liberibacter species to elucidate pathogenesis and culturability

2014 ◽  
Vol 1 (1) ◽  
Author(s):  
Michael T. Leonard ◽  
Jennie R. Fagen ◽  
Connor M. McCullough ◽  
Austin G. Davis-Richardson ◽  
Michael J. Davis ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Comparative Genomics Analysis
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