Assessment of intercontinents mutation hotspots and conserved domains within SARS-CoV-2 genome

Abstract Background Since outbreak in December 2019, the highly infectious and pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over a million deaths globally. With increasing burden, the novel coronavirus has posed a dire threat to public health, social interaction, and global economy. Mutations in the SARS-CoV-2 genome are moderately evolving which might have contributed to its genome variability, transmission, replication efficiency, and virulence in different regions of the world. Results The present study elucidated the mutational landscape in the SARS-CoV-2 genome among the African populace, which may have contributed to the virulence, spread, and pathogenicity observed in the region. A total of 3045 SARS-CoV-2 complete protein sequences with the reference viral sequence (EPI_ISL_402124) were mined and analyzed. SARS-CoV-2 ORF1ab, spike, ORF3, ORF8, and nucleocapsid proteins were observed as mutational hotspots in the African population and may be of keen interest in understanding the viral host relationship, while there is conservation in the ORF6, ORF7a, ORF7b, ORF10, envelope, and membrane proteins. Conclusions The accumulation of moderate mutations (though slowly), in the SARS-CoV-2 genome as seen in this present study, could be a promising strategy to develop antiviral drugs or vaccines. These antiviral interventions should target viral conserved domains and host cellular proteins and/or receptors involved in viral invasion and replication to avoid a new viral wave due to drug resistance and vaccine evasion.

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Recombineering Hunchback identifies two conserved domains required to maintain neuroblast competence and specify early-born neuronal identity

Development ◽

10.1242/dev.048678 ◽

2010 ◽

Vol 137 (9) ◽

pp. 1421-1430 ◽

Cited By ~ 28

Author(s):

K. D. Tran ◽

M. R. Miller ◽

C. Q. Doe

Keyword(s):

Conserved Domains ◽

Neuronal Identity

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Thebric à braclocus consists of two paralogous genes encoding BTB/POZ domain proteins and acts as a homeotic and morphogenetic regulator of imaginal development inDrosophila

Development ◽

10.1242/dev.129.10.2419 ◽

2002 ◽

Vol 129 (10) ◽

pp. 2419-2433 ◽

Cited By ~ 6

Author(s):

Jean-Louis Couderc ◽

Dorothea Godt ◽

Susan Zollman ◽

Jiong Chen ◽

Michelle Li ◽

...

Keyword(s):

Tissue Distribution ◽

Nuclear Protein ◽

Drosophila Species ◽

Sexually Dimorphic ◽

Conserved Domains ◽

Gene Dose ◽

Highly Sensitive ◽

Genes Encoding ◽

Redundant Functions ◽

Related Morphology

The bric à brac (bab) locus acts as a homeotic and morphogenetic regulator in the development of ovaries, appendages and the abdomen. It consists of two structurally and functionally related genes, bab1 and bab2, each of which encodes a single nuclear protein. Bab1 and Bab2 have two conserved domains in common, a BTB/POZ domain and a Psq domain, a motif that characterizes a subfamily of BTB/POZ domain proteins in Drosophila. The tissue distribution of Bab1 and Bab2 overlaps, with Bab1 being expressed in a subpattern of Bab2. Analysis of a series of mutations indicates that the two bab genes have synergistic, distinct and redundant functions during imaginal development. Interestingly, several reproduction-related traits that are sexually dimorphic or show diversity among Drosophila species are highly sensitive to changes in the bab gene dose, suggesting that alterations in bab activity may contribute to evolutionary modification of sex-related morphology.

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Purification of arginase from Aspergillus nidulans.

Acta Biochimica Polonica ◽

10.18388/abp.1994_4700 ◽

1994 ◽

Vol 41 (4) ◽

pp. 467-471 ◽

Cited By ~ 4

Author(s):

A Dzikowska ◽

J P Le Caer ◽

P Jonczyk ◽

P Wëgleński

Keyword(s):

Saccharomyces Cerevisiae ◽

Neurospora Crassa ◽

Molecular Mass ◽

Nitrogen Source ◽

Aspergillus Nidulans ◽

Sole Nitrogen Source ◽

Mass Ratio ◽

Conserved Domains ◽

Native Molecular Mass ◽

High Degree

Arginase (EC 3.5.3.1) of Aspergillus nidulans, the enzyme which enables the fungus to use arginine as the sole nitrogen source was purified to homogeneity. Molecular mass of the purified arginase subunit is 40 kDa and is similar to that reported for the Neurospora crassa (38.3 kDa) and Saccharomyces cerevisiae (39 kDa) enzymes. The native molecular mass of arginase is 125 kDa. The subunit/native molecular mass ratio suggests a trimeric form of the protein. The arginase protein was cleaved and partially sequenced. Two out of the six polypeptides sequenced show a high degree of homology to conserved domains in arginases from other species.

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Identification of Conserved Domains inSalmonella muenchenFlagellin That Are Essential for Its Ability to Activate TLR5 and to Induce an Inflammatory Responsein Vitro

Journal of Biological Chemistry ◽

10.1074/jbc.m307759200 ◽

2003 ◽

Vol 279 (7) ◽

pp. 5667-5675 ◽

Cited By ~ 84

Author(s):

Kanneganti G. K. Murthy ◽

Amitabha Deb ◽

Sunali Goonesekera ◽

Csaba Szabó ◽

Andrew L. Salzman

Keyword(s):

Conserved Domains

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Using the Gibbs Motif Sampler to Find Conserved Domains in DNA and Protein Sequences

Current Protocols in Bioinformatics ◽

10.1002/0471250953.bi0208s10 ◽

2005 ◽

Vol 10 (1) ◽

Cited By ~ 12

Author(s):

William Thompson ◽

Lee Ann McCue ◽

Charles E. Lawrence

Keyword(s):

Protein Sequences ◽

Conserved Domains

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Genome-Wide Identification and Functional Analysis of Chitinase Gene Family in Grape

10.21203/rs.2.22693/v1 ◽

2020 ◽

Author(s):

Ting Zheng ◽

Kekun Zhang ◽

Xudong Zhu ◽

Songtao Jiu ◽

Tianyu Dong ◽

...

Keyword(s):

Gene Family ◽

Fungal Pathogens ◽

Expression Patterns ◽

Hydrolytic Enzymes ◽

Bimolecular Fluorescence Complementation ◽

Microarray Data Analysis ◽

Growth Stages ◽

Transcriptional Level ◽

Fungal Cell ◽

Conserved Domains

Abstract Background: Chitinases, the important resistance-related proteins, are crucial hydrolytic enzymes, which attack fungal pathogens by catalyzing the fungal cell wall degradation. As a large gene family, the VvChis have not been systematically analyzed and effectively investigated in grape. Results: In this study, we identified 42 VvChis in grape by searching the conserved domains, and divided them into A, B, C, D and E groups according to pylogenetic relationships, gene structure and conserved domains analysis. Quantitative real-time PCR (qRT-PCR) and publicly microarray data analysis revealed distinct temporal and spatial expression patterns of VvChis in different tissues at various growth stages. The transcriptional level of most genes was high in the root of ‘Koyho’ and ‘Summer Black’. Combining cis-elements in the promoter, GO and KEGG analysis, and prediction of interaction proteins, we revealed the function of Chitinase. After the pathogen infecting the leaves and berries of grape, the expression levels of VvChis in A, B and E groups showed a significant upward trend, of which VvChi5, VvChi25, VvChi11 (leaf) and VvChi16 (fruit) were the most up-regulated. The interaction between Chi-17 and Metallothionein (MTL) was confirmed by yeast two-hybrid system and bimolecular fluorescence complementation (BiFC). In addition, VvChis in GH18 family were up-regulated under MeJA and ETH treatment, in particular to 500 mg·L -1 ETH、50 μmol·L -1 MeJA; The induction of VvChis by low temperature was more significant than that of high temperature; The expression of VvChis was positively correlated with the concentration of NaCl treatment. Conclusion: This study clarified the member composition and expression pattern of VvChi family in grape, initially explored the disease resistance function of VvChi, and analyzed the response of VvChis to hormones (MeJA and ETH) and environmental stress (temperature and NaCl) signals was analyzed, which laid a foundation for constructing the functional regulation network of VvChi in grapes.

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Comparative characterization of PCDH19 missense and truncating variants in PCDH19-related epilepsy

Journal of Human Genetics ◽

10.1038/s10038-020-00880-z ◽

2020 ◽

Author(s):

Mami Shibata ◽

Atsushi Ishii ◽

Ayako Goto ◽

Shinichi Hirose

Keyword(s):

Distribution Function ◽

Intellectual Disability ◽

Cumulative Distribution Function ◽

Clinical Phenotype ◽

Cytoplasmic Domain ◽

Cumulative Distribution ◽

Clinical Implications ◽

Healthy Individuals ◽

Conserved Domains

AbstractMissense and truncating variants in protocadherin 19 (PCDH19) cause PCDH19-related epilepsy. In this study, we aimed to investigate variations in distributional characteristics and the clinical implications of variant type in PCDH19-related epilepsy. We comprehensively collected PCDH19 missense and truncating variants from the literature and by sequencing six exons and intron–exon boundaries of PCDH19 in our cohort. We investigated the distribution of each type of variant using the cumulative distribution function and tested for associations between variant types and phenotypes. The distribution of missense variants in patients was clearly different from that of healthy individuals and was uniform throughout the extracellular cadherin (EC) domain, which consisted of six highly conserved domains. Truncating variants showed two types of distributions: (1) located from EC domain 1 to EC domain 4, and (2) located from EC domain 5 to the cytoplasmic domain. Furthermore, we also found that later onset seizures and milder intellectual disability occurred in patients with truncating variants located from EC domain 5 to the cytoplasmic domain compared with those of patients with other variants. Our findings provide the first evidence of two types of truncating variants in the PCDH19 gene with regard to distribution and the resulting clinical phenotype.

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