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    Detection of a Usp-like gene in Calotropis procera plant from the de novo assembled genome contigs of the high-throughput sequencing dataset

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    Type
    Article
    Authors
    Shokry, Ahmed M.
    Al-Karim, Saleh
    Ramadan, Ahmed M Ali
    Gadallah, Nour
    Al-Attas, Sanaa G.
    Sabir, Jamal Sabir M
    Hassan, Sabah Mohammed
    Madkour, Loutfy H.
    Bressan, Ray Anthony
    Mahfouz, Magdy M. cc
    Bahieldin, Ahmed M.
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Desert Agriculture Initiative
    Plant Science
    Plant Science Program
    Date
    2014-02
    Permanent link to this record
    http://hdl.handle.net/10754/563379
    
    Metadata
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    Abstract
    The wild plant species Calotropis procera (C. procera) has many potential applications and beneficial uses in medicine, industry and ornamental field. It also represents an excellent source of genes for drought and salt tolerance. Genes encoding proteins that contain the conserved universal stress protein (USP) domain are known to provide organisms like bacteria, archaea, fungi, protozoa and plants with the ability to respond to a plethora of environmental stresses. However, information on the possible occurrence of Usp in C. procera is not available. In this study, we uncovered and characterized a one-class A Usp-like (UspA-like, NCBI accession No. KC954274) gene in this medicinal plant from the de novo assembled genome contigs of the high-throughput sequencing dataset. A number of GenBank accessions for Usp sequences were blasted with the recovered de novo assembled contigs. Homology modelling of the deduced amino acids (NCBI accession No. AGT02387) was further carried out using Swiss-Model, accessible via the EXPASY. Superimposition of C. procera USPA-like full sequence model on Thermus thermophilus USP UniProt protein (PDB accession No. Q5SJV7) was constructed using RasMol and Deep-View programs. The functional domains of the novel USPA-like amino acids sequence were identified from the NCBI conserved domain database (CDD) that provide insights into sequence structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAM). © 2014 Académie des sciences.
    Citation
    Shokry, A. M., Al-Karim, S., Ramadan, A., Gadallah, N., Al Attas, S. G., Sabir, J. S. M., … Bahieldin, A. (2014). Detection of a Usp-like gene in Calotropis procera plant from the de novo assembled genome contigs of the high-throughput sequencing dataset. Comptes Rendus Biologies, 337(2), 86–94. doi:10.1016/j.crvi.2013.12.008
    Sponsors
    This project was funded by the Deanship of Scientific Research (DSR), King Abdulaziz University, Jeddah, under Grant No. 1432-3-15/HiCi. The authors, therefore, acknowledge with thanks DSR technical and financial support.
    Publisher
    Elsevier BV
    Journal
    Comptes Rendus Biologies
    DOI
    10.1016/j.crvi.2013.12.008
    PubMed ID
    24581802
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.crvi.2013.12.008
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Plant Science Program; Desert Agriculture Initiative

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