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

Handle URI:
http://hdl.handle.net/10754/563379
Title:
Detection of a Usp-like gene in Calotropis procera plant from the de novo assembled genome contigs of the high-throughput sequencing dataset
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. ( 0000-0002-0616-6365 ) ; Bahieldin, Ahmed M.
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Plant Science Program; Desert Agriculture Initiative; Bioscience Program
Publisher:
Elsevier BV
Journal:
Comptes Rendus Biologies
Issue Date:
Feb-2014
DOI:
10.1016/j.crvi.2013.12.008
PubMed ID:
24581802
Type:
Article
ISSN:
16310691
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.
Appears in Collections:
Articles; Bioscience Program; Plant Science Program; Desert Agriculture Initiative; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorShokry, Ahmed M.en
dc.contributor.authorAl-Karim, Salehen
dc.contributor.authorRamadan, Ahmed M Alien
dc.contributor.authorGadallah, Nouren
dc.contributor.authorAl-Attas, Sanaa G.en
dc.contributor.authorSabir, Jamal Sabir Men
dc.contributor.authorHassan, Sabah Mohammeden
dc.contributor.authorMadkour, Loutfy H.en
dc.contributor.authorBressan, Ray Anthonyen
dc.contributor.authorMahfouz, Magdy M.en
dc.contributor.authorBahieldin, Ahmed M.en
dc.date.accessioned2015-08-03T11:47:06Zen
dc.date.available2015-08-03T11:47:06Zen
dc.date.issued2014-02en
dc.identifier.issn16310691en
dc.identifier.pmid24581802en
dc.identifier.doi10.1016/j.crvi.2013.12.008en
dc.identifier.urihttp://hdl.handle.net/10754/563379en
dc.description.abstractThe 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.en
dc.description.sponsorshipThis 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.en
dc.publisherElsevier BVen
dc.subject3D Modelingen
dc.subjectAbiotic stressen
dc.subjectBLASTen
dc.subjectGTP-EFTUen
dc.titleDetection of a Usp-like gene in Calotropis procera plant from the de novo assembled genome contigs of the high-throughput sequencing dataseten
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentPlant Science Programen
dc.contributor.departmentDesert Agriculture Initiativeen
dc.contributor.departmentBioscience Programen
dc.identifier.journalComptes Rendus Biologiesen
dc.contributor.institutionDepartment of Biological Sciences, Faculty of Science, King Abdulaziz University (KAU), P.O. Box 80141, Jeddah 21589, Saudi Arabiaen
dc.contributor.institutionAgricultural Genetic Engineering Research Institute (AGERI), Agriculture Research Center (ARC), Giza, Egypten
dc.contributor.institutionGenetics and Cytology Department, Genetic Engineering and Biotechnology Division, National Research Center, Dokki, Egypten
dc.contributor.institutionDepartment of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypten
dc.contributor.institutionArid Lands Agricultural Research Institute, Ain Shams University, Cairo, Egypten
dc.contributor.institutionSchool of Agriculture, Purdue University, West Lafayette, IN, United Statesen
kaust.authorMahfouz, Magdy M.en

Related articles on PubMed

All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.