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Identification of Novel Abiotic Stress Proteins in Triticum aestivum Through Functional Annotation of Hypothetical Proteins

  • Saurabh Gupta
  • Yashbir Singh
  • Himansu Kumar
  • Utkarsh Raj
  • A. R. Rao
  • Pritish Kumar VaradwajEmail author
Original Research Article

Abstract

Cereal grain bread wheat (T. aestivum) is an important source of food and belongs to Poaceae family. Hypothetical proteins (HPs), i.e., proteins with unknown functions, share a substantial portion of wheat proteomes and play important roles in growth and physiology of plant system. Several functional annotations studies utilizing the protein sequences for characterization of role of individual protein in physiology of plant systems were being reported in recent past. In this study, an integrated pipeline of software/servers has been used for the identification and functional annotation of 124 unique HPs of T. aestivum considering available data in NCBI till date. All HPs were broadly annotated, out of which functions of 77 HPs were successfully assigned with high confidence level. Precisely functional annotation of remaining 47 HPs is also characterized with low confidence. Several latest versions of protein family databases, pathways information, genomics context methods and in silico tools were utilized to identify and assign function for individual HPs. Annotation result of several HPs mainly belongs to cellular protein, metabolic enzymes, binding proteins, transmembrane proteins, transcription factors and photosystem regulator proteins. Subsequently, functional analysis has revealed the role of few HPs in abiotic stress, which were further verified by phylogenetic analysis. The functionally associated proteins with each of above-mentioned abiotic stress-related proteins were identified through protein–protein interaction network analysis. The outcome of this study may be helpful for formulating general set pipeline/protocols for a better understanding of the role of HPs in physiological development of various plant systems.

Keywords

Hypothetical proteins Abiotic stress Functional annotations Phylogenetic analysis Protein–protein interaction 

Notes

Acknowledgments

Authors are thankful to the Indian Institute of Information Technology, Allahabad, for providing the required infrastructure and computational facilities to complete this work.

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflict of interest.

Funding Information

This study was not supported by any funding agency.

Human rights and animal statement

This research does not perform any experiment on human and animals. All data used in this in silico work collected from the open sources. Hence, authors declare that there is no compliance with ethical standards.

Supplementary material

12539_2016_178_MOESM1_ESM.xlsx (63 kb)
Supplementary material 1 (XLSX 63 kb)
12539_2016_178_MOESM2_ESM.docx (2 mb)
Supplementary material 2 (DOCX 2047 kb)

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Copyright information

© International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Saurabh Gupta
    • 1
  • Yashbir Singh
    • 1
  • Himansu Kumar
    • 1
  • Utkarsh Raj
    • 1
  • A. R. Rao
    • 2
  • Pritish Kumar Varadwaj
    • 1
    Email author
  1. 1.Department of BioinformaticsIndian Institute of Information Technology-AllahabadAllahabadIndia
  2. 2.Centre for Agricultural BioinformaticsICAR-Indian Agricultural Statistics Research InstituteNew DelhiIndia

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