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Potential SECIS elements in HIV-1 strain HXB2

L Grate1

  • 1Department of Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, USA. leslie@cse.ucsc.edu

Journal of Acquired Immune Deficiency Syndromes and Human Retrovirology : Official Publication of the International Retrovirology Association
|April 30, 1998
PubMed
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Researchers searched the HIV genome for a specific RNA structure, the selenocysteine insertion sequence (SECIS) element, which directs selenocysteine (Sec) incorporation into proteins. A potential SECIS element was identified in HIV-1, suggesting a mechanism for Sec incorporation.

Area of Science:

  • Molecular Biology
  • Virology
  • Bioinformatics

Background:

  • Human Immunodeficiency Virus type 1 (HIV-1) is proposed to encode selenocysteine (Sec), an amino acid incorporated via specific mRNA structures.
  • The selenocysteine insertion sequence (SECIS) element is a known RNA motif that facilitates Sec incorporation during translation.
  • The SECIS element has not been previously identified in the HIV genome using biological or computational methods.

Purpose of the Study:

  • To computationally identify potential SECIS element locations within the HIV-1 HXB2 genome.
  • To assess if identified SECIS elements are positioned to direct Sec incorporation.

Main Methods:

  • Utilized computer-based sequence analysis to search the HIV-1 HXB2 genome.
  • Applied the current model of the SECIS element for sequence matching.

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Main Results:

  • Identified a highly conserved region within the HIV-1 HXB2 genome that closely matches the SECIS element model.
  • This potential SECIS element is located at the junction of the env and nef genes.
  • The identified location is theoretically capable of directing Sec incorporation into a protein.

Conclusions:

  • A potential SECIS element exists in the HIV-1 HXB2 genome, located between the env and nef genes.
  • This finding provides a computational basis for the proposed existence of selenocysteine in HIV-1 proteins.
  • Further biological studies are warranted to confirm the presence and function of this SECIS element and Sec incorporation in HIV-1.