Parts of them are used as epitope tags

Epitope tags, i.e. short peptide tags are commonly used, versatile, and convenient tools for multiple capture and detection applications including immunofluorescence, immunoprecipitation, affinity purification, and Western blotting.

Among those epitope tags, several tags are from virus protein origin, because they likely have unique sequences. Hence, they might have less issues with cross reactivity of antibodies potentially detecting host cell protein background.

Below, an overview of peptide tags that are of virus origin is shown:

• E2 tag / E2 epitope tag

  Applications: Detection and purification
  Sequence: SSTSSDFRDR
  Size: 10 AA, 1.2 kDa
  Tag location: N-, C-terminal or internal
  Origin: transactivator protein E2 of bovine papilloma-virus type-1
  
  

• HA tag

  Applications: Purification and detection
  Sequence: YPYDVPDYA
  Size: 9 AA, 1.1 kDa
  Tag location: N-, C-terminal or internal
  Origin: amino acids 98–106 of the major surface protein glycoprotein hemagglutinin of influenza virus
  Comment: Not suitable for detection or purification of proteins from apoptotic cells because it is cleaved by Caspase-3 / Caspase-7
  
  

• HSV tag

  Applications: Purification
  Sequence: QPELAPEDPED
  Size: 11 AA, 1.2 kDa
  Tag location: C-terminal
  Origin: aa 290–300 of glycoprotein D, a major surface protein of herpes simplex virus type 1 (HSV-1)
  
  

• T7 tag

  Applications: Purification and increased expression
  Sequence: MASMTGGQQMG
  Size: 11 AA, 1.2 kDa
  Tag location: N-, C-terminal or internal
  Origin: N-terminal 11 residues of the major capsid protein gp 10 of T7 phage
  
  

• VSV-G-tag

  Applications: Detection and purification
  Sequence: YTDIEMNRLGK
  Size: 11 AA, 1.3 kDa
  Tag location: C-terminal
  Origin: C terminal aa of virus envelope glycoprotein of vesicular stomatitis virus G
  
  

• V5-tag

  Sequence: GKPIPNPLLGLDST
  Size: 14 AA, 1.4 kDa
  Tag location: N-, C-terminal or internal
  Origin: P and V proteins of Simian virus 5 (SV5) of the Rubulavirus genus in the Paramyxoviridae family

References

Kimple, M.E. et al (2013): Overview of Affinity Tags for Protein Purification
Curr Protoc Protein Sci. 2013; 73: Unit–9.9, DOI 10.1002/0471140864.ps0909s73
and references therein

Boriana Marintcheva, B. (2018) in Harnessing the Power of Viruses, chapter: Viral Tools for Protein Expression and Purification, Academic Press, DOI 10.1016/C2015-0-05654-4

Terpe, K. (2003): Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems, Appl Microbiol Biotechnol. 60:523–533, DOI 10.1007/s00253-002-1158-6

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