Human endogenous retrovirus family HERV-K(HML-5): status, evolution, and reconstruction of an ancient betaretrovirus in the human genome

J Virol. 2004 Aug;78(16):8788-98. doi: 10.1128/JVI.78.16.8788-8798.2004.

Abstract

The human genome harbors numerous distinct families of so-called human endogenous retroviruses (HERV) which are remnants of exogenous retroviruses that entered the germ line millions of years ago. We describe here the hitherto little-characterized betaretrovirus HERV-K(HML-5) family (named HERVK22 in Repbase) in greater detail. Out of 139 proviruses, only a few loci represent full-length proviruses, and many lack gag protease and/or env gene regions. We generated a consensus sequence from multiple alignment of 62 HML-5 loci that displays open reading frames for the four major retroviral proteins. Four HML-5 long terminal repeat (LTR) subfamilies were identified that are associated with monophyletic proviral bodies, implying different evolution of HML-5 LTRs and genes. Sequence analysis indicated that the proviruses formed approximately 55 million years ago. Accordingly, HML-5 proviral sequences were detected in Old World and New World primates but not in prosimians. No recent activity is associated with this HERV family. We also conclude that the HML-5 consensus sequence primer binding site is identical to methionine tRNA. Therefore, the family should be designated HERV-M. Our study provides important insights into the structure and evolution of the oldest betaretrovirus in the primate genome known to date.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Consensus Sequence
  • Endogenous Retroviruses / classification
  • Endogenous Retroviruses / genetics*
  • Evolution, Molecular*
  • Genome, Human*
  • Humans
  • Molecular Sequence Data
  • Phylogeny
  • Proviruses / genetics*
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Terminal Repeat Sequences / genetics
  • Viral Proteins / genetics

Substances

  • Viral Proteins