Ty1-copia retrotransposons Ty1-
copia retrotransposons are abundant in species ranging from single-cell
algae to
bryophytes,
gymnosperms, and
angiosperms. They encode four protein domains in the following order:
protease,
integrase,
reverse transcriptase, and
ribonuclease H. At least two classification systems exist for the subdivision of Ty1-
copia retrotransposons into five lineages:
Sireviruses/Maximus, Oryco/Ivana, Retrofit/Ale, TORK (subdivided in Angela/Sto, TAR/Fourf, GMR/Tork), and Bianca.
Sireviruses/Maximus retrotransposons contain an additional putative envelope gene. This lineage is named for the founder element SIRE1 in the
Glycine max genome, and was later described in many species such as
Zea mays,
Arabidopsis thaliana,
Beta vulgaris, and
Pinus pinaster. Plant
Sireviruses of many sequenced plant genomes are summarized at the MASIVEdb
Sirevirus database.
Ty3-retrotransposons (formally gypsy) Ty3-retrotransposons are widely distributed in the plant kingdom, including both
gymnosperms and
angiosperms. They encode at least four protein domains in the order:
protease,
reverse transcriptase,
ribonuclease H, and
integrase. Based on structure, presence/absence of specific protein domains, and conserved protein sequence motifs, they can be subdivided into several lineages:
Errantiviruses contain an additional defective envelope ORF with similarities to the retroviral envelope gene. First described as Athila-elements in
Arabidopsis thaliana, they have been later identified in many species, such as
Glycine max and
Beta vulgaris.
Chromoviruses contain an additional chromodomain (chromatin organization modifier domain) at the C-terminus of their integrase protein. They are widespread in plants and fungi, probably retaining protein domains during evolution of these two kingdoms. It is thought that the chromodomain directs retrotransposon integration to specific target sites. According to sequence and structure of the chromodomain, chromoviruses are subdivided into the four clades CRM, Tekay, Reina and Galadriel. Chromoviruses from each clade show distinctive integration patterns, e.g. into centromeres or into the rRNA genes. Ogre-elements are gigantic Ty3-retrotransposons reaching lengths up to 25 kb. Ogre elements have been first described in
Pisum sativum.
Metaviruses describe conventional Ty3-
gypsy retrotransposons that do not contain additional domains or ORFs. The Sushi family of Ty3 long terminal repeat retrotransposons were first identified in teleost fish and Sushi-like neogenes were subsequently identified in mammals. Mammalian retrotransposon-derived transcripts (MARTs) cannot transpose but have retained open reading frames, demonstrate high levels of evolutionary conservation and are subject to selective pressures, which suggests some have become neofunctionalized genes with new cellular functions.
Endogenous retroviruses (ERV) Although
retroviruses are often classified separately, they share many features with LTR retrotransposons. A major difference with Ty1-
copia and Ty3-
gypsy retrotransposons is that retroviruses have an envelope protein (ENV). A retrovirus can be transformed into an LTR retrotransposon through inactivation or deletion of the domains that enable extracellular mobility. If such a retrovirus infects and subsequently inserts itself in the genome in germ line cells, it may become transmitted vertically and become an
endogenous retrovirus. Nevertheless, TRIMs can be able to retrotranspose, as they may rely on the coding domains of autonomous Ty1-
copia or Ty3-
gypsy retrotransposons. Among the TRIMs, the Cassandra family plays an exceptional role, as the family is unusually wide-spread among higher plants. In contrast to all other characterized TRIMs, Cassandra elements harbor a 5S rRNA promoter in their LTR sequence. Due to their short overall length and the relatively high contribution of the flanking LTRs, TRIMs are prone to re-arrangements by recombination. ==References==