Table 3 Examples of protein domains found in LTR REs predicted from the genome of Silurana tropicalis which might play a role in gene regulation and transcriptional networking

CHROMO (Chromatin organization modifier)

pfam00385

This domain was exclusively found within Amn-san elements. Circa 80% of these elements within the Silurana genome encode for a chromo domain.

The chromo domain is about 40–50 amino acids long. It is contained in various proteins involved in chromatin remodeling and the regulation of gene expression in eukaryotes during development.

[56–58]

PNMA (Para-neoplastic antigen MA)

pfam14893

Found so far in about 30% of Cer elements and in about 16% of Gmr elements.

This protein domain has so far only been studied in mammals, where it has been associated with neurological disorders.

[59, 60]

Because of the homology between PNMA proteins and an apoptosis inducing protein (MOAP1), the involvement of PNMA proteins in apoptosis is hypothesized.

SCAN

pfam02023 pfam00096

This domain was found in over 50% of Gmr elements only.

The SCAN domain family of Zinc finger transcription factors, they are thought to be implicated in regulating genes involved in lipid metabolism, cell survival, and differentiation.

[61]

Exo/endo phosphatase

pfam03372 pfam14529

Found in about 12% of Mtanga elements.

The exo-/endonuclease phosphatase family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signaling.

[62, 63]

Zinc Fingers Zf-H2C2_2 (Zinc-finger double domain)

Zf-CCHC (Zinc knuckle)

pfam13465

About 40% of SnRVs contained a Zinc-finger double domain; about 20% of XEN1 elements contained a Zinc knuckle.

Zinc finger (Znf) domains are relatively small but very diverse protein motifs which can target specific molecules. Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organization, epithelial development, cell adhesion, protein folding, chromatin remodeling, and Zinc sensing, to name but a few.

[64, 65]

pfam00098

A Zinc knuckle is a Zinc binding motif of the general structure CX2CX4HX4C where X can be any amino acid. The motifs mostly originate from retroviral gag proteins (nucleocapsid). Zinc knuckles are involved in eukaryotic gene regulation.

UBN2 gag-polypeptide of LTR copia-type

pfam14223

Found in Copia-type elements, in about 30% of Mtanga elements and in about 80% of Hydra1.1 elements.

Ubinucleins are members of a protein family that contain a conserved HIRA binding domain which interacts with the N-terminal WD repeats of HIRA/Hir proteins. UBN1 and UBN2 are believed to be the orthologs of Hpc2p, a subunit of a nucleosome assembly complex in budding yeast (HIR), involved in regulation of histone gene transcription.

[66]