SIRE-1, a copia/Ty1-like retroelement from soybean, encodes a retroviral envelope-like protein

Abstract

The soybean genome hosts a family of several hundred, relatively homogeneous copies of a large, copia/Ty1-like retroelement designated SIRE-1. A copy of this element has been recovered from a Glycine max genomic library. DNA sequence analysis of two SIRE-1 subclones revealed that SIRE-1 contains a long, uninterrupted, ORF between the 3' end of the pol ORF and the 3' long terminal repeat (LTR), a region that harbors the env gene in retroviral genomes. Conceptual translation of this second ORF produces a 70-kDa protein. Computer analyses of the amino acid sequence predicted patterns of transmembrane domains, alpha-helices, and coiled coils strikingly similar to those found in mammalian retroviral envelope proteins. In addition, a 65-residue, proline-rich domain is characterized by a strong amino acid compositional bias virtually identical to that of the 60-amino acid, proline-rich neutralization domain of the feline leukemia virus surface protein. The assignment of SIRE-1 to the copia/Ty1 family was confirmed by comparison of the conceptual translation of its reverse transcriptase-like domain with those of other retroelements. This finding suggests the presence of a proretrovirus in a plant genome and is the strongest evidence to date for the existence of a retrovirus-like genome closely related to copia/Ty1 retrotransposons.

Figure 1

Organization of LTR retroelement genes. ♦, tRNA primer binding site; •, polypurine tract. ∗, Some gypsy/Ty3 group members possess an env-like ORF.

Figure 2

Organization of SIRE-1 subclones. ▧, ORF1 (pol); ▨, ORF2; ▥, 3′ LTR; , cDNA overlap; ▩, flanking ORF. H, HindIII; X, XbaI.

Figure 3

Multiple sequence alignment of the second conserved domain in rt by using pileup (32). copia/Ty1 consensus positions are highlighted. Amino acids identical to consensus are highlighted in black; amino acids similar to consensus are highlighted in gray. Opie-2 (18); Art1 (C. Herve, unpublished data, GenBank accession no. Y08010); 1731 (43); Copia (44); Tnt1 (45); Tto1 (46); Hopscotch (17); Tgmr (47); Tst1 (48); Ty1 (49); Ty3 (50); Del (51); Gypsy (21); FIV (52); HIV1 (53). A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; Y, Tyr.

Figure 4

Maximum parsimony tree based on the alignment of seven conserved domains in rt. Numbers above lines are the branch lengths; italicized numbers at nodes are bootstrap values (100 replicates). See Fig. 3 for references.

Figure 5

Conceptual translation of ORF2. Single underline, predicted transmembrane helix (41, 42); double underline, predicted coiled coil (39, 40); dotted underline, proline-rich region; bold, consensus of predicted α-helices (–38); wavy underline, possible fusion peptide. ORFs were generated as described (32). See Fig. 3 for amino acid designations.

Figure 6

Predicted and empirically deduced secondary structure features of retroviral envelope proteins (adapted from refs. and 66). ▩, Predicted α-helices; SP, signal peptide; FP, fusion peptide; CC, coiled coil; AP, anchor peptide; PCS, peptide cleavage site.

Figure 7

Output of coils program search for coiled coils (39) in SIRE-1 and selected retroviral transmembrane proteins. Similar results were obtained with ref. . Results shown are for a window of 21 amino acids. ——, SIRE-1; ⋅ ⋅ ⋅, HIV; - - -, murine leukemia virus; -··-··, influenza A virus. ∗, Numbering from the peptide cleavage site, except for SIRE-1, where residue 1 corresponds to the amino end of the putative hydrophobic fusion peptide.

Figure 8

Heptad repeats in the coiled coil region of retroviral TM proteins. MLV, murine leukemia virus; InflA: influenza virus type A. See Fig. 3 for amino acid designations.

Figure 9

Structural congruence of pol and env-like regions of SIRE-1 from a λ clone and chromosomal copies. (a) Restriction map showing HindIII (H), EcoRI (E), and BamHI (B) sites relative to rt- (▩) and env- (▧) specific probes. BamHI and EcoRI digests of clone and chromosomal (chromo) DNAs sequentially hybridized with rt (b) and ORF2 (c) probes