Abstract
Endogenous Borna-like nucleoprotein (EBLNs) elements were recently discovered as non-retroviral RNA virus elements derived from bornavirus in the genomes of various animals. Most of EBLNs appeared to be defective, but some of primate EBLN-1 to -4, which appeared to be originated from four independent integrations of bornavirus nucleoprotein (N) gene, have retained an open reading frame (ORF) for more than 40 million years. It was therefore possible that primate EBLNs have encoded functional proteins during evolution. To examine this possibility, natural selection operating on all ORFs of primate EBLN-1 to -4 was examined by comparing the rates of synonymous and nonsynonymous substitutions. The expected number of premature termination codons in EBLN-1 generated after the divergence of Old World and New World monkeys under the selective neutrality was also examined by the Monte Carlo simulation. As a result, natural selection was not identified for the entire region as well as parts of ORFs in the pairwise analysis of primate EBLN-1 to -4 and for any branch of the phylogenetic trees for EBLN-1 to -4 after the divergence of Old World and New World monkeys. Computer simulation also indicated that the absence of premature termination codon in the present-day EBLN-1 does not necessarily support the maintenance of function after the divergence of Old World and New World monkeys. These results suggest that EBLNs have not generally encoded functional proteins after the divergence of Old World and New World monkeys.
Highlights
Endogenous Borna-like nucleoprotein (EBLN) elements were recently discovered as non-retroviral RNA virus elements in the genomes of various animals, including primates, rodents, chiropterans, afrotherians, and fishes [1,2,3]
Macaque EBLN-1 and marmoset EBLN-4 contained sequences that were derived from Alu repeat elements (Figure 1), which were characterized as AluMacYa3, belonging to the macaque-specific Alu subfamily [9], and as AluSp or Alu2, respectively
In order to investigate the functionality of primate EBLNs during evolution, a total of 100 open reading frame (ORF) with .50 codons was identified in the orthologous regions of EBLN-1 to -4 in the primate genomes (Figure S1, Table S1)
Summary
Endogenous Borna-like nucleoprotein (EBLN) elements were recently discovered as non-retroviral RNA virus elements in the genomes of various animals, including primates, rodents, chiropterans, afrotherians, and fishes [1,2,3]. Each copy of EBLN-1 to -4 apparently started with the transcription start site of bornavirus N gene and ended with poly-A, and was flanked by the target site duplication, which was specific in length and sequence to each copy These observations indicated that primate EBLN-1 to -4 were originated from four independent integrations of reverse-transcribed mRNA for bornavirus N gene by LINE before the divergence of Old World and New World monkeys (,44.2 million years ago (MYA) in TIMETREE [6]) [1,2]. EBLN1 of human (367 codons), chimpanzee (368 codons), and gorilla (368 codons) encoded an open reading frame (ORF), which was almost equivalent in length to the N gene of bornavirus (371–374 codons), indicating that the ORF has been maintained for more than 40 million years along the evolutionary lineage leading to these organisms This phenomenon was considered unlikely to be observed in the absence of purifying selection on EBLN-1 [1,3]. These observations raised a possibility that primate EBLNs have been functional in the host
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