An RNA-dependent RNA polymerase gene in bat genomes derived from an ancient negative-strand RNA virus

Abstract

Endogenous bornavirus-like L (EBLL) elements are inheritable sequences derived from ancient bornavirus L genes that encode a viral RNA-dependent RNA polymerase (RdRp) in many eukaryotic genomes. Here, we demonstrate that bats of the genus Eptesicus have preserved for more than 11.8 million years an EBLL element named eEBLL-1, which has an intact open reading frame of 1,718 codons. The eEBLL-1 coding sequence revealed that functional motifs essential for mononegaviral RdRp activity are well conserved in the EBLL-1 genes. Genetic analyses showed that natural selection operated on eEBLL-1 during the evolution of Eptesicus. Notably, we detected efficient transcription of eEBLL-1 in tissues from Eptesicus bats. To the best of our knowledge, this study is the first report showing that the eukaryotic genome has gained a riboviral polymerase gene from an ancient virus that has the potential to encode a functional RdRp.

Establishment and characterization of a cell line derived from <i>Eptesicus nilssonii</i>

“…The cells are robust and easy to passage. In addition, eEBLL-1 is present in the genome of HAMOI-EnK cells, which retains a large and intact ORF as previously reported [6]. Furthermore, we demonstrated the presence of sense-oriented eEBLL-1 transcripts in the cells.…”

“…Although we demonstrated that eEBLL-1 is present in the genome of E. nilssonii in the previous study [6], eEBLL-1 might have been lost during long-term passage. Thus, we performed genomic PCR to detect eEBLL-1 in the genome (PCR conditions are available in Supporting information).…”

“…The sequencing revealed that eEBLL-1 in HAMOI-EnK cells retains an intact ORF comprising 1,718 codons and all of the functional motifs in mononegavirus RdRps (see LC122511 in GenBank) that were reported in the previous study [6]. The nucleotide sequence of the putative ORF of eEBLL-1 in HAMOI-EnK cells showed 99.8% (5,146 of 5,157 nucleotides) identity to that of previously reported eEBLL-1 sequence in E. nilssonii (AB921210) [6]. Among the 11 nucleotide differences, 7 are synonymous, and 4 are non-synonymous substitutions.…”

“…Although non-retroviral viruses do not possess reverse transcriptase and/or integrase, recent studies have revealed that non-retroviral EVEs are also present in the genomes of mammals [1, 5, 7, 8, 11]. Notably, several non-retroviral EVEs contain relatively long open reading frames (ORFs) and have evolved under natural selection, suggesting that such EVEs encode functional proteins in the host cells [2, 6, 12]. Indeed, an endogenous bornavirus-like nucleoprotein (EBLN) element in Ictidomys tridecemlineatus showed anti-bornavirus activity in vitro [3].…”

“…Taylor et al [12] reported that an EFL element descended from filoviral VP35 gene has evolved under natural selection in Myotis bats. We also showed that an EBLL in bats of the genus Eptesicus (designated as eEBLL-1), derived from the L gene (encoding RNA-dependent RNA polymerase: RdRp) of an ancient bornavirus, has maintained a large and intact ORF for more than 11.8 million years and evolved under purifying selection in bats of the genus Eptesicus [6]. However, the function of eEBLL-1 is still unclear due to lack of proper research tools.…”