Two Virus-Induced MicroRNAs Known Only from Teleost Fishes Are Orthologues of MicroRNAs Involved in Cell Cycle Control in Humans

Abstract

MicroRNAs (miRNAs) are ~22 base pair-long non-coding RNAs which regulate gene expression in the cytoplasm of eukaryotic cells by binding to specific target regions in mRNAs to mediate transcriptional blocking or mRNA cleavage. Through their fundamental roles in cellular pathways, gene regulation mediated by miRNAs has been shown to be involved in almost all biological phenomena, including development, metabolism, cell cycle, tumor formation, and host-pathogen interactions. To address the latter in a primitive vertebrate host, we here used an array platform to analyze the miRNA response in rainbow trout (Oncorhynchus mykiss) following inoculation with the virulent fish rhabdovirus Viral hemorrhagic septicaemia virus. Two clustered miRNAs, miR-462 and miR-731 (herein referred to as miR-462 cluster), described only in teleost fishes, were found to be strongly upregulated, indicating their involvement in fish-virus interactions. We searched for homologues of the two teleost miRNAs in other vertebrate species and investigated whether findings related to ours have been reported for these homologues. Gene synteny analysis along with gene sequence conservation suggested that the teleost fish miR-462 and miR-731 had evolved from the ancestral miR-191 and miR-425 (herein called miR-191 cluster), respectively. Whereas the miR-462 cluster locus is found between two protein-coding genes (intergenic) in teleost fish genomes, the miR-191 cluster locus is found within an intron of a protein-coding gene (intragenic) in the human genome. Interferon (IFN)-inducible and immune-related promoter elements found upstream of the teleost miR-462 cluster locus suggested roles in immune responses to viral pathogens in fish, while in humans, the miR-191 cluster functionally associated with cell cycle regulation. Stimulation of fish cell cultures with the IFN inducer poly I:C accordingly upregulated the expression of miR-462 and miR-731, while no stimulatory effect on miR-191 and miR-425 expression was observed in human cell lines. Despite high sequence conservation, evolution has thus resulted in different regulation and presumably also different functional roles of these orthologous miRNA clusters in different vertebrate lineages.

Discovery of microRNAs associated with the antiviral immune response of Atlantic cod macrophages

“…Similar motifs were identified in the promoter region of the miRNA-462/731 cluster in rainbow trout (Schyth et al, 2015) and Atlantic salmon , and the potential conservation among species suggests that these motifs may be associated with immune responsiveness of the miRNA-462/731 cluster. These miRNAs also showed a time-dependent upregulation in response to injection of IFNG-expressing plasmids (Bela-ong et al, 2015).…”

“…In Atlantic cod (Andreassen et al, 2016), these miRNAs were found to be clustered in the genome and potentially co-transcribed as in other teleost species, i.e. rainbow trout (Oncorhynchus mykiss) (Schyth et al, 2015), Atlantic salmon and zebrafish (Danio rerio) (Thatcher et al, 2008). These two teleost-specific miRNAs have been reported as virus-and bacteria-responsive in several teleost species .…”

“…in Japanese flounder challenged with megalocytivirus infection (Zhang et al, 2014), rainbow trout challenged with VHSV, RTL-W1 (i.e. rainbow trout liver cell line) stimulated with pIC for 48 h (Schyth et al, 2015) and Atlantic salmon challenged with salmonid alphavirus (SAV) . In addition, these miRNAs were up-regulated in the muscle of VHSV-vaccinated rainbow trout in a timedependent manner, i.e.…”

Never Ending Analysis of a Century Old Evolutionary Debate: “Unringing” the Urmetazoon Bell

“…Nevertheless, microRNAs are not the near-perfect markers for which they are sometimes taken. In some cases they have diverged beyond the point where homology is readily recognized (Schyth et al, 2015). Several clades, in particular Urochordata (Fu et al, 2008) and Platyhelminthes (Fromm et al, 2013), have undergone a massive restructuring of their microRNA repertoire.…”

Pathogenicity-associated protein domains: The fiercely-conserved evolutionary signatures

“…DALR is an anticodon binding domain of tRNA synthetase (arginyl/cysteinyl), made of α helices. In human, this domain-containing protein DALRD3 interacts with protein WDR6 (WD Repeat Domain 6) and C3orf60 (chromosome 3 open reading frame 60), involved in autophagy and protein assembly, respectively (Grinchuk et al, 2010;Schyth et al, 2015). DALR_1 domain detected in pollen might have role in manipulating gene expression.…”