Identification of human microRNA-like sequences embedded within the protein-encoding genes of the human immunodeficiency virus

Abstract

Background: MicroRNAs (miRNAs) are highly conserved, short (18-22 nts), non-coding RNA molecules that regulate gene expression by binding to the 3' untranslated regions (3'UTRs) of mRNAs. While numerous cellular microRNAs have been associated with the progression of various diseases including cancer, miRNAs associated with retroviruses have not been well characterized. Herein we report identification of microRNA-like sequences in coding regions of several HIV-1 genomes.

Results: Based on our earlier proteomics and bioinformatics studies, we have identified 8 cellular miRNAs that are predicted to bind to the mRNAs of multiple proteins that are dysregulated during HIV-infection of CD4+ T-cells in vitro. In silico analysis of the full length and mature sequences of these 8 miRNAs and comparisons with all the genomic and subgenomic sequences of HIV-1 strains in global databases revealed that the first 18/18 sequences of the mature hsa-miR-195 sequence (including the short seed sequence), matched perfectly (100%), or with one nucleotide mismatch, within the envelope (env) genes of five HIV-1 genomes from Africa. In addition, we have identified 4 other miRNA-like sequences (hsa-miR-30d, hsa-miR-30e, hsa-miR-374a and hsa-miR-424) within the env and the gag-pol encoding regions of several HIV-1 strains, albeit with reduced homology. Mapping of the miRNA-homologues of env within HIV-1 genomes localized these sequence to the functionally significant variable regions of the env glycoprotein gp120 designated V1, V2, V4 and V5.

Conclusions: We conclude that microRNA-like sequences are embedded within the protein-encoding regions of several HIV-1 genomes. Given that the V1 to V5 regions of HIV-1 envelopes contain specific, well-characterized domains that are critical for immune responses, virus neutralization and disease progression, we propose that the newly discovered miRNA-like sequences within the HIV-1 genomes may have evolved to self-regulate survival of the virus in the host by evading innate immune responses and therefore influencing persistence, replication and/or pathogenicity.

Figure 1. Phylogenetic Tree of miR-195-like sequences in different HIV clades.

This figure shows the envelope region of the HIV HXB2 genome to which the hsa-miR-195-like seqeunce maps. The area corresponding to the V5 region of HXB2 spans nucleotide positions 7603 through 7632 and is highlighted in yellow. The hsa-miR-195-like region is shown in blue. The mismatches between the HXB2 sequence and the miR-like sequence present in the African strain #GU216763 are due to the sequence variations in envelope regions of all HIV genomes.

Figure 2. Location of hsa-miR-195-like Sequence in HXB2 Env Gene.

Phylogenetic tree was constructed using the hsa-miR-195 sequence TAGCAGCACAGAAATATT for alignment similar to that used in Table 5. This tree was constructed using the treedyn program. Each leaf represents one of the 5 African microRNA-like sequences or one of the 17 reference strains from the 6 clades which were used for alignment. The five sequences highlighted in red represent the 5 African microRNA-like sequences identified in Table 2.

Figure 3. Localization of miR-like sequences in HIV envelope variable regions.

This figure shows the miR–like domains listed in Tables 2 and 3 and mapped to their corresponding positions in the HXB2 envelope gene (at nucleotide positions 6682–6694, 6765–6782, 7386–7398 and 7611–7628). The miR-424-like, miR-374a-like, miR-30d-like, and miR-195-like sequences are embedded in the hypervariable regions corresponding to V1, V2, V4 and V5 respectively and are depicted in blue. No miRNA-like sequence was detected in the V3 region of the envelope.