Identification of Essential cis Element in 5'UTR of Nef mRNA for Nef Translation

Abstract

Nef is one of the accessory proteins of the human immunodeficiency virus type 1 (HIV-1). Nef is translated from multiple-spliced mRNAs transcribed from the viral genome, whose mRNAs have a relatively long 5' untranslated region (5'UTR). Here, we identified a cis element in the 5'UTR of Nef mRNA essential for efficient Nef translation, which was named the Nef-translation essential region (NER). Mutants with a deleted NER in the 5'UTR of the HIV-1 NL4-3 strain showed an almost undetectable Nef expression owing to a low Nef translation efficiency. The NER of the NL4-3 strain was predicted to form putative stem loops. Although the 5'UTR showed significant but relatively low internal ribosome entry site (IRES) activity, the mechanism of 5'cap-dependent translation mainly contributed to the Nef translation from its Nef mRNA. Altogether, it was clarified that not only the 5' cap but also the NER in the 5'UTR is an essential cis element for efficient Nef translation, which is not a typical 5'-cap-dependent mechanism, and that there must be an as yet unknown mechanism using the NER for efficient Nef translation.

HIV UTR, LTR, and Epigenetic Immunity

“…Mutations in the sequence of 5’UTR disrupt the structure of this region and affect the transcription of HIV RNA, reverse transcription, and packaging, as well as the fundamental role of mRNA in protein translation, i.e., the viral protein production. Note that starting at transcription, more than 23 copies of HIV mRNA are produced, which include alternatively spliced isoforms of env mRNA for translation of the regulatory, accessory, and Env proteins, and the gRNA for Gag-Pol structural polyproteins [ 24 , 25 , 26 , 27 ].…”

“…The multiple splice donor (SD) and splice acceptor (SA) sites in the HIV-1 gRNA support alternative splicing for a pool of 4-kb and 2-kb mRNAs that differ in their 5′UTR. These mRNAs contain partly overlapping open reading frames (ORFs), and collectively encode the nine HIV-1 proteins and polyproteins [ 24 , 25 , 26 , 27 ]. In addition, the IRES-dependent translational initiation is a cap-independent translational process.…”