Modulation of vif-mRNA by HIV-1-SA1D2prox
Nomaguchi, Masako Tokushima University Tokushima University Educator and Researcher Directory KAKEN Search Researchers
Doi, Naoya Tokushima University Tokushima University Educator and Researcher Directory
Yoshida, Tomoya Tokushima University
Koma, Takaaki Tokushima University Tokushima University Educator and Researcher Directory KAKEN Search Researchers
Adachi, Shun Tokushima University
Ode, Hirotaka National Hospital Organization Nagoya Medical Center
Iwatani, Yasumasa National Hospital Organization Nagoya Medical Center
Yokoyama, Masaru National Institute of Infectious Diseases
Sato, Hironori National Institute of Infectious Diseases
Adachi, Akio Tokushima University Tokushima University Educator and Researcher Directory KAKEN Search Researchers
secondary RNA structure
Genomic RNA of HIV-1 contains localized structures critical for viral replication. Its structural analysis has demonstrated a stem-loop structure, SLSA1, in a nearby region of HIV-1 genomic splicing acceptor 1 (SA1). We have previously shown that the expression level of vif mRNA is considerably altered by some natural single-nucleotide variations (nSNVs) clustering in SLSA1 structure. In this study, besides eleven nSNVs previously identified by us, we totally found nine new nSNVs in the SLSA1-containing sequence from SA1, splicing donor 2, and through to the start codon of Vif that significantly affect the vif mRNA level, and designated the sequence SA1D2prox (142 nucleotides for HIV-1 NL4-3). We then examined by extensive variant and mutagenesis analyses how SA1D2prox sequence and SLSA1 secondary structure are related to vif mRNA level. While the secondary structure and stability of SLSA1 was largely changed by nSNVs and artificial mutations introduced to restore the original NL4-3 form from altered ones by nSNVs, no clear association of the two SLSA1 properties with vif mRNA level was observed. In contrast, when naturally occurring SA1D2prox sequences that contain multiple nSNVs were examined, we attained significant inverse correlation between the vif level and SLSA1 stability. These results may suggest that SA1D2prox sequence adapts over time, and also that the altered SA1D2prox sequence, SLSA1 stability, and vif level are mutually related. In total, we show here that the entire SA1D2prox sequence and SLSA1 stability critically contribute to the modulation of vif mRNA level.
Frontiers in Microbiology
Frontiers Media S.A.
Copyright © 2017 Nomaguchi, Doi, Yoshida, Koma, Adachi, Ode, Iwatani, Yokoyama, Sato and Adachi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). (https://creativecommons.org/licenses/by/4.0/) The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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