Architecture and secondary structure of an entire HIV-1 RNA genome

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Abstract

Single-stranded RNA viruses encompass broad classes of infectious agents and cause the common cold, cancer, AIDS and other serious health threats. Viral replication is regulated at many levels, including the use of conserved genomic RNA structures. Most potential regulatory elements in viral RNA genomes are uncharacterized. Here we report the structure of an entire HIV-1 genome at single nucleotide resolution using SHAPE, a high-throughput RNA analysis technology. The genome encodes protein structure at two levels. In addition to the correspondence between RNA and protein primary sequences, a correlation exists between high levels of RNA structure and sequences that encode inter-domain loops in HIV proteins. This correlation suggests that RNA structure modulates ribosome elongation to promote native protein folding. Some simple genome elements previously shown to be important, including the ribosomal gag-pol frameshift stem-loop, are components of larger RNA motifs. We also identify organizational principles for unstructured RNA regions, including splice site acceptors and hypervariable regions. These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by previously unrecognized regulatory motifs and that extensive RNA structure constitutes an important component of the genetic code.

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Figure 1: Organization, extent of RNA structure, and relationship to protein structure for an HIV-1 genome.
Figure 2: Structure of the HIV-1 NL4-3 genome.
Figure 3: SHAPE analysis of the signal peptide–gp120 region.
Figure 4: RNA structure in Env hypervariable regions.

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Acknowledgements

This project was supported by the US National Institutes of Health (AI068462 to K.M.W.) and by the National Cancer Institute, under contracts N01-CO-12400 and HHSN261200800001E (to R.J.G. and J.W.B.). J.M.W. was supported as a Fellow of the UNC Lineberger Cancer Center and a National Institutes of Health (NIH) Kirschstein Postdoctoral Fellowship. R.S. and K.K.D. were supported by NIH grants AI44667 and T32 AI07419, respectively. We are indebted to D. Mathews and J. Low for assistance with the RNA structure program and genome secondary structure analysis, respectively. The content of this publication does not necessarily reflect the views or policies of the US Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations indicate endorsement by the US Government.

Author Contributions J.M.W., R.J.G. and K.M.W. conceived of and designed the HIV-1 genome structure analysis project. J.M.W. and K.M.W. analysed and interpreted the HIV SHAPE structure information. K.K.D., R.S. and C.L.B. designed and performed the bioinformatic pairing probability analysis. J.M.W., R.J.G. and C.W.L. performed the experiments. J.M.W., C.L.B. and K.M.W. performed the statistical analyses. J.W.B. produced and purified HIV-1 virions. J.M.W. and K.M.W. wrote the manuscript with contributions from all authors.

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Correspondence to Kevin M. Weeks.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S7 with Legends, Supplementary Tables S1-S2 and Supplementary References. (PDF 686 kb)

Supplementary Data

This file contains dataset S1which is a helix file for the complete NL4-3 RNA genome structure model in tab-delimited ascii format. Columns are: first nucleotide in helix, last nucleotide in helix, number of base pairs in helix. (TXT 5 kb)

Supplementary Data

This file contains dataset S2 which shows all SHAPE reactivities and pairing probabilities for the NL4-3 HIV-1 RNA genome in tab-delimited ascii format. Columns are: nucleotide position, nucleotide identity, SHAPE reactivity, pairing probability (TXT 213 kb)

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Watts, J., Dang, K., Gorelick, R. et al. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature 460, 711–716 (2009) doi:10.1038/nature08237

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