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

Watts JM, Dang KK, Gorelick RJ, Leonard CW, Bess JW, Swanstrom R, Burch CL, Weeks KM - Nature (2009)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.

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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Related in: MedlinePlus

Structure of the HIV-1 NL4-3 genome. The 5′ and 3′ genome halves are shown in panels (a) and (b). Nucleotides are colored by their absolute SHAPE reactivities (see scale in panel a). Every nucleotide is shown explicitly as a sphere; base pairing is indicated by adjacent parallel orientation of the spheres. Protein domains are identified by letters. Important structural landmarks are labeled explicitly. Full nucleotide identities and pairings are provided in the supplementary information (Fig. S7). Intermolecular base pairs involving the tRNALys3 primer and the genomic dimer are shown in gray. Inset shows a box plot illustrating SHAPE reactivities for single stranded versus paired nucleotides in the model. Median reactivities are indicated by bold horizontal lines; the large box spans the central 50% of the reactivity data.
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Figure 2: Structure of the HIV-1 NL4-3 genome. The 5′ and 3′ genome halves are shown in panels (a) and (b). Nucleotides are colored by their absolute SHAPE reactivities (see scale in panel a). Every nucleotide is shown explicitly as a sphere; base pairing is indicated by adjacent parallel orientation of the spheres. Protein domains are identified by letters. Important structural landmarks are labeled explicitly. Full nucleotide identities and pairings are provided in the supplementary information (Fig. S7). Intermolecular base pairs involving the tRNALys3 primer and the genomic dimer are shown in gray. Inset shows a box plot illustrating SHAPE reactivities for single stranded versus paired nucleotides in the model. Median reactivities are indicated by bold horizontal lines; the large box spans the central 50% of the reactivity data.

Mentions: Comprehensive SHAPE reactivity information can also be used to determine a nucleotide-resolution secondary structure model for the entire NL4-3 HIV-1 genome (Fig. 2). SHAPE reactivities are converted to free energy change terms and used to constrain a thermodynamic folding algorithm22,23. The final result is a thermodynamically favored structural model highly reflective of the experimental SHAPE data, at single nucleotide resolution. For example, most nucleotides assigned to single-stranded regions are reactive towards SHAPE (red, orange, and green nucleotides; Fig. 2); whereas, base-paired nucleotides are predominantly unreactive (black nucleotides and inset; Fig. 2). (For a full discussion of SHAPE-directed RNA folding and the fundamental correctness of this model, see the Supporting Methods.)


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

Watts JM, Dang KK, Gorelick RJ, Leonard CW, Bess JW, Swanstrom R, Burch CL, Weeks KM - Nature (2009)

Structure of the HIV-1 NL4-3 genome. The 5′ and 3′ genome halves are shown in panels (a) and (b). Nucleotides are colored by their absolute SHAPE reactivities (see scale in panel a). Every nucleotide is shown explicitly as a sphere; base pairing is indicated by adjacent parallel orientation of the spheres. Protein domains are identified by letters. Important structural landmarks are labeled explicitly. Full nucleotide identities and pairings are provided in the supplementary information (Fig. S7). Intermolecular base pairs involving the tRNALys3 primer and the genomic dimer are shown in gray. Inset shows a box plot illustrating SHAPE reactivities for single stranded versus paired nucleotides in the model. Median reactivities are indicated by bold horizontal lines; the large box spans the central 50% of the reactivity data.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2724670&req=5

Figure 2: Structure of the HIV-1 NL4-3 genome. The 5′ and 3′ genome halves are shown in panels (a) and (b). Nucleotides are colored by their absolute SHAPE reactivities (see scale in panel a). Every nucleotide is shown explicitly as a sphere; base pairing is indicated by adjacent parallel orientation of the spheres. Protein domains are identified by letters. Important structural landmarks are labeled explicitly. Full nucleotide identities and pairings are provided in the supplementary information (Fig. S7). Intermolecular base pairs involving the tRNALys3 primer and the genomic dimer are shown in gray. Inset shows a box plot illustrating SHAPE reactivities for single stranded versus paired nucleotides in the model. Median reactivities are indicated by bold horizontal lines; the large box spans the central 50% of the reactivity data.
Mentions: Comprehensive SHAPE reactivity information can also be used to determine a nucleotide-resolution secondary structure model for the entire NL4-3 HIV-1 genome (Fig. 2). SHAPE reactivities are converted to free energy change terms and used to constrain a thermodynamic folding algorithm22,23. The final result is a thermodynamically favored structural model highly reflective of the experimental SHAPE data, at single nucleotide resolution. For example, most nucleotides assigned to single-stranded regions are reactive towards SHAPE (red, orange, and green nucleotides; Fig. 2); whereas, base-paired nucleotides are predominantly unreactive (black nucleotides and inset; Fig. 2). (For a full discussion of SHAPE-directed RNA folding and the fundamental correctness of this model, see the Supporting Methods.)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA.

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.

Show MeSH
Related in: MedlinePlus