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New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation.

Kieft JS, Rabe JL, Chapman EG - RNA Biol (2015)

Bottom Line: We recently solved the crystal structure of a functional xrRNA, revealing a novel fold that provides a mechanistic model for Xrn1 resistance.Continued analysis and interpretation of the structure reveals that the tertiary contacts that knit the xrRNA fold together are shared by a wide variety of arthropod-borne FVs, conferring robust Xrn1 resistance in all tested.However, there is some variability in the structures that correlates with unexplained patterns in the viral 3' UTRs.

View Article: PubMed Central - PubMed

Affiliation: a Department of Biochemistry and Molecular Genetics.

ABSTRACT
Arthropod-borne flaviviruses (FVs) are a growing world-wide health threat whose incidence and range are increasing. The pathogenicity and cytopathicity of these single-stranded RNA viruses are influenced by viral subgenomic non-protein-coding RNAs (sfRNAs) that the viruses produce to high levels during infection. To generate sfRNAs the virus co-opts the action of the abundant cellular exonuclease Xrn1, which is part of the cell's normal RNA turnover machinery. This exploitation of the cellular machinery is enabled by discrete, highly structured, Xrn1-resistant RNA elements (xrRNAs) in the 3'UTR that interact with Xrn1 to halt processive 5' to 3' decay of the viral genomic RNA. We recently solved the crystal structure of a functional xrRNA, revealing a novel fold that provides a mechanistic model for Xrn1 resistance. Continued analysis and interpretation of the structure reveals that the tertiary contacts that knit the xrRNA fold together are shared by a wide variety of arthropod-borne FVs, conferring robust Xrn1 resistance in all tested. However, there is some variability in the structures that correlates with unexplained patterns in the viral 3' UTRs. Finally, examination of these structures and their behavior in the context of viral infection leads to a new hypothesis linking RNA tertiary structure, overall 3' UTR architecture, sfRNA production, and host adaptation.

No MeSH data available.


Related in: MedlinePlus

Hypothesis linking xrRNA tertiary structure, sfRNA formation, and host adaptation. (A) Northern blot analysis of RNA produced during WNVKUN infection in human cells. Wild-type (WT) virus and 2 mutants in which the S1-S3 tertiary interaction was abrogated in either the first xrRNA or second xrRNA are shown. These data were previously published.35 (B) Secondary structure of the MVExrRNA2 as in Figure 2B. The regions of the second DENV xrRNA in which mutations accumulate during infection in mosquito cells are shaded green. These mutations would effectively abrogate tertiary interactions. (C) A model for how these mutations could alter sfRNA production as DENV cycles between human (left) and mosquito (right) hosts. “Strong” and “weak” refer to the efficiency of halting Xrn1, green shading shows where the second xrRNA builds up mutations, and hypothetical Northern blot analyses of noncoding sfRNA production are shown.
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f0006: Hypothesis linking xrRNA tertiary structure, sfRNA formation, and host adaptation. (A) Northern blot analysis of RNA produced during WNVKUN infection in human cells. Wild-type (WT) virus and 2 mutants in which the S1-S3 tertiary interaction was abrogated in either the first xrRNA or second xrRNA are shown. These data were previously published.35 (B) Secondary structure of the MVExrRNA2 as in Figure 2B. The regions of the second DENV xrRNA in which mutations accumulate during infection in mosquito cells are shaded green. These mutations would effectively abrogate tertiary interactions. (C) A model for how these mutations could alter sfRNA production as DENV cycles between human (left) and mosquito (right) hosts. “Strong” and “weak” refer to the efficiency of halting Xrn1, green shading shows where the second xrRNA builds up mutations, and hypothetical Northern blot analyses of noncoding sfRNA production are shown.

Mentions: We do not yet understand how an individual xrRNA tertiary structure relates to the full architecture of a FV 3′ UTR and to patterns of sfRNA production during infection, but recent observations from several papers lead to an interesting model. First, when we infected human cells with the Kunjin strain of WNV (WNVKUN), the pattern of sfRNA production demonstrated that the first xrRNA (WNVxrRNA1) was very efficient in halting Xrn1, with most of the sfRNAs produced by this upstream xrRNA (Fig. 6A).35,36 Consistent with previous studies, when this xrRNA was mutated to disrupt its tertiary structure, this sfRNA disappeared as expected, but levels of the second sfRNA that results from the action of the downstream xrRNA (WNVxrRNA2) increased only marginally.19,33,35,36 Thus, the downstream xrRNA is less efficient in its ability to halt Xrn1. More surprising, when WNVxrRNA2 was mutated to disrupt its tertiary structure the amount of sfRNA produced from WNVxrRNA1 also decreased, an effect noted previously but not yet explained.19,33,35,36 This suggests that the efficiency of sfRNA production from WNVxrRNA1 is coupled to the integrity of the tertiary structure of WNVxrRNA2 by some completely unknown mechanism (Fig. 6A). To date, this coupling has only been examined or detected in WNV, clearly more exploration is needed to assess its significance.Figure 6.


New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation.

Kieft JS, Rabe JL, Chapman EG - RNA Biol (2015)

Hypothesis linking xrRNA tertiary structure, sfRNA formation, and host adaptation. (A) Northern blot analysis of RNA produced during WNVKUN infection in human cells. Wild-type (WT) virus and 2 mutants in which the S1-S3 tertiary interaction was abrogated in either the first xrRNA or second xrRNA are shown. These data were previously published.35 (B) Secondary structure of the MVExrRNA2 as in Figure 2B. The regions of the second DENV xrRNA in which mutations accumulate during infection in mosquito cells are shaded green. These mutations would effectively abrogate tertiary interactions. (C) A model for how these mutations could alter sfRNA production as DENV cycles between human (left) and mosquito (right) hosts. “Strong” and “weak” refer to the efficiency of halting Xrn1, green shading shows where the second xrRNA builds up mutations, and hypothetical Northern blot analyses of noncoding sfRNA production are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4829329&req=5

f0006: Hypothesis linking xrRNA tertiary structure, sfRNA formation, and host adaptation. (A) Northern blot analysis of RNA produced during WNVKUN infection in human cells. Wild-type (WT) virus and 2 mutants in which the S1-S3 tertiary interaction was abrogated in either the first xrRNA or second xrRNA are shown. These data were previously published.35 (B) Secondary structure of the MVExrRNA2 as in Figure 2B. The regions of the second DENV xrRNA in which mutations accumulate during infection in mosquito cells are shaded green. These mutations would effectively abrogate tertiary interactions. (C) A model for how these mutations could alter sfRNA production as DENV cycles between human (left) and mosquito (right) hosts. “Strong” and “weak” refer to the efficiency of halting Xrn1, green shading shows where the second xrRNA builds up mutations, and hypothetical Northern blot analyses of noncoding sfRNA production are shown.
Mentions: We do not yet understand how an individual xrRNA tertiary structure relates to the full architecture of a FV 3′ UTR and to patterns of sfRNA production during infection, but recent observations from several papers lead to an interesting model. First, when we infected human cells with the Kunjin strain of WNV (WNVKUN), the pattern of sfRNA production demonstrated that the first xrRNA (WNVxrRNA1) was very efficient in halting Xrn1, with most of the sfRNAs produced by this upstream xrRNA (Fig. 6A).35,36 Consistent with previous studies, when this xrRNA was mutated to disrupt its tertiary structure, this sfRNA disappeared as expected, but levels of the second sfRNA that results from the action of the downstream xrRNA (WNVxrRNA2) increased only marginally.19,33,35,36 Thus, the downstream xrRNA is less efficient in its ability to halt Xrn1. More surprising, when WNVxrRNA2 was mutated to disrupt its tertiary structure the amount of sfRNA produced from WNVxrRNA1 also decreased, an effect noted previously but not yet explained.19,33,35,36 This suggests that the efficiency of sfRNA production from WNVxrRNA1 is coupled to the integrity of the tertiary structure of WNVxrRNA2 by some completely unknown mechanism (Fig. 6A). To date, this coupling has only been examined or detected in WNV, clearly more exploration is needed to assess its significance.Figure 6.

Bottom Line: We recently solved the crystal structure of a functional xrRNA, revealing a novel fold that provides a mechanistic model for Xrn1 resistance.Continued analysis and interpretation of the structure reveals that the tertiary contacts that knit the xrRNA fold together are shared by a wide variety of arthropod-borne FVs, conferring robust Xrn1 resistance in all tested.However, there is some variability in the structures that correlates with unexplained patterns in the viral 3' UTRs.

View Article: PubMed Central - PubMed

Affiliation: a Department of Biochemistry and Molecular Genetics.

ABSTRACT
Arthropod-borne flaviviruses (FVs) are a growing world-wide health threat whose incidence and range are increasing. The pathogenicity and cytopathicity of these single-stranded RNA viruses are influenced by viral subgenomic non-protein-coding RNAs (sfRNAs) that the viruses produce to high levels during infection. To generate sfRNAs the virus co-opts the action of the abundant cellular exonuclease Xrn1, which is part of the cell's normal RNA turnover machinery. This exploitation of the cellular machinery is enabled by discrete, highly structured, Xrn1-resistant RNA elements (xrRNAs) in the 3'UTR that interact with Xrn1 to halt processive 5' to 3' decay of the viral genomic RNA. We recently solved the crystal structure of a functional xrRNA, revealing a novel fold that provides a mechanistic model for Xrn1 resistance. Continued analysis and interpretation of the structure reveals that the tertiary contacts that knit the xrRNA fold together are shared by a wide variety of arthropod-borne FVs, conferring robust Xrn1 resistance in all tested. However, there is some variability in the structures that correlates with unexplained patterns in the viral 3' UTRs. Finally, examination of these structures and their behavior in the context of viral infection leads to a new hypothesis linking RNA tertiary structure, overall 3' UTR architecture, sfRNA production, and host adaptation.

No MeSH data available.


Related in: MedlinePlus