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Abstract
RNA viruses encode the information required to usurp cellular metabolism and gene regulation and to enable their own replication in two ways: in the linear sequence of their RNA genomes and in higher-order structures that form when the genomic RNA strand folds back on itself. Application of high-resolution SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) structure probing to viral RNA genomes has identified numerous new regulatory elements, defined new principles by which viral RNAs interact with the cellular host and evade host immune responses, and revealed relationships between virus evolution and RNA structure. This review summarizes our current understanding of genome structure-function interrelationships for RNA viruses, as informed by SHAPE structure probing, and outlines opportunities for future studies.
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Affiliation(s)
- Mark A Boerneke
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA; , ,
| | - Jeffrey E Ehrhardt
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA; , ,
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA; , ,
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2
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Abstract
BACKGROUND Despite the long-anticipated possibility of putting sequence alignment on the same footing as statistical phylogenetics, theorists have struggled to develop time-dependent evolutionary models for indels that are as tractable as the analogous models for substitution events. MAIN TEXT This paper discusses progress in the area of insertion-deletion models, in view of recent work by Ezawa (BMC Bioinformatics 17:304, 2016); (BMC Bioinformatics 17:397, 2016); (BMC Bioinformatics 17:457, 2016) on the calculation of time-dependent gap length distributions in pairwise alignments, and current approaches for extending these approaches from ancestor-descendant pairs to phylogenetic trees. CONCLUSIONS While approximations that use finite-state machines (Pair HMMs and transducers) currently represent the most practical approach to problems such as sequence alignment and phylogeny, more rigorous approaches that work directly with the matrix exponential of the underlying continuous-time Markov chain also show promise, especially in view of recent advances.
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Affiliation(s)
- Ian H. Holmes
- 0000 0001 2181 7878grid.47840.3fDept of Bioengineering, University of California, Berkeley, 94720 USA
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3
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Santiago-Ortiz J, Ojala DS, Westesson O, Weinstein JR, Wong SY, Steinsapir A, Kumar S, Holmes I, Schaffer DV. AAV ancestral reconstruction library enables selection of broadly infectious viral variants. Gene Ther 2015; 22:934-46. [PMID: 26186661 PMCID: PMC4509550 DOI: 10.1038/gt.2015.74] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/22/2015] [Accepted: 07/08/2015] [Indexed: 01/19/2023]
Abstract
Adeno-associated virus (AAV) vectors have achieved clinical efficacy in treating several diseases. However, enhanced vectors are required to extend these landmark successes to other indications and protein engineering approaches may provide the necessary vector improvements to address such unmet medical needs. To generate new capsid variants with potentially enhanced infectious properties and to gain insights into AAV's evolutionary history, we computationally designed and experimentally constructed a putative ancestral AAV library. Combinatorial variations at 32 amino acid sites were introduced to account for uncertainty in their identities. We then analyzed the evolutionary flexibility of these residues, the majority of which have not been previously studied, by subjecting the library to iterative selection on a representative cell line panel. The resulting variants exhibited transduction efficiencies comparable to the most efficient extant serotypes and, in general, ancestral libraries were broadly infectious across the cell line panel, indicating that they favored promiscuity over specificity. Interestingly, putative ancestral AAVs were more thermostable than modern serotypes and did not use sialic acids, galactose or heparan sulfate proteoglycans for cellular entry. Finally, variants mediated 19- to 31-fold higher gene expression in the muscle compared with AAV1, a clinically used serotype for muscle delivery, highlighting their promise for gene therapy.
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Affiliation(s)
- J Santiago-Ortiz
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - D S Ojala
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - O Westesson
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - J R Weinstein
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - S Y Wong
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - A Steinsapir
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - S Kumar
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - I Holmes
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - D V Schaffer
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
- The Helen Wills Neuroscience Institute, University of California, Berkeley, CA, USA
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4
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Burrill CP, Westesson O, Schulte MB, Strings VR, Segal M, Andino R. Global RNA structure analysis of poliovirus identifies a conserved RNA structure involved in viral replication and infectivity. J Virol 2013; 87:11670-83. [PMID: 23966409 PMCID: PMC3807356 DOI: 10.1128/jvi.01560-13] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/15/2013] [Indexed: 01/06/2023] Open
Abstract
The genomes of RNA viruses often contain RNA structures that are crucial for translation and RNA replication and may play additional, uncharacterized roles during the viral replication cycle. For the picornavirus family member poliovirus, a number of functional RNA structures have been identified, but much of its genome, especially the open reading frame, has remained uncharacterized. We have now generated a global RNA structure map of the poliovirus genome using a chemical probing approach that interrogates RNA structure with single-nucleotide resolution. In combination with orthogonal evolutionary analyses, we uncover several conserved RNA structures in the open reading frame of the viral genome. To validate the ability of our global analyses to identify functionally important RNA structures, we further characterized one of the newly identified structures, located in the region encoding the RNA-dependent RNA polymerase, 3D(pol), by site-directed mutagenesis. Our results reveal that the structure is required for viral replication and infectivity, since synonymous mutants are defective in these processes. Furthermore, these defects can be partially suppressed by mutations in the viral protein 3C(pro), which suggests the existence of a novel functional interaction between an RNA structure in the 3D(pol)-coding region and the viral protein(s) 3C(pro) and/or its precursor 3CD(pro).
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Affiliation(s)
- Cecily P. Burrill
- Tetrad Graduate Program, University of California, San Francisco, California, USA
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
| | - Oscar Westesson
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Michael B. Schulte
- Tetrad Graduate Program, University of California, San Francisco, California, USA
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
| | - Vanessa R. Strings
- Tetrad Graduate Program, University of California, San Francisco, California, USA
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
| | - Mark Segal
- Department of Epidemiology & Biostatistics, University of California, San Francisco, California, USA
| | - Raul Andino
- Department of Microbiology & Immunology, University of California, San Francisco, California, USA
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