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Bao Q, Hotz-Wagenblatt A, Betts MJ, Hipp M, Hugo A, Pougialis G, Lei-Rossmann J, Löchelt M. Shared and cell type-specific adaptation strategies of Gag and Env yield high titer bovine foamy virus variants. INFECTION GENETICS AND EVOLUTION 2020; 82:104287. [PMID: 32179148 DOI: 10.1016/j.meegid.2020.104287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 03/05/2020] [Accepted: 03/11/2020] [Indexed: 12/27/2022]
Abstract
During in vitro selection and evolution screens to adapt the tightly cell-associated bovine foamy virus BFV to high titer cell-free transmission, common, cell-type specific and concurrent adaptive changes in Gag and Env, the major players of foamy virus particle assembly and release, were detected. Upon early establishment of cell type-independent pioneering mutations in Env and, subsequently in Gag, a diverse virus pool emerged that was characterized by the occurrence of shared and additional cell type-specific exchanges. At late passages and saturated titers, remarkably homogeneous virus populations characterized by functionally important mutations developed which may be partly due to stochastic evolutionary events that occurred earlier during adaptation. Reverse genetics showed that defined mutations were functionally important for high titer cell-free transmission.
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Affiliation(s)
- Qiuying Bao
- Division of Viral Transformation Mechanisms, Research Focus Infection, Inflammation and Cancer, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany.
| | | | - Matthew J Betts
- CellNetworks, Bioquant, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
| | - Michaela Hipp
- Division of Viral Transformation Mechanisms, Research Focus Infection, Inflammation and Cancer, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany.
| | - Annette Hugo
- Division of Viral Transformation Mechanisms, Research Focus Infection, Inflammation and Cancer, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany.
| | - Georgios Pougialis
- Division of Viral Transformation Mechanisms, Research Focus Infection, Inflammation and Cancer, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany.
| | - Janet Lei-Rossmann
- Division of Viral Transformation Mechanisms, Research Focus Infection, Inflammation and Cancer, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany.
| | - Martin Löchelt
- Division of Viral Transformation Mechanisms, Research Focus Infection, Inflammation and Cancer, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany.
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Klaver B, van der Velden Y, van Hemert F, van der Kuyl AC, Berkhout B. HIV-1 tolerates changes in A-count in a small segment of the pol gene. Retrovirology 2017; 14:43. [PMID: 28870251 PMCID: PMC5583962 DOI: 10.1186/s12977-017-0367-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/30/2017] [Indexed: 11/21/2022] Open
Abstract
Background The HIV-1 RNA genome has a biased nucleotide composition with a surplus of As. Several hypotheses have been put forward to explain this striking phenomenon, but the A-count of the HIV-1 genome has thus far not been systematically manipulated. The reason for this reservation is the likelihood that known and unknown sequence motifs will be affected by such a massive mutational approach, thus resulting in replication-impaired virus mutants. We present the first attempt to increase and decrease the A-count in a relatively small polymerase (pol) gene segment of HIV-1 RNA. Results To minimize the mutational impact, a new mutational approach was developed that is inspired by natural sequence variation as present in HIV-1 isolates. This phylogeny-instructed mutagenesis allowed us to create replication-competent HIV-1 mutants with a significantly increased or decreased local A-count. The local A-count of the wild-type (wt) virus (40.2%) was further increased to 46.9% or reduced to 31.7 and 26.3%. These HIV-1 variants replicate efficiently in vitro, despite the fact that the pol changes cause a quite profound move in HIV–SIV sequence space. Conclusions Extrapolating these results to the complete 9 kb RNA genome, we may cautiously suggest that the A-rich signature does not have to be maintained. This survey also provided clues that silent codon changes, in particular from G-to-A, determine the subtype-specific sequence signatures.
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Affiliation(s)
- Bep Klaver
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Yme van der Velden
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Formijn van Hemert
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Antoinette C van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, K3-110, Meibergdreef 15, 1105 AZ, Amsterdam, The Netherlands.
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van Bel N, Ghabri A, Das AT, Berkhout B. The HIV-1 leader RNA is exquisitely sensitive to structural changes. Virology 2015; 483:236-52. [DOI: 10.1016/j.virol.2015.03.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/05/2015] [Accepted: 03/27/2015] [Indexed: 01/14/2023]
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Cantara WA, Olson ED, Musier-Forsyth K. Progress and outlook in structural biology of large viral RNAs. Virus Res 2014; 193:24-38. [PMID: 24956407 PMCID: PMC4252365 DOI: 10.1016/j.virusres.2014.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/11/2014] [Accepted: 06/12/2014] [Indexed: 02/05/2023]
Abstract
The field of viral molecular biology has reached a precipice for which pioneering studies on the structure of viral RNAs are beginning to bridge the gap. It has become clear that viral genomic RNAs are not simply carriers of hereditary information, but rather are active players in many critical stages during replication. Indeed, functions such as cap-independent translation initiation mechanisms are, in some cases, primarily driven by RNA structural determinants. Other stages including reverse transcription initiation in retroviruses, nuclear export and viral packaging are specifically dependent on the proper 3-dimensional folding of multiple RNA domains to recruit necessary viral and host factors required for activity. Furthermore, a large-scale conformational change within the 5'-untranslated region of HIV-1 has been proposed to regulate the temporal switch between viral protein synthesis and packaging. These RNA-dependent functions are necessary for replication of many human disease-causing viruses such as severe acute respiratory syndrome (SARS)-associated coronavirus, West Nile virus, and HIV-1. The potential for antiviral development is currently hindered by a poor understanding of RNA-driven molecular mechanisms, resulting from a lack of structural information on large RNAs and ribonucleoprotein complexes. Herein, we describe the recent progress that has been made on characterizing these large RNAs and provide brief descriptions of the techniques that will be at the forefront of future advances. Ongoing and future work will contribute to a more complete understanding of the lifecycles of retroviruses and RNA viruses and potentially lead to novel antiviral strategies.
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Affiliation(s)
| | | | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, United States
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van Bel N, Das AT, Cornelissen M, Abbink TEM, Berkhout B. A short sequence motif in the 5' leader of the HIV-1 genome modulates extended RNA dimer formation and virus replication. J Biol Chem 2014; 289:35061-74. [PMID: 25368321 DOI: 10.1074/jbc.m114.621425] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 5' leader of the HIV-1 RNA genome encodes signals that control various steps in the replication cycle, including the dimerization initiation signal (DIS) that triggers RNA dimerization. The DIS folds a hairpin structure with a palindromic sequence in the loop that allows RNA dimerization via intermolecular kissing loop (KL) base pairing. The KL dimer can be stabilized by including the DIS stem nucleotides in the intermolecular base pairing, forming an extended dimer (ED). The role of the ED RNA dimer in HIV-1 replication has hardly been addressed because of technical challenges. We analyzed a set of leader mutants with a stabilized DIS hairpin for in vitro RNA dimerization and virus replication in T cells. In agreement with previous observations, DIS hairpin stability modulated KL and ED dimerization. An unexpected previous finding was that mutation of three nucleotides immediately upstream of the DIS hairpin significantly reduced in vitro ED formation. In this study, we tested such mutants in vivo for the importance of the ED in HIV-1 biology. Mutants with a stabilized DIS hairpin replicated less efficiently than WT HIV-1. This defect was most severe when the upstream sequence motif was altered. Virus evolution experiments with the defective mutants yielded fast replicating HIV-1 variants with second site mutations that (partially) restored the WT hairpin stability. Characterization of the mutant and revertant RNA molecules and the corresponding viruses confirmed the correlation between in vitro ED RNA dimer formation and efficient virus replication, thus indicating that the ED structure is important for HIV-1 replication.
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Affiliation(s)
- Nikki van Bel
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
| | - Atze T Das
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
| | - Marion Cornelissen
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
| | - Truus E M Abbink
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and the Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 0SP, United Kingdom
| | - Ben Berkhout
- From the Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands and
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Herrera-Carrillo E, Liu YP, Berkhout B. The impact of unprotected T cells in RNAi-based gene therapy for HIV-AIDS. Mol Ther 2014; 22:596-606. [PMID: 24336172 PMCID: PMC3944328 DOI: 10.1038/mt.2013.280] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 12/01/2013] [Indexed: 12/18/2022] Open
Abstract
RNA interference (RNAi) is highly effective in inhibiting human immunodeficiency virus type 1 (HIV-1) replication by the expression of antiviral short hairpin RNA (shRNA) in stably transduced T-cell lines. For the development of a durable gene therapy that prevents viral escape, we proposed to combine multiple shRNAs against highly conserved regions of the HIV-1 RNA genome. The future in vivo application of such a gene therapy protocol will reach only a fraction of the T cells, such that HIV-1 replication will continue in the unmodified T cells, thereby possibly frustrating the therapy by generation of HIV-1 variants that escape from the inhibition imposed by the protected cells. We studied virus inhibition and evolution in pure cultures of shRNA-expressing cells versus mixed cell cultures of protected and unprotected T cells. The addition of the unprotected T cells indeed seems to accelerate HIV-1 evolution and escape from a single shRNA inhibitor. However, expression of three antiviral shRNAs from a single lentiviral vector prevents virus escape even in the presence of unprotected cells. These results support the idea to validate the therapeutic potential of this anti-HIV approach in appropriate in vivo models.
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Affiliation(s)
- Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ying Poi Liu
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
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Fernández N, Fernandez-Miragall O, Ramajo J, García-Sacristán A, Bellora N, Eyras E, Briones C, Martínez-Salas E. Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation. Nucleic Acids Res 2011; 39:8572-85. [PMID: 21742761 PMCID: PMC3201876 DOI: 10.1093/nar/gkr560] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RNA structure plays a fundamental role in internal initiation of translation. Picornavirus internal ribosome entry site (IRES) are long, efficient cis-acting elements that recruit the ribosome to internal mRNA sites. However, little is known about long-range constraints determining the IRES RNA structure. Here, we sought to investigate the functional and structural relevance of the invariant apical stem of a picornavirus IRES. Mutation of this apical stem revealed better performance of G:C compared with C:G base pairs, demonstrating that the secondary structure solely is not sufficient for IRES function. In turn, mutations designed to disrupt the stem abolished IRES activity. Lack of tolerance to accept genetic variability in the apical stem was supported by the presence of coupled covariations within the adjacent stem-loops. SHAPE structural analysis, gel mobility-shift and microarrays-based RNA accessibility revealed that the apical stem contributes to maintain IRES RNA structure through the generation of distant interactions between two adjacent stem-loops. Our results demonstrate that a highly interactive structure constrained by distant interactions involving invariant G:C base pairs plays a key role in maintaining the RNA conformation necessary for IRES-mediated translation.
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Affiliation(s)
- Noemí Fernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Kortekaas J, Vloet RPM, Weerdmeester K, Ketelaar J, van Eijk M, Loeffen WL. Rational design of a classical swine fever C-strain vaccine virus that enables the differentiation between infected and vaccinated animals. J Virol Methods 2009; 163:175-85. [PMID: 19770004 DOI: 10.1016/j.jviromet.2009.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Revised: 09/05/2009] [Accepted: 09/10/2009] [Indexed: 11/25/2022]
Abstract
The C-strain of the classical swine fever virus (CSFV) is considered the gold standard vaccine for the control of CSF. This vaccine, however, does not enable the serological differentiation between infected and vaccinated animals (DIVA). Consequently, its use can impose severe trade restrictions. The immunodominant and evolutionarily conserved A-domain of the E2 structural glycoprotein is an important target in CSFV-specific ELISAs. With the ultimate aim to render the C-strain suitable as a DIVA vaccine, mutations were introduced that were expected to dampen the immunogenicity of the A-domain. In the first of two approaches, the feasibility of shielding the A-domain by N-linked glycans was evaluated, whereas in the second approach C-strain mutants were created with targeted deletions in the A-domain. Analysis of the antibody responses elicited in rabbits suggested that shielding of the A-domain by an N-linked glycan had a minor effect on the immune response against the A-domain, whereas a targeted deletion of only a single amino acid severely dampened this response. C-strain mutants with larger deletions were highly debilitated and incapable of sustained growth in vitro. By providing the viruses with the opportunity to increase their fitness by mutation, a mutant was rescued that found a way to compensate for the imposed fitness cost. Most of the identified mutations occurred in several independently evolved viruses, demonstrating parallel evolution. By virtue of this compensatory evolution, a well replicating and genetically stable C-strain mutant was produced that can be serologically differentiated from wildtype CSFV. The findings provide the molecular basis for the development of a novel, genetically stable, live attenuated CSF DIVA vaccine.
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Affiliation(s)
- J Kortekaas
- Virology Division, Central Veterinary Institute of Wageningen University Research Centre, P.O. Box 65, 8200 AB Lelystad, The Netherlands.
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Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships. J Virol 2009; 83:6326-34. [PMID: 19369331 DOI: 10.1128/jvi.00251-09] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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