RNA Regulatory Elements in the Genomes of Simple Retroviruses

Wiley Interdisciplinary Reviews - Rna, 2013

After reverse transcription of the retroviral RNA genome and integration of the DNA provirus into the host genome, host machinery is used for viral gene expression along with viral proteins and RNA regulatory elements. Here, we discuss co-transcriptional and posttranscriptional regulation of retroviral gene expression, comparing simple and complex retroviruses. Cellular RNA polymerase II synthesizes full-length viral primary RNA transcripts that are capped and polyadenylated. All retroviruses generate a singly spliced env mRNA from this primary transcript, which encodes the viral glycoproteins. In addition, complex viral RNAs are alternatively spliced to generate accessory proteins, such as Rev, which is involved in posttranscriptional regulation of HIV-1 RNA. Importantly, the splicing of all retroviruses is incomplete; they must maintain and export a fraction of their primary RNA transcripts. This unspliced RNA functions both as the major mRNA for Gag and Pol proteins and as the packaged genomic RNA. Different retroviruses export their unspliced viral RNA from the nucleus to the cytoplasm by either Tap-dependent or Rev/CRM1-dependent routes. Translation of the unspliced mRNA involves frame-shifting or termination codon suppression so that the Gag proteins, which make up the capsid, are expressed more abundantly than the Pol proteins, which are the viral enzymes. After the viral polyproteins assemble into viral particles and bud from the cell membrane, a viral encoded protease cleaves them. Some retroviruses have evolved mechanisms to protect their unspliced RNA from decay by nonsense-mediated RNA decay and to prevent genome editing by the cellular APOBEC deaminases.

Mobile Genetic Elements, 2015

Wiley Interdisciplinary Reviews: RNA, 2013

After reverse transcription of the retroviral RNA genome and integration of the DNA provirus into the host genome, host machinery is used for viral gene expression along with viral proteins and RNA regulatory elements. Here, we discuss co-transcriptional and posttranscriptional regulation of retroviral gene expression, comparing simple and complex retroviruses. Cellular RNA polymerase II synthesizes full-length viral primary RNA transcripts that are capped and polyadenylated. All retroviruses generate a singly spliced env mRNA from this primary transcript, which encodes the viral glycoproteins. In addition, complex viral RNAs are alternatively spliced to generate accessory proteins, such as Rev, which is involved in posttranscriptional regulation of HIV-1 RNA. Importantly, the splicing of all retroviruses is incomplete; they must maintain and export a fraction of their primary RNA transcripts. This unspliced RNA functions both as the major mRNA for Gag and Pol proteins and as the packaged genomic RNA. Different retroviruses export their unspliced viral RNA from the nucleus to the cytoplasm by either Tap-dependent or Rev/CRM1-dependent routes. Translation of the unspliced mRNA involves frame-shifting or termination codon suppression so that the Gag proteins, which make up the capsid, are expressed more abundantly than the Pol proteins, which are the viral enzymes. After the viral polyproteins assemble into viral particles and bud from the cell membrane, a viral encoded protease cleaves them. Some retroviruses have evolved mechanisms to protect their unspliced RNA from decay by nonsense-mediated RNA decay and to prevent genome editing by the cellular APOBEC deaminases.

Journal of virology, 1996

It was previously shown that a 240-nucleotide (nt) RNA element (cis-acting transactivation element [CTE]) located between the env gene and the 3' long terminal repeat of simian retrovirus type 1 (SRV-1) can functionally replace posttranscriptional activation directed by Rev and the Rev-responsive element (RRE) when inserted into a Rev- and RRE-deficient molecular clone of human immunodeficiency virus type 1, resulting in efficient virus replication. Here, we analyze the molecular and structural requirements for function of this RNA element. Deletion mutagenesis demonstrated that the core element spans 173 nt. SRV-2 and Mason-Pfizer monkey virus have highly homologous elements, which function similarly when inserted into the Rev/RRE-deficient human immunodeficiency virus type 1. Computer prediction indicated that the core CTEs of all three viruses have similar extensive secondary structures. Mutagenesis of the SRV-1 CTE revealed that both sequence and secondary structure are esse...

The Retroviridae, 1992

The retrovirus family encompasses a diverse group of metazoan viruses that have a replication step whereby DNA is synthesized from virion RNA in a process designated reverse transcription (Temin and Baltimore, 1972) (Fig. 1; Table I) (see Chapter 1). Molecular mechanisms in the virus life cycle are reviewed in this chapter, and the focus is on retroviruses containing genes for virion proteins but lacking genes that regulate viral expression. Retroviruses with simple genomes express the polyproteins (i.e., precursor polypeptides) encoded by the following genes: gag for group-specific antigen in the virion core, pol for RNAdependent DNA polymerase, and env for the viral envelope glycoprotein (Fig. 2). This genome organization is a feature of three genera in the retrovirus family, and both horizontally transmitted exogenous viruses and vertically transmitted endogenous viruses are included (Table II) (see Chapters 1 and 2) (Coffin, 1982b; Coffin and Stoye, 1985). Retroviruses with complex genomes (i.e., lentiviruses, spumaviruses, and certain oncoviruses) encode regulatory genes as well as virion proteins;

RNA Biology, 2011

Nature Reviews Microbiology, 2007

Retroviruses are a unique family of RNA viruses that use virally encoded reverse transcriptase (RT) to replicate genomic RNA through a full-length viral DNA intermediate. These viruses have been shown to be present in the genomes of many vertebrates, including fish, rodents, birds, cats, ungulants, non-human primates and humans. Infection by retroviruses causes a wide variety of pathologies, most commonly cancers, such as leukaemias, sarcomas and mammary carcinomas, but retroviral infection can also cause immunodeficiencies, anaemias, arthritis and pneumonia 1. The retroviridae are classified into seven different genera that are named α through to ε retroviruses, as well as the lentiviruses and spumaviruses (see the International Committee on Taxonomy of Viruses database). Historically, retroviruses have been the source of many key discoveries in biology during the twentieth century, including cell transformation, viral and cellular oncogenes, RT and viral transduction, which paved the way to cDNA cloning and design of retroviral vectors for gene therapy 1. This Review will focus on the mechanisms used by retroviruses to ensure the correct viral protein synthesis within the cytoplasm of the host infected cell with particular emphasis on αand γ-retroviruses (whose prototypes are the avian leukosis virus (ALV) and murine leukaemia virus (MLV), respectively) and primate lentiviruses (HIV-1, HIV-2 and simian immunodeficiency virus (SIV)). An overview of the retroviral life cycle. Retroviruses are enveloped RNA viruses that encapsidate two copies of the same capped and polyadenylated (positive sense) RNA molecule that ranges from 8,000 to 11,000

Journal of virology, 1988

Virology, 2005

Ineffective transgene expression in a sufficient amount of target cells is still a limitation in retroviral vector mediated gene therapy. Thus, we systematically evaluated four genetic modulators, (i) the woodchuck posttranscriptional regulatory element (WPRE), (ii) the mouse RNA transport element (RTE), (iii) the constitutive transport element (CTE) of the simian retrovirus type 1 (SRV-1), and (iv) the 5V untranslated region of the human heat shock protein 70 (Hsp70 5VUTR), all of them involved in the posttranscriptional control of mRNA nucleo/ cytoplasmatic transport, RNA stability, and translation efficiency, in an MLV-based retrovirus vector context. Insertion of the WPRE into the retrovirus vector resulted in enhancement of transgene expression (EGFP) both in transfected virus producing cells as well as in infected recipient cells irrespective of the location in the vector. The best effect was observed with two copies of the WPRE, 3V of the transgene and in the 3V untranslated region of the vector backbone. However, oligomerization of this element does not further increase transgene expression. Presence of the WPRE resulted also in an increase in virus production. Introduction of the CTE and/or RTE in the retroviral vector did not alter transgene expression and infectious particle production. Positive effects were observed only in vectors harboring the CTE and/or RTE in combination with the WPRE. The activity of the Hsp70 5VUTR as a translational enhancer was found to be negligible in the context of the retroviral vector. However, interference of the Hsp70 5VUTR strong secondary structure with the packaging sequence of the viral RNA was experimentally excluded as being the cause of this. These data suggest that only the WPRE is a suitable element for the improvement of transgene expression and oncoretroviral vector production. D

Journal of virology, 1996

All retroviruses need mechanisms for nucleocytoplasmic export of their unspliced RNA and for maintenance of this RNA in the cytoplasm, where it is either translated to produce Gag and Pol proteins or packaged into viral particles. The complex retroviruses encode Rev or Rex regulatory proteins, which interact with cis-acting viral sequences to promote cytoplasmic expression of incompletely spliced viral RNAs. Since the simple retroviruses do not encode regulatory proteins, we proposed that they might contain cis-acting sequences that could interact with cellular Rev-like proteins. To test this possibility, we initially looked for a cis-acting sequence in avian retroviruses that could substitute for Rev and the Rev response element in human immunodeficiency virus type 1 expression constructs. A cis-acting element in the 3' untranslated region of Rous sarcoma virus (RSV) RNA was found to promote Rev-independent expression of human immunodeficiency virus type 1 Gag proteins. This el...