In this review, we focus on the roles of lncRNAs, including cellular and viral lncRNAs, in virus replication in infected cells. We survey the interactions and functions of several cellular lncRNAs such as XIST, HOTAIR, NEAT1, BIC and several virus encoded lncRNAs.
Autophagy, a general homeostatic process for degradation of cytosolic proteins or organelles, has been reported to modulate the replication of many viruses. The role of autophagy in human T-cell leukemia virus type 1 (HTLV-1) replication has, however, been uncharacterized. Here, we report that HTLV-1 infection increases the accumulation of autophagosomes and that this accumulation increases HTLV-1 production. We found that the HTLV-1 Tax protein increases cellular autophagosome accumulation by acting to block the fusion of autophagosomes to lysosomes, preventing the degradation of the former by the latter. Interestingly, the inhibition of cellular autophagosome-lysosome fusion using bafilomycin A increased the stability of the Tax protein, suggesting that cellular degradation of Tax occurs in part through autophagy. Our current findings indicate that by interrupting the cell's autophagic process, Tax exerts a positive feedback on its own stability.
Most of the human genome is transcribed into protein-noncoding RNAs (ncRNAs), including small ncRNAs and long ncRNAs (lncRNAs). Over the past decade, rapidly emerging evidence has increasingly supported the view that lncRNAs serve key regulatory and functional roles in mammal cells. HIV-1 replication relies on various cell functions. To date, while the involvement of host protein factors and microRNAs (miRNAs) in the HIV-1 life cycle has been extensively studied, the relationship between lncRNAs and HIV-1 remains uncharacterized. Here, we have profiled 83 disease-related lncRNAs in HIV-1-infected T cells. We found NEAT1 to be one of several lncRNAs whose expression is changed by HIV-1 infection, and we have characterized its role in HIV-1 replication. We report here that the knockdown of NEAT1 enhances virus production through increased nucleus-to-cytoplasm export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs.
Long protein-noncoding RNAs (lncRNAs) play roles in regulating gene expression and modulating protein activities. There is emerging evidence that lncRNAs are involved in the replication of viruses. To our knowledge, this report is the first to characterize a role contributed by an lncRNA, NEAT1, to HIV-1 replication. NEAT1 is essential for the integrity of the nuclear paraspeckle substructure. Based on our findings from NEAT1 knockdown, we have identified the nuclear paraspeckle body as another important subcellular organelle for HIV-1 replication.
Viral replication requires the use of host cell proteins and enzymes. Many viruses utilize viral helicases at various stages of their life cycle; these viruses have evolved to encode directly helicase or helicase-like proteins. In contrast, the genomes of retroviruses are devoid of viral helicases. Human immunodeficiency virus (HIV-1) has adopted the ability to use one or more cellular RNA helicases for its replicative life cycle. In this chapter, we briefly summarize the approach for assaying the RNA unwinding activity of RNA helicasesd and measurement of the effect helicase inhibitors on HIV-1 replication.
RNA helicases; Human immunodeficiency virus type 1 (HIV-1); DEAD-Box domain; DDX3
The human T – cell leukemia virus type 1 (HTLV-1) was the first retrovirus discovered to be causative of a human cancer, Adult T-cell leukemia (ATL). The transforming entity of HTLV-1 has been attributed to the virally-encoded oncoprotein, Tax. Unlike the v-onc proteins encoded by other oncogenic animal retroviruses that transform cells, Tax does not originate from a c-onc counterpart. In this article, we review progress in our understanding of HTLV-1 infectivity, cellular transformation, anti-sense transcription, and therapy, thirty years after the original discovery of this virus.
human T-cell leukemia virus type 1 (HTLV-1); adult T cell leukemia (ATL); Tax; HTLV-1 bZIP factor (HBZ); aneuploidy
The post-transcriptional export of spliced and unspliced HIV-1 (human immunodeficiency virus type 1) RNAs from the nucleus to the cytoplasm is a complex process. Part of the complexity arises from the fact that eukaryotic cells normally retain unspliced RNAs in the nucleus preventing their exit into the cytoplasm. HIV-1 has evolved a protein, Rev, that participates in the export of unspliced/partially spliced viral RNAs from the nucleus. It has been documented that several cellular factors cooperate in trans with Rev, and certain cis-RNA motifs/features are important for transcripts to be recognized by Rev and its co-factors. Here, the post-transcriptional activities of Rev are discussed in the context of a recent finding that an RNA cap methyltransferase contributes to the expression of unspliced/partially spliced HIV-1 transcripts.
PIMT; TGS1; HIV-1; Rev; CRM1; RNA export
Choosing the right laboratory in which to do postdoctoral training is perhaps one of the most important decisions that a scientist makes in his or her career. Does one choose a laboratory based on the research topic or the research style of the mentor? Does one choose a large laboratory or a small one? How does one fit the selection of a postdoctoral laboratory into the context of one’s long-range career goals? Here, I briefly discuss three points worth considering in seeking a research laboratory for postdoctoral training after the completion of a graduate degree.
education; postdoctoral training; mentoring
Human tumor viruses are associated with a variety of human malignancies, and it is estimated that 15% of all human cancers have a viral etiology. An abnormality in chromosomal ploidy or aneuploidy is a hallmark of cancers. In normal cells, euploidy is governed by several factors including an intact spindle assembly checkpoint (SAC), accurate centrosome duplication, and proper cytokinesis. Viral oncoproteins are suggested to perturb the cellular machineries for chromosomal segregation creating aneuploidy which can lead to the malignant transformation of infected cells. Here we review in brief some of the mechanisms employed by viruses that can cause cellular aneuploidy.
Spindle assembly checkpoint; centrosome; aneuploidy; human T-cell leukemia virus type I (HTLV-I); Tax
The mechanism of HTLV-1 transformation of cells to Adult T cell leukemia (ATL) remains not fully understood. Currently, the viral Tax oncoprotein is known to be required to initiate transformation. Emerging evidence suggests that Tax is not needed to maintain the transformed ATL phenotype. Recent studies have shown that HTLV-1 transformed cells show deregulated expression of cellular microRNAs (miRNAs). Here we discuss the possibility that early ATL cells are Tax-oncogeneaddicted while late ATL cells are oncogenic microRNA (oncomiR) – addicted. The potential utility of interrupting oncomiR addiction as a cancer treatment is broached.
HTLV; ATL; MicroRNAs; Leukemia; oncogene
Mutations in the LMNA gene are associated with a spectrum of human dystrophic diseases termed the “nuclear laminopathies.” We recently found that the accumulation of the inner nuclear envelope proteins SUN1 is pathogenic in progeric and dystrophic laminopathies. This conclusion arose from the unexpected observation that the deletion of Sun1, instead of accelerating aging, actually ameliorated the progeric and dystrophic phenotypes in Lmna-deficient mice. In human cells, knocking down SUN1 corrected the nuclear aberrancies and the senescent tendencies of HGPS (Hutchinson-Gilford progeria syndrome) skin fibroblasts. Here we offer additional comments on the contributions of SUN1 and the process of normal protein turnover to cellular aging.
SUN1; nuclear envelope; progeria; lamin; aging
Human LMNA gene mutations result in laminopathies that include Emery-Dreifuss Muscular Dystrophy (AD-EDMD) and Hutchinson-Gilford Progeria, the premature aging syndrome (HGPS). The Lmna null (Lmna−/−) and progeroid LmnaΔ9 mutant mice are models for AD-EDMD and HGPS respectively. Both animals develop severe tissue pathologies with abbreviated life spans. Like HGPS cells, Lmna−/− and LmnaΔ9 fibroblasts have typically misshapen nuclei. Unexpectedly, Lmna−/− or LmnaΔ9 mice that are also deficient for the inner nuclear membrane protein Sun1 show markedly reduced tissue pathologies and enhanced longevity. Concordantly, reduction of SUN1 over-accumulation in LMNA mutant fibroblasts and in HGPS cells corrected nuclear defects and cellular senescence. Collectively, these findings implicate Sun1 protein accumulation as a common pathogenic event in Lmna−/−, LmnaΔ9, and HGPS disorders.
Retrovirology would like to thank the following for their assistance with peer review of manuscripts for the journal in 2012.
Hereditary hearing loss is the most common sensory deficit. We determined that progressive high-frequency hearing loss in 2 families of Iraqi Jewish ancestry was due to homozygosity for the protein truncating mutation SYNE4 c.228delAT. SYNE4, a gene not previously associated with hearing loss, encodes nesprin-4 (NESP4), an outer nuclear membrane (ONM) protein expressed in the hair cells of the inner ear. The truncated NESP4 encoded by the families’ mutation did not localize to the ONM. NESP4 and SUN domain–containing protein 1 (SUN1), which localizes to the inner nuclear membrane (INM), are part of the linker of nucleoskeleton and cytoskeleton (LINC) complex in the nuclear envelope. Mice lacking either Nesp4 or Sun1 were evaluated for hair cell defects and hearing loss. In both Nesp4–/– and Sun1–/– mice, OHCs formed normally, but degenerated as hearing matured, leading to progressive hearing loss. The nuclei of OHCs from mutant mice failed to maintain their basal localization, potentially affecting cell motility and hence the response to sound. These results demonstrate that the LINC complex is essential for viability and normal morphology of OHCs and suggest that the position of the nucleus in sensory epithelial cells is critical for maintenance of normal hearing.
Retroviruses have an intricate life cycle. There is much to be learned from studying retrovirus-host interactions. Among retroviruses, the primate lentiviruses have one of the more complex genome structures with three categories of viral genes: structural, regulatory, and accessory genes. Over time, we have gained increasing understanding of the lentivirus life cycle from studying host factors that support virus replication. Similarly, studies on host restriction factors that inhibit viral replication have also made significant contributions to our knowledge. Here, we review recent progress on the rapidly growing field of restriction factors, focusing on the antiretroviral activities of APOBEC3G, TRIM5, tetherin, SAMHD1, MOV10, and cellular microRNAs (miRNAs), and the counter-activities of Vif, Vpu, Vpr, Vpx, and Nef.
The importance of geographic diversity in publishing is emphasized in this editorial.
Human T-cell Leukemia Virus type 1 (HTLV-1) and 2 (HTLV-2) are two closely related human retroviruses. HTLV-1 is associated with an aggressive Adult T-cell Leukemia (ATL) while there is no evidence for an association of HTLV-2 with any human malignancies. The two viruses encode transactivator proteins, Tax-1 and Tax-2 respectively. In ATL, Tax-1 is thought to play a central role in the transformation of a normal T-cell into a leukemic cell; however, it has not been entirely clear how post-translational modifications of Tax-1 influence its transforming activity. Here, we discuss three recent papers that report on the ubiquitination and sumoylation of Tax-1 and Tax-2. We comment on their divergent findings implicating the importance (or lack of importance) of these modifications and other events on Tax activation of NF-κB as related to cellular transformation.
HTLV-1; HTLV-2; Tax; ATL; Cell transformation; NF-κB; Sumoylation; Ubiquitination
Tombusvirus P19 is a protein encoded by tomato bushy stunt virus and related tombusviruses. Earlier studies have demonstrated that P19 is an RNA silencing suppressor (RSS) in plant cells. However, it has not been systematically investigated how P19 suppresses RNA interference in various mammalian cell settings.
We have studied the RSS effect of P19 in mammalian cells, HEK293T, HeLa, and mouse embryonic fibroblasts. We have individually mutated 18 positively charged residues in P19 and found that 6 of these charged residues in P19 reduce its ability to suppress RNA interference. In each case, the reduction of silencing of RNA interference correlated with the reduced ability by these P19 mutants to bind siRNAs (small interfering RNAs).
Our findings characterize a class of RNA-binding proteins that function as RSS moieties. We find a tight correlation between positively charged residues in P19 accounting for siRNA-binding and their RSS activity. Because P19’s activity is conserved in plant and animal cells, we conclude that its RSS function unlikely requires cell type-specific co-factors and likely arises from direct RNA-binding.
Recent literature highlights at Retrovirology are described. Predictions are made regarding “hot” retrovirology research trends for the coming year based on recent journal access statistics. Changes in Retrovirology editor and the frequency of the Retrovirology Prize are announced.
MicroRNAs (miRNAs) are small non-coding RNAs that control a multitude of critical processes in mammalian cells. Increasing evidence has emerged that host miRNAs serve in animal cells to restrict viral infections. In turn, many viruses encode RNA silencing suppressors (RSS) which are employed to moderate the potency of the cell’s miRNA selection against viral replication. Some viruses also encode viral miRNAs. In this review, we summarize findings from human immunodeficiency virus type 1 (HIV-1) and human T-cell leukemia virus type 1 (HTLV-1) that illustrate examples of host cell miRNAs that target the viruses, of RSS encoded by viruses, and of host cell miRNA profile changes that are seen in infected cells.
microRNA; virus replication; innate immunity; RNA silencing suppressors; viral gene expression; virus-host interaction
Autophagy is a protein degradative process important for normal cellular metabolism. It is apparently used also by cells to eliminate invading pathogens. Interestingly, many pathogens have learned to subvert the cell’s autophagic process. Here, we review the interactions between viruses and cells in regards to cellular autophagy. Using findings from hepatitis B virus and human retroviruses, HIV-1 and HTLV-1, we discuss mechanisms used by viruses to usurp cellular autophagy in ways that benefit viral replication.
Cell and Bioscience is on track to receive its first Impact Factor in mid-2013. What is the role of the Impact Factor as a measure of a journal’s success?
MicroRNAs (miRNAs) are 22-nt non-coding RNAs involved in the regulation of cellular gene
expression and potential cellular defense against viral infection. Using in
silico analyses, we predicted target sites for 22 human miRNAs in the HIV
genome. Transfection experiments using synthetic miRNAs showed that five of these miRNAs
capably decreased HIV replication. Using one of these five miRNAs, human miR-326 as an
example, we demonstrated that the degree of complementarity between the predicted viral
sequence and cellular miR-326 correlates, in a Dicer-dependent manner, with the potency of
miRNA-mediated restriction of viral replication. Antagomirs to miR-326 that knocked down
this cell endogenous miRNA increased HIV-1 replication in cells, suggesting that miR-326
is physiologically functional in moderating HIV-1 replication in human cells.
A major challenge in studies of human diseases involving macrophages is low yield and heterogeneity of the primary cells and limited ability of these cells for transfections and genetic manipulations. To address this issue, we developed a simple and efficient three steps method for somatic 293T cells reprogramming into monocytes and macrophage-like cells. First, 293T cells were reprogrammed into induced pluripotent stem cells (iPSCs) through a transfection-mediated expression of two factors, Oct-4 and Sox2, resulting in a high yield of iPSC. Second, the obtained iPSC were differentiated into monocytes using IL-3 and M-CSF treatment. And third, monocytes were differentiated into macrophage-like cells in the presence of M-CSF. As an example, we developed HIV-1-resistant macrophage-like cells from 293T cells with knockdown of CDK2, a factor critical for HIV-1 transcription. Our study provides a proof-of-principle approach that can be used to study the role of host cell factors in HIV-1 infection of human macrophages.
HIV-1 resistant macrophage-like cells; CDK2 knockdown; iPSC
Nine years after its founding, Retrovirology has moved to the forefront of virology journals in Impact Factor.