1
|
Zhao H, Punga T, Pettersson U. Adenovirus in the omics era - a multipronged strategy. FEBS Lett 2020; 594:1879-1890. [PMID: 31811727 DOI: 10.1002/1873-3468.13710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/21/2019] [Accepted: 11/28/2019] [Indexed: 01/15/2023]
Abstract
Human adenoviruses (HAdVs) are common pathogens associated with a wide variety of respiratory, ocular, and gastrointestinal diseases. To achieve its effective lytic mode of replication, HAdVs have to reprogram host-cell gene expression and fine-tune viral gene expression in a temporal manner. In two decades, omics revolution has advanced our knowledge about the HAdV and host-cell interplay at the RNA and protein levels. This review summarizes the current knowledge from large-scale datasets on how HAdV infections adjust coding and noncoding RNA expression, as well as how they reprogram host-cell proteome during the lytic course of infection.
Collapse
Affiliation(s)
- Hongxing Zhao
- Beijer Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Sweden
| | - Ulf Pettersson
- Beijer Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Sweden
| |
Collapse
|
2
|
Alvesalo J, Greco D, Leinonen M, Raitila T, Vuorela P, Auvinen P. Microarray Analysis of aChlamydia pneumoniae–Infected Human Epithelial Cell Line by Use of Gene Ontology Hierarchy. J Infect Dis 2008; 197:156-62. [DOI: 10.1086/524142] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
3
|
Bishopric NH, Zeng GQ, Sato B, Webster KA. Adenovirus E1A inhibits cardiac myocyte-specific gene expression through its amino terminus. J Biol Chem 1997; 272:20584-94. [PMID: 9252373 DOI: 10.1074/jbc.272.33.20584] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Adenovirus E1A oncoproteins inhibit muscle-specific gene expression and myogenic differentiation by suppressing the transcriptional activating functions of basic helix-loop-helix proteins. As one approach to identifying cardiac-specific gene regulatory proteins, we analyzed the functional regions of E1A proteins that are required for muscle gene repression in cardiac cells. Myocyte-specific promoters, including the alpha-actins and alpha-myosin heavy chain, were selectively and potently inhibited (>90%) by E1A, while the ubiquitously expressed beta-actin promoter was only partially ( approximately 30%) repressed; endogenous gene expression was also affected. Distinct E1A protein binding sites mediated repression of muscle-specific and ubiquitous actin promoters. E1A-mediated inhibition of beta-actin required both an intact binding site for the tumor repressor proteins pRb and p107 and a second E1A domain (residues 15-35). In contrast, cardiac-specific promoter repression required the E1A amino-terminal residues 2-36. The proximal skeletal actin promoter (3' to base pair -153) was a target for repression by E1A. Although E1A binding to p300 was not required for inhibition of either promoter, co-expression of p300 partially reversed E1A-mediated transcriptional repression. We conclude that cardiac-specific and general promoter inhibition by E1A occurs by distinct mechanisms and that cardiac-specific gene expression is modulated by cellular factors interacting with the E1A p300/CBP-binding domain.
Collapse
Affiliation(s)
- N H Bishopric
- Molecular Cardiology Laboratory, SRI International, Menlo Park, California 94125, USA
| | | | | | | |
Collapse
|
4
|
Yang UC, Huang W, Flint SJ. mRNA export correlates with activation of transcription in human subgroup C adenovirus-infected cells. J Virol 1996; 70:4071-80. [PMID: 8648745 PMCID: PMC190288 DOI: 10.1128/jvi.70.6.4071-4080.1996] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
To investigate the mechanisms by which viral mRNA species are distinguished from their cellular counterparts for export to the cytoplasm during the late phase of subgroup C adenovirus infection, we have examined the metabolism of several cellular and viral mRNAs in human cells productively infected by adenovirus type 5 (Ad5). Several cellular mRNAs that were refractory to, or could escape from, adenovirus-induced inhibition of export of mRNA from the nucleus have been identified. This group includes Hsp70 mRNAs synthesized upon heat shock of Ad5-infected 293 or HeLa cells during the late phase of infection. However, successful export in Ad5-infected cells is not a specific response to heat shock, for beta-tubulin and interferon-inducible mRNAs were also refractory to virus-induced export inhibition. The export of these cellular mRNAs, like that of viral late mRNAs, required the E1B 55-kDa protein. Export to the cytoplasm during the late phase of Ad5 infection of several cellular mRNAs, including members of the Hsp70 family whose export was inhibited under some, but not other, conditions, indicates that viral mRNA species cannot be selectively exported by virtue of specific sequence or structural features. Cellular and viral late mRNAs that can be exported from the nucleus to the cytoplasm were expressed from genes whose transcription was induced or activated during the late phase of Ad5 infection. Consistent with the possibility that successful export is governed by transcriptional activation in the late phase of adenovirus infection, newly synthesized viral early E1A mRNA was subject to export inhibition during the late phase of infection.
Collapse
Affiliation(s)
- U C Yang
- Department of Molecular Biology, Princeton University, New Jersey 08544-1014, USA
| | | | | |
Collapse
|
5
|
Smiley JK, Young MA, Bansbach CC, Flint SJ. The metabolism of small cellular RNA species during productive subgroup C adenovirus infection. Virology 1995; 206:100-7. [PMID: 7831765 DOI: 10.1016/s0042-6822(95)80024-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
During the late phase of subgroup C adenovirus infection, export of cellular mRNA from the nucleus to the cytoplasm is inhibited. In one approach to investigate the mechanism whereby viral late mRNAs are selected for export, we have examined the metabolism of small cellular RNA species transcribed by all three RNA polymerases during the late phase of Ad5 infection. No changes in the quantities of [3H]uridine-labeled 5S rRNA or tRNAs entering the cytoplasm were observed in infected cells. Adenovirus type 5 infection reduced the nuclear and cytoplasmic populations of the newly synthesized, snRNP-associated snRNAs U1, U2, U4, U5, and U6. Transcription of a representative snRNA, U1 RNA, was not inhibited, indicating that the post-transcriptional metabolism of snRNAs was perturbed during the late phase of infection. The increased cytoplasmic concentration of newly synthesized U1 RNA in Ad5- compared to mock-infected cells, and the greater reduction of the snRNP-associated compared to the total U1 RNA population, indicated that snRNP assembly in the cytoplasm was impaired. As adenovirus infection does not perturb export from the nucleus of small cellular mRNAs transcribed by RNA polymerases II and III, viral mRNA must be distinguished for selective export at a nuclear step upstream of translocation to the cytoplasm via nuclear pore complexes.
Collapse
Affiliation(s)
- J K Smiley
- Department of Molecular Biology, Princeton University, New Jersey 08544-1014
| | | | | | | |
Collapse
|
6
|
Affiliation(s)
- L Philipson
- Skirball Institute of Biomolecular Medicine, New York University Medical Center, New York 10016, USA
| |
Collapse
|
7
|
Abstract
Treatment of Hela cells infected with adenovirus 5 wild type (Ad5WT) with the tumor-promoting phorbol ester TPA (12-O-tetradecanoyl phorbol-13-acetate), accelerated as well as stimulated expression of viral early genes EII and EIII but not that of EIA. TPA treatment of HeLa cells infected with dl312, an Ad5 EIA deletion mutant, activated expression of EIII but not EII. Stimulation of EII and EIII expression was blocked by H7 (1-5-isoquinolinyl sulfonyl-2-methyl piperazine), a specific inhibitor of protein kinase c (PKc). Nuclear run off assays demonstrated that TPA exerted a stimulatory effect at the level of transcription. PKc inhibitor alone reduced transcription of early genes in the absence of TPA activation. Phosphorylation of EIA 35 kDa but not 40- to 45-kDa proteins was dramatically increased by TPA. Three cellular proteins of 200, 24, and 20 kDa which coprecipitated with EIA proteins underwent enhanced and preferential phosphorylation by activated PKc. Inhibitor of PKc blocked phosphorylation of cellular proteins and reduced phosphorylation of EIA 35 kDa but not EIA 40- to 45-kDa proteins. These results tend to indicate that TPA stimulates adenovirus early gene expression through activation of protein kinase c and further suggest but do not prove that this may be due to specific phosphorylation of EIA 35 kDa and cellular proteins of 200, 24, and 20 kDa.
Collapse
Affiliation(s)
- A Mirza
- Institut für Molekularbiologie (Tumorforschung), Universitätsklinikum, Essen, Germany
| |
Collapse
|
8
|
Maine AB, Ciejek-Baez E. Distinct developmental regulatory mechanisms for two members of the aldolase gene family. DEVELOPMENTAL GENETICS 1991; 12:431-6. [PMID: 1822433 DOI: 10.1002/dvg.1020120608] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The aldolase isozyme family is composed of three members, A, B, and C, which are encoded by separate genes. The proteins are expressed in a tissue-restricted manner during development and in the adult. To elucidate the regulation of aldolase mRNA in the mouse liver, we analyzed its expression by a number of methods including Northern blot, RNA dot blot, and nuclear run-on assays. Our experiments demonstrate that the expression of aldolase A in the liver is primarily regulated by post-transcriptional control. In contrast, we found that changes in the level of aldolase B mRNA are due to changes in the rate of initiation of transcription. In addition, we examined the regulation of aldolase expression in the adult kidney. We found that although the kidney has eight times more aldolase B than the liver, the rate of initiation of transcription is similar in both tissues. Also, the rate of initiation of transcription of aldolase A is the same in the adult kidney and liver although there is 40 times more steady state aldolase A mRNA in the kidney than in the liver.
Collapse
Affiliation(s)
- A B Maine
- Department of Biochemistry, University of Rochester School of Medicine and Dentistry, New York 14642
| | | |
Collapse
|
9
|
Abstract
The intracellular location of the adenovirus type 5 E1B 55-kilodalton (kDa) protein, particularly the question of whether it is associated with nuclear pore complexes, was examined. Fractionation of adenovirus type 5-infected HeLa cell nuclei by an established procedure (N. Dwyer and G. Blobel, J. Cell. Biol. 70:581-591, 1976) yielded one population of E1B 55-kDa protein molecules released by digestion of nuclei with RNase A and a second population recovered in the pore complex-lamina fraction. Free and E1B 55-kDa protein-bound forms of the E4 34-kDa protein (P. Sarnow, C. A. Sullivan, and A. J. Levine, Virology 120:387-394, 1982) were largely recovered in the pore complex-lamina fraction. Nevertheless, the association of E1B 55-kDa protein molecules with this nuclear envelope fraction did not depend on interaction of the E1B 55-kDa protein with the E4 34-kDa protein. Comparison of the immunofluorescence patterns observed with antibodies recognizing the E1B 55-kDa protein or cellular pore complex proteins and of the behavior of these viral and cellular proteins during in situ fractionation suggests that the E1B 55-kDa protein does not become intimately or stably associated with pore complexes in adenovirus-infected cells.
Collapse
Affiliation(s)
- J K Smiley
- Department of Biology, Princeton University, New Jersey 08544
| | | | | |
Collapse
|
10
|
Stein GS, Stein JL, Lian JB, Van Wijnen AJ, Wright KL, Pauli U. Modifications in molecular mechanisms associated with control of cell cycle regulated human histone gene expression during differentiation. CELL BIOPHYSICS 1989; 15:201-23. [PMID: 2480181 DOI: 10.1007/bf02989684] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Histone proteins are preferentially synthesized during the S-phase of the cell cycle, and the temporal and functional coupling of histone gene expression with DNA replication is mediated at both the transcriptional and posttranscriptional levels. The genes are transcribed throughout the cell cycle, and a 3-5-fold enhancement in the rate of transcription occurs during the first 2 h following initiation of DNA synthesis. Control of histone mRNA stability also accounts for some of the 20-100fold increase in cellular histone mRNA levels during S-phase and for the rapid and selective degradation of the mRNAs at the natural completion of DNA replication or when DNA synthesis is inhibited. Two segments of the proximal promoter, designated Sites I and II, influence the specificity and rate of histone gene transcription. Occupancy of Sites I and II during all periods of the cell cycle by three transacting factors (HiNF-A, HiNF-C, and HiNF-D) suggests that these protein-DNA interactions are responsible for the constitutive transcription of histone genes. Binding of HiNF-D in Site II is selectively lost, whereas occupancy of Site I by HiNF-A and -C persists when histone gene transcription is down regulated when cells terminally differentiate. These results are consistent with a primary role for interactions of HiNF-D with a proximal promoter element in rendering cell growth regulated human histone genes transcribable in proliferating cells.
Collapse
Affiliation(s)
- G S Stein
- Department of Cell Biology, University of Massachusetts Medical Center, Worcester
| | | | | | | | | | | |
Collapse
|
11
|
Adenovirus transcriptional complexes contain EIa encoded tumour antigens physically bound to cellular proteins. Arch Virol 1988; 102:245-62. [PMID: 2974276 DOI: 10.1007/bf01310829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Adenovirus type 12 transcriptional complexes were isolated from cells during the early phase of infection. Sedimentation analysis identified a fast sedimenting complex type I and a slow sedimenting complex type II. Both complexes made virus specific RNA complementary to all the early genes and both contained viral DNA, which in type II but not in type I had nucleosome like configuration. Analysis of the proteins of the complexes with antiserum against Ad 12 EIa-beta-galactosidase fusion protein expressed in E. coli demonstrated the following: (a) type I complex contained EIa 45 K protein, which co-precipitated with cellular proteins of mol. wt. 42, 58, and 60 K, (b) type II complex contained EIa 47 K protein, which co-precipitated with major cellular proteins of 35, 40-46 K and minor proteins of 58, 60, 68, 76, 86, and 120-150 K. Association of EIa specific and cellular proteins to transcriptional complexes was sensitive to both 1 M NaCl and DNAse I indicating the DNA binding nature of these proteins. Treatment of transcriptional complexes with 1 M NaCl or DNase I released EIa proteins, which still remained strongly bound to cellular proteins. These findings suggested that EIa proteins bind to viral DNA and that this binding is probably mediated by cellular proteins.
Collapse
|
12
|
Yager DR, Bachenheimer SL. Synthesis and metabolism of cellular transcripts in HSV-1 infected cells. Virus Genes 1988; 1:135-48. [PMID: 2853485 DOI: 10.1007/bf00555933] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The effects of productive herpes simplex virus infection on host gene expression were examined by measuring the rates of synthesis and subsequent fates of several Vero cell mRNAs. The rates of transcription of actin, beta-tubulin, and histone-3 and -4 RNAs were measured by pulse-labeling of intact cells as well as by run-on transcription in isolated nuclei. At both early (2 hr) and late (6 hr) times, the relative rates of transcription of these RNAs were greater than in uninfected cells. Kinetic labeling experiments performed at late times also revealed increased turnover rates of nuclear RNAs. That the rate of appearance of these RNAs in the cytoplasm was also reduced suggests that these cellular RNAs are being specifically retained and degraded in the nucleus. Levels of pre-existing cytoplasmic RNAs as measured by Northern blot analysis declined rapidly after infection though the nuclear steady-state levels of these RNAs increased up to 3 hr postinfection and then declined between 3 and 10 hr postinfection. At no time was the accumulation of processing intermediates detectable. Finally, we also determined that, consistent with the decline in levels of histone mRNA, rates of histone protein synthesis declined rapidly after infection.
Collapse
Affiliation(s)
- D R Yager
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill 27599
| | | |
Collapse
|
13
|
Young DC, Tobin GJ, Flanegan JB. Characterization of product RNAs synthesized in vitro by poliovirus RNA polymerase purified by chromatography on hydroxylapatite or poly(U) Sepharose. J Virol 1987; 61:611-4. [PMID: 3027390 PMCID: PMC253991 DOI: 10.1128/jvi.61.2.611-614.1987] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The size of the product RNA synthesized by the poliovirus RNA polymerase and host factor was significantly affected by the type of column chromatography used to purify the polymerase. Dimer length product RNA was synthesized by the polymerase purified by chromatography on hydroxylapatite. This contrasted with the monomer length product RNA synthesized by the polymerase purified by chromatography on poly(U) Sepharose. The poly(U) Sepharose-purified polymerase was shown to contain oligo(U) that functioned as a primer. The addition of host factor to reactions containing the poly(U) Sepharose-purified polymerase significantly increased the synthesis of monomer length product RNA, in agreement with previous studies. This product RNA, however, did not immunoprecipitate with anti-VPg antibody and thus was not linked to VPg or a VPg-related protein. Thus, it was concluded that the synthesis of monomer length product RNA by the poly(U) Sepharose-purified polymerase and host factor was caused by oligo(U) priming rather than VPg priming.
Collapse
|
14
|
Ross J, Kobs G. H4 histone messenger RNA decay in cell-free extracts initiates at or near the 3' terminus and proceeds 3' to 5'. J Mol Biol 1986; 188:579-93. [PMID: 3525849 DOI: 10.1016/s0022-2836(86)80008-0] [Citation(s) in RCA: 146] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The relative decay of four human messenger RNAs, gamma globin, delta globin, c-myc and H4 histone, were compared in a cell-free system. Under appropriate conditions, they are degraded in vitro in approximately the same relative order as in vivo: histone faster than c-myc and delta globin faster than gamma globin. Degradation of polysome-associated H4 histone mRNA and of deproteinized histone mRNA begins at or near the 3' terminus. At least a portion of the mRNA then continues to be degraded in a 3' to 5' direction. Discrete 3'-terminal degradation hold-up points are observed, suggesting that 3' to 5' degradation occurs non-uniformly. Cycloheximide and puromycin inhibit protein synthesis but do not affect the rate or directionality of histone mRNA decay in vitro. We conclude that the rate-limiting step in H4 histone mRNA decay occurs at or near the 3' terminus and that at least a portion of the mRNA molecule is subsequently degraded 3' to 5', probably via a processive exonuclease.
Collapse
|
15
|
Abstract
This chapter summarizes the structural features that govern the translation of viral mRNAs: where the synthesis of a protein starts and ends, how many proteins can be produced from one mRNA, and how efficiently. It focuses on the interplay between viral and cellular mRNAs and the translational machinery. That interplay, together with the intrinsic structure of viral mRNAs, determines the patterns of translation in infected cells. It also points out some possibilities for translational regulation that can only be glimpsed at present, but are likely to come into focus in the future. The mechanism of selecting the initiation site for protein synthesis appears to follow a single formula. The translational machinery displays a certain flexibility that is exploited more frequently by viral than by cellular mRNAs. Although some of the parameters that determine efficiency have been identified, how efficiently a given mRNA will be translated cannot be predicted by summing the known parameters.
Collapse
|
16
|
MESH Headings
- Adenovirus Infections, Human/genetics
- Adenoviruses, Human/genetics
- Cell Line
- Cells, Cultured
- DNA, Viral/biosynthesis
- Enhancer Elements, Genetic
- Gene Expression Regulation
- Genes, Viral
- Humans
- Promoter Regions, Genetic
- RNA Processing, Post-Transcriptional
- RNA, Messenger/biosynthesis
- RNA, Viral/biosynthesis
- Transcription, Genetic
- Viral Proteins/genetics
Collapse
|
17
|
Abstract
The effects of productive adenovirus infection on host gene expression were studied by using a line of methotrexate-resistant HeLa cells with amplified dihydrofolate reductase (DHFR) genes. We have previously reported that synthesis of DHFR is induced threefold early in infection and is shut off late in infection (Yoder et al., Mol. Cell. Biol. 3:819-828, 1983). These changes in DHFR protein synthesis are accompanied by changes in both the steady-state cytoplasmic levels of DHFR mRNA and in the rate of appearance of DHFR mRNA in the cytoplasm. In this report, we examined the mechanism of nuclear control of DHFR mRNA levels. Transcription of DHFR-specific sequences continued at a constant rate throughout infection, representing 0.015% of the total transcriptional activity. In contrast, nuclear steady-state levels of DHFR sequences changed in correspondence to the changing rate of appearance of DHFR mRNA in the cytoplasm. That is, nuclear levels of DHFR-specific sequences rose 2.5-fold early in infection and declined to a level below that found in uninfected cells late in infection. Thus, the relative nuclear stability of DHFR sequences changed throughout the course of infection such that during the time of induction, DHFR sequences were preferentially stabilized. This stabilization was transient, however, and was no longer observed by the time of shutoff. These data indicate that posttranscriptional nuclear events are important in the regulation of DHFR gene expression by adenovirus.
Collapse
|
18
|
Stein GS, Stein JL. The relationship between human histone gene expression and DNA replication. Bioessays 1984. [DOI: 10.1002/bies.950010505] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|