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Kamel, Wael
Publications (10 of 11) Show all publications
Younis, S., Kamel, W., Falkeborn, T., Wang, H., Yu, D., Daniels, R., . . . Andersson, L. (2018). Multiple nuclear-replicating viruses require the stress-induced protein ZC3H11A for efficient growth. Proceedings of the National Academy of Sciences of the United States of America, 115(16), E3808-E3816
Open this publication in new window or tab >>Multiple nuclear-replicating viruses require the stress-induced protein ZC3H11A for efficient growth
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2018 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 16, p. E3808-E3816Article in journal (Refereed) Published
Abstract [en]

The zinc finger CCCH-type containing 11A (ZC3H11A) gene encodes a well-conserved zinc finger protein that may function in mRNA export as it has been shown to associate with the transcription export (TREX) complex in proteomic screens. Here, we report that ZC3H11A is a stress-induced nuclear protein with RNA-binding capacity that localizes to nuclear splicing speckles. During an adenovirus infection, the ZC3H11A protein and splicing factor SRSF2 relocalize to nuclear regions where viral DNA replication and transcription take place. Knockout (KO) of ZC3H11A in HeLa cells demonstrated that several nuclear-replicating viruses are dependent on ZC3H11A for efficient growth (HIV, influenza virus, herpes simplex virus, and adenovirus), whereas cytoplasmic replicating viruses are not (vaccinia virus and Semliki Forest virus). High-throughput sequencing of ZC3H11A-cross-linked RNA showed that ZC3H11A binds to short purine-rich ribonucleotide stretches in cellular and adenoviral transcripts. We show that the RNA-binding property of ZC3H11A is crucial for its function and localization. In ZC3H11A KO cells, the adenovirus fiber mRNA accumulates in the cell nucleus. Our results suggest that ZC3H11A is important for maintaining nuclear export of mRNAs during stress and that several nuclear-replicating viruses take advantage of this mechanism to facilitate their replication.

Keywords
ZC3H11A, mRNA export, stress response, virus infection
National Category
Microbiology in the medical area Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-354118 (URN)10.1073/pnas.1722333115 (DOI)000430191900026 ()29610341 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation
Note

De 2 första författarna delar förstaförfattarskapet.

Available from: 2018-06-19 Created: 2018-06-19 Last updated: 2018-06-19Bibliographically approved
Kamel, W. & Akusjärvi, G. (2017). An Ago2-associated capped transcriptional start site small RNA suppresses adenovirus DNA replication. RNA: A publication of the RNA Society, 23(11), 1700-1711
Open this publication in new window or tab >>An Ago2-associated capped transcriptional start site small RNA suppresses adenovirus DNA replication
2017 (English)In: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 23, no 11, p. 1700-1711Article in journal (Refereed) Published
Abstract [en]

Here we show that the adenovirus major late promoter produces a 31-nucleotide transcriptional start site small RNA (MLP-TSS-sRNA) that retains the 7-methylguanosine (m7G)-cap and is incorporated onto Ago2-containing RNA-induced silencing complexes (RISC) in human adenovirus-37 infected cells. RNA polymerase II CLIP (UV-cross linking immunoprecipitation) experiments suggest that the MLP-TSS-sRNA is produced by promoter proximal stalling/termination of RNA polymerase II transcription at the site of the small RNA 3' end. The MLP-TSS-sRNA is highly stable in cells and functionally active, down-regulating complementary targets in a sequence and dose-dependent manner. The MLP-TSS-sRNA is transcribed from the opposite strand to the adenoviral DNA polymerase and preterminal protein mRNAs, two essential viral replication proteins. We show that the MLP-TSS-sRNA act in trans to reduce DNA polymerase and preterminal protein mRNA expression. As a consequence of this, the MLP-TSS-sRNA has an inhibitory effect on the efficiency of viral DNA replication. Collectively, our results suggest that this novel sRNA may serve a regulatory function controlling viral genome replication during a lytic and/or persistent adenovirus infection in its natural host.

Keywords
adenovirus, Ago2, m7G-cap, small RNA
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-339747 (URN)10.1261/rna.061291.117 (DOI)000412996100009 ()28839112 (PubMedID)
Funder
Swedish Cancer Society, 130469Swedish Research Council, 2006-5038-36531-16
Available from: 2018-01-25 Created: 2018-01-25 Last updated: 2018-01-25Bibliographically approved
Assadian, F., Kamel, W., Laurell, G., Svensson, C., Punga, T. & Akusjärvi, G. (2017). Expression profile of Epstein-Barr virus and human adenovirus small RNAs in tonsillar B and T lymphocytes. PLoS ONE, 12(5), Article ID e0177275.
Open this publication in new window or tab >>Expression profile of Epstein-Barr virus and human adenovirus small RNAs in tonsillar B and T lymphocytes
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2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 5, article id e0177275Article in journal (Refereed) Published
Abstract [en]

We have used high-throughput small RNA sequencing to characterize viral small RNA expression in purified tonsillar B and T lymphocytes isolated from patients tested positive for Epstein-Barr virus (EBV) or human adenovirus (HAdV) infections, respectively. In the small set of patients analyzed, the expression profile of EBV and HAdV miRNAs could not distinguish between patients diagnosed with tonsillar hypertrophy or chronic/recurrent tonsillitis. The EBV miR-BART expression profile among the patients diagnosed with tonsillar diseases resembles most closely the pattern seen in EBV+ tumors (Latency II/I). The miRBARTs that appear to be absent in normal EBV infected cells are essentially all detectable in the diseased tonsillar B lymphocytes. In the EBV+ B cells we detected 44 EBV miRBARTs derived from the proposed BART precursor hairpins whereof five are not annotated in miRBase v21. One previously undetected miRNA, BART16b-5p, originates from the miR-BART16 precursor hairpin as an alternative 5 A miR-BART16 located precisely upstream of the annotated miR-BART16-5p. Further, our analysis revealed an extensive sequence variation among the EBV miRNAs with isomiRs having a constant 5 A end but alternative 3 A ends. A range of small RNAs was also detected from the terminal stem of the EBER RNAs and the 3 A part of v-snoRNA1. During a lytic HAdV infection in established cell lines the terminal stem of the viral non-coding VA RNAs are processed to highly abundant viral miRNAs (mivaRNAs). In contrast, mivaRNA expression in HAdV positive tonsillar T lymphocytes was very low. The small RNA profile further showed that the 5 A mivaRNA from VA RNAI and the 3 A mivaRNA from VA RNAII were as predicted, whereas the 3 A mivaRNA from VA RNAI showed an aberrant processing upstream of the expected Dicer cleavage site.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2017
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-326234 (URN)10.1371/journal.pone.0177275 (DOI)000402062800013 ()28542273 (PubMedID)
Funder
Swedish Cancer Society, 120678, 130469
Available from: 2017-07-06 Created: 2017-07-06 Last updated: 2017-11-29Bibliographically approved
Lan, S., Kamel, W., Punga, T. & Akusjärvi, G. (2017). The adenovirus L4-22K protein regulates transcription and RNA splicing via a sequence-specific single-stranded RNA binding. Nucleic Acids Research, 45(4), 1731-1742
Open this publication in new window or tab >>The adenovirus L4-22K protein regulates transcription and RNA splicing via a sequence-specific single-stranded RNA binding
2017 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 45, no 4, p. 1731-1742Article in journal (Refereed) Published
Abstract [en]

The adenovirus L4-22K protein both activates and suppresses transcription from the adenovirus major late promoter (MLP) by binding to DNA elements located downstream of the MLP transcriptional start site: the so-called DE element ( positive) and the R1 region ( negative). Here we show that L4-22K preferentially binds to the RNA form of the R1 region, both to the double-stranded RNA and the single-stranded RNA of the same polarity as the nascent MLP transcript. Further, L4-22K binds to a 5'-CAAA-3' motif in the single-stranded RNA, which is identical to the sequence motif characterized for L4-22K DNA binding. L4-22K binding to single-stranded RNA results in an enhancement of U1 snRNA recruitment to the major late first leader 5' splice site. This increase in U1 snRNA binding results in a suppression of MLP transcription and a concurrent stimulation of major late first intron splicing.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-318946 (URN)10.1093/nar/gkw1145 (DOI)000396055400023 ()27899607 (PubMedID)
Funder
Swedish Cancer Society, 120678, 130410Swedish Research Council, 2006-5038-36531-16
Available from: 2017-04-03 Created: 2017-04-03 Last updated: 2017-11-29Bibliographically approved
Kamel, W. (2016). Adenoviral small non-coding RNAs: A Structural and Functional Charaterization. (Doctoral dissertation). Uppsala: Acta Universitatis Upsaliensis
Open this publication in new window or tab >>Adenoviral small non-coding RNAs: A Structural and Functional Charaterization
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Since their discovery in 1953, adenoviruses have significantly contributed to the understanding of virus-host cell interactions, including mechanistic details of cellular processes such as cell cycle control and alternative RNA splicing. Among the first characterized adenoviral genes were the virus-associated RNAs (VA RNAI/II), which are produced in massive amount during a lytic infection. The VA RNAs perform multiple functions and are required for a successful adenovirus life cycle. More recently, it was shown that the VA RNAs are processed into small viral miRNAs, so-called mivaRNAs, which interfere with the function of the cellular RNAi/miRNA machinery.

In papers I and II, we focused on a structural and functional characterization of the mivaRNAs using two approaches. Firstly, we created a model system where the predicted miRNA-like function of mivaRNAI could be investigated, without interfering with other VA RNA functions. This was accomplished by construction of recombinant adenoviruses, in which the seed sequence of mivaRNAI was altered. The results showed that in cell culture experiments the mivaRNAI seed sequence mutants grew as the wild type virus, suggesting that the mivaRNAs are not required during the lytic phase of an adenovirus infection. Secondly, we showed that the VA RNAs from different human adenoviruses (Ad4, Ad5, Ad11 and Ad37) undergo the same type of Dicer-dependent processing into mivaRNAs, which subsequently are loaded onto the RNA induced silencing complex (RISC), albeit with different efficiencies.

In paper III, we demonstrated that the promoter proximal region of the adenovirus major late promoter (MLP) produces a novel non-canonical class of small RNAs, which we termed the MLP-TSS-sRNAs. Surprisingly the MLP-TSS-sRNA maintains the m7G-cap structure while bound to Ago2 containing RISC. These complexes are functional suppressing expression of target mRNAs with complementary binding site. Most importantly, the MLP-TSS-sRNA limits the efficiency of viral DNA replication probably through a targeting of the E2B mRNAs, which are transcribed in the antisense orientation. In conclusion, the MLP-TSS-sRNA represents the first viral small RNA, which has been shown to have a function as a regulator of an adenovirus infection.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2016. p. 49
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 1216
Keywords
non-coding RNA miRNA mivaRNA canonical Dicer Ago2 TSS m7G Cap Adenovirus replication E2B
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-283080 (URN)978-91-554-9556-5 (ISBN)
Public defence
2016-06-02, B/A1:111a, BMC, Uppsala, 13:15 (English)
Opponent
Supervisors
Available from: 2016-05-11 Created: 2016-04-11 Last updated: 2016-06-01
Inturi, R., Kamel, W., Akusjärvi, G. & Punga, T. (2015). Complementation of the human adenovirus type 5 VA RNAI defect by the Vaccinia virus E3L protein and serotype-specific VA RNAIs. Virology, 485, 25-35
Open this publication in new window or tab >>Complementation of the human adenovirus type 5 VA RNAI defect by the Vaccinia virus E3L protein and serotype-specific VA RNAIs
2015 (English)In: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 485, p. 25-35Article in journal (Refereed) Published
Abstract [en]

Human adenoviruses (HAdVs) encode for multifunctional non-coding virus-associated (VA) RNAs, which function as powerful suppressors of the cellular interferon (IFN) and RNA interference (RNAi) systems. In this study we tested the ability of various plant and animal virus encoded RNAi and IFN suppressor proteins to functionally substitute for the HAdV-5 VA RNAI. Our results revealed that only the Vaccinia virus (VACV) E3L protein was able to substitute for the HAdV-5 VA RNAI functions in virus-infected cells. Interestingly, the E3L protein rescues the translational defect but does not stimulate viral capsid mRNA accumulation observed with VA RNA. We further show that the E3L C-terminal region containing the dsRNA-binding domain is needed to enhance VA RNAI mutant virus replication. Additionally, we show that the HAdV-4 and HAdV-37 VA RNAI are more effective than the HAdV-5 VA RNAI in rescuing virus replication.

Keywords
Adenovirus, Vaccinia virus, interferon, PKR, RNAi
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Medical Virology
Identifiers
urn:nbn:se:uu:diva-258879 (URN)10.1016/j.virol.2015.07.002 (DOI)000363993100003 ()
Funder
Swedish Cancer Society, 12 0504, 13 0469Swedish Research Council, K2012–999X-21959-01-301–3Åke Wiberg Foundation, M14-01555
Available from: 2015-07-21 Created: 2015-07-21 Last updated: 2017-12-04Bibliographically approved
Pickl, J. M., Kamel, W., Ciftci, S., Punga, T. & Akusjärvi, G. (2015). Opposite expression of CYP51A1 and its natural antisense transcript AluCYP51A1 in adenovirus type 37 infected retinal pigmented epithelial cells. FEBS Letters, 589(12), 1383-1388
Open this publication in new window or tab >>Opposite expression of CYP51A1 and its natural antisense transcript AluCYP51A1 in adenovirus type 37 infected retinal pigmented epithelial cells
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2015 (English)In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 589, no 12, p. 1383-1388Article in journal (Refereed) Published
Abstract [en]

Cytochrome P450 family member CYP51A1 is a key enzyme in cholesterol biosynthesis whose deregulation is implicated in numerous diseases, including retinal degeneration. Here we describe that HAdV-37 infection leads to downregulation of CYP51A1 expression and overexpression of its antisense non-coding Alu element (AluCYP51A1) in retinal pigment epithelium (RPE) cells. This change in gene expression is associated with a reversed accumulation of a positive histone mark at the CYP51A1 and AluCYP51A1 promoters. Further, transient AluCYP51A1 RNA overexpression correlates with reduced CYP51A1 mRNA accumulation. Collectively, our data suggest that AluCYP51A1 might control CYP51A1 gene expression in HAdV-37-infected RPE cells. (C) 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Keywords
Adenovirus, Human adenovirus type 37, Retinal pigment epithelium, Alu element, CYP51A1
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-255066 (URN)10.1016/j.febslet.2015.04.018 (DOI)000354290500014 ()25907535 (PubMedID)
Funder
Swedish Research Council, K2012-99X-21959-01-3Swedish Research Council, 2006-5038-36531-16
Available from: 2015-06-22 Created: 2015-06-12 Last updated: 2017-12-04Bibliographically approved
Kamel, W., Segerman, B., Punga, T. & Akusjärvi, G. (2014). Small RNA Sequence Analysis of Adenovirus VA RNA-Derived MiRNAs Reveals an Unexpected Serotype-Specific Difference in Structure and Abundance. PLoS ONE, 9(8), e105746
Open this publication in new window or tab >>Small RNA Sequence Analysis of Adenovirus VA RNA-Derived MiRNAs Reveals an Unexpected Serotype-Specific Difference in Structure and Abundance
2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 8, p. e105746-Article in journal (Refereed) Published
Abstract [en]

Human adenoviruses (HAds) encode for one or two highly abundant virus-associated RNAs, designated VA RNAI and VA RNAII, which fold into stable hairpin structures resembling miRNA precursors. Here we show that the terminal stem of the VA RNAs originating from Ad4, Ad5, Ad11 and Ad37, all undergo Dicer dependent processing into virus-specific miRNAs (so-called mivaRNAs). We further show that the mivaRNA duplex is subjected to a highly asymmetric RISC loading with the 3'-strand from all VA RNAs being the favored strand, except for the Ad37 VA RNAII, where the 5'-mivaRNAII strand was preferentially assembled into RISC. Although the mivaRNA seed sequences are not fully conserved between the HAds a bioinformatics prediction approach suggests that a large fraction of the VA RNAII-, but not the VA RNAI-derived mivaRNAs still are able to target the same cellular genes. Using small RNA deep sequencing we demonstrate that the Dicer processing event in the terminal stem of the VA RNAs is not unique and generates 3'-mivaRNAs with a slight variation of the position of the 5'-terminal nucleotide in the RISC loaded guide strand. Also, we show that all analyzed VA RNAs, except Ad37 VA RNAI and Ad5 VA RNAII, utilize an alternative upstream A start site in addition to the classical +1 G start site. Further, the 5'-mivaRNAs with an A start appears to be preferentially incorporated into RISC. Although the majority of mivaRNA research has been done using Ad5 as the model system our analysis demonstrates that the mivaRNAs expressed in Ad11- and Ad37-infected cells are the most abundant mivaRNAs associated with Ago2-containing RISC. Collectively, our results show an unexpected variability in Dicer processing of the VA RNAs and a serotype-specific loading of mivaRNAs into Ago2-based RISC.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-233020 (URN)10.1371/journal.pone.0105746 (DOI)000341106100115 ()
Funder
Swedish Cancer Society, 13 0469, 12 0504Swedish Research Council, K2012-99X-21959-01-3, 2006-5038-36531-16
Available from: 2014-10-07 Created: 2014-09-29 Last updated: 2017-12-05Bibliographically approved
Punga, T., Kamel, W. & Akusjarvi, G. (2013). Old and new functions for the adenovirus virus-associated RNAs. Future Virology, 8(4), 343-356
Open this publication in new window or tab >>Old and new functions for the adenovirus virus-associated RNAs
2013 (English)In: Future Virology, ISSN 1746-0794, Vol. 8, no 4, p. 343-356Article, review/survey (Refereed) Published
Abstract [en]

Adenovirus type 5 encodes two short, highly structured noncoding RNAs, the virus-associated (VA) RNAI and VA RNAII. These RNAs are expressed in large amounts late during a lytic infection. Early studies established an important role for VA RNAI in maintaining efficient translation in late virus-infected cells by blocking activation of the key interferon-induced PKR protein kinase. More recent studies have demonstrated that the VA RNAs also target the RNAi/miRNA pathway. Collectively, available data suggest that the VA RNAs are multifunctional RNAs suppressing the activity of three dsRNA-sensing enzyme systems in human cells. Here, the known functions of the VA RNAs are summarized and the interplay between VA RNA expression and the activity of the interferon and RNAi pathways are discussed in more detail.

Keywords
adenovirus, Ago2, Dicer, interferon, mivaRNA, OAS, PKR, RISC, RNAi, VA RNA
National Category
Natural Sciences Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-200272 (URN)10.2217/FVL.13.19 (DOI)000317344000008 ()
Available from: 2013-05-24 Created: 2013-05-24 Last updated: 2013-05-24Bibliographically approved
Kamel, W., Segerman, B., Oberg, D., Punga, T. & Akusjärvi, G. (2013). The adenovirus VA RNA-derived miRNAs are not essential for lytic virus growth in tissue culture cells. Nucleic Acids Research, 41(9), 4802-4812
Open this publication in new window or tab >>The adenovirus VA RNA-derived miRNAs are not essential for lytic virus growth in tissue culture cells
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2013 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 41, no 9, p. 4802-4812Article in journal (Refereed) Published
Abstract [en]

At late times during a lytic infection human adenovirus type 5 produces ∼10(8) copies per cell of virus-associated RNA I (VA RNAI). This short highly structured RNA polymerase III transcript has previously been shown to be essential for lytic virus growth. A fraction of VA RNAI is processed by Dicer into small RNAs, so-called mivaRNAIs, which are efficiently incorporated into the RNA-induced silencing complex. Here, we constructed recombinant adenoviruses with mutations in the seed sequence of both the 5'- and the 3'-strand of the mivaRNAI duplex. The results showed that late viral protein synthesis, as well as new virus progeny formation, was essentially unaffected by the seed sequence mutations under lytic replicative conditions in HeLa or HEK293 cells. Collectively, our results suggest that either strand of the mivaRNAI duplex does not have target mRNA interactions that are critical for the establishment of virus growth under lytic conditions. Further, by depletion of protein kinase R (PKR) in HEK293 cells, we show that the suppressive effect of VA RNAI on the interferon-induced PKR pathway is most critical for late gene expression.

National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-198031 (URN)10.1093/nar/gkt172 (DOI)000318570000013 ()23525465 (PubMedID)
Available from: 2013-04-08 Created: 2013-04-08 Last updated: 2017-12-06Bibliographically approved
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