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Article ; Online: Phosphorylation regulates viral biomolecular condensates to promote infectious progeny production.

Grams, Nicholas / Charman, Matthew / Halko, Edwin / Lauman, Richard / Garcia, Benjamin A / Weitzman, Matthew D

2024 Volume 43, Issue 2, Page(s) 277–303

Abstract: Biomolecular condensates (BMCs) play important roles in diverse biological processes. Many viruses form BMCs which have been implicated in various functions critical for the productive infection of host cells. The adenovirus L1-52/55 kilodalton protein ( ... ...

Abstract	Biomolecular condensates (BMCs) play important roles in diverse biological processes. Many viruses form BMCs which have been implicated in various functions critical for the productive infection of host cells. The adenovirus L1-52/55 kilodalton protein (52K) was recently shown to form viral BMCs that coordinate viral genome packaging and capsid assembly. Although critical for packaging, we do not know how viral condensates are regulated during adenovirus infection. Here we show that phosphorylation of serine residues 28 and 75 within the N-terminal intrinsically disordered region of 52K modulates viral condensates in vitro and in cells, promoting liquid-like properties. Furthermore, we demonstrate that phosphorylation of 52K promotes viral genome packaging and the production of infectious progeny particles. Collectively, our findings provide insights into how viral condensate properties are regulated and maintained in a state conducive to their function in viral progeny production. In addition, our findings have implications for antiviral strategies aimed at targeting the regulation of viral BMCs to limit viral multiplication.
MeSH term(s)	Phosphorylation ; Biomolecular Condensates ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Virus Replication ; Viruses
Chemical Substances	Viral Proteins
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	586044-1
ISSN	1460-2075 ; 0261-4189
ISSN (online)	1460-2075
ISSN	0261-4189
DOI	10.1038/s44318-023-00021-0
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Article ; Online: Unraveling the RNA modification code with mass spectrometry.

Lauman, Richard / Garcia, Benjamin A

Molecular omics

2020 Volume 16, Issue 4, Page(s) 305–315

Abstract: The discovery and analysis of modifications on proteins and nucleic acids has provided functional information that has rapidly accelerated the field of epigenetics. While protein post-translational modifications (PTMs), especially on histones, have been ... ...

Abstract	The discovery and analysis of modifications on proteins and nucleic acids has provided functional information that has rapidly accelerated the field of epigenetics. While protein post-translational modifications (PTMs), especially on histones, have been highlighted as critical components of epigenetics, the post-transcriptional modification of RNA has been a subject of more recently emergent interest. Multiple RNA modifications have been known to be present in tRNA and rRNA since the 1960s, but the exploration of mRNA, small RNA, and inducible tRNA modifications remains nascent. Sequencing-based methods have been essential to the field by creating the first epitranscriptome maps of m
MeSH term(s)	Animals ; Humans ; Mass Spectrometry ; Molecular Structure ; Nucleosides ; Nucleotides ; Protein Processing, Post-Translational ; RNA/chemistry ; RNA/genetics ; RNA/metabolism ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Ribosomal/chemistry ; RNA, Ribosomal/genetics ; RNA, Ribosomal/metabolism ; RNA, Transfer/chemistry ; RNA, Transfer/genetics ; RNA, Transfer/metabolism
Chemical Substances	Nucleosides ; Nucleotides ; RNA, Messenger ; RNA, Ribosomal ; RNA (63231-63-0) ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2020-04-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2515-4184
ISSN (online)	2515-4184
DOI	10.1039/c8mo00247a
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Article ; Online: Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography.

Lauman, Richard / Kim, Hee Jong / Pino, Lindsay K / Scacchetti, Alessandro / Xie, Yixuan / Robison, Faith / Sidoli, Simone / Bonasio, Roberto / Garcia, Benjamin A

Analytical chemistry

2023 Volume 95, Issue 12, Page(s) 5187–5195

Abstract: Post-transcriptional modifications of RNA strongly influence the RNA structure and function. Recent advances in RNA sequencing and mass spectrometry (MS) methods have identified over 140 of these modifications on a wide variety of RNA species. Most next- ... ...

Abstract	Post-transcriptional modifications of RNA strongly influence the RNA structure and function. Recent advances in RNA sequencing and mass spectrometry (MS) methods have identified over 140 of these modifications on a wide variety of RNA species. Most next-generation sequencing approaches can only map one RNA modification at a time, and while MS can assign multiple modifications simultaneously in an unbiased manner, MS cannot accurately catalog and assign RNA modifications in complex biological samples due to limitations in the fragment length and coverage depth. Thus, a facile method to identify novel RNA modifications while simultaneously locating them in the context of their RNA sequences is still lacking. We combined two orthogonal modes of RNA ion separation before MS identification: high-field asymmetric ion mobility separation (FAIMS) and electrochemically modulated liquid chromatography (EMLC). FAIMS RNA MS increases both coverage and throughput, while EMLC LC-MS orthogonally separates RNA molecules of different lengths and charges. The combination of the two methods offers a broadly applicable platform to improve the length and depth of MS-based RNA sequencing while providing contextual access to the analysis of RNA modifications.
MeSH term(s)	Base Sequence ; Mass Spectrometry/methods ; Chromatography, Liquid ; Ion Mobility Spectrometry/methods ; RNA
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2023-03-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04114
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Article ; Online: Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography

Lauman, Richard / Kim, Hee Jong / Pino, Lindsay K. / Scacchetti, Alessandro / Xie, Yixuan / Robison, Faith / Sidoli, Simone / Bonasio, Roberto / Garcia, Benjamin A.

Analytical Chemistry. 2023 Mar. 14, v. 95, no. 12 p.5187-5195

2023

Abstract	Post-transcriptional modifications of RNA strongly influence the RNA structure and function. Recent advances in RNA sequencing and mass spectrometry (MS) methods have identified over 140 of these modifications on a wide variety of RNA species. Most next-generation sequencing approaches can only map one RNA modification at a time, and while MS can assign multiple modifications simultaneously in an unbiased manner, MS cannot accurately catalog and assign RNA modifications in complex biological samples due to limitations in the fragment length and coverage depth. Thus, a facile method to identify novel RNA modifications while simultaneously locating them in the context of their RNA sequences is still lacking. We combined two orthogonal modes of RNA ion separation before MS identification: high-field asymmetric ion mobility separation (FAIMS) and electrochemically modulated liquid chromatography (EMLC). FAIMS RNA MS increases both coverage and throughput, while EMLC LC–MS orthogonally separates RNA molecules of different lengths and charges. The combination of the two methods offers a broadly applicable platform to improve the length and depth of MS-based RNA sequencing while providing contextual access to the analysis of RNA modifications.
Keywords	RNA ; analytical chemistry ; electrochemistry ; liquid chromatography ; mass spectrometry
Language	English
Dates of publication	2023-0314
Size	p. 5187-5195.
Publishing place	American Chemical Society
Document type	Article ; Online
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c04114
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Article ; Online: Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation.

Pino, Lindsay K / Baeza, Josue / Lauman, Richard / Schilling, Birgit / Garcia, Benjamin A

Journal of proteome research

2021 Volume 20, Issue 4, Page(s) 1918–1927

Abstract: Stable isotope labeling by amino acids in cell culture (SILAC) coupled to data-dependent acquisition (DDA) is a common approach to quantitative proteomics with the desirable benefit of reducing batch effects during sample processing and data acquisition. ...

Abstract	Stable isotope labeling by amino acids in cell culture (SILAC) coupled to data-dependent acquisition (DDA) is a common approach to quantitative proteomics with the desirable benefit of reducing batch effects during sample processing and data acquisition. More recently, using data-independent acquisition (DIA/SWATH) to systematically measure peptides has gained popularity for its comprehensiveness, reproducibility, and accuracy of quantification. The complementary advantages of these two techniques logically suggests combining them. Here we develop a SILAC-DIA-MS workflow using free, open-source software. We empirically determine that using DIA achieves similar peptide detection numbers as DDA and that DIA improves the quantitative accuracy and precision of SILAC by an order of magnitude. Finally, we apply SILAC-DIA-MS to determine protein turnover rates of cells treated with bortezomib, an FDA-approved 26S proteasome inhibitor for multiple myeloma and mantle cell lymphoma. We observe that SILAC-DIA produces more sensitive protein turnover models. Of the proteins determined to be differentially degraded by both acquisition methods, we find known proteins that are degraded by the ubiquitin-proteasome pathway, such as HNRNPK, EIF3A, and IF4A1/EIF4A-1, and a slower turnover for CATD, a protein implicated in invasive breast cancer. With improved quantification from DIA, we anticipate that this workflow will make SILAC-based experiments like protein turnover more sensitive.
MeSH term(s)	Bortezomib/pharmacology ; Proteolysis ; Proteome ; Reproducibility of Results ; Tandem Mass Spectrometry
Chemical Substances	Proteome ; Bortezomib (69G8BD63PP)
Language	English
Publishing date	2021-03-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.0c00938
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Article ; Online: Regulation of eDHFR-tagged proteins with trimethoprim PROTACs.

Etersque, Jean M / Lee, Iris K / Sharma, Nitika / Xu, Kexiang / Ruff, Andrew / Northrup, Justin D / Sarkar, Swarbhanu / Nguyen, Tommy / Lauman, Richard / Burslem, George M / Sellmyer, Mark A

Nature communications

2023 Volume 14, Issue 1, Page(s) 7071

Abstract: Temporal control of protein levels in cells and living animals can be used to improve our understanding of protein function. In addition, control of engineered proteins could be used in therapeutic applications. PRoteolysis-TArgeting Chimeras (PROTACs) ... ...

Abstract	Temporal control of protein levels in cells and living animals can be used to improve our understanding of protein function. In addition, control of engineered proteins could be used in therapeutic applications. PRoteolysis-TArgeting Chimeras (PROTACs) have emerged as a small-molecule-driven strategy to achieve rapid, post-translational regulation of protein abundance via recruitment of an E3 ligase to the target protein of interest. Here, we develop several PROTAC molecules by covalently linking the antibiotic trimethoprim (TMP) to pomalidomide, a ligand for the E3 ligase, Cereblon. These molecules induce degradation of proteins of interest (POIs) genetically fused to a small protein domain, E. coli dihydrofolate reductase (eDHFR), the molecular target of TMP. We show that various eDHFR-tagged proteins can be robustly degraded to 95% of maximum expression with PROTAC molecule 7c. Moreover, TMP-based PROTACs minimally affect the expression of immunomodulatory imide drug (IMiD)-sensitive neosubstrates using proteomic and biochemical assays. Finally, we show multiplexed regulation with another known degron-PROTAC pair, as well as reversible protein regulation in a rodent model of metastatic cancer, demonstrating the formidable strength of this system. Altogether, TMP PROTACs are a robust approach for selective and reversible degradation of eDHFR-tagged proteins in vitro and in vivo.
MeSH term(s)	Animals ; Tetrahydrofolate Dehydrogenase/genetics ; Tetrahydrofolate Dehydrogenase/metabolism ; Proteolysis Targeting Chimera ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Trimethoprim/pharmacology ; Proteomics ; Ubiquitin-Protein Ligases/metabolism ; Proteolysis
Chemical Substances	Tetrahydrofolate Dehydrogenase (EC 1.5.1.3) ; Proteolysis Targeting Chimera ; Escherichia coli Proteins ; Trimethoprim (AN164J8Y0X) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2023-11-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-42820-3
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Article ; Online: Transcription factors interact with RNA to regulate genes.

Oksuz, Ozgur / Henninger, Jonathan E / Warneford-Thomson, Robert / Zheng, Ming M / Erb, Hailey / Vancura, Adrienne / Overholt, Kalon J / Hawken, Susana Wilson / Banani, Salman F / Lauman, Richard / Reich, Lauren N / Robertson, Anne L / Hannett, Nancy M / Lee, Tong I / Zon, Leonard I / Bonasio, Roberto / Young, Richard A

Molecular cell

2023 Volume 83, Issue 14, Page(s) 2449–2463.e13

Abstract: Transcription factors (TFs) orchestrate the gene expression programs that define each cell's identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or ... ...

Abstract	Transcription factors (TFs) orchestrate the gene expression programs that define each cell's identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA, and TF on chromatin. TF-RNA interactions are a conserved feature important for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA, and protein is a general property of many TFs and is fundamental to their gene regulatory function.
MeSH term(s)	Transcription Factors/metabolism ; RNA/metabolism ; Binding Sites ; Protein Binding ; DNA/genetics
Chemical Substances	Transcription Factors ; RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2023-07-03
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.06.012
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Article ; Online: Novel viral splicing events and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts.

Price, Alexander M / Steinbock, Robert T / Lauman, Richard / Charman, Matthew / Hayer, Katharina E / Kumar, Namrata / Halko, Edwin / Lum, Krystal K / Wei, Monica / Wilson, Angus C / Garcia, Benjamin A / Depledge, Daniel P / Weitzman, Matthew D

PLoS pathogens

2022 Volume 18, Issue 9, Page(s) e1010797

Abstract: Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and polyadenylation sites have been characterized using low- ... ...

Abstract	Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and polyadenylation sites have been characterized using low-throughput biochemical techniques or short read cDNA-based sequencing, these technologies do not fully capture the complexity of the adenoviral transcriptome. By combining Illumina short-read and nanopore long-read direct RNA sequencing approaches, we mapped transcription start sites and RNA cleavage and polyadenylation sites across the adenovirus genome. In addition to confirming the known canonical viral early and late RNA cassettes, our analysis of splice junctions within long RNA reads revealed an additional 35 novel viral transcripts that meet stringent criteria for expression. These RNAs include fourteen new splice junctions which lead to expression of canonical open reading frames (ORFs), six novel ORF-containing transcripts, and 15 transcripts encoding for messages that could alter protein functions through truncation or fusion of canonical ORFs. In addition, we detect RNAs that bypass canonical cleavage sites and generate potential chimeric proteins by linking distinct gene transcription units. Among these chimeric proteins we detected an evolutionarily conserved protein containing the N-terminus of E4orf6 fused to the downstream DBP/E2A ORF. Loss of this novel protein, E4orf6/DBP, was associated with aberrant viral replication center morphology and poor viral spread. Our work highlights how long-read sequencing technologies combined with mass spectrometry can reveal further complexity within viral transcriptomes and resulting proteomes.
MeSH term(s)	Adenoviridae/genetics ; DNA, Complementary ; Humans ; Open Reading Frames/genetics ; Proteome/metabolism ; RNA Splicing/genetics ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Recombinant Fusion Proteins/metabolism ; Sequence Analysis, RNA/methods ; Transcriptome
Chemical Substances	DNA, Complementary ; Proteome ; RNA, Viral ; Recombinant Fusion Proteins
Language	English
Publishing date	2022-09-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1010797
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Article ; Online: Transcription factors interact with RNA to regulate genes

Oksuz, Ozgur / Henninger, Jonathan E. / Warneford-Thomson, Robert / Zheng, Ming M. / Erb, Hailey / Vancura, Adrienne / Overholt, Kalon J. / Hawken, Susana Wilson / Banani, Salman F. / Lauman, Richard / Reich, Lauren N. / Robertson, A. L. / Hannett, Nancy M. / Lee, Tong I. / Zon, Leonard I. / Bonasio, Roberto / Young, Richard A.

Molecular Cell. 20232023 July 03, July 03, v. 83, no. 14 p.2449-2463.e13

2023

Abstract: Transcription factors (TFs) orchestrate the gene expression programs that define each cell’s identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or ... ...

Abstract	Transcription factors (TFs) orchestrate the gene expression programs that define each cell’s identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA, and TF on chromatin. TF-RNA interactions are a conserved feature important for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA, and protein is a general property of many TFs and is fundamental to their gene regulatory function.
Keywords	DNA ; RNA ; chromatin ; gene expression ; genes ; transactivators ; vertebrates ; transcription factor ; gene regulation ; RNA-binding proteins ; arginine-rich motif ; single-molecule imaging ; development ; zebrafish
Language	English
Dates of publication	2023-0703
Size	p. 2449-2463.e13.
Publishing place	Elsevier Inc.
Document type	Article ; Online
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.06.012
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Article: Adenovirus Remodeling of the Host Proteome and Host Factors Associated with Viral Genomes.

Dybas, Joseph M / Lum, Krystal K / Kulej, Katarzyna / Reyes, Emigdio D / Lauman, Richard / Charman, Matthew / Purman, Caitlin E / Steinbock, Robert T / Grams, Nicholas / Price, Alexander M / Mendoza, Lydia / Garcia, Benjamin A / Weitzman, Matthew D

mSystems

2021 , Page(s) e0046821

Abstract: Viral infections are associated with extensive remodeling of the cellular proteome. Viruses encode gene products that manipulate host proteins to redirect cellular processes or subvert antiviral immune responses. Adenovirus (AdV) encodes proteins from ... ...

Abstract	Viral infections are associated with extensive remodeling of the cellular proteome. Viruses encode gene products that manipulate host proteins to redirect cellular processes or subvert antiviral immune responses. Adenovirus (AdV) encodes proteins from the early E4 region which are necessary for productive infection. Some cellular antiviral proteins are known to be targeted by AdV E4 gene products, resulting in their degradation or mislocalization. However, the full repertoire of host proteome changes induced by viral E4 proteins has not been defined. To identify cellular proteins and processes manipulated by viral products, we developed a global, unbiased proteomics approach to analyze changes to the host proteome during infection with adenovirus serotype 5 (Ad5) virus. We used whole-cell proteomics to measure total protein abundances in the proteome during Ad5 infection. Since host antiviral proteins can antagonize viral infection by associating with viral genomes and inhibiting essential viral processes, we used Isolation of Proteins on Nascent DNA (iPOND) proteomics to identify proteins associated with viral genomes during infection with wild-type Ad5 or an E4 mutant virus. By integrating these proteomics data sets, we identified cellular factors that are degraded in an E4-dependent manner or are associated with the viral genome in the absence of E4 proteins. We further show that some identified proteins exert inhibitory effects on Ad5 infection. Our systems-level analysis reveals cellular processes that are manipulated during Ad5 infection and points to host factors counteracted by early viral proteins as they remodel the host proteome to promote efficient infection.
Language	English
Publishing date	2021-08-31
Publishing country	United States
Document type	Journal Article
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00468-21
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