From A to m6A: The Emerging Viral Epitranscriptome

Belinda Baquero-Perez; Daryl Geers; Juana Díez

doi:10.3390/v13061049

From A to m6A: The Emerging Viral Epitranscriptome

Viruses ◽

10.3390/v13061049 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1049

Author(s):

Belinda Baquero-Perez ◽

Daryl Geers ◽

Juana Díez

Keyword(s):

Nuclear Export ◽

Current Knowledge ◽

Rna Modification ◽

Structure Stability ◽

Rna Modifications ◽

Viral Mrnas ◽

Dna Viruses ◽

Mrna Structure ◽

Cellular Mrnas ◽

Rna And Dna

There are over 100 different chemical RNA modifications, collectively known as the epitranscriptome. N6-methyladenosine (m6A) is the most commonly found internal RNA modification in cellular mRNAs where it plays important roles in the regulation of the mRNA structure, stability, translation and nuclear export. This modification is also found in viral RNA genomes and in viral mRNAs derived from both RNA and DNA viruses. A growing body of evidence indicates that m6A modifications play important roles in regulating viral replication by interacting with the cellular m6A machinery. In this review, we will exhaustively detail the current knowledge on m6A modification, with an emphasis on its function in virus biology.

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Post-Transcriptional Regulation of Viral RNA through Epitranscriptional Modification

Cells ◽

10.3390/cells10051129 ◽

2021 ◽

Vol 10 (5) ◽

pp. 1129

Author(s):

David G. Courtney

Keyword(s):

Transcriptional Regulation ◽

Viral Replication ◽

Viral Rna ◽

Rna Modifications ◽

Exact Role ◽

Dna Viruses ◽

Wide Range ◽

Cellular Mrnas ◽

Post Transcriptional Regulation ◽

Rna And Dna

The field of mRNA modifications has been steadily growing in recent years as technologies have improved and the importance of these residues became clear. However, a subfield has also arisen, specifically focused on how these modifications affect viral RNA, with the possibility that viruses can also be used as a model to best determine the role that these modifications play on cellular mRNAs. First, virologists focused on the most abundant internal mRNA modification, m6A, mapping this modification and elucidating its effects on the RNA of a wide range of RNA and DNA viruses. Next, less common RNA modifications including m5C, Nm and ac4C were investigated and also found to be present on viral RNA. It now appears that viral RNA is littered with a multitude of RNA modifications. In biological systems that are under constant evolutionary pressure to out compete both the host as well as newly arising viral mutants, it poses an interesting question about what evolutionary benefit these modifications provide as it seems evident, at least to this author, that these modifications have been selected for. In this review, I discuss how RNA modifications are identified on viral RNA and the roles that have now been uncovered for these modifications in regard to viral replication. Finally, I propose some interesting avenues of research that may shed further light on the exact role that these modifications play in viral replication.

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Strength in Diversity: Nuclear Export of Viral RNAs

Viruses ◽

10.3390/v12091014 ◽

2020 ◽

Vol 12 (9) ◽

pp. 1014 ◽

Cited By ~ 1

Author(s):

Jón Pol Gales ◽

Julie Kubina ◽

Angèle Geldreich ◽

Maria Dimitrova

Keyword(s):

Nuclear Export ◽

Influenza Viruses ◽

Adapter Proteins ◽

Viral Mrnas ◽

Dna Viruses ◽

Complex Process ◽

Cellular Mrnas ◽

Rna Export ◽

Synthesis And Processing ◽

Nuclear Rna Export

The nuclear export of cellular mRNAs is a complex process that requires the orchestrated participation of many proteins that are recruited during the early steps of mRNA synthesis and processing. This strategy allows the cell to guarantee the conformity of the messengers accessing the cytoplasm and the translation machinery. Most transcripts are exported by the exportin dimer Nuclear RNA export factor 1 (NXF1)–NTF2-related export protein 1 (NXT1) and the transcription–export complex 1 (TREX1). Some mRNAs that do not possess all the common messenger characteristics use either variants of the NXF1–NXT1 pathway or CRM1, a different exportin. Viruses whose mRNAs are synthesized in the nucleus (retroviruses, the vast majority of DNA viruses, and influenza viruses) exploit both these cellular export pathways. Viral mRNAs hijack the cellular export machinery via complex secondary structures recognized by cellular export factors and/or viral adapter proteins. This way, the viral transcripts succeed in escaping the host surveillance system and are efficiently exported for translation, allowing the infectious cycle to proceed. This review gives an overview of the cellular mRNA nuclear export mechanisms and presents detailed insights into the most important strategies that viruses use to export the different forms of their RNAs from the nucleus to the cytoplasm.

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Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach

Molecules ◽

10.3390/molecules25153344 ◽

2020 ◽

Vol 25 (15) ◽

pp. 3344

Author(s):

Karolina Bartosik ◽

Katarzyna Debiec ◽

Anna Czarnecka ◽

Elzbieta Sochacka ◽

Grazyna Leszczynska

Keyword(s):

Functional Groups ◽

Fluorescent Dyes ◽

Building Blocks ◽

Rna Modification ◽

Spin Labels ◽

Structure Stability ◽

Synthetic Approach ◽

Rna Modifications ◽

Powerful Approach ◽

Nitroxide Spin Labels

The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA modifications have been proven to enhance the drug-like properties of RNA oligomers providing the oligonucleotide-based therapeutic agents in the antisense and siRNA technologies. The important sites of RNA modification/functionalization are the nucleobase residues. Standard phosphoramidite RNA chemistry allows the site-specific incorporation of a large number of functional groups to the nucleobase structure if the building blocks are synthetically obtainable and stable under the conditions of oligonucleotide chemistry and work-up. Otherwise, the chemically modified RNAs are produced by post-synthetic oligoribonucleotide functionalization. This review highlights the post-synthetic RNA modification approach as a convenient and valuable method to introduce a wide variety of nucleobase modifications, including recently discovered native hypermodified functional groups, fluorescent dyes, photoreactive groups, disulfide crosslinks, and nitroxide spin labels.

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Structural–functional interactions of NS1-BP protein with the splicing and mRNA export machineries for viral and host gene expression

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1818012115 ◽

2018 ◽

Vol 115 (52) ◽

pp. E12218-E12227 ◽

Cited By ~ 6

Author(s):

Ke Zhang ◽

Guijun Shang ◽

Abhilash Padavannil ◽

Juan Wang ◽

Ramanavelan Sakthivel ◽

...

Keyword(s):

Nuclear Export ◽

Matrix Protein ◽

Mrna Export ◽

Splicing Factors ◽

Ns1 Protein ◽

Viral Mrnas ◽

Hnrnp K ◽

Kelch Domain ◽

Cellular Mrnas ◽

Alternatively Spliced

The influenza virulence factor NS1 protein interacts with the cellular NS1-BP protein to promote splicing and nuclear export of the viral M mRNAs. The viral M1 mRNA encodes the M1 matrix protein and is alternatively spliced into the M2 mRNA, which is translated into the M2 ion channel. These proteins have key functions in viral trafficking and budding. To uncover the NS1-BP structural and functional activities in splicing and nuclear export, we performed proteomics analysis of nuclear NS1-BP binding partners and showed its interaction with constituents of the splicing and mRNA export machineries. NS1-BP BTB domains form dimers in the crystal. Full-length NS1-BP is a dimer in solution and forms at least a dimer in cells. Mutations suggest that dimerization is important for splicing. The central BACK domain of NS1-BP interacts directly with splicing factors such as hnRNP K and PTBP1 and with the viral NS1 protein. The BACK domain is also the site for interactions with mRNA export factor Aly/REF and is required for viral M mRNA nuclear export. The crystal structure of the C-terminal Kelch domain shows that it forms a β-propeller fold, which is required for the splicing function of NS1-BP. This domain interacts with the polymerase II C-terminal domain and SART1, which are involved in recruitment of splicing factors and spliceosome assembly, respectively. NS1-BP functions are not only critical for processing a subset of viral mRNAs but also impact levels and nuclear export of a subset of cellular mRNAs encoding factors involved in metastasis and immunity.

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Control of mRNA Export by Adenovirus E4orf6 and E1B55K Proteins during Productive Infection Requires E4orf6 Ubiquitin Ligase Activity

Journal of Virology ◽

10.1128/jvi.02309-07 ◽

2008 ◽

Vol 82 (6) ◽

pp. 2642-2651 ◽

Cited By ~ 53

Author(s):

Paola Blanchette ◽

Kathrin Kindsmüller ◽

Peter Groitl ◽

Frédéric Dallaire ◽

Thomas Speiseder ◽

...

Keyword(s):

Ubiquitin Ligase ◽

Nuclear Export ◽

Mrna Export ◽

Productive Infection ◽

Specific Substrate ◽

Viral Mrnas ◽

Ubiquitin Ligase Activity ◽

Cullin 5 ◽

Cellular Mrnas ◽

Virus Mutant

ABSTRACT During the adenovirus infectious cycle, the early proteins E4orf6 and E1B55K are known to perform several functions. These include nuclear export of late viral mRNAs, a block of nuclear export of the bulk of cellular mRNAs, and the ubiquitin-mediated degradation of selected proteins, including p53 and Mre11. Degradation of these proteins occurs via a cellular E3 ubiquitin ligase complex that is assembled through interactions between elongins B and C and BC boxes present in E4orf6 to form a cullin 5-based ligase complex. E1B55K, which has been known for some time to associate with the E4orf6 protein, is thought to bind to specific substrate proteins to bring them to the complex for ubiquitination. Earlier studies with E4orf6 mutants indicated that the interaction between the E4orf6 and E1B55K proteins is optimal only when E4orf6 is able to form the ligase complex. These and other observations suggested that most if not all of the functions ascribed to E4orf6 and E1B55K during infection, including the control of mRNA export, are achieved through the degradation of specific substrates by the E4orf6 ubiquitin ligase activity. We have tested this hypothesis through the generation of a virus mutant in which the E4orf6 product is unable to form a ligase complex and indeed have found that this mutant behaves identically to an E4orf6− virus in production of late viral proteins, growth, and export of the late viral L5 mRNA.

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PIAS1 potentiates the anti-EBV activity of SAMHD1 through SUMOylation

Cell & Bioscience ◽

10.1186/s13578-021-00636-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Farjana Saiada ◽

Kun Zhang ◽

Renfeng Li

Keyword(s):

Lytic Replication ◽

Dependent Manner ◽

Dna Viruses ◽

Post Translational Modifications ◽

Protein Protein Interaction ◽

Barr Virus ◽

Sumo Ligase ◽

Lysine Residues ◽

Epstein Barr ◽

Rna And Dna

Abstract Background Sterile alpha motif and HD domain 1 (SAMHD1) is a deoxynucleotide triphosphohydrolase (dNTPase) that restricts the infection of a variety of RNA and DNA viruses, including herpesviruses. The anti-viral function of SAMHD1 is associated with its dNTPase activity, which is regulated by several post-translational modifications, including phosphorylation, acetylation and ubiquitination. Our recent studies also demonstrated that the E3 SUMO ligase PIAS1 functions as an Epstein-Barr virus (EBV) restriction factor. However, whether SAMHD1 is regulated by PIAS1 to restrict EBV replication remains unknown. Results In this study, we showed that PIAS1 interacts with SAMHD1 and promotes its SUMOylation. We identified three lysine residues (K469, K595 and K622) located on the surface of SAMHD1 as the major SUMOylation sites. We demonstrated that phosphorylated SAMHD1 can be SUMOylated by PIAS1 and SUMOylated SAMHD1 can also be phosphorylated by viral protein kinases. We showed that SUMOylation-deficient SAMHD1 loses its anti-EBV activity. Furthermore, we demonstrated that SAMHD1 is associated with EBV genome in a PIAS1-dependent manner. Conclusion Our study reveals that PIAS1 synergizes with SAMHD1 to inhibit EBV lytic replication through protein–protein interaction and SUMOylation.

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Phenoxazine nucleoside derivatives with a multiple activity against RNA and DNA viruses

European Journal of Medicinal Chemistry ◽

10.1016/j.ejmech.2021.113467 ◽

2021 ◽

Vol 220 ◽

pp. 113467

Author(s):

Liubov I. Kozlovskaya ◽

Viktor P. Volok ◽

Anna A. Shtro ◽

Yulia V. Nikolaeva ◽

Alexey A. Chistov ◽

...

Keyword(s):

Dna Viruses ◽

Rna And Dna

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Hypoxia-induced alteration of RNA modifications in the mouse testis and sperm

Biology of Reproduction ◽

10.1093/biolre/ioab142 ◽

2021 ◽

Author(s):

Tong He ◽

Huanping Guo ◽

Xipeng Shen ◽

Xiao Wu ◽

Lin Xia ◽

...

Keyword(s):

Hypobaric Hypoxia ◽

Environmental Changes ◽

Epigenetic Inheritance ◽

Transcriptional Regulators ◽

Extreme Environment ◽

Mouse Testis ◽

Rna Modification ◽

Rna Modifications ◽

Sperm Counts ◽

Health Studies

Abstract Hypobaric hypoxia as an extreme environment in a plateau may have deleterious effects on human health. Studies have indicated that rush entry into a plateau may reduce male fertility and manifest in decreased sperm counts and weakened sperm motility. RNA modifications are sensitive to environmental changes and have recently emerged as novel post-transcriptional regulators in male spermatogenesis and intergenerational epigenetic inheritance. In the present study, we generated a mouse hypoxia model simulating the environment of 5500 meters in altitude for 35 days, which led to compromised spermatogenesis, decreased sperm counts, and an increased sperm deformation rate. Using this hypoxia model, we further applied our recently developed high-throughput RNA modification quantification platform based on LC–MS/MS, which exhibited the capacity to simultaneously examine 25 types of RNA modifications. Our results revealed an altered sperm RNA modifications signature in the testis (6 types) and mature sperm (11 types) under the hypoxia model, with 4 types showing overlap (Am, Gm, m7G, and m22G). Our data first drew the signature of RNA modification profiles and comprehensively analyzed the alteration of RNA modification levels in mouse testis and sperm under a mouse hypoxia model. These data may be highly related to human conditions under a similar hypoxia environment.

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RNA Modification Level Estimation with pulseR

Genes ◽

10.3390/genes9120619 ◽

2018 ◽

Vol 9 (12) ◽

pp. 619

Author(s):

Etienne Boileau ◽

Christoph Dieterich

Keyword(s):

Experimental Approach ◽

High Efficiency ◽

Rna Modification ◽

Model Parameters ◽

Metabolic Labeling ◽

Rna Seq ◽

Rna Modifications ◽

Log Odds ◽

Pros And Cons ◽

Wide Scale

RNA modifications regulate the complex life of transcripts. An experimental approach called LAIC-seq was developed to characterize modification levels on a transcriptome-wide scale. In this method, the modified and unmodified molecules are separated using antibodies specific for a given RNA modification (e.g., m6A). In essence, the procedure of biochemical separation yields three fractions: Input, eluate, and supernatent, which are subjected to RNA-seq. In this work, we present a bioinformatics workflow, which starts from RNA-seq data to infer gene-specific modification levels by a statistical model on a transcriptome-wide scale. Our workflow centers around the pulseR package, which was originally developed for the analysis of metabolic labeling experiments. We demonstrate how to analyze data without external normalization (i.e., in the absence of spike-ins), given high efficiency of separation, and how, alternatively, scaling factors can be derived from unmodified spike-ins. Importantly, our workflow provides an estimate of uncertainty of modification levels in terms of confidence intervals for model parameters, such as gene expression and RNA modification levels. We also compare alternative model parametrizations, log-odds, or the proportion of the modified molecules and discuss the pros and cons of each representation. In summary, our workflow is a versatile approach to RNA modification level estimation, which is open to any read-count-based experimental approach.

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