Insights into the molecular mechanisms of the n6-methyladenosine (m6a) methylation machinery in the regulation of the infection cycle of rna plant viruses
- Autores: Luis Alvarado Marchena
- Directores de la Tesis: Vicente Pallás Benet (dir. tes.), Frederic Aparicio Herrero (dir. tes.)
- Lectura: En la Universitat Politècnica de València ( España ) en 2022
- Idioma: español
- Tribunal Calificador de la Tesis: Francisco Tenllado Peralo (presid.), Carmelo López del Rincón (secret.), María Soledad Sacristán Benayas (voc.)
- Programa de doctorado: Programa de Doctorado en Biotecnología por la Universitat Politècnica de València
- Materias:
- Enlaces
- Tesis en acceso abierto en: RiuNet
- Resumen
N6-methyladenosine (m6A) is a widespread modification on cellular RNAs of different organisms that can impact many cellular processes and pathways. In plants, m6A-methylation is mainly installed by a methylation complex containing several proteins: MTA, MTB, FIP37, VIR, and HAKAI. This modification is removed by demethylases of the AlkB family, and members of the ECT family are the best described proteins that recognize and process m6A-modified RNAs. Studies of viral epitransciptomics have revealed an equally important role of m6A during virus infection; however, there is no global pro- or antiviral role of m6A that can be generalized. The laboratory where this work was carried out has been a pioneer in the study of the effect of m6A on plant-viruses, using AMV as a model-virus. AMV belongs to the Bromoviridae family and, as the rest of the members of this family, its genome consists of three (+)ssRNAs. RNA1 and RNA2 encode the replicase subunits (P1 and P2), whereas RNA 3 encodes the MP and serves as a template for the synthesis of sgRNA 4, which encodes CP. At the beginning of this thesis, our laboratory had already reported on: the presence of putative m6A-motifs in the 3'UTR RNA3, a critical region for AMV replication, the first Arabidopsis m6A-demethylase (ALKBH9B), the functional relevance of ALKBH9B to maintain adequate m6A/A levels for correct AMV replication, the ability of AMV-CP to interact with ALKBH9B, possibly to usurp ALKBH9B activity, and the capability of Arabidopsis ECT2/3/5 to interact with m6A-containing AMV vRNAs. Given the functional relevance of m6A on the biology of AMV, in this thesis it was decided to deepen the knowledge of the implications of the m6A regulation mechanism on the viral infectious cycle of AMV. For this, it was decided: deepen the functional understanding of the m6A-demethylase ALKBH9B, evaluate the in vivo function of the putative two m6A-sites present in the 3'UTR-RNA 3, and explore a possible involvement of some m6A-methyltransferases in infection caused by AMV.
We mapped functional subdomains in the atALKBH9B m6A-demethylase required for its binding to the vRNA and to the CP of AMV. Remarkably, it was observed the presence of IDRs in the N-terminal region, within the internal domain like AlkB and in the C-terminal region. About 78% of the RBD identified in ALKBH9B is contained in the C-terminal IDR. In this context, it has been proposed that the capability to specifically target different RNAs in RBPs containing IDRs is due to conformational flexibility as well as the establishment of extended conserved electrostatic interfaces with RNAs. Additionally, due that IDRs are frequently localized in proteins that undergo LLPS, a process that likely contributes to the formation and stability of RNA granules, it's possible that the IDRs and the RBD of ALKBH9B could act cooperatively to promote RNA granule formation.
The analysis of the putative DRACH-motifs located in the hpB loop and the lower-stem of hpE in the 3'UTR RNA 3 present hot sites involved in AMV replication in vivo. The identity of residues 2012A, 2013A and 2014A in the hpB loop appears to be a key structural requirement for AMV replication and/or accumulation. Regarding hpE, our results determined that the putative m6A-residue 1902A, as well as the base pairing of the lower-stem of hpE, are also essential requirements for the in vivo plus-strand synthesis in AMV. To our knowledge, this is the first evidence in AMV to show that the hpB loop and the lower-stem of hpE are involved in viral replication/accumulation and plus-strand synthesis, respectively.
Finally, regarding the study of the influence of m6A-methyltransferases on the viral infection cycle of AMV, a non-proviral and/or antiviral effect was determined in the m6A-mRNA methyltransferase complex made up of atMTA:atMTB, nor of the putative m6A-rRNA methyltransferase complex made up of atMETTL5-like:atTRMT112-like on the biology of AMV.
