Insights into the specificity for the interaction of the promiscuous SARS-CoV-2 nucleocapsid protein N-terminal domain with deoxyribonucleic acids

The SARS-CoV-2 nucleocapsid protein (N) is a multifunctional promiscuous nucleic acid-binding protein, which plays a major role in nucleocapsid assembly and discontinuous RNA transcription, facilitating the template switch of transcriptional regulatory sequences (TRS). Here, we dissect the structura...

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Detalles Bibliográficos
Autores: Caruso, Icaro Putinhon [UNESP], dos Santos Almeida, Vitor, do Amaral, Mariana Juliani, de Andrade, Guilherme Caldas, de Araújo, Gabriela Rocha, de Araújo, Talita Stelling, de Azevedo, Jéssica Moreira, Barbosa, Glauce Moreno, Bartkevihi, Leonardo, Bezerra, Peter Reis, dos Santos Cabral, Katia Maria, de Lourenço, Isabella Otênio [UNESP], Malizia-Motta, Clara L.F., de Luna Marques, Aline, Mebus-Antunes, Nathane Cunha, Neves-Martins, Thais Cristtina, de Sá, Jéssica Maróstica [UNESP], Sanches, Karoline [UNESP], Santana-Silva, Marcos Caique, Vasconcelos, Ariana Azevedo, da Silva Almeida, Marcius, de Amorim, Gisele Cardoso, Anobom, Cristiane Dinis, Da Poian, Andrea T., Gomes-Neto, Francisco, Pinheiro, Anderson S., Almeida, Fabio C.L.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:Brasil
Institución:Universidade Estadual Paulista (UNESP)
Repositorio:Repositório Institucional da UNESP
Idioma:inglés
OAI Identifier:oai:repositorio.unesp.br:11449/223395
Acceso en línea:http://dx.doi.org/10.1016/j.ijbiomac.2022.01.121
http://hdl.handle.net/11449/223395
Access Level:acceso abierto
Palabra clave:Binding specificity
DNA/RNA binding protein
SARS-CoV-2 nucleocapsid protein
Descripción
Sumario:The SARS-CoV-2 nucleocapsid protein (N) is a multifunctional promiscuous nucleic acid-binding protein, which plays a major role in nucleocapsid assembly and discontinuous RNA transcription, facilitating the template switch of transcriptional regulatory sequences (TRS). Here, we dissect the structural features of the N protein N-terminal domain (N-NTD) and N-NTD plus the SR-rich motif (N-NTD-SR) upon binding to single and double-stranded TRS DNA, as well as their activities for dsTRS melting and TRS-induced liquid-liquid phase separation (LLPS). Our study gives insights on the specificity for N-NTD(-SR) interaction with TRS. We observed an approximation of the triple-thymidine (TTT) motif of the TRS to β-sheet II, giving rise to an orientation difference of ~25° between dsTRS and non-specific sequence (dsNS). It led to a local unfavorable energetic contribution that might trigger the melting activity. The thermodynamic parameters of binding of ssTRSs and dsTRS suggested that the duplex dissociation of the dsTRS in the binding cleft is entropically favorable. We showed a preference for TRS in the formation of liquid condensates when compared to NS. Moreover, our results on DNA binding may serve as a starting point for the design of inhibitors, including aptamers, against N, a possible therapeutic target essential for the virus infectivity.

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