Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (2024)

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Volume 46

Issue 6

10.3390/cimb46060344

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Article

by

Yahaira de J. Tamayo-Ordóñez

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (5)Yahaira de J. Tamayo-Ordóñez

1,

Ninfa M. Rosas-García

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (6)Ninfa M. Rosas-García

1,*Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (7),

Francisco A. Tamayo-Ordoñez

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (8)Francisco A. Tamayo-Ordoñez

2Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (9),

Benjamín A. Ayil-Gutiérrez

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (10)Benjamín A. Ayil-Gutiérrez

3,

Juan M. Bello-López

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (11)Juan M. Bello-López

4Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (12),

Gerardo de J. Sosa-Santillán

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (13)Gerardo de J. Sosa-Santillán

5Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (14),

Erika Acosta-Cruz

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (15)Erika Acosta-Cruz

6Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (16),

Francisco Anguebes-Franseschi

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (17)Francisco Anguebes-Franseschi

2,

Siprian Damas-Damas

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (18)Siprian Damas-Damas

2,

Angel V. Domínguez-May

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (19)Angel V. Domínguez-May

7Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (20),

Atl Victor Córdova-Quiroz

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (21)Atl Victor Córdova-Quiroz

2 and

María Concepción Tamayo-Ordóñez

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (22)María Concepción Tamayo-Ordóñez

8,*Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (23)

1

Laboratorio de Biotecnología Ambiental del Centro de Biotecnología Genómica del Instituto Politécnico Nacional, Reynosa 88710, Tamps, Mexico

2

Facultad de Química, Universidad Autónoma del Carmen, Calle 56 N. 4, Av. Concordia Col. Benito Juárez, Ciudad del Carmen 24180, Campeche, Mexico

3

CONAHCYT—Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Biotecnología Vegetal, Reynosa 88710, Tamps, Mexico

4

División de Investigación, Hospital Juárez de México, Ciudad de México 07760, Mexico

5

Laboratorio de Microbiología y Biosíntesis, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico

6

Laboratorio de Microbiología Molecular, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico

7

TecNM, Instituto Tecnológico Superior del Sur del Estado de Yucatán, Road Muna-Felipe Carrillo Puerto, Stretch Oxkutzcab-Akil Km 41+400, Oxkutzcab 97880, Yucatán, Mexico

8

Laboratorio de Ingeniería Genética, Departamento de Biotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Coahuila, Saltillo 25280, Coahuila, Mexico

*

Authors to whom correspondence should be addressed.

Curr. Issues Mol. Biol. 2024, 46(6), 5744-5776; https://doi.org/10.3390/cimb46060344

Submission received: 10 April 2024/Revised: 14 May 2024/Accepted: 26 May 2024/Published: 9 June 2024

(This article belongs to the Special Issue Structure and Function of Proteins: From Bioinformatics Insights)

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Abstract

In the SARS-CoV-2 lineage, RNA elements essential for its viral life cycle, including genome replication and gene expression, have been identified. Still, the precise structures and functions of these RNA regions in coronaviruses remain poorly understood. This lack of knowledge points out the need for further research to better understand these crucial aspects of viral biology and, in time, prepare for future outbreaks. In this research, the in silico analysis of the cis RNA structures that act in the alpha-, beta-, gamma-, and deltacoronavirus genera has provided a detailed view of the presence and adaptation of the structures of these elements in coronaviruses. The results emphasize the importance of these cis elements in viral biology and their variability between different viral variants. Some coronavirus variants in some groups, depending on the cis element (stem-loop1 and -2; pseudoknot stem-loop1 and -2, and s2m), exhibited functional adaptation. Additionally, the conformation flexibility of the s2m element in the SARS variants was determined, suggesting a coevolution of this element in this viral group. The variability in secondary structures suggests genomic adaptations that may be related to replication processes, genetic regulation, as well as the specific pathogenicity of each variant. The results suggest that RNA structures in coronaviruses can adapt and evolve toward different viral variants, which has important implications for viral adaptation, pathogenicity, and future therapeutic strategies.

Keywords: SARS-CoV-2; RNA structures; cis elements; coevolution

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MDPI and ACS Style

Tamayo-Ordóñez, Y.d.J.; Rosas-García, N.M.; Tamayo-Ordoñez, F.A.; Ayil-Gutiérrez, B.A.; Bello-López, J.M.; Sosa-Santillán, G.d.J.; Acosta-Cruz, E.; Anguebes-Franseschi, F.; Damas-Damas, S.; Domínguez-May, A.V.;et al. Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements. Curr. Issues Mol. Biol. 2024, 46, 5744-5776.https://doi.org/10.3390/cimb46060344

AMA Style

Tamayo-Ordóñez YdJ, Rosas-García NM, Tamayo-Ordoñez FA, Ayil-Gutiérrez BA, Bello-López JM, Sosa-Santillán GdJ, Acosta-Cruz E, Anguebes-Franseschi F, Damas-Damas S, Domínguez-May AV,et al. Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements. Current Issues in Molecular Biology. 2024; 46(6):5744-5776.https://doi.org/10.3390/cimb46060344

Chicago/Turabian Style

Tamayo-Ordóñez, Yahaira de J., Ninfa M. Rosas-García, Francisco A. Tamayo-Ordoñez, Benjamín A. Ayil-Gutiérrez, Juan M. Bello-López, Gerardo de J. Sosa-Santillán, Erika Acosta-Cruz, Francisco Anguebes-Franseschi, Siprian Damas-Damas, Angel V. Domínguez-May,and et al. 2024. "Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements" Current Issues in Molecular Biology 46, no. 6: 5744-5776.https://doi.org/10.3390/cimb46060344

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MDPI and ACS Style

Tamayo-Ordóñez, Y.d.J.; Rosas-García, N.M.; Tamayo-Ordoñez, F.A.; Ayil-Gutiérrez, B.A.; Bello-López, J.M.; Sosa-Santillán, G.d.J.; Acosta-Cruz, E.; Anguebes-Franseschi, F.; Damas-Damas, S.; Domínguez-May, A.V.;et al. Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements. Curr. Issues Mol. Biol. 2024, 46, 5744-5776.https://doi.org/10.3390/cimb46060344

AMA Style

Tamayo-Ordóñez YdJ, Rosas-García NM, Tamayo-Ordoñez FA, Ayil-Gutiérrez BA, Bello-López JM, Sosa-Santillán GdJ, Acosta-Cruz E, Anguebes-Franseschi F, Damas-Damas S, Domínguez-May AV,et al. Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements. Current Issues in Molecular Biology. 2024; 46(6):5744-5776.https://doi.org/10.3390/cimb46060344

Chicago/Turabian Style

Tamayo-Ordóñez, Yahaira de J., Ninfa M. Rosas-García, Francisco A. Tamayo-Ordoñez, Benjamín A. Ayil-Gutiérrez, Juan M. Bello-López, Gerardo de J. Sosa-Santillán, Erika Acosta-Cruz, Francisco Anguebes-Franseschi, Siprian Damas-Damas, Angel V. Domínguez-May,and et al. 2024. "Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements" Current Issues in Molecular Biology 46, no. 6: 5744-5776.https://doi.org/10.3390/cimb46060344

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Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements (24)

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