In Silico Characterization of the RCC1 Family and the UVR8 Gene in Chenopodium quinoa Willd

Paredes Malca, Jean Carlo; Fuentes Apaza, Michell Maheba; Valderrama-Valencia, María Rosario Elsa; Bardales Álvarez, Roxana; Condori Mamani, Eloy; Condori-Pacsi, Sandro Jhonatan

doi:10.3390/ijms262311657

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In Silico Characterization of the RCC1 Family and the UVR8 Gene in Chenopodium quinoa Willd

by

Jean Carlo Paredes Malca

,

Michell Maheba Fuentes Apaza

,

María Rosario Elsa Valderrama-Valencia

,

Roxana Bardales Álvarez

,

Eloy Condori Mamani

and

Sandro Jhonatan Condori-Pacsi

^*

Laboratorio de Recursos Genéticos y Genética Molecular, Universidad Nacional de San Agustín, Arequipa 04001, Peru

^*

Author to whom correspondence should be addressed.

Int. J. Mol. Sci. 2025, 26(23), 11657; https://doi.org/10.3390/ijms262311657 (registering DOI)

Submission received: 15 October 2025 / Revised: 23 November 2025 / Accepted: 27 November 2025 / Published: 1 December 2025

(This article belongs to the Special Issue Screening and Identification of Crop Abiotic Stress Tolerance Functional Genes)

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Abstract

Quinoa (Chenopodium quinoa Willd.), an Andean crop with exceptional nutritional value, thrives in ecosystems exposed to intense ultraviolet-B (UV-B) radiation; yet the molecular mechanisms underlying its photoreception remain largely unknown. The UV Resistance locus 8 (UVR8) protein, a member of the Regulator of Chromosome Condensation 1 (RCC1) family, is the primary UV-B photoreceptor in plants. Here, we report the first in silico characterization of the RCC1 gene family in C. quinoa, aimed at identifying and structurally analyzing UVR8 homologs. Genomic analysis uncovered 40 CqRCC1 genes, exhibiting extensive structural diversity. Phylogenetic reconstruction identified two proteins, CqRCC1_20 and CqRCC1_23, as the closest homologs of AtUVR8 from Arabidopsis thaliana. Homology modeling revealed that CqRCC1_20 maintains the canonical seven-bladed β-propeller architecture of UVR8, whereas CqRCC1_23 carries a deletion leading to a six-bladed structure. Both isoforms retain the critical tryptophan residues (W233, W285, W337) and the C-terminal Valine-Proline (VP) motif required for photoperception and Constitutive Photomorphogenic 1 (COP1) interaction. Notably, the CqRCC1_23 model predicts fewer hydrogen bonds at the dimer interface and structural alterations at key regulatory interaction sites. Collectively, these results indicate that quinoa harbors functionally conserved UVR8 isoforms with structural divergence, such as CqRCC1_23, which may influence photoreceptor stability and enable a sustained UV-B response, potentially conferring an adaptive advantage in high-radiation environments.

Keywords: Chenopodium quinoa; UVR8; RCC1; bioinformatic; photoreceptor UV-B; comparative modeling; abiotic stress

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MDPI and ACS Style

Paredes Malca, J.C.; Fuentes Apaza, M.M.; Valderrama-Valencia, M.R.E.; Bardales Álvarez, R.; Condori Mamani, E.; Condori-Pacsi, S.J. In Silico Characterization of the RCC1 Family and the UVR8 Gene in Chenopodium quinoa Willd. Int. J. Mol. Sci. 2025, 26, 11657. https://doi.org/10.3390/ijms262311657

AMA Style

Paredes Malca JC, Fuentes Apaza MM, Valderrama-Valencia MRE, Bardales Álvarez R, Condori Mamani E, Condori-Pacsi SJ. In Silico Characterization of the RCC1 Family and the UVR8 Gene in Chenopodium quinoa Willd. International Journal of Molecular Sciences. 2025; 26(23):11657. https://doi.org/10.3390/ijms262311657

Chicago/Turabian Style

Paredes Malca, Jean Carlo, Michell Maheba Fuentes Apaza, María Rosario Elsa Valderrama-Valencia, Roxana Bardales Álvarez, Eloy Condori Mamani, and Sandro Jhonatan Condori-Pacsi. 2025. "In Silico Characterization of the RCC1 Family and the UVR8 Gene in Chenopodium quinoa Willd" International Journal of Molecular Sciences 26, no. 23: 11657. https://doi.org/10.3390/ijms262311657

APA Style

Paredes Malca, J. C., Fuentes Apaza, M. M., Valderrama-Valencia, M. R. E., Bardales Álvarez, R., Condori Mamani, E., & Condori-Pacsi, S. J. (2025). In Silico Characterization of the RCC1 Family and the UVR8 Gene in Chenopodium quinoa Willd. International Journal of Molecular Sciences, 26(23), 11657. https://doi.org/10.3390/ijms262311657

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In Silico Characterization of the RCC1 Family and the UVR8 Gene in Chenopodium quinoa Willd

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