Identification of regulatory motifs in putative coding genes of small Heat Shock Proteins in Chenopodium quinoa

COSTA TÁRTARA SABRINA M.; ARCE, DÉBORA P.; CACCHIARELLI, PAOLO; TOLOSA, GABRIEL H.; PRATTA, GUILLERMO R.

Rosario, Santa Fé

Congreso; XIII Argentine Congress of Bioinformatics and Computational Biology, XIII International Conference of the Iberoamerican Society of Bioinformatics and III Annual Meeting of the Ibero-American Artificial Intelligence Network for Big Biodata; 2023

Asociación Argentina de Bioinformática y Biología Computacional

BACKGROUNDHeat Shock Elements (HSE) are conserved motif sequences of DNA (GAA..TTC) present in gene regulatory regions of Heat Shock Proteins (HSPs). HSE interact with Heat Shock transcription Factors (Hsfs) to trigger HSP transcription depending on heat, abiotic or oxidative stress response. In plants, HSPs are chaperones that assist in protein folding, preventing their irreversible aggregation during stress. However, it is currently known that they are present in cells during other biological processes like germination and fruit maturation. Chenopodium quinoa (quinoa) is an allotetraploid (2n = 4x = 36) crop species belonging to the Chenopodiacea family, whose grains are consumed as cereal, although they are a good quality protein source. Quinoa represents a model to study HSPs because of an intrinsic tolerance to abiotic stress, like high salinity, water shortage and light intensity. At the same time, it is sensitive to high temperatures. We already reported 75 putative small (s) HSP coding gene sequences about genome (v2) and in this work we explored the upstream region, defined in 1000 pb, of a group of genes closely located in chromosome 4B (Cq4B). Each upstream sequence was retrieved and filtered with an ad-hoc Python script. HSE were scanned in each gene´s putative promoter region using the RSAT platform. RESULTSThe high number of sHSP sequences reported is congruent with other plant species, which show 20 to 70 members, approximately. We also observed possible duplication events in some chromosomes, an evolutionary mechanism reported in the expansion of the HSP gene family. Among the tandem copy arranged selected genes CQ020271 (567 bp), CQ020272 (549 bp), CQ020274 (555 bp), CQ020275 (522 bp), CQ020276 (552 bp), CQ020278 (609 bp) located in Cq4B, HSEs were only detected in CQ020272 and CQ020276 promoters, indicating a possible Hsf-dependent regulation characterized in the HSP gene family. CONCLUSIONSThese observations support previous findings on sHSP subfamily characterization in other plant species of agronomic interest including Arabidopsis sp., tomato, potato, cotton, wheat, barley or sorghum. Further approaches could be conducted to characterize gene expression profiles of nearly duplicated genes (or tandem copy-located genes).