Genome-wide identification and characterization of Solanum tuberosum BiP genes reveal the role of the promoter architecture in BiP gene diversity

Abstract

The endoplasmic reticulum (ER) immunoglobulin binding proteins (BiPs) are molecular chaperones involved in normal protein maturation and refolding malformed proteins through the unfolded protein response (UPR). Plant BiPs belong to a multi-gene family contributing to development, immunity, and responses to environmental stresses. This study identified three BiP homologs in the Solanum tuberosum (potato) genome using phylogenetic, amino acid sequence, 3-D protein modeling, and gene structure analysis. These analyses revealed that StBiP1 and StBiP2 grouped with AtBiP2, whereas StBiP3 grouped with AtBiP3. While the protein sequences and folding structures are highly similar, these StBiPs are distinguishable by their expression patterns in different tissues and in response to environmental stressors such as treatment with heat, chemicals, or virus elicitors of UPR. Ab initio promoter analysis revealed that potato and Arabidopsis BiP1 and BiP2 promoters were highly enriched with cis-regulatory elements (CREs) linked to developmental processes, whereas BiP3 promoters were enriched with stress related CREs. The frequency and linear distribution of these CREs produced two phylogenetic branches that further resolve the groups identified through gene phylogeny and exon/intron phase analysis. These data reveal that the CRE architecture of BiP promoters potentially define their spatio-temporal expression patterns under developmental and stress related cues.

The Endoplasmic Reticulum Role in the Plant Response to Abiotic Stress

“…Recently, research in citrus species reported the presence of CsBiP1 and CsBiP2 genes and showed that under drought stress the expression of CsBiP1 is upregulated in C. limonia, and CsBiP2 was observed to be upregulated in C. sinensis seedlings under cold and osmotic stress (Guimarães et al, 2018), an interesting observation that offers a unique opportunity to study the regulation and role of BiP on different stresses. A similar observation has been made on Solanum tuberosum, where three candidates BiPs; StBiP1, StBiP2, and StBiP3 have been identified and only StBiP3 is upregulated under salt stress (Herath et al, 2020). Overall, these reports provide strong evidence that BiP proteins are linked with different types of abiotic stresses, nevertheless none of them identified or associated any client(s) protein(s) to the observed phenotype, so further research into client(s) of these chaperones, and the search for new BiPs in other plants, would contribute to a better understanding of the role of BiP under stress.…”

Genome-wide identification of heat shock factors and heat shock proteins in response to UV and high intensity light stress in lettuce

“…Hsp70s are molecular regulators of stress responses, as they maintain protein homeostasis by mediating protein folding and/or protein denaturation [ 29 ]. Hsp70 family is comprised of DnaK subfamily including cytoplasmic Hsp70 (Hsp70), truncated Hsp70 (Hsp70t), plastidic Hsp70 (cpHsp70), mitochondrial Hsp70 (mtHsp70), endoplasmic reticulum-localized immunoglobin binding protein (BiP), and the Hsp110/SSE subfamily [ 30 ]. We found that the Hsp70 subfamily was largely expanded in lettuce (Fig.…”

Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum

“…The bZIP TF family is central to the regulation of developmental and physiological responses as well as abiotic and biotic stress responses [ 36 , 37 , 38 ]. Five of TFs ( StbZIP37 , StbZIP42 , StbZIP46 , StbZIP58 , and StbZIP61 ) are upregulated early in PVX infection and only one ( StbZIP72 ) is downregulated ( Tables S4 and S5 ).…”