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

Sci Rep. 2020 Jul 9;10(1):11327. doi: 10.1038/s41598-020-68407-2.

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis Proteins / genetics
  • Carrier Proteins / genetics*
  • Endoplasmic Reticulum / metabolism
  • Gene Expression Regulation, Plant
  • Molecular Chaperones / genetics*
  • Plant Proteins / genetics*
  • Promoter Regions, Genetic*
  • Protein Conformation
  • Solanum tuberosum / genetics*
  • Stress, Physiological

Substances

  • Arabidopsis Proteins
  • BiP1 protein, Arabidopsis
  • BiP2 protein, Arabidopsis
  • BiP3 protein, Arabidopsis
  • Carrier Proteins
  • Molecular Chaperones
  • Plant Proteins