Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function.

Venura Herath,Jeanmarie Verchot

doi:10.3390/ijms22010253

Abstract

The basic region-leucine zipper (bZIP) transcription factors (TFs) form homodimers and heterodimers via the coil–coil region. The bZIP dimerization network influences gene expression across plant development and in response to a range of environmental stresses. The recent release of the most comprehensive potato reference genome was used to identify 80 StbZIP genes and to characterize their gene structure, phylogenetic relationships, and gene expression profiles. The StbZIP genes have undergone 22 segmental and one tandem duplication events. Ka/Ks analysis suggested that most duplications experienced purifying selection. Amino acid sequence alignments and phylogenetic comparisons made with the Arabidopsis bZIP family were used to assign the StbZIP genes to functional groups based on the Arabidopsis orthologs. The patterns of introns and exons were conserved within the assigned functional groups which are supportive of the phylogeny and evidence of a common progenitor. Inspection of the leucine repeat heptads within the bZIP domains identified a pattern of attractive pairs favoring homodimerization, and repulsive pairs favoring heterodimerization. These patterns of attractive and repulsive heptads were similar within each functional group for Arabidopsis and S. tuberosum orthologs. High-throughput RNA-seq data indicated the most highly expressed and repressed genes that might play significant roles in tissue growth and development, abiotic stress response, and response to pathogens including Potato virus X. These data provide useful information for further functional analysis of the StbZIP gene family and their potential applications in crop improvement.

Highlights

Introduction nal affiliationsBroad networks of transcription factors (TFs) exert basal control of gene expression, acting at the core promoter and engaging with RNA polymerase to initiate transcription.Regulatory TFs bind proximal and distal promoter regions to stimulate gene expression in a spatiotemporal and tissue-specific manner
We identified 67 basic region-leucine zipper (bZIP) genes in the S. tuberosum genome (EnsemblPlants SolTub_3.0 assembly) by restricting our query to the predicted domain model (IPR004827)
We examined transcript profiles derived from leaves that were inoculated with Potato Virus X (PVX) and harvested at 2 and 3 dpi to identify the StbZIP factors whose expression is altered early in virus infection

Summary

Introduction

Broad networks of transcription factors (TFs) exert basal control of gene expression, acting at the core promoter and engaging with RNA polymerase to initiate transcription. Regulatory TFs bind proximal and distal promoter regions to stimulate gene expression in a spatiotemporal and tissue-specific manner. They often recognize consensus sequences in promoters and can act on multiple genes. Such regulatory TFs are the master controllers of transcription networks and are fundamental for plant growth, development, and responses to environmental factors [1,2]. The bZIP family is central to the regulation of developmental and physiological processes as well as abiotic and biotic stress responses [4]

Methods

Results

Conclusion