Large-scale analyses of heat shock transcription factors and database construction based on whole-genome genes in horticultural and representative plants

The heat shock transcription factors (Hsfs) are members of a key transcription factor gene family that responds to heat stress and plays an important role in heat resistance. Previous reports have shown that Hsf family genes contain several conserved domains. At the N terminus is a DNA-binding domain (DBD) that can recognize promoter elements of heat-responsive genes. An adjacent oligomerization domain (OD or HR-A/B) is found in all Hsf family genes and comprises mainly hydrophobic heptad repeats. HSFs are sequence-specific DNA binding proteins that bind specifically to heat-shock elements (HSEs) with high affinity. The activation of HSFs and their subsequent binding to HSEs are key steps in regulating the expression of almost all heat shock genes. Until now, the Hsf gene family has been characterized in whole genomes of many plant species, including Arabidopsis thaliana (21 genes), Oryza sativa (25), Solanum lycopersicum, and others. However, no database has previously been created specifically for the Hsf gene family, and some detailed information on this family is still absent.

Recently, scientists from the North China University of Science and Technology constructed an Hsf database (http://hsfdb.bio2db.com) from which researchers can retrieve information on Hsf family genes in order to explore their expression patterns and evolutionary mechanisms. They identified 2950 Hsf family genes from 111 horticultural species and other representative plants. A phylogenetic tree of all the Hsf genes was constructed, which indicated that the Hsf genes of each branch had evolved independently after species differentiation. The evolutionary trajectories of Hsf genes were also uncovered by motif analysis, and a heat response network was constructed using 24 Hsf genes and 2421 downstream and 222 upstream genes from A. thaliana. Further analysis showed that Hsf genes and other transcription factors interacted with one another during the heat stress response. Syntenic and phylogenetic analyses were performed using Hsf genes from A. thaliana and a pan-genome from 18 Brassica rapa accessions. The researchers also performed expression pattern analysis of Hsf and six Hsp family genes using expression values from different tissues and heat treatments in B. rapa. An interaction network was constructed among Hsf and Hsp gene families from B. rapa, and several core genes were identified in the network.

“We performed comprehensive analyses of the Hsf gene family in 111 horticultural and other representative plants, especially for the study of the horticultural plant B. rapa. We also constructed a database for all identified Hsf family genes,” Dr. Song said. This study will serve as a useful resource for future studies on the biological functions and evolutionary history of the Hsf gene family.

###

Reference

Authors

Tong Yu¹, Yun Bai¹, Zhuo Liu¹, Zhiyuan Wang¹, Qihang Yang¹, Tong Wu¹, Shuyan Feng¹, Yu Zhang¹, Shaoqin Shen¹, Qiang Li², Liqiang Gu² and Xiaoming Song^1,3,4,*

Affiliations

1 School of Life Sciences, North China University of Science and Technology, Tangshan 063210, Hebei, China

2 Faculty of Life Science, Tangshan Normal University, Tangshan 063000, Hebei, China

3 School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China

4 Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68588, USA

About Dr. Xiaoming Song

Dr. Xiaoming Song graduated from Nanjing University of Horticulture and Genomics in June 2015. From July 2015 to now, he has worked in the School of Life Sciences at North China University of Technology. Dr. Song is mainly engaged in comparative genomics and functional genomics research. He has published more than 40 articles to date, and his SCI papers have been cited more than 1000 times. He serves as a reviewer for SCI journals such as Plant Physiology and Biochemistry. His doctoral dissertation was honored as one of the one hundred excellent doctoral theses in Jiangsu Province. He presided over a Youth Top Talent Project of the Provincial Department of Education, a Provincial Natural Science Foundation project, and a municipal department-level scientific research project, as well as participating in several national scientific research projects.