Genome-wide analysis of the heat shock transcription factors in Populus trichocarpa and Medicago truncatula

Abstract

Research has provided substantial evidences that heat shock proteins (HSPs) play essential roles in extreme physiological conditions. Heat shock transcription factors (HSFs) are important HSPs regulators, but their functions are poorly understood, particularly in Populus and Medicago. In this study, a comprehensive bioinformatics analysis of the HSFs was performed in Populus trichocarpa and Medicago truncatula. Twenty-eight Populus HSFs and 16 Medicago HSFs were identified, and comparative analyzes of the two plants were carried out subsequently. HSFs were divided into three different classes and they were diverse and complicated transcription factors. The results of semi-quantitative RT-PCR in Populus suggested six genes (PtHSF-03, PtHSF-13, PtHSF-15, PtHSF-21, PtHSF-22 and PtHSF-23) were markedly increased by heat stress. The results presented here provide an important clue for cloning, expression and functional studies of the HSFs in Populus and Medicago.

Genome-wide identification, classification, and analysis of heat shock transcription factor family in Chinese cabbage (Brassica rapa pekinensis)

“…All paraologous genes appeared between chromosomes, providing information regarding the evolutionary process of the Chinese cabbage Hsf family and indicating that genome duplication likely occurred. In contrast, in maize and Populus, segmental Hsf gene duplications and tandem duplications coexisted, with the former more prevalent than the latter (Lin et al, 2011;Wang et al, 2012). Gene duplication is a major mechanism through which genomic rearrangement and expansion occur; however, diversification of gene function is also generated during molecular evolution.…”

“…To date, a variety of heat stress transcription factors have been successfully identified and investigated in some plants, including tomato (Scharf et al, 1990), Arabidopsis (Nover et al, 2001), rice (Guo et al, 2008), maize (Lin et al, 2011), Malus domestica (Giorno et al, 2012), soybean (Glycine max) (Chung et al, 2012), Medicago truncatula, and polar (Populus tricocarpa) (Wang et al, 2012). For example, Arabidopsis, which served as the prototype for the Hsf family, contains a set of 21 Hsf-encoding genes with 15 members belonging to class A, 5 members to class B, and 1 to class C, which are the smallest families observed thus far.…”

Systematic analysis of maize class III peroxidase gene family reveals a conserved subfamily involved in abiotic stress response

“…wur.nl/uk/software_mapinspect.html) according to their starting positions on the maize chromosomes. Duplications of ZmPRXs were identified using MCScanX software (http://chibba.pgml.uga.edu/mcscan2/) (Wang et al, 2012a(Wang et al, , 2012b. First, whole-genome protein sequences from maize were merged and searched against themselves using BLASTP with an E-value cutoff of 1 × 10 −10 .…”

“…First, whole-genome protein sequences from maize were merged and searched against themselves using BLASTP with an E-value cutoff of 1 × 10 −10 . Then, the default parameters of MCScanX were applied to identify the synteny regions in accordance with some studies (Wang et al, 2012a(Wang et al, , 2012b. Finally, the duplicated PRXs from these duplicated regions were identified using an in-house Perl script, and the duplicated genes were classified into groups with various types of duplications including collinearity, tandem and so on.…”

Genome wide analysis of heat shock transcription factor (HSF) family in chickpea and its comparison with Arabidopsis

“…In response to heat stress, these chaperone complexes are converted from a transcriptional inactive monomer to an active trimmer through combination of their oligomerization domains. As sequence-specific trimeric DNA binding proteins, the active HSFs are capable of recognizing and combining HSEs in the HSF-inducible gene promoters (Wang et al, 2012). HSEs are formed of repetitive palindromic binding motifs of the 5'-AGAAnnTTCT-3' sequence upstream of the TATA box in the HSF-inducible genes (Pelham, 1982;Santoro et al, 1998;Akerfelt, 2010).…”