Genome-wide identification, classification and analysis of heat shock transcription factor family in maize

Abstract

BackgroundHeat shock response in eukaryotes is transcriptionally regulated by conserved heat shock transcription factors (Hsfs). Hsf genes are represented by a large multigene family in plants and investigation of the Hsf gene family will serve to elucidate the mechanisms by which plants respond to stress. In recent years, reports of genome-wide structural and evolutionary analysis of the entire Hsf gene family have been generated in two model plant systems, Arabidopsis and rice. Maize, an important cereal crop, has represented a model plant for genetics and evolutionary research. Although some Hsf genes have been characterized in maize, analysis of the entire Hsf gene family were not completed following Maize (B73) Genome Sequencing Project.ResultsA genome-wide analysis was carried out in the present study to identify all Hsfs maize genes. Due to the availability of complete maize genome sequences, 25 nonredundant Hsf genes, named ZmHsfs were identified. Chromosomal location, protein domain and motif organization of ZmHsfs were analyzed in maize genome. The phylogenetic relationships, gene duplications and expression profiles of ZmHsf genes were also presented in this study. Twenty-five ZmHsfs were classified into three major classes (class A, B, and C) according to their structural characteristics and phylogenetic comparisons, and class A was further subdivided into 10 subclasses. Moreover, phylogenetic analysis indicated that the orthologs from the three species (maize, Arabidopsis and rice) were distributed in all three classes, it also revealed diverse Hsf gene family expression patterns in classes and subclasses. Chromosomal/segmental duplications played a key role in Hsf gene family expansion in maize by investigation of gene duplication events. Furthermore, the transcripts of 25 ZmHsf genes were detected in the leaves by heat shock using quantitative real-time PCR. The result demonstrated that ZmHsf genes exhibit different expression levels in heat stress treatment.ConclusionsOverall, data obtained from our investigation contributes to a better understanding of the complexity of the maize Hsf gene family and provides the first step towards directing future experimentation designed to perform systematic analysis of the functions of the Hsf gene family.

Genome-wide analysis, expression profile of heat shock factor gene family (CaHsfs) and characterisation of CaHsfA2 in pepper (Capsicum annuum L.)

“…Most HsfBs, except HsfB5, contain the tetrapeptide LFGV in the C-terminal domain, which is assumed to function as a repressor motif in the transcriptional machinery [8]. The expression patterns of most CaHsfB members under HS could be explained by a report in tomato.…”

“…The Hsf gene family has, so far, been fully characterised only in a few model species, such as Arabidopsis , rice, maize, wheat and Chinese cabbage [8, 20, 39–41]. The genome sequence of pepper has been published recently [42, 43], which enables the characterisation of the pepper Hsf family and their responses to various stresses at the molecular level.…”

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.…”

Genome Duplication and Gene Loss Affect the Evolution of Heat Shock Transcription Factor Genes in Legumes

“…On the basis of sequence divergence, three Hsf classes (A, B and C) and several subgroups are currently recognized [22]. Previous studies have shown that there are no apparent tandem duplications, and no clustered organization, in the Hsf families of several monocot and eudicot species [35], [37]. How did the members of this gene family arise, and how are the copy numbers of genes in this family maintained?…”