A genome-wide survey of HD-Zip genes in rice and analysis of drought-responsive family members

Abstract

The homeodomain leucine zipper (HD-Zip) genes encode transcription factors that have diverse functions in plant development and have often been implicated in stress adaptation. The HD-Zip genes are the most abundant group of homeobox (HB) genes in plants and do not occur in other eukaryotes. This paper describes the complete annotation of the HD-Zip families I, II and III from rice and compares these gene families with Arabidopsis in a phylogeny reconstruction. Orthologous pairs of rice and Arabidopsis HD-Zip genes were predicted based on neighbour joining and maximum parsimony (MP) trees with support of conserved intron-exon organization. Additionally, a number of HD-Zip genes appeared to be unique to rice. Searching of EST and cDNA databases and expression analysis using RT-PCR showed that 30 out of 31 predicted rice HD-Zip genes are expressed. Most HD-Zip genes were broadly expressed in mature plants and seedlings, but others showed more organ specific patterns. Like in Arabidopsis and other dicots, a subset of the rice HD-Zip I and II genes was found to be regulated by drought stress. We identified both drought-induced and drought-repressed HD-Zip genes and demonstrate that these genes are differentially regulated in drought-sensitive versus drought-tolerant rice cultivars. The drought-repressed HD-Zip family I gene, Oshox4, was selected for promoter-GUS analysis, showing that drought-responsiveness of Oshox4 is controlled by the promoter and that Oshox4 expression is predominantly vascular-specific. Loss-of-function analysis of Oshox4 revealed no specific phenotype, but overexpression analysis suggested a role for Oshox4 in elongation and maturation processes.

Genome-wide analysis of the homeodomain-leucine zipper (HD-ZIP) gene family in peach (Prunus persica)

“…The MEME result revealed that HD-ZIP III proteins have a C-terminal extension of about 150 amino acids termed MEKHLA. This region was also well conserved in the HD-ZIP III proteins from both monocots (O. sativa) and dicots (Arabidopsis) (Prigge et al, 2005;Agalou et al, 2008).…”

“…The availability of the complete genome sequences of peach and the previous identification of HD-ZIP family genes from some plant species (Aso et al, 1999;Agalou et al, 2008;Övernäs, 2010;Hu et al, 2012) enabled a comparison of individual families and groups of these genes with those in Arabidopsis (Henriksson et al, 2005;Prigge et al, 2005;Nakamura et al, 2006;Ciarbelli et al, 2008). Although peach has a large genome of 220-230 Mbp (Jung et al, 2008), which is larger than that of A. thaliana (145 Mbp) (Huala et al, 2001) and smaller than that of O. sativa (430 Mbp) (Goff et al, 2002), the number of genes in the HD-ZIP family in peach (33) is not more than that in A. thaliana (47) and is not much less than that in O. sativa (38).…”

A genome-wide survey of homeodomain-leucine zipper genes and analysis of cold-responsive HD-Zip I members’ expression in tomato

“…The original β clade was also divided into β1 and β2 clades as reported in maize and rice. 42,43) β2, φ1, ε clades were grouped by tomato and Arabidopsis genes. SlHZ12 in β1 clade, SlHZ08, -13 and -28,-01 in α clade, SlHZ16, -17, -18, -19 in δ clade, SlHZ20, -32, -41, -05 in γ clade were clustered with Arabidopsis and rice in their clades.…”

“…41) However, in this study, ATHB54 did not had any counterparts of two other species or did not belong to any clade as Agalou reported. 42) ATHB54 is a atypical HD-Zip I protein with an extremely long CTR (325aa) which a RNA recognition motif can be identified in. 10) In class II, HD-Zip genes of three species were divided into several subclasses as reported in Arabidopsis.…”

Identification of drought, cadmium and root-lesion nematode infection stress-responsive transcription factors in ramie

“…Many members of MYB, AP2/ERF, bZIP, and HD-ZIP families not only play important roles in the regulation of plant tolerance to abiotic stresses, but also function as regulators of responses to biotic stress, particularly with respect to activation of anti-pathogen defenses [30][31][32][33][34][35][36][37][38][39]. In rice, transgenic technology approaches indicated that at least five bZIP genes, nine AP2/ERF genes, and one MYB genes regulated tolerance to drought [40].…”