The Arabidopsis Homeodomain-leucine Zipper II gene family: diversity and redundancy

Abstract

The Arabidopsis genome contains 10 genes belonging to the HD-Zip II family including ATHB2 and HAT2. Previous work has shown that ATHB2 is rapidly and strongly induced by light quality changes that provoke the shade avoidance response whereas HAT2 expression responds to auxin. Here, we present a genome-wide analysis of the HD-Zip II family. Phylogeny reconstruction revealed that almost all of the HD-Zip II genes can be subdivided into 4 clades (alpha-delta), each clade comprising 2-3 paralogs. Gene expression studies demonstrated that all the gamma and delta genes are regulated by light quality changes. Kinetics of induction, low R/FR/high R/FR reversibility and auxin response analyses strongly suggested that HAT1, HAT3 and ATHB4, as ATHB2, are under the control of the phytochrome system whereas HAT2 is up-regulated by low R/FR as a consequence of the induction of the auxin signaling pathway provoked by FR-rich light. Root and shoot digital in situ revealed that gamma and delta genes are also tightly regulated during plant development with both distinct and overlapping patterns. Phenotypes of gain of function and dominant negative lines demonstrated that one or more of the HD-Zip II gamma genes negatively regulate cell proliferation during leaf development in a high R/FR light environment. Finally, target gene analysis using a chimeric transcription factor (HD-Zip2-V-G), known to activate ATHB2 target genes in a glucocorticoid-dependent manner, revealed that all the 10 HD-Zip II genes can be recognized by the HD-Zip 2 domain in vivo, implying an intricate negative feedback network.

Green Light Induces Shade Avoidance Symptoms

“…HAT4 and PIL1 are strongly induced during shade avoidance responses to far-red light (Devlin et al, 2003). HAT4 is a member of the homeodomain Leu zipper family of transcription factors, binding DNA via the 9-bp sequence CAATNATTG (Henriksson et al, 2005;Ciarbelli et al, 2008). Analysis of multiple phytochrome-deficient mutants revealed that HAT4 expression is redundantly suppressed by PHYB and PHYE (Franklin et al, 2003).…”

COP1 mediates the coordination of root and shoot growth by light through modulation of PIN1- and PIN2-dependent auxin transport in Arabidopsis

“…Images were taken with a Jenoptik ProgRes C10 camera mounted either on a Zeiss Axioskop 2+ microscope equipped with Nomarski optics or on a Leica MZ12 stereomicroscope. RNA extraction and quantitative reverse transcription PCR (qRT-PCR) were performed as previously described using the ACTIN 2 gene as a reference (Ciarbelli et al, 2008) and analyzed according to Pfaffl (Pfaffl, 2001). Primer sequences and Universal Probe Library (UPL) probes are given in the supplementary material Table S2.…”

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

“…Some HD-ZIP I genes not only are reported to be involved in abscisic acid and sucrose signaling pathways but are also critical to plant abiotic stress responses, embryogenesis, and cotyledon and leaf development (Himmelbach et al, 2002;Johannesson et al, 2003). The HD-ZIP II subfamily consists of 9 members (ATHB2/HAT4, ATHB4, HAT9,HAT14,HAT17,and HAT22) (Ciarbelli et al, 2008). All the 9 members possess a set of conserved cysteine molecules in and outside the LZ motif (Tron et al, 2002).…”