Analysis of the arabidopsis REM gene family predicts functions during flower development

Abstract

Background and aims: The REM (Reproductive Meristem) gene family of Arabidopsis thaliana is part of the B3 DNA-binding domain superfamily. Despite the fact that several groups have worked on the REM genes for many years, little is known about the function of this transcription factor family. This study aims to identify a set of REM genes involved in flower development and to characterize their function.

Methods: In order to provide an overview of the REM gene family, a detailed expression analysis for all REM genes of A. thaliana was performed and combined with a meta-analysis of ChIP-sequencing and microarray experiments.

Key results: Two sets of phylogenetically closely related REM genes, namely REM23, REM24 and REM25, and REM34, REM35 and REM36, were identified as possibly being involved in the early stages of flower development. Single- and double-mutant combinations were analysed for these genes, and no phenotypic effects were detected during flower development.

Conclusions: The data suggest that the REM34, REM35 and REM36 group is the most interesting one, as REM34 is co-expressed with the floral meristem identity (FMI) genes, they are bound by AP1, SVP, AP3 and PI, and they are expressed in the floral meristem and during the earliest stages of flower development. However, it appears that high levels of functional redundancy may conceal the exact function of these transcription factor genes.

Keywords: Arabidopsis thaliana; B3 domain; FMI; REM gene; floral meristem identity; flower development; reproductive meristem; transcription factor.

Fig. 1.

Distribution of REM genes on Arabidopsis chromosomes indicating the phylogenetic relationships (coloured lines).

Fig. 2.

Heatmaps for expression levels of REM genes. (A) REM gene expression levels measured by microarray; data are shown as log₁₀ transformed absolute values from the AtGeneExpress developmental series; the ‘Roots’ sample corresponds to the ATGE_93 microarray experiment, the ‘Rosette leaves’ sample is the ATGE_13 experiment, the ‘Cauline leaves’ sample is the ATGE_26 experiment, the ‘shoot apex - inflorescence’ sample is the ATGE_29 experiment, the ‘Flowers stage 9’ sample is the ATGE_31 experiment, the ‘Flowers stage 10–11’ sample is the ATGE_32 experiment, the ‘Flowers stage 12’ sample is the ATGE_33 experiment, the ‘Flowers stage 15’ sample is the ATGE_39 experiment, the ‘Silique/Seeds stage 3’ sample is the ATGE_76 experiment, the ‘Silique/Seeds stage 4’ sample is the ATGE_77 experiment, the ‘Silique/Seeds stage 5’ sample is the ATGE_78 experiment, the ‘Seeds stage 6’ sample is the ATGE_79 experiment, and the ‘Seeds stage 7’ sample is the ATGE_81 experiment. (B) REM gene expression levels measured by quantitative real-time PCR (data are shown as square root-transformed 2^–ΔCT values).

Fig. 3.

Co-expression matrix for REM genes and key regulators of reproductive development (same data as in Fig 3) after hierarchical clustering with the Euclidean distance as metric and the average linkage method. The values visualized in the heatmap represent the Pearson correlation between the expression values of each gene pair calculated using almost 2000 microarray hybridization experiments.

Fig. 4.

Graphical representation of the co-expression among REM genes and selected reproductive markers. Only pairs of genes with co-expression levels (r) that are ≥ 0·75 are shown. Co-expressed genes are linked by lines, the length of the line being negatively correlated with co-expression levels.

Fig. 5.

High confidence AP1-, SVP-, PI- and AP3-binding sites in the cluster of REM34 homologues on chromosome 4.

Fig. 6.

Expression analysis by in situ hybridization for selected REM genes in wild-type Col inflorescences. REM23 (A), REM24 (B) and REM25 (C) are expressed from stage 7–8 of flower development. REM23 and REM24 expression is detectable in developing stamens (st), whereas REM25 is expressed from stage 7 of flower development in developing carpels (ca) and stamens. REM34 (D), REM35 (E) and REM36 (F) are all expressed in the inflorescence meristem (im) and floral meristems at stages 1 (fm), 2, 3 and 4. During later stages of flower development, the expression is detectable in the inner floral whorls and excluded from the sepals (se). Scale bars = 50 μm.