Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids

Polyploidization is an abrupt speciation mechanism for eukaryotes and is especially common in plants. However, little is known about patterns and mechanisms of gene regulation during early stages of polyploid formation. Here we analyzed differential expression patterns of the progenitors' genes among successive selfing generations and independent lineages. The synthetic Arabidopsis allotetraploid lines were produced by a genetic cross between A. thaliana and A. arenosa autotetraploids. We found that some progenitors' genes are differentially expressed in early generations, whereas other genes are silenced in late generations or among different siblings within a selfing generation, suggesting that the silencing of progenitors' genes is rapidly and/or stochastically established. Moreover, a subset of genes is affected in autotetraploid and multiple independent allotetraploid lines and in A. suecica, a natural allotetraploid derived from A. thaliana and A. arenosa, indicating locus-specific susceptibility to ploidy-dependent gene regulation. The role of DNA methylation in silencing progenitors' genes is tested in DNA-hypomethylation transgenic lines of A. suecica using RNA interference (RNAi). Two silenced genes are reactivated in both ddm1- and met1-RNAi lines, consistent with the demethylation of centromeric repeats and gene-specific regions in the genome. A rapid and stochastic process of differential gene expression is reinforced by epigenetic regulation during polyploid formation and evolution.     

Temporal lag between gene expression and metabolite accumulation in flavonol biosynthesis of Arabidopsis roots

The temporal lag between gene expression and metabolite accumulation has been estimated in flavonol biosynthesis, but the time difference between these events is unclear. In the present study, we investigated the expression of flavonol biosynthetic genes ELONGATED HYPOCOTYL5, MYELOBLASTOSIS PROYEIN12/PRODUCTION OF FLAVONOL GLYCOSYDES1, CHALCONE SYNTHASE, CHALCONE ISOMERASE, FLAVANONE 3-HYDROXYLASE, and FLAVONOL SYNTHASE1, and the accumulation of flavonol glycosides (kaempferol and quercetin glycosides) in time-series samples of Arabidopsis thaliana roots. All genes started to be expressed within 3 h after sequential light irradiation (HAS) and reached their maximum expression levels at 12 HAS, and the accumulation of the flavonol glycosides started at 6 HAS. Metabolome analysis using liquid chromatography-mass spectrometry showed that the accumulation of kaempferol 3-O-glucoside-7-O-rhamnoside and kaempferol 3-O-rhamnosyl (1 → 2) glucoside-7-O-rhamnoside reached their maximum levels at 48 HAS, whereas other flavonol glycosides, such as kaempferol/quercetin 3-O-rhamnoside-7-O-rhamnoside, quercetin 3-O-glucoside-7-O-rhamnoside and quercetin 3-O-rhamnosyl (1 → 2) glucoside-7-O-rhamnoside, increased gradually until 96 HAS. These results show that the expression of the flavonol genes is an early response against light exposure, and that the accumulation of the flavonol glycosides is a late response.     

ABI4 downregulates expression of the sodium transporter HKT1;1 in Arabidopsis roots and affects salt tolerance

A plant's ability to cope with salt stress is highly correlated with their ability to reduce the accumulation of sodium ions in the shoot. Arabidopsis mutants affected in the ABSCISIC ACID INSENSITIVE (ABI) 4 gene display increased salt tolerance, whereas ABI4‐overexpressors are hypersensitive to salinity from seed germination to late vegetative developmental stages. In this study we demonstrate that abi4 mutant plants accumulate lower levels of sodium ions and higher levels of proline than wild‐type plants following salt stress. We show higher HKT1;1 expression in abi4 mutant plants and lower levels of expression in ABI4‐overexpressing plants, resulting in reduced accumulation of sodium ions in the shoot of abi4 mutants. HKT1;1 encodes a sodium transporter which is known to unload sodium ions from the root xylem stream into the xylem parenchyma stele cells. We have shown recently that ABI4 is expressed in the root stele at various developmental stages and that it plays a key role in determining root architecture. Thus ABI4 and HKT1;1 are expressed in the same cells, which suggests the possibility of direct binding of ABI4 to the HKT1;1 promoter. In planta chromatin immunoprecipitation and in vitro electrophoresis mobility shift assays demonstrated that ABI4 binds two highly related sites within the HKT1;1 promoter. These sites, GC(C/G)GCTT(T), termed ABI4‐binding element (ABE), have also been identified in other ABI4‐repressed genes. We therefore suggest that ABI4 is a major modulator of root development and function.     

The RETINOBLASTOMA-RELATED gene regulates stem cell maintenance in Arabidopsis roots

The maintenance of stem cells in defined locations is crucial for all multicellular organisms. Although intrinsic factors and signals for stem cell fate have been identified in several species, it has remained unclear how these connect to the ability to reenter the cell cycle that is one of the defining properties of stem cells. We show that local reduction of expression of the RETINOBLASTOMA-RELATED (RBR) gene in Arabidopsis roots increases the amount of stem cells without affecting cell cycle duration in mitotically active cells. Conversely, induced RBR overexpression dissipates stem cells prior to arresting other mitotic cells. Overexpression of D cyclins, KIP-related proteins, and E2F factors also affects root stem cell pool size, and genetic interactions suggest that these factors function in a canonical RBR pathway to regulate somatic stem cells. Expression analysis and genetic interactions position RBR-mediated regulation of the stem cell state downstream of the patterning gene SCARECROW.     

The monosaccharide transporter(-like) gene family in Arabidopsis

The availability of complete plant genomes has greatly influenced the identification and analysis of phylogenetically related gene clusters. In Arabidopsis, this has revealed the existence of a monosaccharide transporter(-like) gene family with 53 members, which play a role in long-distance sugar partitioning or sub-cellular sugar distribution and catalyze the transport of hexoses, but also polyols and in one case also pentoses and tetroses. An update on the currently available information on these Arabidopsis monosaccharide transporters, on their sub-cellular localization and physiological function will be given.