The Autonomous Pathway

Mutations that delay flowering under any photoperiod and confer a response to vernalisation were placed in the autonomous pathway.

Genes in the autonomous pathway include LD, FCA, FY, FPA, FVE, FLD and FLK. Mutations in each of these genes lead to an increase in the levels of FLC mRNA and FLC protein (Michaels and Amasino, 1999; Sheldon et al., 1999; Rouse et al., 2002) . Most of the genes in this group have been cloned and suggest that the autonomous pathway represents different biological processes. FCA contains an RNA binding motif and a WW domain, which is thought to be involved in protein-protein interactions (Bork et al., 1994; Macknight et al., 1997) . FCA is able to bind to RNA in vitro (Macknight et al., 1997; Macknight et al., 2002) . FCA is able to regulate its own expression by promoting cleavage and polyadenylation of its own third intron; this auto-regulation is under developmental control and requires the WW domain (Quesada et al., 2003) .

The FVE proteins represents a second biochemical function involved in FLC regulation. FVE encodes AtMSI4, a putative retinoblastoma-associated protein that participates in a protein complex that represses FLC transcription through a histone deacetylation mechanism (Ausin et al., 2004). Additionally, it has recently been shown to be a negative regulator of the CBF/DREB pathway involved in the cold acclimatisation (Ausin et al., 2004; Kim et al., 2004) .

Autonomous Pathway Genes

Double mutant analysis suggests that autonomous pathway genes do not act in a linear hierarchy. For example, the fy mutation does not enhance the flowering phenotype seen in fca plants, suggesting that they act in the same pathway. Similar logic suggests that FVE and FPA act in a linear pathway. The double mutant fpa fy is lethal, and the combination of fve with either fca or fy mutants leads to a later flowering time than is seen in the single mutants alone (Koornneef et al., 1998b) . FY binds to the WW domain of FCA, and is involved in the processing of the 3' end of transcripts (Simpson et al., 2003) . FLC seems to be particularly sensitive to the impairment of the function of this complex, causing an increase in FLC mRNA abundance. From work on perichimal chimaeras, in which flowering was not delayed when FCA was expressed in epidermal cell layers, it is thought that FCA promotes flowering in a cell non-autonomous manner (Furner et al., 1996) .

RNA recognition

Like FCA, FPA also contains a RNA recognition motif. Mutations in FPA result in extremely delayed flowering, whilst overexpression of FPA in Arabidopsis causes early flowering in noninductive short days. Like FCA, FPA is expressed most strongly in developing tissues (Schomburg et al., 2001) .

Autonomous pathway: FLK

The FLK gene is a recently identified autonomous pathway gene. It encodes a putative RNA binding protein and the mutant form has a late flowering phenotype in both long and short-day photoperiods. Vernalisation and the application of exogenous gibberellins are able to suppress the late flowering-time phenotype. Like other autonomous pathway genes, FLC mRNA levels increased in the flk mutant, whilst those of ft and soc1 were reduced (Lim et al., 2004) .

FLD encodes a protein that is a homologue of a protein found in mammalian histone deacetylase complexes (He et al., 2003) , emphasising the importance of histone modification in FLC regulation. Mutations in FLD result in delayed flowering, an increase in FLC expression and hyper acetylation of histones present in FLC chromatin. Therefore some genes assigned to the autonomous pathway encode negative regulators of FLC that act to cause histone deacetylation (He et al., 2003) .


LUMINIDEPENDENS (LD) was cloned through the use of T-DNA mutagenesis (Redei, 1962; Lee et al., 1994) . LD contains both a nucleic acid-binding homeodomain and an acidic rich carboxyl terminal, enriched with homopolymeric glutamine residues. These features are related to transcriptional activators of genes from Drosophila, Yeast and Antennapedia (van Nocker, 2001). Therefore, LD probably acts as a transcriptional regulator, the LD protein is localised to the nucleus, is expressed ubiquitously, and is involved in the regulation of the meristem identity gene LEAFY (LFY) (Aukerman et al., 1999) .

Therefore genes assigned to the autonomous pathway seem to represent protein complexes involved in RNA processing or histone modification and FLC expression seems particularly sensitive to disruption of these processes.

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