Conservation and Divergence of FCA Function between Arabidopsis and Rice

Abstract

Although several genes have been identified in rice which are functionally equivalent to the flowering time genes in Arabidopsis, primarily genes involved in the photoperiod pathway, little data is available regarding the genes that function in the autonomous pathway in rice. In order to acquire further insight into the control of heading dates in rice, we isolated and conducted an expression analysis on OsFCA, which exhibited 38% sequence homology with Arabidopsis FCA. The N-terminal region of the OsFCA protein appears to be unusually rich in glycine-residues, unlike the N-terminal region found in FCA. However, the genetic structure of OsFCA is, in general, similar to that of FCA. RT-PCR and in silico analyses also showed that alternative splicing and polyadenylation at intron3 were conserved in the genetic expression of OsFCA. We were able to detect alpha, beta, and gamma transcripts, but not the delta transcript, of the OsFCA gene. The beta and gamma transcripts of the OsFCA gene were detected via Northern analysis in the leaves, roots, and flowers of the plant. Flowers in younger stages exhibited higher transcript levels. These data suggest that intron3 may constitute a primary control point in the OsFCA pre-mRNA processing of rice. The overexpression of OsFCA cDNA, driven by the 35S promoter, was shown to partially rescue the late flowering phenotype of the fca mutant, suggesting that the functions of the OsFCA and the FCA are partially overlapped, despite the lack of an apparent FLC homologue in the rice genome. The constitutive expression of OsFCA resulted in no downregulation of FLC, but did result in the weak upregulation of SOC1 in the transgenic Arabidopsis. OsFCA overexpression did not result in a reduction of the gamma transcript levels of FCA in the transgenic Arabidopsis either, thereby suggesting that OsFCA had no effects on the autoregulation of Arabidopsis FCA. All of these results imply conservation and divergence in the functions of FCA between rice and Arabidopsis.

PtFLC homolog from trifoliate orange (Poncirus trifoliata) is regulated by alternative splicing and experiences seasonal fluctuation in expression level

“…PtFLC is regulated post-transcriptionally by alternative splicing Alternative splicing is a common regulatory mechanism of gene expression at posttranscriptional stage in eukaryotic organisms (Simpson and Filipowicz 1996;Lee et al 2005;Wang and Brendel 2006). Although several thousand plant genes were now known to produce multiple transcripts (Reddy 2001;Wang and Brendel 2006), the precise function of most splicing variants and their encoded proteins were not known, in Xowering plants, functional studies Fig.…”

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

“…Extending this type of analysis to identify specific AS events that are conserved among multiple species will identify those "ancestral" candidate AS events that are more likely to be functionally significant. For example, one of the FCA gene AS events involved in flowering control (see above) is conserved between Arabidopsis and rice (Lee et al 2005). Computationally identifying conserved AS events requires the identification of robust cross-species orthologous gene sets.…”

Genome-wide multilocus analysis of intraspecific differentiation in Oryza rufipogon Griff. from China and the influence of introgression from O. sativa L.

“…Previous studies have identified the genes controlling flowering time in rice (Shinozuka et al, 1999;Izawa et al, 2003;Doi et al, 2004;Lee et al, 2005;Lu et al, 2006;Kim et al, 2007;Tamaki et al, 2007). The DNA sequences of these genes in strain 9311 of indica and strain Nipponbare of japonica were acquired by a rice genome search in the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/), the BGI-RIS (http://rise.genomics.org.cn/rice/index2.jsp), and the GRAMENE (http://www.gramene.org/ genome_browser/index.html) databases.…”

“…Eighteen flowering time-controlling genes were selected according to published references (Shinozuka et al, 1999;Izawa et al, 2003;Doi et al, 2004;Lee et al, 2005;Lu et al, 2006;Kim et al, 2007;Tamaki et al, 2007). The sequences of these genes in Nipponbare (japonica) and 9311 (indica) were acquired by a search of rice genome in public databases (NCBI, BGI-RIS, and GRAMENE) and were aligned using Vector NTI advance 10 (data not shown).…”