LUMINIDEPENDENS (LD)

From Purdue Genomics Database Facility

Victor A. Albert

(NB: IN PROGRESS; see bold text)

LUMINIDEPENDENS (LD) is a single-copy gene in Arabidopsis that is a positive regulator of flowering in the autonomous pathway. LD may be a transcriptional regulator that operates via supression of the MADS box protein FLOWERING LOCUS C (FLC). As such, mutations in LD cause late flowering.

LD encodes a protein with unique features. An LD homolog has been identified in maize, ZmLD. It shares the same domain structure as LD. Other angiosperm sequences in the database, albeit partials, show high conservation in these domains. The conserved domains, however, match nothing else in the NCBI CDD.

Selaginella has one locus (2 alleles: e_gw1.10.267.1 and e_gw1.14.273.1) encoding a protein that has strong sequence similarity to the 2 major, conserved domains of LD-like proteins. The Selaginella locus [may! -- see below] lack the long N- and C-terminal tails of LD and ZmLD, however. Interestingly, Physcomitrella posesses a LD-like protein with extensive N- and C-terminal tails, with the N-terminus significantly longer than Arabidopsis LD.

FLC homologs are not known outside of Arabidopsis and other core eudicots (Reeves PA, He Y, Schmitz RJ, Amasino RM, Panella LW, Richards CM. Evolutionary conservation of the FLOWERING LOCUS C-mediated vernalization response: evidence from the sugar beet (Beta vulgaris). Genetics. 2007 May;176(1):295-307.) Therefore, LD probably has another target in monocots and perhaps basal angiosperms. Likewise, given the likely absence of a true FLC homolog in Physcomitrella, its LD-like protein must have another target.

All LD homologs and LD-like proteins isolated so far are single-copy, which is suggestive of dosage-dependent effect (similarly to the LFY and GIGANTEA proteins). As such, the single Selaginella protein could share this interesting dosage dependence, perhaps in a related function in reproductive promotion.

[NOTE: The Selaginella genome browser Vista Selmo1 vs. Physcomitrella panel suggests that C-terminal exons with high similarity to the Physco LD-like protein AND Arabidopsis LD were missed in gene model prediction! See scaffold_10:539785-545952.]

Below is a preliminary phylogenetic tree of LD-like proteins, and an alignment of them from Jalview.

Note GI numbers in tree and below. Arabidopsis LD is boxed.