Academic journal article Genetics

The Conserved PFT1 Tandem Repeat Is Crucial for Proper Flowering in Arabidopsis Thaliana

Academic journal article Genetics

The Conserved PFT1 Tandem Repeat Is Crucial for Proper Flowering in Arabidopsis Thaliana

Article excerpt

ABSTRACT It is widely appreciated that short tandem repeat (STR) variation underlies substantial phenotypic variation in organisms. Some propose that the high mutation rates of STRs in functional genomic regions facilitate evolutionary adaptation. Despite their high mutation rate, some STRs show little to no variation in populations. One such STR occurs in the Arabidopsis thaliana gene PFT1 (MED25), where it encodes an interrupted polyglutamine tract. Although the PFT1 STR is large (~270 bp), and thus expected to be extremely variable, it shows only minuscule variation across A. thaliana strains. We hypothesized that the PFT1 STR is under selective constraint, due to previously undescribed roles in PFT1 function. We investigated this hypothesis using plants expressing transgenic PFT1 constructs with either an endogenous STR or synthetic STRs of varying length. Transgenic plants carrying the endogenous PFT1 STR generally performed best in complementing a pft1 null mutant across adult PFT1-dependent traits. In stark contrast, transgenic plants carrying a PFT1 transgene lacking the STR phenocopied a pft1 loss-of-function mutant for flowering time phenotypes and were generally hypomorphic for other traits, establishing the functional importance of this domain. Transgenic plants carrying various synthetic constructs occupied the phenotypic space between wild-type and pft1 loss-of-function mutants. By varying PFT1 STR length, we discovered that PFT1 can act as either an activator or repressor of flowering in a photoperiod-dependent manner. We conclude that the PFT1 STR is constrained to its approximate wild-type length by its various functional requirements. Our study implies that there is strong selection on STRs not only to generate allelic diversity, but also to maintain certain lengths pursuant to optimal molecular function.

SHORT tandem repeats (STRs, microsatellites) are ubiq- uitous and unstable genomic elements that have ex- tremely high mutation rates (Subramanian et al. 2003; Legendre et al. 2007; Eckert and Hile 2009), leading to STR unit number variation within populations. STR varia- tion in coding and regulatory regions can have significant phenotypic consequences (Gemayel et al. 2010). For exam- ple, several devastating human diseases, including Huntington's disease and spinocerebellar ataxias, are caused by expanded STR alleles (Hannan 2010). However, STR variation can also confer beneficial phenotypic variation and may facili- tate adaptation to new environments (Fondon et al. 2008; Gemayel et al. 2010). For example, in Saccharomyces cerevisiae natural polyQ variation in the FLO1 protein underlies var- iation in flocculation, which is important for stress resis- tance and biofilm formation in yeasts (Verstrepen et al. 2005). Natural STR variants of the Arabidopsis thaliana gene ELF3, which encode variable polyQ tracts, can pheno- copy elf3 loss-of-function phenotypes in a common reference background (Undurraga et al. 2012). Moreover, the pheno- typic effects of ELF3 STR variants differed dramatically be- tween the divergent backgrounds Col and Ws, consistent with the existence of background-specific modifiers. Genetic incompatibilities involving variation in several other STRs have been described in plants, flies, and fish (Peixoto et al. 1998; Scarpino et al. 2013; Rosas et al. 2014). Taken to- gether, these observations argue that STR variation under- lies substantial phenotypic variation and may also underlie some genetic incompatibilities.

The A. thaliana gene PHYTOCHROME AND FLOWERING TIME 1 (PFT1, MEDIATOR 25, MED25) contains an STR of unknown function. In contrast to the comparatively short and pure ELF3 STR, the PFT1 STR encodes a long (~90 amino acids in PFT1, vs. 7-29 for ELF3), periodically inter- rupted polyQ tract (See Figure S1). The far greater length of the PFT1 STR leads to the prediction that its allelic variation should be greater than that of the highly variable ELF3 STR (Legendre et al. …

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