Abstract
Genomic interactions in allopolyploids create expression variation of homoeologous alleles through protein-protein and protein-DNA interactions. However, the molecular basis for this is largely unknown. Here we investigated the protein-protein and protein-DNA interactions among homoeologous transcription factors in the circadian-clock feedback loop, consisting of CCA1 HIKING EXPEDITION (CHE), CIRCADIAN CLOCK ASSOCIATED1 (CCA1), and TIMING OF CAB EXPRESSION1 (TOC1), plus the interaction with a chromatin factor, HISTONE DEACETYLASE1 (HD1). In the allotetraploids formed between A. thaliana (At) and Arabidopsis arenosa (Aa), AtCCA1 is expressed at lower levels than AaCCA1, which could alter clock output traits. The reduced AtCCA1 expressions in the allotetraploids are consistent with the biochemical data that AaCHE showed preferential binding to the AtCCA1 promoter, in which AaCHE interacts with a higher affinity to AtHD1 than AtCHE. AaCHE also showed a higher affinity to TOC1 than AtCHE, consistent with the effect of TOC1 on repressing CCA1. Thus, stronger AaCHE-TOC1 and AaCHE-AtHD1 interactions reduce AtCC1 allelic expression. Our current data suggest a biochemical basis for protein interactions in trans with a preference to the cis-acting elements in heterologous combinations to reduce AtCCA1 expression, while altered CCA1 expression has been shown to affect metabolic and biomass heterosis in interspecific hybrids or allotetraploids.
Highlights
Heterosis refers to superior growth and fitness in the offspring relative to one or both parents
We tested if the A. thaliana Histone Deacetyase1 (AtHD1) affects clock gene expression and vice versa, if the circadian clock affects AtHD1 expression
This is consistent with the reported CLOCK ASSOCIATED1 (CCA1) HIKING EXPEDITION (CHE) expression to which it peaked at 9 hours after the subjective dark period under continuous light[22]
Summary
Heterosis refers to superior growth and fitness in the offspring relative to one or both parents. The morning-phased clock regulators are down-regulated, while the evening-phased ones are activated in Arabidopsis intraspecific hybrids[25,26] and allotetraploids (doubled interspecific hybrids)[14], which are formed by pollinating Arabidopsis thaliana with Arabidopsis arenosa pollen[27] Both A. thaliana CCA1 (AtCCA1) and A. arenosa CCA1 (AaCCA1) are down-regulated in the allotetraploids during the day, which correlates with increased levels of chlorophyll and starch, promoting growth vigor[26]. We take the advantage of the circadian transcriptional feedback loop to test a biochemical model for homoeologous protein-protein interactions and protein-DNA (cis-regulatory element) recognition in altering allelic expression levels. This biochemical model could explain a molecular basis for heterosis in interspecific hybrids and allotetraploids
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