Abstract
Plants have evolved genome complexity through iterative rounds of single gene and whole genome duplication. This has led to substantial expansion in transcription factor numbers following preferential retention and subsequent functional divergence of these regulatory genes. Here we review how this simple evolutionary network rewiring process, regulatory gene duplication followed by functional divergence, can be used to inspire synthetic biology approaches that seek to develop novel phenotypic variation for future trait based breeding programs in plants.
Highlights
Single nucleotide variants are amongst the most prevalent modifications in genomes (Altshuler et al, 2010)
Rewiring Transcriptomes, a Phenotype Paradox the promoter of QPT2 contains three sequence motifs that the ERF189, a positive regulator of nicotine biosynthesis, binds to in vitro. These three motifs provide graded positive activation of QPT2. Overall this suggests that transcription factor binding sites (TFBS) bound by ERF189 evolved within the promoter of QPT2 facilitating its integration into the nicotine biosynthesis regulon (Shoji and Hashimoto, 2011)
Whilst it has been observed that transcription factors (TFs) duplicates are more often retained after whole genome duplication (WGD) rather than smaller duplication events (Maere et al, 2005), studies looking at domestication traits reveal a plethora of underlying single TFs with altered promoter sequences, appearing to drive TF expression divergence (Swinnen et al, 2016)
Summary
Single nucleotide variants are amongst the most prevalent modifications in genomes (Altshuler et al, 2010). Diversity and cellular plasticity are attained purely through differential regulation of duplicate gene sets This could occur through sequential evolution of cistronic transcription factor binding sites (TFBS) that bring target genes under coordinated regulatory control, as may have been the case for certain metabolic pathways in plants (Shoji, 2019). Gene duplicates experience a relatively relaxed period of selection before they are either silenced or take on novel, redundant or semi-redundant roles (Lynch and Conery, 2000; Blanc and Wolfe, 2004; Maere et al, 2005; Jiao et al, 2011) During this evolutionary filtering process it is noteworthy that regulatory genes are often preferentially retained whilst their paralogs often undergo gene expression divergence (Blanc and Wolfe, 2004; Maere et al, 2005). We show how this synthetic biology approach offers a novel way to optimise plant responses to environmental stimuli
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