Abstract
Identification of potential cis-regulatory motifs controlling the development of C4 photosynthesis is a major focus of current research. In this study, we used time-series RNA-seq data collected from etiolated maize and rice leaf tissues sampled during a de-etiolation process to systematically characterize the expression patterns of C4-related genes and to further identify potential cis elements in five different genomic regions (i.e. promoter, 5'UTR, 3'UTR, intron, and coding sequence) of C4 orthologous genes. The results demonstrate that although most of the C4 genes show similar expression patterns, a number of them, including chloroplast dicarboxylate transporter 1, aspartate aminotransferase, and triose phosphate transporter, show shifted expression patterns compared with their C3 counterparts. A number of conserved short DNA motifs between maize C4 genes and their rice orthologous genes were identified not only in the promoter, 5'UTR, 3'UTR, and coding sequences, but also in the introns of core C4 genes. We also identified cis-regulatory motifs that exist in maize C4 genes and also in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution.
Highlights
Many of the world’s most productive crop species, such as maize, sorghum, and miscanthus, use C4 photosynthesis (Brown, 1999)
We identified cis-regulatory motifs that exist in maize C4 genes and in genes showing similar expression patterns as maize C4 genes but that do not exist in rice C3 orthologs, suggesting a possible recruitment of pre-existing cis-elements from genes unrelated to C4 photosynthesis into C4 photosynthesis genes during C4 evolution
We first studied the responses of C4 genes in de-etiolated leaves during the greening process; we used computational approaches to predict potential cis-regulatory elements in different segments of major C4-related genes; we examined the likelihood of the recruitment of pre-existing cis-regulatory elements into C4 metabolic genes during C4 evolution, and we provide a list of potential recruited cis-elements that might serve for further experimental validation
Summary
Many of the world’s most productive crop species, such as maize, sorghum, and miscanthus, use C4 photosynthesis (Brown, 1999). This higher photosynthetic efficiency is achieved by concentrating CO2 at the site of RuBisCO, thereby minimizing the rate of photorespiration (Leegood, 2002) These modifications probably required the evolution of new regulatory mechanisms, in the form of either cis- or trans-regulatory factors or elements (Sheen, 1999; Hibberd and Covshoff, 2010; Kajala et al, 2012; Griffiths et al, 2013; Aubry, et al, 2014). Elucidation of these regulatory mechanisms underlying cell-specific expression of C4-related genes is a major focus of current C4 photosynthesis research
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