Searching for Novel Transcriptional Regulators of Lignin Deposition Within the PIRIN Family in the Model C4 Grass Setaria Viridis

Abstract

PIRINs (PRNs) comprise a family of cupin domain-containing proteins that are conserved between prokaryotic and eukaryotic organisms, but whose functions remain largely elusive. A member of the PIRIN family has been recently characterized as a transcriptional co-regulator of lignin deposition in the eudicot Arabidopsis thaliana, consisting of another player in the complex regulatory mechanism controlling the timing, localization and final structure of the lignin polymer. However, a similar regulatory function for PRNs in other plant species remains to be determined. Here, we characterized the PIRIN gene family in the C4 model grass Setaria viridis and further identified members potentially involved in lignification. A total of 4 genes encoding PRNs (SvPRN1 to SvPRN4) were found in the genome of S. viridis, similar to the number found in other grasses. Phylogenetic analysis using 39 plant species depicted three groups of PRN proteins, not equally conserved across the plant kingdom. SvPRN2 clustered into Group 1 together with other PRNs from eudicots and grasses, whereas the other SvPRNs clustered into Group 3, consisting mainly of PRNs from grasses. Group 2 was exclusively composed of PRN proteins from eudicot species, together with PRN from the basal Angiosperm Amborella trichopoda. Predictive structural analysis suggests that PRN proteins belonging to Group 3 harbor distinct structural features potentially related to functional diversification. The identification of SvPRN genes potentially involved in lignification in S. viridis was based on the following criteria: i) similar expression pattern to lignin biosynthetic genes in a set of different S. viridis tissues; ii) similar expression pattern to lignin biosynthetic genes in the elongating internode of S. viridis; iii) co-expression with secondary cell wall- (SCW) and lignin-related genes in co-expression databases; iv) presence of SCW-related cis elements in its promoter region; v) high expression in S. viridis tissues undergoing active lignification. These analyses suggest that SvPRN2 is the strongest candidate to play a role in the regulation of lignin deposition in S. viridis, although other members of the family met some of these criteria and might also function in this biological process. Functional studies are necessary to confirm and further characterize the precise role of these SvPRN genes in S. viridis.