Comprehensive Evolutionary and Expression Analysis of FCS-Like Zinc finger Gene Family Yields Insights into Their Origin, Expansion and Divergence

Abstract

Plant evolution is characterized by frequent genome duplication events. Expansion of habitat resulted in the origin of many novel genes and genome duplication events which in turn resulted in the expansion of many regulatory gene families. The plant-specific FCS-Like Zinc finger (FLZ) gene family is characterized by the presence of a FCS-Like Zinc finger (FLZ) domain which mediates the protein-protein interaction. In this study, we identified that the expansion of FLZ gene family size in different species is correlated with ancestral and lineage-specific whole genome duplication events. The subsequent gene loss found to have a greater role in determining the size of this gene family in many species. However, genomic block duplications played the significant role in the expansion of FLZ gene family in some species. Comparison of Arabidopsis thaliana and Oryza sativa FLZ gene family revealed monocot and dicot specific evolutionary trends. The FLZ genes were found to be under high purifying selection. The spatiotemporal expression analyses of Arabidopsis thaliana FLZ gene family revealed that majority of the members are highly expressed in reproductive organs. FLZ genes were also found to be highly expressed during vegetative-to-reproductive phase transition which is correlated with the proposed role of this gene family in sugar signaling. The comparison of sequence, structural and expression features of duplicated genes identified lineage-specific redundancy and divergence. This extensive evolutionary analysis and expression analysis of Arabidopsis thaliana FLZ genes will pave the way for further functional analysis of FLZ genes.

FCS‐like zinc finger 6 and 10 repress SnRK1 signalling in Arabidopsis

“…In an earlier quantitative (q)RT‐PCR study we found that FLZ6 is expressed more in flowers, silique and seedling stages. FLZ10 also showed a very similar expression pattern (Jamsheer K et al ., ). To get a more detailed picture of the tissue‐ and developmental stage‐specific expression patterns we constructed promoter:GUS reporter lines for both the genes (Figure ).…”

“…flz10.2 showed reduced biomass and lateral root number, but there was no significant change in primary root length, suggesting that the truncated transcript in this line might be functional to some extent. The phylogenetic analysis suggests that FLZ genes originated in terrestrial plants (Jamsheer K et al ., ). The regulation of SnRK1 signalling by FLZ genes might have originated in land plants, which provide an additional layer of control over the SnRK1 signalling in plants (Figure ).…”

“…FLZ6 and FLZ10 are phylogenetically distant FLZ proteins (Jamsheer K et al ., ). Interestingly, reduced expression of these genes in their respective mutants resulted in the accumulation of SnRK1α1, suggesting that neither of these genes can completely replace the other in function.…”

“…Protein–protein interaction studies identified that the Arabidopsis FCS‐like zinc finger (FLZ) proteins interact with the kinase subunits of SnRK1 and may act as adaptors to facilitate the interaction of SnRK1 with other proteins (Arabidopsis Interactome Mapping Consortium, ; Nietzsche et al ., ). They are found to be small proteins with a solitary FLZ domain which functions as the canonical interaction module (Jamsheer K and Laxmi, ; Nietzsche et al ., ; Jamsheer K et al ., ). The expression of FLZ genes is highly regulated by energy status and abiotic stress (Jamsheer K and Laxmi, ).…”

The FCS-like zinc finger scaffold of the kinase SnRK1 is formed by the coordinated actions of the FLZ domain and intrinsically disordered regions

“…The plasticity and adaptability of scaffold proteins are usually achieved by the presence of intrinsically disordered regions (IDRs) in these proteins (16). FLZ proteins show low sequence conservation outside the FLZ domain indicating that these regions might be enriched with disordered regions (6,7). IDRs lack fixed secondary or tertiary structures.…”