Abstract
As part of large protein complexes, Snf2 family ATPases are responsible for energy supply during chromatin remodeling, but the precise mechanism of action of many of these proteins is largely unknown. They influence many processes in plants, such as the response to environmental stress. This analysis is the first comprehensive study of Snf2 family ATPases in plants. We here present a comparative analysis of 1159 candidate plant Snf2 genes in 33 complete and annotated plant genomes, including two green algae. The number of Snf2 ATPases shows considerable variation across plant genomes (17-63 genes). The DRD1, Rad5/16 and Snf2 subfamily members occur most often. Detailed analysis of the plant-specific DRD1 subfamily in related plant genomes shows the occurrence of a complex series of evolutionary events. Notably tomato carries unexpected gene expansions of DRD1 gene members. Most of these genes are expressed in tomato, although at low levels and with distinct tissue or organ specificity. In contrast, the Snf2 subfamily genes tend to be expressed constitutively in tomato. The results underpin and extend the Snf2 subfamily classification, which could help to determine the various functional roles of Snf2 ATPases and to target environmental stress tolerance and yield in future breeding.
Highlights
Genomic DNA is organized into chromatin, which is physically restricting the access of regulatory proteins to the genome [1]
Tomato (S. lycopersicum) assembly release 2.40 and iTAG annotation release 2.3 [12] were retrieved from the SGN network.The potato (S. tuberosum group Phureja DM1-3 516R44 (CIP801092)) genome assembly v3 and annotation v3.4 [13] were retrieved from the Potato Genome Sequencing Consortium
The Snf2 family of ATPases is a large family of chromatin remodeling enzymes that have versatile roles in a variety of fundamental processes in growth and development
Summary
Genomic DNA is organized into chromatin, which is physically restricting the access of regulatory proteins to the genome [1]. The access to the genome can be changed by chromatin modifying activities, altering histone tails or the histone cores covalently; and chromatin remodeling activities, altering DNA–histone interactions non-covalently [1]. Both provide important epigenetic mechanisms to regulate gene expression [2]. The associated ATP-dependent changes in nucleosome organization catalyzed by Snf2-family ATPases accounts for a large part of chromatin remodeling activities [2]. Snf ATPases show broad functional diversity and are involved in a variety of genome-wide processes involving DNA, such as transcription, replication, repair and recombination. The Snf ATPases shape the functionality of a complex
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