Snf2 family gene distribution in higher plant genomes reveals DRD1 expansion and diversification in the tomato genome

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.

Figure 1. Distribution of Snf2 family members in plant genomes.

Groupings and subfamilies on the left are named according to the Arabidopsis subfamily classification [3]. Species names on the top are organized on the basis of their phylogenetic relationship according to Phytozome [14]. Snf2 candidate member Cre09.g390000.t1.1 (Chlamydomonas reinhardtii) could not be assigned to any subfamily and was excluded. Subfamily counts are shaded according to the deviation from the subfamily mean in standard deviations (sd). The total count is given on the top right cell. Mean and standard deviations per subfamily are indicated in the last column.

Figure 2. Unrooted phylogenetic tree of all candidate Snf2 genes in plant genomes.

The full tree from which this subset was extracted is presented in Figure S3. The subfamily branches were collapsed to a single node that represents the first split that is part of the subfamily branch. Confidence values (50-100) are indicated at the relevant splits of the branches. The tree is based on 100 bootstrap replicates. The leaf tagged ‘not classified’ indicates candidate Snf2 members that are not part of a known subfamily, including Cre09.g390000.t1.1 (Chlamydomonas reinhardtii) and members of sequence databases.

Figure 3. Analysis of the DRD1 subfamily in tomato, potato, Mimulus and Arabidopsis.

The left side shows a detailed view of the DRD1 subfamily branch of an unrooted tree based on 1000 bootstraps of Snf2 data from Arabidopsis thaliana (Ath), Mimulus guttatus (Mgu), Solanum lycopersicum (Sly) and Solanum tuberosum (Stu). Confidence values (50-100) are given at the relevant branches of the tree. Identifiers give the name of the organism in three-letter abbreviations together with gene identifiers. The individual branches identified are indicated by letters in lowercase on the right side. To increase readability, some branch edges have been extended by dotted grey lines. These grey dotted lines are therefore not part of the estimated branch length. The right side shows structural elements (domains and unfolded regions) in the protein sequence of the DRD1 subfamily members in Arabidopsis, Mimulus, tomato and potato. Besides the ATPase region no other domains are present in these genes. A black dot at the right end of the figure indicates the expression of the respective gene in tomato based on the analysis of RNA-seq data.

Figure 4. RT-PCR expression analysis of DRD1 and Snf2 subfamilies of tomato Snf2 ATPase genes.

The tissue used is indicated on the x-axis. The individual genes are indicated of the right, the branches identified on the left. The expression of the actin gene (25 cycles) was used as control (lower panel). The number of PCR cycles used for the analysis of the individual gene was adjusted to generate a detectable amount of PCR product. For most of genes, 35 cycles were used. Genes marked with superscript a (^a) were amplified with 29 cycles. For the actin gene 25 cycles were used.