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

Bargsten JW, Folta A, Mlynárová L, Nap JP - PLoS ONE (2013)

Bottom Line: Notably tomato carries unexpected gene expansions of DRD1 gene members.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.

View Article: PubMed Central - PubMed

Affiliation: Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands ; Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands ; Laboratory for Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands.

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.

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Related in: MedlinePlus

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.
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pone-0081147-g001: 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.

Mentions: Snf2 family members in the predicted proteomes of 33 plant genomes including two green algae, were identified (Table S2). To prevent the inclusion of peptide fragments in the gene predictions, a cut-off of 200 amino acids (aa) was used, given that the conserved ATPase region has a length of about 400 aa [7]. All protein sequences longer than 200 aa were analyzed for the presence of the SNF2_N and Helicase_C domain. To be considered present, domains required a match in the protein sequence with an E-value smaller than 1e-3. Protein sequences containing at least one SNF2_N domain and one Helicase_C domain were listed as candidate Snf2 ATPase. To improve accuracy, a HMM model spanning the conserved ATPase region was created. The initial result set was filtered with this model and only candidates with a bitscore of at least 200 were used for further analyses. For Arabidopsis, all (41) previously known Snf2 genes (ChromDB; [41]) were identified (Figure 1). In total, 1159 family members were identified (Figure 1).


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

Bargsten JW, Folta A, Mlynárová L, Nap JP - PLoS ONE (2013)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3842944&req=5

pone-0081147-g001: 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.
Mentions: Snf2 family members in the predicted proteomes of 33 plant genomes including two green algae, were identified (Table S2). To prevent the inclusion of peptide fragments in the gene predictions, a cut-off of 200 amino acids (aa) was used, given that the conserved ATPase region has a length of about 400 aa [7]. All protein sequences longer than 200 aa were analyzed for the presence of the SNF2_N and Helicase_C domain. To be considered present, domains required a match in the protein sequence with an E-value smaller than 1e-3. Protein sequences containing at least one SNF2_N domain and one Helicase_C domain were listed as candidate Snf2 ATPase. To improve accuracy, a HMM model spanning the conserved ATPase region was created. The initial result set was filtered with this model and only candidates with a bitscore of at least 200 were used for further analyses. For Arabidopsis, all (41) previously known Snf2 genes (ChromDB; [41]) were identified (Figure 1). In total, 1159 family members were identified (Figure 1).

Bottom Line: Notably tomato carries unexpected gene expansions of DRD1 gene members.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.

View Article: PubMed Central - PubMed

Affiliation: Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands ; Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands ; Laboratory for Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands.

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.

Show MeSH
Related in: MedlinePlus