A family portrait: structural comparison of the Whirly proteins from Arabidopsis thaliana and Solanum tuberosum

Abstract

DNA double-strand breaks are highly detrimental genomic lesions that routinely arise in genomes. To protect the integrity of their genetic information, all organisms have evolved specialized DNA-repair mechanisms. Whirly proteins modulate DNA repair in plant chloroplasts and mitochondria by binding single-stranded DNA in a non-sequence-specific manner. Although most of the results showing the involvement of the Whirly proteins in DNA repair have been obtained in Arabidopsis thaliana, only the crystal structures of the potato Whirly proteins WHY1 and WHY2 have been reported to date. The present report of the crystal structures of the three Whirly proteins from A. thaliana (WHY1, WHY2 and WHY3) reveals that these structurally similar proteins assemble into tetramers. Furthermore, structural alignment with a potato WHY2-DNA complex reveals that the residues in these proteins are properly oriented to bind single-stranded DNA in a non-sequence-specific manner.

Keywords: Arabidopsis; DNA repair; WHY1; WHY2; WHY3; Whirly proteins; ssDNA-binding proteins.

Figure 1

Tetramers of (a) WHY2, (b) WHY1 and (c) WHY3 in cartoon representation. WHY2 tetramers are present in the asymmetric unit. Tetramers of WHY1 and WHY3 were generated by applying the appropriate crystallographic symmetries.

Figure 2

(a) Sequence alignment of the Whirly domains of chloroplast-directed Whirlies. AtWhy1, Arabidopsis WHY1; AtWhy2, Arabidopsis WHY2; StWhy1, S. tuberosum WHY1. (b) Structural alignment of chloroplast-directed Whirly proteins in cartoon representation with WHY1 in green, WHY3 in cyan and potato WHY1 (PDB entry 1l3a) in orange.

Figure 3

(a) Sequence alignment of the Whirly domains of mitochondria-directed Whirlies. AtWhy2, Arabidopsis WHY2; StWhy2, S. tuberosum WHY2. (b) Structural alignment of mitochondria-directed Whirly proteins in cartoon representation with WHY2 in yellow and potato WHY2 (PDB entry 3n1h) in light blue. The black arrows point to the β-hairpin encompassing residues 74–90.

Figure 4

(a) Alignment of Arabidopsis Whirly ssDNA-binding sites. Proteins are shown in cartoon representation and residues equivalent to those of potato WHY2 (PDB entry 3n1i) that contact ssDNA are shown in stick representation with C atoms in grey. Those of WHY1, WHY2 and WHY3 are shown in cyan, magenta and green, respectively. The potato WHY2 nomenclature was used for clarity. The ssDNA is shown in stick representation with its C atoms in yellow. (b) Close-up of residues Trp100 and Trp110. The representation is similar to that in (a).