Protein disorder in plants: a view from the chloroplast

1 .pdf with the full text of article (13 Pags., 5 Figs.) + Supplemental data into 8 Additional Files (1 Fig., 7 Tabls.)The intrinsically unstructured state of some proteins, observed in all living organisms, is essential for basic cellular functions. In this field the available information from plants is limited but it has been reached a point where these proteins can be comprehensively classified on the basis of disorder, function and evolution.ResultsOur analysis of plant genomes confirms that nuclear-encoded proteins follow the same trend than other multi-cellular eukaryotes; however, chloroplast- and mitochondria- encoded proteins conserve the patterns of Archaea and Bacteria, in agreement with their phylogenetic origin. Based on current knowledge about gene transference from the chloroplast to the nucleus, we report a strong correlation between the rate of disorder of transferred and nuclear-encoded proteins, even for polypeptides that play functional roles back in the chloroplast. We further investigate this trend by reviewing the set of chloroplast ribosomal proteins, one of the most representative transferred gene clusters, finding that the ribosomal large subunit, assembled from a majority of nuclear-encoded proteins, is clearly more unstructured than the small one, which integrates mostly plastid-encoded proteins.ConclusionsOur observations suggest that the evolutionary dynamics of the plant nucleus adds disordered segments to genes alike, regardless of their origin, with the notable exception of proteins currently encoded in both genomes, probably due to functional constraints.This work was supported by grants from Ministerio de Economía y Competitividad (MAT2011-23861 to I.Y.) and Gobierno de Aragón (DGA-GC B18 to I.Y. and DGA-GC A06 to B.C-M). All these grants were partially financed by the EU FEDER Program.Peer Reviewe