title: Protein disorder in plants: a view from the chloroplast.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  Our 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.
  
  
  CONCLUSIONS
  Our 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.
authors.affiliation: Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Avda, Montañana, 1005, Zaragoza 50059, Spain. yruela@eead.csic.es
authors.forename: Inmaculada
authors.initials: I
authors.lastname: Yruela
authors.forename: Bruno
authors.initials: B
authors.lastname: Contreras-Moreira
mesh_terms: D000595:Amino Acid Sequence; D002467:Cell Nucleus / Q000235:genetics / Q000378:metabolism*; D060365:Chloroplast Proteins / Q000235:genetics / Q000378:metabolism*; D002736:Chloroplasts / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology; D019143:Evolution, Molecular; D018745:Genome, Plant; D008928:Mitochondria / Q000235:genetics / Q000378:metabolism; D024101:Mitochondrial Proteins / Q000235:genetics / Q000378:metabolism; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D010944:Plants / Q000235:genetics / Q000378:metabolism*; D021381:Protein Transport; D012269:Ribosomal Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D060365:Chloroplast Proteins; D024101:Mitochondrial Proteins; D009687:Nuclear Proteins; D010940:Plant Proteins; D012269:Ribosomal Proteins