Structural Disorder in Eukaryotes

Citation: Pancsa R, Tompa P ( Structural Disorder in Eukaryotes Rita Pancsa 0 Peter Tompa 0 Laszlo Buday, Hungarian Academy of Sciences, Hungary 0 1 VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium, 2 Institute of Enzymology, Hungarian Academy of Sciences , Budapest , Hungary Based on early bioinformatic studies on a handful of species, the frequency of structural disorder of proteins is generally thought to be much higher in eukaryotes than in prokaryotes. To refine this view, we present here a comparative prediction study and analysis of 194 fully described eukaryotic proteomes and 87 reference prokaryotes for structural disorder. We found that structural disorder does distinguish eukaryotes from prokaryotes, but its frequency spans a very wide range in the two superkingdoms that largely overlap. The number of disordered binding regions and different Pfam domain types also contribute to distinguish eukaryotes from prokaryotes. Unexpectedly, the highest levels - and highest variability - of predicted disorder is found in protists, i.e. single-celled eukaryotes, often surpassing more complex eukaryote organisms, plants and animals. This trend contrasts with that of the number of domain types, which increases rather monotonously toward more complex organisms. The level of structural disorder appears to be strongly correlated with lifestyle, because some obligate intracellular parasites and endosymbionts have the lowest levels, whereas host-changing parasites have the highest level of predicted disorder. We conclude that protists have been the evolutionary hot-bed of experimentation with structural disorder, in a period when structural disorder was actively invented and the major functional classes of disordered proteins established. - Deciphering protein structures has been instrumental in understanding the molecular principles of life. Yet, the recent most exciting development in structural biology is the recognition that many proteins (intrinsically disordered proteins, IDPs) or regions of proteins (intrinsically disordered regions, IDRs) exist and function without a well-defined structure [1,2,3]. The existence and functioning of IDPs/IDRs demand a radical extension of the structure-function paradigm to encompass their non-conventional functional modes. The functional advantages of structural disorder are manifested either directly, in functions termed entropic chains, or in molecular recognition, in the form of adaptable binding [4], uncoupling specificity from binding strength [5] or increasing the speed of interactions [6,7], among others. Due to these advantages, an elevated level of structural disorder can be found in proteins involved in signaling and regulation, and structural disorder is often associated with disease, such as cancer and neurodegeneration [7]. The functional advantages and functional types of IDPs/IDRs predisposes them for roles in complex organisms, in broad agreement with the observed phylogenetic distribution of structural disorder [8,9,10]. Based on previous studies on a few genomes available at the time (usually comparing predicted disorder in 45 eukaryotes to bacteria and archea), it has become generally accepted that structural disorder is significantly higher in eukarytoes than in prokaryotes, expressed by the notion that structural disorder correlates with complexity. Besides these comparative studies, the level of disorder was only addressed in particular phylogenetic groups, such as bacteria [11,12], archaea [13] or a few protists within eukaryotes [14,15]. More recent studies presented large-scale analyses, without trying to derive general conclusions [16]. The suggested correlation with complexity was directly addressed for organisms of known complexity measures (number of different cell types) [17]. It was found that disorder has a tendency to increase in evolution, but its correlation with complexity within eukaryotes is marginal. Therefore, even these limited studies have raised certain caveats to the above generalizations, and suggested exceptions to the seemingly simple and general rule. For example, studies on the distribution of predicted structural disorder in prokaryotes has shown wide variations as a function of growth temperature, with mesophiles an thermophyles covering a very broad range from ,1.5% to ,25% but hyperthermophiles having much less [11,12]. Archaea were also found to show wide disorder distribution, with strong genomic variations depending on habitat and lifestyle [13]. Turning to eukaryotes, Apicomplexan protists single-celled eukaryotes - have shown unexpectedly high levels of predicted disorder, way exceeding that of apparently more complex metazoan organisms [14]. Similar conclusions were drawn in a study of a handful of early-branching protists [15], which again showed a high level of predicted disorder surpassing the average of eukaryotic proteins in SwissProt. It was raised that structural disorder may be associated with the parasitic lifestyle of these organisms. As apparent from this short overview, structural disorder has not been systematically and comparatively analyzed in eukaryotes. Apparently, one of the reasons is a very fast advance in sequencing efforts, due to which about two-thirds of known eukaryotic genomes became available in the past five years or so. Furthermore, the results of distinct studies are hard to compare, because they rely on different disorder predictors usually based on different principles and having significantly different rates of confidence [18,19,20]. In addition, often related but different measures of structural disorder (frequency of disordered residues, frequency of proteins with a long IDR, or frequency of mostly disordered proteins) are applied, which again impedes comparisons and sound generalizations. Therefore, we decided to predict and compare structural disorder in 194 available eukaryotic proteomes (and 87 reference prokaryotes) with the IUPred algorithm [21,22]. We extended and complemented these calculations with predictions of the prevalence of Pfam domains and comparing disorder within and outside domains, because: i) disordered regions often harbor binding motifs for domains [23], ii) disordered regions often function by acting as linkers between flanking domains, and iii) structural disorder may also be present in Pfam domains themselves [24]. The novel data on the phylogenetic distribution of structural disorder, Pfam domain types, and their varied correlation in different types of species refine previous limited generalizations and provide novel insight into the evolutionary and functional implications of structural disorder. Eukaryotic, prokaryotic and archaeal proteomes Most of the eukaryotic proteomes were downloaded from the complete proteome set of the UniProt database [25], and some additional ones from the RefSeq database [26]. To avoid redundancy, we usually used only one proteome for specie (...truncated)