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. 2010 May 28;4 Suppl 1(Suppl 1):S1.
doi: 10.1186/1752-0509-4-S1-S1.

Archaic chaos: intrinsically disordered proteins in Archaea

Bin Xue  1 , Robert W Williams, Christopher J Oldfield, A Keith Dunker, Vladimir N Uversky
Affiliations

Archaic chaos: intrinsically disordered proteins in Archaea

Bin Xue et al. BMC Syst Biol. .

Abstract

Background: Many proteins or their regions known as intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack unique 3D structure in their native states under physiological conditions yet fulfill key biological functions. Earlier bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. Archaea belong to an intriguing domain of life whose members, being microbes, are characterized by a unique mosaic-like combination of bacterial and eukaryotic properties and include inhabitants of some of the most extreme environments on the planet. With the expansion of the archaea genome data (more than fifty archaea species from five different phyla are known now), and with recent improvements in the accuracy of intrinsic disorder prediction, it is time to re-examine the abundance of IDPs and IDRs in the archaea domain.

Results: The abundance of IDPs and IDRs in 53 archaea species is analyzed. The amino acid composition profiles of these species are generally quite different from each other. The disordered content is highly species-dependent. Thermoproteales proteomes have 14% of disordered residues, while in Halobacteria, this value increases to 34%. In proteomes of these two phyla, proteins containing long disordered regions account for 12% and 46%, whereas 4% and 26% their proteins are wholly disordered. These three measures of disorder content are linearly correlated with each other at the genome level. There is a weak correlation between the environmental factors (such as salinity, pH and temperature of the habitats) and the abundance of intrinsic disorder in Archaea, with various environmental factors possessing different disorder-promoting strengths. Harsh environmental conditions, especially those combining several hostile factors, clearly favor increased disorder content. Intrinsic disorder is highly abundant in functional Pfam domains of the archaea origin. The analysis based on the disordered content and phylogenetic tree indicated diverse evolution of intrinsic disorder among various classes and species of Archaea.

Conclusions: Archaea proteins are rich in intrinsic disorder. Some of these IDPs and IDRs likely evolve to help archaea to accommodate to their hostile habitats. Other archaean IDPs and IDRs possess crucial biological functions similar to those of the bacterial and eukaryotic IDPs/IDRs.

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Figures

Figure 1
Figure 1
Comparison of disorder prediction between PONDR-VLXT and PONDR-VSL2 for (a) Q971E4 and (b) Q9YC05: The solid line is the disorder score of PONDR-VLXT, while the dashed line is from PONDR-VSL2. The line at (a) shows a dip in VLXT prediction while VSL2 predicts the long segment to be disordered. The circle in (b) represents a long disordered region predicted by VLXT, but missed by VSL2.
Figure 2
Figure 2
Size of proteome of each species: The X-axis is the index of the number of each species, while the Y-axis is the number of proteins. Filled circles represent the size of the proteome of each species. Filled squares indicate the taxonomy of archaea with similar species together and on same level. (1), (3)-(5) indicate species in four phyla: Crenarchaeota, Korarchaeota, Nanoarcgaeota, and Thaumarchaeota. (2.1) - (2.8) are eight different classes in the phylum of Euryarchaeota as shown in Table. 1.
Figure 3
Figure 3
Length distribution of proteins in five phyla (a) and eight classes (b) of Euryarchaeota. X-axis: “X” length of protein; Y-axis: percentage of proteins with “X” length. The upper limit of the x-axis is taken as 1500 residues for visualization purposes. However, there are still scattered distributions of proteins beyond this uplimit.
Figure 4
Figure 4
Composition profile of amino acids for (a) five phyla, and (b) eight classes in Euryarchaeota: Residues on the X-axis are arranged according to the increasing disorder tendency. Y-axis: the relative compositional profile compared to a fully disordered dataset.
Figure 5
Figure 5
Various measures of intrinsic disorder content in 53 species: (a), Ratio of disordered residues in each species; (b), Percentage of proteins with long disordered regions (>30aa) in each species; (c), Ratio of fully disordered proteins in each species. In all figures above, the X-axis is the index number of each species. Filled squares indicate the taxonomy of archaea with similar species together and on the same level. (1), (3)-(5) indicate species in four phyla: Crenarchaeota, Korarchaeota, Nanoarcgaeota, and Thaumarchaeota. (2.1) - (2.8) are eight different classes in the phylum of Euryarchaeota. (d), Correlation among various disordered contents. X-axis: the ratio of disordered residues. Y-axis: percentage of proteins with long disordered regions and percentage of fully disordered proteins, accordingly.
Figure 6
Figure 6
Averaged CH-CDF plots for (a) five phyla and (b) eight classes in Euryarchaeota. Various symbols indicate the averaged values of CH- and CDF-distances of all proteins in that species. Error bars are calculated from the root mean square deviation of the same set of proteins.
Figure 7
Figure 7
The distribution of intrinsic disorder content in the Archaea as a function of optimal pH. Three measures of intrinsic disorder: (a) overall percentage of intrinsically disordered residues (IDAA); (a) percentage of proteins with long disordered regions (IDP >30 aa); (c) and the percentage of wholly disordered proteins (WIDP).
Figure 8
Figure 8
The distribution of intrinsic disorder content in the Archaea as a function of salinity of their habitats. Three measures of intrinsic disorder: (a) overall percentage of intrinsically disordered residues (IDAA); (b) percentage of proteins with long disordered regions (IDP >30 aa); (c) and the percentage of wholly disordered proteins (WIDP).
Figure 9
Figure 9
The distribution of intrinsic disorder content in the Archaea as a function of temperature of their habitats. Three measures of intrinsic disorder: (a) overall percentage of intrinsically disordered residues (IDAA); (b) percentage of proteins with long disordered regions (IDP >30 aa); (c) and the percentage of wholly disordered proteins (WIDP).
Figure 10
Figure 10
PONDR® prediction and experimentally solved structure of aIF2β from Sulfolobus solfataricus. The PONDR® VSL2 prediction is given in the plot, where scores greater than 0.5 are predictions of disordered residues and scores less then 0.5 are predictions of ordered residues. Horizontal bars represent regions with known structure, or are likely to be structured, which are (from N- to C- termini): the aIF2γ-binding MoRF region (red bar), the core domain (cyan bar), and the C-terminal zinc finger domain (green bar). Additionally, structures of the aIF2γ-binding MoRF region (red ribbon) bound to aIF2γ (blue surface) and aIF2α (green surface), and of the core domain (cyan ribbon) are shown (coordinates from PDB entries 2QN6 and 2NXU, respectively).
Figure 11
Figure 11
Intrinsic disorder and phylogenetic tree of Archaea. This schematic figure is made manually by taking the figure in http://archaea.ucsc.edu as a template. Several species not analyzed in our study were removed. Distances between very similar species were also intentionally increased. Numbers nearby the species name represent the relative content of disordered residues in that species. Colors of the tree are assigned according to the abundance of disordered residues (red:>30%; orange: >21%; yellow: >17%; light blue: >14%; dark blue:<=14%).
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