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Comparative Study
. 2003;4(6):R40.
doi: 10.1186/gb-2003-4-6-r40. Epub 2003 May 30.

A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes

Paul M Harrison  1 , Mark Gerstein
Affiliations
Comparative Study

A method to assess compositional bias in biological sequences and its application to prion-like glutamine/asparagine-rich domains in eukaryotic proteomes

Paul M Harrison et al. Genome Biol. 2003.

Abstract

We have derived a novel method to assess compositional biases in biological sequences, which is based on finding the lowest-probability subsequences for a given residue-type set. As a case study, the distribution of prion-like glutamine/asparagine-rich ((Q+N)-rich) domains (which are linked to amyloidogenesis) was assessed for budding and fission yeasts and four other eukaryotes. We find more than 170 prion-like (Q+N)-rich regions in budding yeast, and, strikingly, many fewer in fission yeast. Also, some residues, such as tryptophan or isoleucine, are unlikely to form biased regions in any eukaryotic proteome.

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Figures

Figure 1
Figure 1
Histogram of the lengths of the (Q+N)-rich domains for budding yeast, fruit fly and human. The distribution of sequence lengths for the (Q+N)-rich domains are shown for budding yeast (top panel), fruit fly (middle panel) and human (bottom panel). The y-axis is the number of regions per bin, and the x-axis is for bins with labels x such that each bin contains all sequences with length x to x + 24 inclusive. The mean and median lengths for each of these distributions are as follows (organism, mean (± SD), median): budding yeast, 209 ± 209, 116; fruit fly, 236 ± 389, 89; human, 553 ± 730, 268. Only the distributions up to bin x = 275 are shown; a sizeable proportion of each distribution is longer than 275 residues (budding yeast 30% of sequences, fruit fly 22% and human 44%).
Figure 2
Figure 2
Each proteome has a characteristic distribution of biases. The proportion of bias residues (y-axis) counted up for each of the following seven residues (S, Q, N, L, I, D, C) are shown as a function of the bias probability (x-axis). The x-axis comprises bins labeled with -log(P) such that all regions with probabilities from -log(P) to 3.0 -log(P) are included. The end (right-most) bin includes all regions with log probability greater than -log(P). From left to right, the first set of panels is for budding yeast, the second set for fission yeast, the third set for fruit fly and the fourth for human. The rows of panels are labeled at the far right with the appropriate one-letter amino-acid symbol (S, Q, N, L, I, D and C).
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References

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