Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes

Abstract

Based on searches for disabled homologs to known proteins, we have identified a large population of pseudogenes in four sequenced eukaryotic genomes-the worm, yeast, fly and human (chromosomes 21 and 22 only). Each of our nearly 2500 pseudogenes is characterized by one or more disablements mid-domain, such as premature stops and frameshifts. Here, we perform a comprehensive survey of the amino acid and nucleotide composition of these pseudogenes in comparison to that of functional genes and intergenic DNA. We show that pseudogenes invariably have an amino acid composition intermediate between genes and translated intergenic DNA. Although the degree of intermediacy varies among the four organisms, in all cases, it is most evident for amino acid types that differ most in occurrence between genes and intergenic regions. The same intermediacy also applies to codon frequencies, especially in the worm and human. Moreover, the intermediate composition of pseudogenes applies even though the composition of the genes in the four organisms is markedly different, showing a strong correlation with the overall A/T content of the genomic sequence. Pseudogenes can be divided into 'ancient' and 'modern' subsets, based on the level of sequence identity with their closest matching homolog (within the same genome). Modern pseudogenes usually have a much closer sequence composition to genes than ancient pseudogenes. Collectively, our results indicate that the composition of pseudogenes that are under no selective constraints progressively drifts from that of coding DNA towards non-coding DNA. Therefore, we propose that the degree to which pseudogenes approach a random sequence composition may be useful in dating different sets of pseudogenes, as well as to assess the rate at which intergenic DNA accumulates mutations. Our compositional analyses with the interactive viewer are available over the web at http://genecensus.org/pseudogene.

Figure 1

(A) Gene and (B) intergenic region composition for the 20 amino acids and stop signal (*) in the four eukaryotes. Residues are sorted in decreasing order by standard deviation of gene frequencies across the organisms. Human genes are taken from GenomeScan predictions along chromosomes 21 and 22; for other organisms the available complete proteomes have been used. Some gene sequences may include the terminating stop codon, thus there is some variation in the frequency shown for this signal.

Figure 2

Compositon of ΨG in the eukaryotes. The amino acid content of pseudogene predictions is compared with the implied translation of unmasked chromosomes and identified genes. For the human, only chromosomes 21 and 22 are used in the plot shown. In each case, residues have been sorted in order of the difference in frequency between genes and chromosomes [ΔF(genes,intergenic)].

Figure 3

Classifications of pseudogenes. Residues are sorted as above by ΔF(genes,intergenic). (A) Pseudogenes divided into putative processed and duplicated sets. (B) Processed pseudogenes divided into recent and ancient sets based on a median FASTA identity value of 79%.

Figure 4

Arginine codon bias in human chromosomes 21 and 22. Frequency is out of all Arg codons, or F_codon/F_Arg.

Figure 5

Sample screen of the online composition browser. The database is accessible through a form that allows selection of any combination of features for which amino acid composition has been determined. Included in the display is a plot of the compositions and statistics for each feature.