Comparison of the complete protein sets of worm and yeast: orthology and divergence

Abstract

Comparative analysis of predicted protein sequences encoded by the genomes of Caenorhabditis elegans and Saccharomyces cerevisiae suggests that most of the core biological functions are carried out by orthologous proteins (proteins of different species that can be traced back to a common ancestor) that occur in comparable numbers. The specialized processes of signal transduction and regulatory control that are unique to the multicellular worm appear to use novel proteins, many of which re-use conserved domains. Major expansion of the number of some of these domains seen in the worm may have contributed to the advent of multicellularity. The proteins conserved in yeast and worm are likely to have orthologs throughout eukaryotes; in contrast, the proteins unique to the worm may well define metazoans.

Fig. 1

Distribution of core biological functions conserved in both yeast and worm. Yeast and worm protein sequences were clustered into closely related groups (BLASTP P < 1 × 10⁻⁵⁰, with the >80% aligned length constraint) as described in the legend to Table 1. Each sequence group (including groups with two or more sequences) was assigned into a single functional category, relying primarily on the functional annotations for the yeast genes in SGD when available (44). The unclassified category contains groups of sequences without annotation. The boxed number within each category reflects the ratio of worm to yeast proteins for that category.

Fig. 2

Orthologous core biological functions in yeast and worm. Representative sequence groups are shown as rooted CLUSTALW Neighbor-Joining trees, clustered as described in the legend to Table 1, at a similarity level indicated after each description. Gene names are color-coded (blue, S. cerevisiae; red, C. elegans). (A) RNA polymerase. (B) Replication factor C. (C) Proteasome subunits. (D) Tubulin. (E) HSP70 heat shock proteins. (F) Actin and actin-related proteins. Hyperlinked versions of these figures are available at the SGD Web site described in the text. Trees were created by means of CLUSTALW (14) with default parameters, which use the BLOSUM series of weight matrices. Trees were drawn with a combination of the Phylip (22) and gd (Boutell.Com, www.boutell.com) software packages. This table gives only examples from the table on the Web site.

Fig. 3

Normalized counts of the common regulatory and signal transduction domains in yeast and the nematode C. elegans. The data are from the complete version of Table 2 that is available on the Web site. The axes show the number of proteins with the given domain per 1000 genes. 1, POZ domains; 2, EGF; 3, MATH domain; 4, phosphotyrosine phosphatase; 5, homeodomains; 6, leucine-rich repeats; 7, calmodulin; 8, PDZ domains; 9, voltage-gated channels; 10, ankyrin repeats; 11, RING domain; 12, C6 fingers; 13, nuclear hormone receptors; 14, AAA-type ATPases. The two domains that are most abundant in yeast, namely serine-threonine protein kinases and WD40 domains (Table 2), were not used for this plot, in order to improve resolution for the other points.