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Protein sets (proteomes) from the following pairs of complete genome sequences were compared in order to identify orthologous sequences: S. cerevisiae - S. pombe , S. cerevisiae - C. elegans , H. pylori strain 26695 - H. pylori strain J99, H. pylori strain 26695 - C. jejuni . Pairs of proteomes were compared using the BLASTP program [ 18 ] , with post-processing of results done using the SEALS package [ 19 ] . For each proteome, individual proteins were used as queries in BLASTP searches against the entire proteome of the other analyzed species (or strain).
A total of 1,879 pairs of orthologous proteins, one from S. cerevisiae and one from S. pombe , were identified (see Methods), and for 1,004 of these, there was data on protein-protein interactions of the S. cerevisiae member in the MIPS database [ 5 ] . For these 1,004 orthologous pairs, the number of protein-protein interactions detected for the S. cerevisiae protein was plotted against the calculated substitution rates between orthologs (Figure 1a).
Immunoblotting of protein lysates prepared from S. pombe cells, whose pcu3 chromosomal locus was modified to encode Pcu3p with thirteen copies of the Myc epitope attached to its C-terminus, revealed two distinct species of Pcu3p, which migrated on SDS gels as two closely spaced species of roughly equal abundance (Fig.
In addition to CUL1, the human genome contains at least five other cullins, CUL 2, 3, 4A, 4B, and 5. This diversity is partially recapitulated in S. pombe , which encodes pcu3 and pcu4 , homologues of human CUL3 and CUL4, for which there are no direct correlates in budding yeast [ 6].
Sequences were the APE1 protein from human, bovine, monkey, rat murine, Arabidopsis thaliana (Mouse-ear cress) Dictyostelium discoideum (Slime mold), Schizosaccharomyces pombe (Fission yeast), Caenorhabditis elegans , Saccharomyces cerevisiae (Baker's yeast), Thermoplasma acidophilum , Neisseria meningitidis . Methanobacterium thermoautotrophicum , Leishmania major , Trypanosoma cruzi , Coxiella burnetii ; the Rrp1 protein of Drosophilia ; exonuclease III from E. coli , Bacillus subtilis , Mycobacterium tuberculosis , Haemophilus influenzae , Salmonella typhimurium , Helicobacter pylori , Rickettsia prowazekii , Archaeoglobus fulgidus , Actinobacillus actinomycetemcomitans , Streptomyces coelicolor , Synechocystis sp.
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