Assigning protein functions by comparative genome analysis: protein phylogenetic profiles

Abstract

Determining protein functions from genomic sequences is a central goal of bioinformatics. We present a method based on the assumption that proteins that function together in a pathway or structural complex are likely to evolve in a correlated fashion. During evolution, all such functionally linked proteins tend to be either preserved or eliminated in a new species. We describe this property of correlated evolution by characterizing each protein by its phylogenetic profile, a string that encodes the presence or absence of a protein in every known genome. We show that proteins having matching or similar profiles strongly tend to be functionally linked. This method of phylogenetic profiling allows us to predict the function of uncharacterized proteins.

Figure 1

Our method of analyzing protein phylogenetic profiles is illustrated schematically for the hypothetical case of four fully sequenced genomes (from E. coli, Saccharomyces cerevisiae, Haemophilus influenzae, and Bacillus subtilis) in which we focus on seven proteins (P1–P7). For each E. coli protein, we construct a profile, indicating which genomes code for homologs of the protein. We next cluster the profiles to determine which proteins share the same profiles. Proteins with identical (or similar) profiles are boxed to indicate that they are likely to be functionally linked. Boxes connected by lines have phylogenetic profiles that differ by one bit and are termed neighbors.

Figure 2

Proteins with phylogenetic profiles in the neighborhood of ribosomal protein RL7 (A), flagellar structural protein FlgL (B), and histidine biosynthetic protein His5 (C). In each case, we first found all proteins with profiles identical to our query proteins; the proteins we found are shown in the double boxes. We then found all the proteins with profiles that differed from our query proteins by one bit; these are shown in the single boxes. Proteins in bold participate in the same complex or pathway as the query protein, and proteins in italics participate in a different but related complex or pathway. Proteins with identical profiles are shown within the same box. Single lines between boxes represent a one-bit difference between the two profiles. All neighboring proteins whose profiles differ by one bit from the query protein are shown. Homologous proteins are connected by a dashed line or are indented. Each protein is labeled by a four-digit E. coli gene number, a SwissProt gene name, and a brief description. Note that proteins within a box or in boxes connected by a line have similar functions. Hypothetical proteins (i.e., those of unknown function) are prime candidates for functional and structural studies. Proteins in the double boxes in A, B, and C have 11, 6, and 10 ones, respectively, in their phylogenetic profiles, of a possible 16 for the 17 genomes presently sequenced.