Functional Divergence Prediction from Evolutionary Analysis: A Case Study of Vertebrate Hemoglobin Simonetta Gribaldo,1 Didier Casane,1 Philippe Lopez, and Hervé Philippe Phylogénie, Bioinformatique et Génome, Université Pierre et Marie Curie, Paris, France Introduction The prediction and analysis of functional subtypes in protein families is one of the highest priorities of postgenomics studies (Eisenberg et al. 2000; Enright and Ouzounis 2001; Bickel et al. 2002; Gaucher et al. 2002b; Jensen, Skovgaard, and Brunak 2002; Lichtarge and Sowa 2002; Yang 2002; Blouin, Boucher, and Roger 2003). Besides predicting specialization in subgroups of homologs, it is of the utmost importance to devise in silico methodologies aimed at identifying the residues involved in such a process. This is just beginning to become possible, given the large number of sequences necessary to such analyses. Diverse approaches have been proposed, mostly based on multiple alignments (Casari, Sander, and Valencia 1995; Lichtarge, Bourne, and Cohen 1996; Hannenhalli and Russell 2000). It is well established that many aspects of comparative biology can benefit from evolutionary studies (Felsenstein 1985), and evolutionary information is very helpful in the prediction of gene function (Eisen 1998; Marcotte et al. 1999; Pellegrini et al. 1999). Recently, molecular phylogenetics tools have been used to tackle this issue via the identification of changes in rates of substitutions over time, under the principle that site-specific switches in evolutionary rates in a member of a duplicated gene couple are a signature of functional diversification (Gu 1999, 2001; Naylor and Gerstein 2000; Gaucher, Miyamoto, and Benner 2001; Knudsen and 1 These authors contributed equally to this work. Key words: covarion, evolutionary rate, hemoglobin, heterotachy, protein function, tertiary structures. E-mail: [email protected]. Mol. Biol. Evol. 20(11):1754–1759. 2003 DOI: 10.1093/molbev/msg171 Molecular Biology and Evolution, Vol. 20, No. 11, Ó Society for Molecular Biology and Evolution 2003; all rights reserved. 1754 Miyamoto 2001; Gaucher et al. 2002a, 2002b; Blouin, Boucher, and Roger 2003). The switch of constraints on positions over time is a poorly understood phenomenon. Indeed, although the notion that not all sites in a protein are subjected to the same evolutionary forces is well established (Kimura 1983), a site can show dramatic changes in substitution rates on separate parts of a phylogeny. Evidence for such behavior dates as early as the 1970s, with the formulation of Fitch’s covarion model of molecular evolution (Fitch and Markowitz 1970). The term heterotachy (Greek for different speed) was recently coined to refine the description of this phenomenon (Philippe and Lopez 2001), as opposed to homotachy, which indicates a homogeneous substitution rate. Because heterotachy (i.e., lineage-specific substitution rate shifts) reflects constraint variation on specific sites of a protein structure across time, it is generally indicated as a landmark of functional divergence (Gaucher et al. 2002b). Under this reasoning, the identification of heterotachous profiles between paralogous genes would be potentially informative for structure/function prediction analyses, because gene duplication is a major source of functional innovation (Ohno, Wolf, and Atkin 1968). Various approaches have been applied to a number of paralogous families in order to identify shifts in replacement rates that may be indicative of their functional diversification after duplication (Gu 1999, 2001; Gaucher, Miyamoto, and Benner 2001; Knudsen and Miyamoto 2001; Gaucher et al. 2002a, 2002b). Recently, Naylor and Gerstein (2000) employed Gu’s coefficient of functional divergence (Gu 1999) to identify shifts in variability profiles between alpha and beta globins for three groups of mammals as a measure of their specialization over evolutionary time. Because they observed marked rate shifts between alpha and beta globins, but not within each subunit, they concluded that this approach can Downloaded from http://mbe.oxfordjournals.org/ by guest on September 7, 2013 It is a central assumption of evolution that gene duplications provide the genetic raw material from which to create proteins with new functions. The increasing availability in multigene family sequences that has resulted from genome projects has inspired the creation of novel in silico approaches to predict details of protein function. The underlying principle of all such approaches is to compare the evolutionary properties of homologous sequence positions in paralogous proteins. It has been proposed that the positions that show switches in substitution rate over time—i.e., ‘‘heterotachous sites,’’ are good indicators of functional divergence. Here, we analyzed the a and b paralogous subunits of hemoglobin in search for such signatures. We found as many heterotachous sites in comparisons between groups of paralogous subunits (a/b) as between orthologous ones (a/a, b/b). Thus, the importance of substitution rate shifts as predictors of specialization between protein subfamilies might be reconsidered. Instead, such shifts may reflect a more general process of protein evolution, consistent with the fact that they can be compatible with function conservation. As an alternative, we focused on those residues showing highly constrained states in two sequence groups, but different in each group, and we named them CBD (for ‘‘constant but different’’). As opposed to heterotachous positions, CBD sites were markedly overrepresented in paralogous (a/b) comparisons, as opposed to orthologous ones (a/a, b/b), identifying them as likely signatures of functional specialization between the two subunits. When superimposed onto the threedimensional structure of hemoglobin, CBD positions consistently appeared to cluster preferentially on inter-subunit surfaces, two contact areas crucial to function in vertebrate tetrameric hemoglobin. The identification and analysis of CBD sites by complementing structural information with evolutionary data may represent a promising direction for future studies dealing with the functional characterization of a growing number of multigene families identified by complete genome analyses. Functional Divergence Prediction 1755 Methods Sequence Retrieval, Alignment, and Taxon Sampling Vertebrate globin homologs were obtained from public databases (http://www.ncbi.nlm.nih.gov/) by using the automatic retrieving program AliBaba (Lopez, unpublished), and manually aligned by the aid of the ED program included in the MUST suite (Philippe 1993). We discarded 7 alpha and 8 beta globin sequences, as they belonged to poorly sampled monophyletic groups (chondrichthyans, coelacanths, dipnoi, amphibians). We retained a and b subunit sequences from three large monophyletic groups, mammals, teleost fishes, and Sauropsida (birds, crocodiles, lepidosaurs, and turtles). After removal of ambiguously aligned regions, a data set was assembled comprising 234 a and 213 b sequences totaling 132 amino acid positions. The data set was subdivided into six subalignments corresponding to either a and b sequences from each taxonomic group (145 a and 145 b from mammals; 46 a and 57 b from teleosts; 45 a and 49 b from Sauropsida). Alignments and accession numbers are available as online Supplementary Material. Phylogenetic Analyses and Study of Site-Specific Evolutionary Behavior Heterotachy was tested as previously described (Lopez, Casane, and Philippe 2002). Briefly, the number of substitutions at each site was calculated on a phylogenetic tree obtained from each of the six subalignments (corresponding to 3 a and 3 b sequence groups for each taxonomic cluster). Substitution numbers were inferred by maximum likelihood (ML) using PAML (Yang 1997) with the JTT þ F þ ÿ model. Each position was described by a profile indicating the numbers of inferred substitutions for every group. The program HTACH (Philippe, unpublished) was then employed for all possible binary comparisons to identify positions as either (1) homotachous, (2) heterotachous, (3) constant, and (4) constant but different (CBD). Positions displaying less than a total of three substitutions were classified as untestable, because no statistical test can detect a difference in such cases (this corresponds to the criterion ‘‘a total number of substitutions smaller than half the number of groups’’ used by (Lopez, Forterre, and Philippe 1999)). Positions with only one change in one terminal branch were considered for categories (3) or (4), because this difference is likely the result of sequencing error. Structure Analyses The different classes of sites were superimposed onto three-dimensional hemoglobin structures retrieved from the Protein Data Bank (Berman et al. 2000), by using the user script option in RasMol (Sayle and Milner-White 1995). Side chain solvent accessibility was calculated by the program Access (http://www.csb.yale.edu/userguides/ datamanip/access/access_descrip.html), but because various types of positions display similar values, this is not discussed here (see table S1 in the online Supplementary Material). Mutational data were retrieved from the Databases of Human Hemoglobin Variants and Other Resources through the Globin Gene Server at http://globin.cse. psu.edu/hbvar/menu.html (Hardison et al. 2002). Downloaded from http://mbe.oxfordjournals.org/ by guest on September 7, 2013 successfully pinpoint functional differentiation. However, because a very large number of sequences are needed to assess site-specific rate shifts with statistical confidence (Lopez, Casane, and Philippe 2002), these results might have been biased by both a scarce sampling and limited evolutionary distances. In addition to sites with replacement rate switches, highly constrained residues may also hold information regarding functional divergence. For instance, sites that switched state between two diverging proteins, but that nonetheless conserved a high evolutionary constraint and are consequently not identified in analyses of heterotachous positions, might be potentially important in the process of functional specialization. Although pinpointed by different approaches (Lichtarge, Bourne, and Cohen 1996; Gu 2001), this type of site remains poorly investigated in functional genomics studies. We applied an approach coupling evolutionary and structural knowledge to survey the sites potentially responsible for functional specialization in the two subunits of vertebrate hemoglobin. Recently, such an approach was employed to investigate the fine functional differences between elongation factor homologs in bacteria and eukarya (Gaucher, Miyamoto, and Benner 2001; Gaucher et al. 2002a). Our choice was driven by the considerable representation of hemoglobin sequences in molecular databases, and by the vast amount of structural and functional information available. Tetrameric vertebrate hemoglobin consists of two identical a subunits of 141 residues and of two identical b subunits of 146 residues, each containing one heme group. Subunits a and b are paralogous peptides arising from an ancient gene duplication at the base of jawed vertebrates. Oxygen binding is cooperative and is associated with a large shift in the quaternary structure of the heterotetramer, from the deoxy (T) to the oxy (R) forms, as one dimer rotates relative to the other. Two types of subunit interfaces are implicated in such transition, namely a1b1 (or a2b2) and a1b2 (or a2b1), also referred to as packing and sliding surfaces, respectively (Perutz 1970). During the transition from the T to R state, the a1b2-subunit interface undergoes a dramatic sliding movement, whereas the a1b1-subunit interface remains essentially unchanged. Mutational studies have demonstrated the importance of both inter-subunit and intra-subunit contact regions for critical hemoglobin properties such as oxygen affinity and cooperativity (Shionyu, Takahashi, and Go 2001). We sought to identify and study the set of positions potentially implicated in the development of such highly functional interactions over the divergence of a and b subunits. We first studied heterotachous positions and found a similar level of variabilityprofile shift between orthologs and between paralogs, suggesting that heterotachous positions may be poor signatures of functional divergence. Then we turned instead to examining more constrained positions, which appeared to be much more reliable predictors. 1756 Gribaldo et al. Results and Discussion FIG. 1.—Distribution of heterotachous (H) and conserved but different (CBD) sites in paired orthologous and paralogous comparisons. (a) Schematic phylogenetic representation of a and b vertebrate globin families. The numbers of taxa used for each group are given in parentheses. (b) Distribution of H sites in orthologous (open circles) and in paralogous (solid circles) comparisons. Values on the Y axis indicate numbers of sites, and values on the X axis are the average Kimura distances between the two corresponding groups. (c) Distribution of CBD sites in orthologous (open circles) and in paralogous (solid circles) comparisons. Values on Y and X axes are as in (b). 1991), whereas the a55 homolog does not appear to be involved in any essential interaction. Nevertheless, these examples should be considered as special cases in which substitution rate shifts are linked to function. In fact, the similar levels of heterotachy observed in both ortholog (i.e., no functional divergence) and paralog (i.e., functional divergence) comparisons (fig. 1a), coupled with the fact that H sites were evenly dispersed over the three-dimensional structure (fig. 2a), indicate that, overall, the use of heterotachy as a reliable indicator of functional divergence should be reconsidered. Downloaded from http://mbe.oxfordjournals.org/ by guest on September 7, 2013 We retrieved and aligned a large sample of a and b globins from three vertebrate lineages—mammals, Sauropsida (reptiles and birds), and teleost fishes, totaling 487 taxa. This data set was subdivided into six sequence groups (corresponding to a and b globin clusters from each lineage), and evolutionary rates at each site were determined in each group by maximum likelihood (Yang 1997). By comparing these rates between groups of either paralogous and orthologous sequences (fig. 1a), we were thus able to follow the evolutionary behavior of each site in both a and b globins over time. Because our goal was to identify sites important in the functional divergence of the two globins, while we considered orthologous comparisons as a negative control, we looked for those sites harboring different properties in paralogous groups of sequences. We first studied heterotachous (H) sites, because a number of analyses have suggested that changes in variability profiles over time harbor a strong signal of functional differentiation (Gu 1999, 2001; Naylor and Gerstein 2000; Gaucher, Miyamoto, and Benner 2001; Knudsen and Miyamoto 2001; Gaucher et al. 2002a, 2002b; Blouin, Boucher, and Roger 2003). We followed the frequency of H sites over the evolution of a and b globins (fig. 1b). Unexpectedly, we found similar proportions of H positions in both orthologous and paralogous comparisons, with a mean of ;30% and ;34%, respectively. The nonparametric Mann-Whitney rank test suggested that the difference was not significant (w ¼ 40; P , 0.45). In fact, the highest value of heterotachy in paralogous comparisons is likely due to the greater evolutionary distances (Lopez, Casane, and Philippe 2002). Sometimes, the level of heterotachy was even higher between orthologs than between paralogs. For example, we found 45 H sites in orthologous comparisons between mammals and teleosts, but only 21 in paralogous comparisons within teleosts. The significance of these findings was investigated further by observing the structural distribution of the 40 H positions identified in mammalian paralogous comparisons (fig. 2a; for a detailed list, see table S2 in the online Supplementary Material). These positions appeared evenly dispersed all over the structure, both at internal and external locations (fig. 2a). Within the pool of H positions there were some likely to hold high functional significance, as they presented strong constraints in one subunit and much higher variability in the other. Consistently, the function of such residues was critical to only one chain (see table S2 in the online Supplementary Material). This was the case of six positions lying at inter-subunit contact surfaces. For example, leucine a40 presented no substitutions over the whole mammalian tree, whereas its b39 homolog was much more variable. This site is crucial in the a chain as it interacts with histidine b146 at the sliding interface. Instead, we found no functional indication for residue b39. Similarly, position b60 displayed a remarkably conserved valine over the whole mammalian tree, whereas its a homolog switched to variable amino acids on different branches. A valine to glutamate mutation at this site is reported to lead to a highly unstable b globin responsible for a severe form of thalassemia (Podda et al. Functional Divergence Prediction 1757 Downloaded from http://mbe.oxfordjournals.org/ by guest on September 7, 2013 FIG. 2.—Distribution of mammalian heterotachous and constant but different (CBD) sites onto human hemoglobin 3D structure. Sites belonging to a subunits (A and D chains) are colored in yellow and green, respectively; sites belonging to b subunits (B and D chains) are colored in blue and magenta, respectively; hemes are in red. H (a) and CBD (b) sites are displayed with the spacefill option, whereas only the backbone of the molecules is shown. The structure presented is a human adult hemoglobin in the deoxy conformation (Tame and Vallone 2000), with PDB accession number: 1A3N. The four types of categories (constant, homotachous, heterotachous, and CBD) between mammalian hemoglobin a and b are shown in fig. S1 (see Supplementary Material online). This might be the case for a number of previous studies (Gu 1999, 2001; Gaucher, Miyamoto, and Benner 2001; Knudsen and Miyamoto 2001; Gaucher et al. 2002a, 2002b), and for a recent analysis of globins (Naylor and Gerstein 2000). However, compared to this analysis, our substitution rate estimates were more accurate because they were calculated by using about four times as many sequences and much larger evolutionary distances (i.e., a broader taxonomic sampling). Moreover, none of the above studies challenged the reciprocal hypothesis, i.e., that heterotachy is absent when function is preserved. Indeed, the opposite was recently demonstrated when ;95% of variable positions in vertebrate cytochrome b were found to be heterotachous, using a sample of 2,000 sequences (Lopez, Casane, and Philippe 2002), even though a functional change of this enzyme within vertebrates is unlikely. Then, although heterotachy certainly harbors a strong functional component, this may not be specifically related to functional divergence. Instead, it may more generally reflect a less specific process related to the many intramolecular and intermolecular interactions compatible with a range of equally viable protein conformations. This latter hypothesis is consistent with Fitch’s pioneering theory on the non-independence of substitutions in proteins (Fitch and Markowitz 1970). To find more genuine signatures of functional divergence between the two globin subunits, we turned to positions harboring strong evolutionary constraints in both paralogs. Among them, we selected those that displayed different amino acid states in each paralog. Accordingly, we named them ‘‘conserved but different’’ (CBD). As shown in figure 1c, we found that, in contrast to H sites, CBD sites were overrepresented in paralogous comparisons with respect to orthologous ones, with a mean of ;10% and ;2%, respectively. The nonparametric Mann-Whitney rank test suggested that the difference was significant (w ¼ 23; P , 0.002). For example, although a total of 15 and 13 such positions were identified in paralogous comparisons in Sauropsida and mammals, respectively, only one was found in orthologous comparisons between Sauropsida and mammals (see fig. 1c). This evidence seems to indicate a likely involvement of CBD positions in the specialization of the two globin families. To confirm this prediction, we studied the distribution of CBD sites onto the hemoglobin quaternary structure. When superimposed onto the 3D structure of human adult hemoglobin, the 13 CBD sites identified in mammalian paralogous comparisons (for a detailed list, see table S2 in the online Supplementary Material) were concentrated at non-exposed locations (fig. 2b). This concentration was confirmed by the fact that almost all of them (10/13) were indeed reported to occupy contact surfaces (see table S2 in the online Supplementary Material), such as central cavity, ligand binding pockets, and inter-subunit contacts. In particular, six CBD sites were directly involved in both a1b2 (sliding) and a1b1 (packing) interfaces (Perutz 1970; Shionyu, Takahashi, and Go 2001). For example, tyrosine a41 and its homolog arginine b40 were identified as a highly constrained CBD couple in mammals. These sites interact with each other at the sliding surface in the oxy state. Another case is that of arginine a141 and its 1758 Gribaldo et al. Supplementary Material The following material is available online: figure S1: Distribution on human hemoglobin 3D structure of the four evolutionary categories of mammalian globins sites, H, CBD, homotachous, and constant; table S1: Solvent accessibility and site categories for all the positions of mammalian globins; table S2: Structural and mutational data for mammalian CBD and H sites. Also, alignments and accession numbers are available as online Supplementary Material. Acknowledgments We acknowledge Pierre Tuffery for kindly calculating side chain solvent accessibility, and Eric Bapteste and Franz Lang for careful reading of the manuscript. S.G. was supported by a poste de chercheur associé from CNRS. This work was supported by a grant from the programme inter-EPST bioinformatique. Literature Cited Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235–242. Bickel, P. 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Nat. 125:1–15. Fitch, W. M., and E. Markowitz. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4:579–593. Gaucher, E. A., U. K. Das, M. M. Miyamoto, and S. A. Benner. 2002a. The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors. Mol. Biol. Evol. 19:569–573. Gaucher, E. A., X. Gu, M. M. Miyamoto, and S. A. Benner. 2002b. Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem. Sci. 27:315–321. Gaucher, E. A., M. M. Miyamoto, and S. A. Benner. 2001. Function-structure analysis of proteins using covarion-based evolutionary approaches: elongation factors. Proc. Natl. Acad. Sci. USA 98:548–552. Gu, X. 1999. Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16:1664–1674. ———. 2001. Maximum-likelihood approach for gene family evolution under functional divergence. Mol. Biol. Evol. 18:453–464. Hannenhalli, S. S., and R. B. Russell. 2000. Analysis and prediction of functional sub-types from protein sequence alignments. J. Mol. Biol. 303:61–76. Hardison, R. C., D. H. Chui, B. Giardine, C. Riemer, G. P. Patrinos, N. Anagnou, W. Miller, and H. Wajcman. 2002. HbVar: a relational database of human hemoglobin variants and thalassemia mutations at the globin gene server. Hum. Mutat. 19:225–233. Jensen, L. J., M. Skovgaard, and S. Brunak. 2002. Prediction of novel archaeal enzymes from sequence-derived features. Protein Sci. 11:2894–2898. Kimura, M. 1983. The neutral theory of molecular evolution, Cambridge University Press, Cambridge. Knudsen, B., and M. M. Miyamoto. 2001. A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc. Natl. Acad. Sci. USA 98:14512–14517. Lichtarge, O., H. R. Bourne, and F. E. Cohen. 1996. An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol. 257:342–358. Lichtarge, O., and M. E. Sowa. 2002. Evolutionary predictions of binding surfaces and interactions. Curr. Opin. Struct. Biol. 12:21–27. Lopez, P., D. Casane, and H. Philippe. 2002. Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19: 1–7. Lopez, P., P. Forterre, and H. Philippe. 1999. The root of the tree of life in the light of the covarion model. J. Mol. Evol. 49:496–508. Marcotte, E. M., M. Pellegrini, H. L. Ng, D. W. Rice, T. O. Yeates, and D. Eisenberg. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285:751–753. Downloaded from http://mbe.oxfordjournals.org/ by guest on September 7, 2013 homolog histidine b146, both of which presented no substitutions over the whole mammalian tree. These sites are involved in crucial interactions with different residues in the deoxy state. The high proportion of CBD positions at inter-subunit surfaces supports their role as potential indicators of functional divergence, because the refinement of interactions at these interfaces played a fundamental role in the evolution of critical functions such as modulation of oxygen affinity and cooperative binding (Perutz 1970). It will be interesting to verify whether CBD sites have the same critical role in proteins that do not oligomerize, when their representation in public databases will be sufficient to allow an analysis similar to that presented here. Only three CBD sites occupied external locations on human hemoglobin (fig. 2b; see also table S2 in the Supplementary Material online). Because the reason for their strong conservation on the heterotetramer surface is not obvious, and because they are probably involved in functional divergence, they might represent promising candidates for further experimental studies. 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