Coevolution analyses illuminate the dependencies between amino acid sites in the chaperonin system GroES-L
© Ruiz-González and Fares; licensee BioMed Central Ltd. 2013
Received: 25 March 2013
Accepted: 18 July 2013
Published: 22 July 2013
GroESL is a heat-shock protein ubiquitous in bacteria and eukaryotic organelles. This evolutionarily conserved protein is involved in the folding of a wide variety of other proteins in the cytosol, being essential to the cell. The folding activity proceeds through strong conformational changes mediated by the co-chaperonin GroES and ATP. Functions alternative to folding have been previously described for GroEL in different bacterial groups, supporting enormous functional and structural plasticity for this molecule and the existence of a hidden combinatorial code in the protein sequence enabling such functions. Describing this plasticity can shed light on the functional diversity of GroEL. We hypothesize that different overlapping sets of amino acids coevolve within GroEL, GroES and between both these proteins. Shifts in these coevolutionary relationships may inevitably lead to evolution of alternative functions.
We conducted the first coevolution analyses in an extensive bacterial phylogeny, revealing complex networks of evolutionary dependencies between residues in GroESL. These networks differed among bacterial groups and involved amino acid sites with functional importance and others with previously unsuspected functional potential. Coevolutionary networks formed statistically independent units among bacterial groups and map to structurally continuous regions in the protein, suggesting their functional link. Sites involved in coevolution fell within narrow structural regions, supporting dynamic combinatorial functional links involving similar protein domains. Moreover, coevolving sites within a bacterial group mapped to regions previously identified as involved in folding-unrelated functions, and thus, coevolution may mediate alternative functions.
Our results highlight the evolutionary plasticity of GroEL across the entire bacterial phylogeny. Evidence on the functional importance of coevolving sites illuminates the as yet unappreciated functional diversity of proteins.
Heat-shock proteins, also known as molecular chaperones, belong to a highly conserved set of protein families that perform essential functions to the cell in prokaryotes and eukaryotes . These functions include, but are not limited to, protein folding, assembly, and transport [2–9]. While the folding function of GroEL has been extensively characterized, emerging literature uncover many alternative functions and structures for this protein (For a recent review see ). Mutations in this molecule that are responsible for the emergence of alternative functions remain uncharacterized. Therefore, the potential evolvability of this essential protein is largely unexplored.
GroES and GroEL, also known as cpn10 and cpn60 respectively, are expressed at constitutive levels under physiological conditions and their expression increases at high temperatures, allowing the growth and survival of bacteria at a broad range of temperatures [11–13]. Both chaperonins are encoded by the operon groE and they form a homotetradecamer organized into two back-to-back oriented rings. Each of the rings comprises seven identical GroEL subunits, with each subunit being divided into three domains: the apical, which binds unfolded proteins and GroES, the intermediate, which acts as a hinge allowing the movement of the apical domain as well as the transition between trans and cis conformations needed for GroEL function, and the equatorial which is responsible for the ATPase and the folding activities that take place in the central cavity of the ringed complex [14–16].
The main function of GroEL has been considered to be the folding of other proteins in the cell [6, 14, 17–20], although evidence supports other folding-unrelated roles for GroEL, such as immune response in humans [21–23] or growth and biofilm formation in bacteria, among others [24–30]. These functions are context dependent and may vary from one organism to another. Alternative functions may emerge in proteins after the duplication and evolution of their encoding gene or through amino acid replacements that impinge on the protein structure. The gene groEL has undergone many duplications in bacteria , adaptive evolution  and functional divergence . Moreover, structural evolutionary changes have been recently described for GroEL, according to which changes in the amino acid composition of its co-chaperonin GroES can determine GroEL functioning as a single instead of double ring .
The strong evolutionary sequence conservation of groEL and the high number of interactions it establishes with other proteins in the cell [13, 34] contrast with GroEL´s functional and structural plasticity and its propensity to persist in duplicate in some bacteria. Particularly striking is the fact that, while performing essential functions in the cell, GroEL presents alternative functions . The trade-off between groEL´s high conservation at the sequence and functional levels and its high propensity to evolve novel functions remains poorly understood.
Researchers have attempted to uncover GroEL’s multi-functionality through the testing of the effects of directed mutagenesis of GroEL amino acids under laboratory-controlled conditions. However, the multifunctional nature of GroEL suggests the existence of a reservoir of functionalities resulting from the interaction between distinct sets of amino acids in different bacteria. Here we propose the hypothesis that the functional plasticity of GroEL is mediated by an evolutionary plasticity of potentially functional amino acids. In support of this hypothesis, bacteria growing under different physiological conditions present GroEL variants with functions alternative to folding and which involve different sets of amino acids. The strong selective constraints acting on GroEL imply important functional and structural links between amino acids. These links impose reciprocal selection pressures among amino acid sites. Therefore, changes on GroEL functions from one bacterial group to another should be reflected in strong coevolutionary signatures between linked amino acids whose evolvability is co-regulated by selection in a particular bacterial clade.
In this study we performed an exhaustive coevolutionary analysis using an extensive bacterial phylogeny to uncover the evolutionary, hence functional, dependencies among amino acid residues within GroES, GroEL and between both these proteins. The coevolutionary networks identified in these chaperonins from hundreds of bacteria reveal the complexity underlying the evolution of this essential protein and shed light on the functional importance of previously uncharacterized residues.
Sequence data and coevolution analyses
GroES (Cpn10) and GroEL (Cpn60) sequences used in our analysis
Proteobacteria (α, β, γ, δ, ϵ)
Evolutionary dependencies between functional sites within GroES and GroEL
To determine the magnitude of the evolutionary plasticity of GroEL and GroES, we first conducted a coevolutionary analysis to determine the network of residues dependencies in all bacteria. We performed intra-protein coevolution analyses in a 519 sequences based GroES alignment and 505 sequences based GroEL alignment, representing the 6 major bacterial groups. We also calculated the support of each pair of coevolutionary sites taking into account the phylogenetic relationships using a non-parametric bootstrap approach (see Material and Methods for details). All amino acid sites numbering and composition are referred throughout the text to the numbering in the crystal structure of GroESL from E. coli (1AON.pdb).
Interestingly, Leu27 and Gly29, two amino acids known to be involved in the interaction between GroES and GroEL [35, 36] are the most central in the coevolution network (Additional file 1: Figure S1a to c). The dependency of these two essential amino acids on other functionally uncharacterized ones hints possible functional links between both sets of amino acid sites. Indeed, Lys13, Thr36, Arg37, Gly39, Arg47 and Lys74, while lacking apparent functions, they form a structural cluster establishing important contacts among GroES subunits (Figure 1b). Amino acid sites within each of the structural clusters were in close proximity to each other (for example, their proximal carbon atoms were less than 4 Å distant, against an average distance of 40 Å between all pairs of amino acids). Coevolution among structurally proximal amino acid sites is a general pattern  and suggests compensatory relationships, hence functional or structural links, between amino acids [38–40].
In GroEL, we identified 21 coevolving amino acid residues (Figure 1c), of which Leu116, Ala127, Ser135, Arg231, Lys245, Gln319, Arg350, Ala443, and Asn487 were the most central residues to the network (Additional file 1: Figure S1d to 1f). Arg231, Val236, and Lys245 are involved or close to (less than 4 Å distance in the structure) sites mediating substrate and GroES binding. Other positions were either included or close to charged amino acid sites that were facing the central GroEL cavity (for example, Gln290, Val300, Lys311, and Arg350). Finally, Asn487 is located in the ATP and Mg2+ binding site, while other amino acid sites, such as Ala443 and Ala466, are at the rings interface and likely involved in protein folding within the GroES-L ring complex. All 21 amino acids are distributed into two structural groups: one in the apical and another in the equatorial domains (Figure 1d). Remarkably, coevolving sites are very close to sites involved in protein folding, substrate and GroES binding, ATP binding and hydrolysis, or inter-subunits contacts, thus, suggesting that changes at these amino acids may have important functional consequences (Figure 1d).
Coevolution of GroES with GroEL
The interaction of GroES and GroEL is essential to induce the conformational changes needed for the folding cycle. These conformational changes may force coadaptation dynamics between GroES and GroEL.
In support of the structural and functional communication between the coevolving sites of GroES and GroEL, coevolving amino acids formed structural clusters within GroESL (Figure 2b). In addition to their clustering, coevolving sites were either functionally relevant or were close to sites with reported functional importance. Taken together, these results support the hypothesis that the coevolutionary relationships are the result of selective constraints on amino acid sites that are structurally or functionally linked in the GroES-L complex.
Shifts of GroES-GroEL coevolutionary relationships during bacterial evolution
We tested whether the coevolutionary relationships among amino acid sites have changed among the different bacterial groups, which would indicate functional changes in GroES-L. Functional shifts in GroEL have been previously documented and linked to events of GroEL gene duplication  and to changes in the organismal lifestyle [10, 32]. However, a precise analysis of the sites potentially driving GroEL functional changes in major bacterial groups has not been conducted before.
We identified evolutionary dependencies between amino acid sites that were specific to a particular bacterial group but not to others. Previous studies have shown that the number of sequences in the alignment may undermine the accuracy of coevolution-detection methods . To avoid such size-dependent effects, we performed bootstrap analyses of the coevolving pairs of sites (see material and methods). Amino acid sites identified as coevolving presented high bootstrap values (Additional file 3: Figure S3 and Additional file 4: Figure S4 for the coevolution results of GroES and GroEL, respectively). Amino acid sites detected in coevolution analyses between GroES and GroEL (Additional file 5: Figure S5) were not detected in intra-protein coevolution analyses, and thus, were not the result of indirect evolutionary dependencies.
Coevolving sites are three-dimensionally proximal in the structure of GroES and GroEL. For example, His7 and Asn68 from Actinobacteria that are strongly proximal in the structure (mean Euclidean distance between their proximal atoms is less than 4 Å) were coevolving with two sets of amino acids from GroEL. One set included Tyr478, Ala481 and Cys519, all three being very proximal to one another in the equatorial domain of GroEL, and another set comprised Cys138 and His401, which were proximal in the intermediate domain.
To determine the functional meaning of the groupings of coevolving sites in each bacterial clade, we performed two different analyses. First, we followed a previously published approach to define functional sectors in GroEL and GroES . In this study, sectors are characterized by statistical independence, structural continuity, biochemical independence and divergence independence. Halabi and colleagues  showed that statistical protein sectors correspond to functional sectors. We tested three of the sectors properties using computational means: statistical and divergence independences and structural continuity. Second, we mapped sites identified as coevolving in one bacterial group but not in other into those protein regions known to have shifted GroEL function to other folding unrelated functions in that bacterial group.
Groups of coevolution form protein sectors statistically independent among bacteria
Functional links between sites impose correlation in their entropies . To test this, we measured the amount of conservation (D i ) for the sites of each GroEL protein domain as a function of Entropy (see Material and Methods for details). Then, we calculated the correlation entropy (I i ) for each group of coevolving sites (see Material and methods). To determine if the group of coevolving sites within a bacterial clade is independent from that of another bacterial clade, we compared the correlation entropy of groups of different bacterial clades for each of the GroEL domains. Three were the domains compared (apical, equatorial and intermediate domains) between bacterial groups. If the change in the sites composition of coevolution networks is the result of functional shifts between bacteria, sites within a network in a bacterial group (g1) should correlate in their entropies (I i ) more than with any of the sites of the network of the other bacterial group (g2). That is, the entropy correlation of one group should be independent of that of the other group (I g1-g2 ≈ I g1 +I g2 ).
A main difference between our approach and that of the previous study  is that sectors in our approach are defined based on coevolution analyses derived from CAPS, while those of Halabi and colleagues  were identified using statistical coupling analyses (SCA) to determine the contribution of correlations to conservation profiles.
Groups of coevolution present structural continuity
Coevolution of GroEL sites with folding-independent functions
GroEL regions responsible for functional differences among bacteria are reported in Figure 4 of . We have compared the sites coevolving in one bacterial clade but not another and plotted these sites in the different domains known to confer GroEL alternative non-folding functions. Many of the sites involved in a coevolutionary relationship in a bacterial group have been reported to be involved in a GroEL function alternative to protein folding (Figure 3). For example, two of the coevolving sites in Actinobacteria are directly involved in monocyte modulation by the Actinobacterium Micobacterium tuberculosis (, figure 3). Moreover, a number of the amino acids identified as coevolving exclusively in proteobacteria map to a region from GroEL previously found to bind to potato leafroll virus and to facilitate its movement in the plant [45, 46] (Figure 3). The extensive list of coevolving amino acid sites mapping within these folding-alternative functions (Figure 3) is testament to the important implications of groups of coevolution in the functional plasticity of GroEL.
Complex coevolutionary networks in GroESL define the functional boundaries of amino acid sites
Our analyses of the coevolutionary dynamics within GroES and GroEL as well as between both these interacting proteins uncover a complex network of evolutionary dependencies among amino acid sites. These dependencies often involve sets of sites with known functional relevance but also comprise other sites with unknown importance. However, the functional importance of these untested sites is supported by a number of observations and tests made in this study. First, we show that most amino acids involved in coevolutionary dynamics are three-dimensionally clustered in the protein structure and closely located to functionally or structurally important sites. As a case in point, functionally important sites in GroES present the largest centrality values in GroES coevolutionary network, indicating their greater evolutionary dependencies with other sites closely located in the protein structure. The coevolution of sites surrounding important functional regions may compensate the effects of mutations at these functional sites or near functional and catalytic pockets, thereby maintaining an overall volume or shape for that pocket . Our results on the proximity of coevolving sites to functional domains support previous studies claiming that covarying groups of amino acid sites are often identified at critical protein regions [37, 40, 47–52]. Second, covarying amino acid sites identified in this study are part of networks that correspond to structural clusters, that is, these sites fall close to each other in the protein structure. In conclusion, the low number of sites identified in our coevolutionary analyses, their structural clustering, and their proximity to functional or proteins interface regions point to their functional or structural importance. This is supported by previous studies indicating that sites coevolving with few others within the protein are likely to represent functional dependencies [49, 53, 54].
Most covarying amino acid sites in GroEL were identified in the equatorial and apical domains and only few sites were located in the intermediate domain. Apical and equatorial domains perform most functions in GroEL. It is remarkable that many of the amino acids from the equatorial domain involved in coevolutionary relationships belong to the most carboxi-terminal GroEL tail. Indeed, the folding of substrates within the central GroEL cavity is favoured by the limited size and hydrophobicity of the cavity [6, 20]. The C-terminal tail of GroEL define the environment within the central cavity of GroEL with regards to its hydrophobicity, which would impact on both the size and nature of the substrate proteins folded by the chaperonin . Collectively, our results uncover a list of amino acid sites that might have profound implications on the functions of GroES and GroEL.
The evolutionary dependencies between GroES and GroEL provide information on the structural consequences of their interaction
Our coevolutionary analyses in GroES and GroEL identified several sets of sites with apparently distinct roles. First, GroES amino acid regions coevolving with residues from GroEL are all located in the interface between the GroES subunits. Second, GroEL residues coevolving with GroES are distributed among the three domains, apical, intermediate and equatorial. In the apical domain, two amino acid residues coevolving with GroES are involved in substrate binding. One site is located at the interface between the two GroEL heptameric rings and may be involved in the stabilization of these domains. Indeed, the folding reaction cycle requires the double ring of GroEL, in which the information passes between the rings to signal the ATP hydrolysis progress in one ring and which causes important conformational changes in the opposite ring [56, 57]. One such change involves the weakening of GroES-GroEL binding, which ends with the binding of an ATP to the opposite ring . The inter-ring amino acid contacts are, therefore, essential for the folding cycle completion and release of GroES from the cis ring once ATP has been bound to the opposite ring. Arguably, coevolution between the interface of the rings and GroES may be the result of the constraints to maintain the structural communication between the two GroEL rings upon the interaction with GroES.
Amino acids coevolution underlies the functional plasticity of GroES and GroEL in bacteria
Our results bring forward the controversial, although intuitive, suggestion that the function of a protein may change across an evolutionary scale leading to a plastic fitness landscape in which constraints on amino acids can vary dramatically. Against the static view of one protein one function, we propose that proteins have the potential to perform many alternative functions. Leaping from one function to another requires the correlated evolution of key amino acids in the protein. GroEL, and its co-chaperonin GroES, offer a unique system to test this hypothesis because, despite its essentiality to the cell, this protein has evolved many alternative functions in other bacteria [21–30]. The performance of alternative functions is dependent on the fixation of mutations in genes. Since amino acids are constrained by their interactions with other amino acids, fixation of mutations at sites with functional relevance must be accompanied by mutations in other sites of the protein through molecular coadaptation dynamics—that is, amino acids that are structurally or functionally linked exercise reciprocal natural selection on one another .
The groups of amino acids identified in the intra-protein and inter-protein coevolution analyses differed between bacterial groups, in good agreement with the apparent difference in functions of GroEL in these bacteria. Groups of coevolving amino acids in one domain of a bacterial group showed statistical and structural independence of that in the same domain from another bacterial group. Many of the coevolution groups found in one bacterial group map to regions of groEL that are known to encode functions alternative to protein folding. Other coevolving amino acids could not be directly mapped to domains with known alternative functions, though their structural proximity to these domains hints potential roles for these sites. Remarkably, the set of amino acid sites involved in an evolutionary dependency in one bacterial group was close in the protein structure to the set of amino acids detected for another bacterial group. In fact, in some cases, the same amino acid was detected as coevolving with different sets of amino acids in two bacterial groups, thereby acting as evolutionary hinges of alternative functional protein sectors. For example, in the intra-GroEL coevolution analysis, Met514 was detected in Actinobacteria and Bacteroidetes, but it was coevolving with different amino acids in these two groups. The general trend was that alternative sets of coevolving sites identified in different bacteria were closely located in the structure. This supports the plausible hypothesis that shifts in the selective constraints on amino acid sites of GroEL are subtle between bacteria, and affect the same structural regions; probably those regions undergoing conformational changes when GroEL interacts with GroES.
To conclude, we provide evidence of the plasticity of the evolutionary relationships between the amino acid sites in an essential protein. We also list a set of coevolving sites that might be worth testing for addressing important questions regarding the functional promiscuity of GroEL and its evolvability under different conditions. Experimental studies aimed at determining the importance of the amino acid sites listed in this study may aid the development of mechanistic models of protein folding in the cell and the evolution of alternative functions from highly conserved ones.
Our results map genetic diversity in GroESL to its functional promiscuity. While different functional sectors in GroESL can be assigned to distinct functions, the overlap in the amino acids sets of these sectors put forward the conclusion that functional leaps in proteins can be driven by subtle sequence compositional differences. Our results highlight the evolutionary plasticity of GroEL across the entire bacterial phylogeny. Evidence on the functional importance of coevolving sites illuminates the as yet unappreciated functional diversity of proteins.
Sequences, alignments and phylogenetic inference
All GroES and GroEL (also known as cpn10 and cpn60, respectively) sequences where downloaded from the OMA browser site (http://omabrowser.org). We used either cpn10 or cpn60 and Rhizobium as keywords. Then we chose the link to the page with the highest number of orthologs, RHIL300891 (Q1MKX3), with 903 orthologs (01/04/2011) for cpn10 and RHIL300890 (CH601_RHIL3), with 870 orthologs (23/03/2011). We removed all eukaryotic and archaeal sequences prior to the analysis. Then, we aligned all sequences using ClustalX2 [60, 61]. The output alignment was manually refined using GeneDoc 2.6  and this new alignment was used to build a neighbor-joining tree with 1000 bootstrap replicates in ClustalX2. The trees were visualized with FigTree 1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/) and all redundant sequences (same amino acidic sequences) were detected and deleted but leaving a representative one. Then, we removed the sequences belonging to duplicated genes within all given species, ending with a final alignment that included 519 sequences for the cpn10 and 505 sequences for the cpn60 (see Table 1). We used CAPS  to analyse the intra-protein coevolution clustering of amino acids for both the cpn10 and cpn60 alignments. For both alignments we used a threshold α value of 0.001, a random sampling of 100000, and a bootstrap value of 100. In addition to these two alignments, we prepared new alignments for those taxonomic groups with at least 10 sequences for both cpn10 and cpn60 proteins (sample sizes in Table 1): Actinobacteria, Bacteroidetes/Chlorobi group, Cyanobacteria, Firmicutes, all Proteobacteria together, and Spirochaetes. In these analyses the bootstrap values were adapted to the sample sizes (20, 80, 100, 20, 10, and 9, respectively).
To conduct coevolution analysis between GroES and GroEL, we built multiple sequence alignments for both of the proteins, which comprised the sequences belonging to the same organismal source (a total of 381 sequences for GroES and GroEL, Table 1). We downloaded the sequences for the crystallized cpn10 and cpn60 proteins of Escherichia coli (PDB ID: 1AON, MMDB ID: 47936) from the NCBI site (http://www.ncbi.nlm.nih.gov/sites/structure) to map the coevolving amino acidic sites detected using CAPS in the protein structure. Since the output amino acidic sites detected by CAPS correspond to the position in the input alignment, which included gaps, we wrote a script in C++ (Microsoft Visual C++ Standard Edition 6.0, available from authors upon request) to identify the coevolving sites in the sequence of the published structure of the protein. The networks of coevolving amino acids were performed using Cytoscape 2.8.2 . The crystal structure of GroESL complex was represented using the software imol (P. Rotkiewicz, http://www.pirx.com/iMol/index.shtml).
Coevolution analyses, that is the correlated variation of two amino acid sites throughout the multiple sequence alignment, was performed using a previously published coevolution method  implemented in the program CAPS . Other Mutual Information methods were used as well but their performance was significantly poorer, providing large sets of sites and false positive results in agreement with a previous study . Briefly, this method estimates how correlated is the evolutionary variability at two sites of the same or different protein-coding multiple sequence alignments. To account for the strength of the amino acids transitions in a site, the BLOSUM score of amino acid transitions of a site between two sequences was corrected by the time since the divergence of the two sequences compared. Time of divergence was calculated using the Li’s corrected synonymous nucleotide substitutions. Phylogenetic artifacts—phylogeny asymmetries, long-branch attractions, and unequal codon and base composition biases among the bacterial clades—were accounted for by conducting the same coevolution analyses in a set of neutrally evolving simulated alignments, which bear the same evolutionary features as the real sequence alignments. A pair of sites was considered to coevolve if the probability of their correlation coefficient was lower than 0.001 when compared to the null distribution of such coefficients drawn from the simulated sequence alignments. Moreover, to identify coevolving pairs of sites that may be functionally or structurally linked across the bacterial phylogeny, we conducted non-parametric bootstrap analyses of covariation (see next section).
Bootstrapping the pairs of coevolving sites
In this study, we have devised a new method to determine the reliability of a coevolution pair of amino acid sites. This test is based upon the assumption that pairs of sites involved in important functional roles within a phylogenetic group should be inextricably linked between each other with regards to their evolutionary patterns, such that the two sites of the pair should be evolutionarily dependent on one another through their reciprocal natural selection. That is, a change in one amino acid should be accompanied by a compensatory (coadaptive) change in its coevolving amino acid partner. Making the inverse rationale, pairs of amino acid sites that are consistently detected as coevolving in a phylogenetic context should be functionally related.
For each of the pairs of amino acid sites detected in our coevolutionary analyses, we performed a non-parametric bootstrapping, that is we randomly sampled sequences from the phylogenetic tree, performed the coevolutionary analyses for those sampled sequences using CAPS and, then, checked whether a particular pair of sites detected in the real coevolutionary analyses was also detected in this new sampled dataset. We replicated this procedure a 1000 times and, then, asked how many times each of the pairs of sites detected as coevolving in the real multiple sequence alignments was detected as significantly supporting coevolution. Those pairs that were identified in more than 70% of the phylogenetic random samples were deemed as consistently coevolving amino acid sites.
Measuring statistical independence of coevolutionary groups among bacteria
Here is the frequency of the most represented amino acid (a) in each of the sites under coevolution (i, j, …, S) within the group. This frequency is compared to the frequency of the amino acid (a) in all the proteins (q (a) ).
To determine the significance of the difference between both sides of equation 4, we built 1000 groups, each with the same size as the coevolution group; then, we estimated I S(g1) and I S(g2) , and compared this to I S(g1,g2) .
This study was supported by Science Foundation Ireland (10/RFP/GEN2685) and a grant from the Ministerio de Ciencia e Innovación (BFU2009-12022) to MAF. MXRG is supported by the JAE DOC-2009, Ministerio de Ciencia e Innovación. We thank two anonymous reviewers for useful comments to improve this study presentation.
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