Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin, Ireland
Correspondence: E-mail: faresm{at}tcd.ie.
![]() |
Abstract |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Key Words: CCT duplication positive selection functional divergence convergent evolution protein folding
![]() |
Introduction |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Unlike for GroEL, the number of substrates that bind to CCT is small (Kim, Willison, and Horwich 1994), the best characterized interactions being those of tubulins, actins, and a very small number of other proteins (Sternlicht et al. 1993; Kubota, Hynes, and Willison 1995; Hynes et al. 1996; Lewis et al. 1996; Thulasiraman, Yang, and Frydman 1999). Nonetheless, the list of known CCT-substrates continues to growth with the addition of proteins such as luciferase (Frydman et al. 1994), G--transducin (Farr et al. 1997), hepatitis B virus capsid protein (Lingappa et al. 1994), cyclin E (Won et al. 1998), the EBNA1 viral protein (Kashuba et al. 1999), myosin (Srikakulam and Winkelmann 1999), and the tumor-suppressor protein VHL (Feldman et al. 1999). Klumpp, Baumeister, and Essen (1997) suggested that the high flexibility of the CCT apical protrusion would accommodate a wide variety of different substrates.
The specificity of the interaction between CCT subunits and -actins was previously demonstrated by electron microscopy (Llorca et al. 1999a). The description of the interaction between actin and CCT by Llorca et al. (1999a, 2000) and Hynes and Willison (2000) has been refined by McCormack, Rohman, and Willison (2001), who defined the main actin domains that bind to specific CCT subunits. Furthermore, the similarity of actin and tubulin domains that bind to CCT has been demonstrated in several biochemical studies (Hynes and Willison 2000; Llorca et al. 2000; Ritco-Vonsovici and Willison 2000). It has been demonstrated that the small N-terminal domain of actin binds to the CCT
subunit, and the large C-terminal domain binds mainly CCT
but also CCTß (Llorca et al. 1999b; Hynes and Willison 2000). Tubulin establishes two possible binding arrangements, but uses CCTß and CCT
with the highest affinity. In contrast to GroEL, in which substrate-binding sites seem to accommodate many different amino acid sequences by means of hydrophobic interactions (Fenton et al. 1994), there is biochemical evidence that specific subunits of CCT establish nonhydrophobic interactions with their protein substrates (Hynes and Willison 2000). Most interesting is that most of the amino acid differences among CCT subunits reside in the apical domain, which contains the substrate-binding sites (Kim, Willison, and Horwich 1994; Pappenberger et al. 2002), and that the different subunits are positioned in a specific arrangement (Liou and Willison 1997; Llorca et al. 1999a; Grantham et al. 2000). Although the CCT subunits are very divergent from one another, a detailed phylogenetic analysis revealed that each CCT subunit group of sequences can be distinguished by a conserved set of amino acid residue "signatures" located in the three protein domains (Archibald, Blouin, and Doolittle 2001). The existence of these amino acid signatures supports the hypothesis of functional divergence between the different CCT subunits, which was previously suggested by Kubota et al. (1994). Interestingly, some of these slowly evolving amino acid signatures are located in ATP-binding and hydrolysis motifs mapped onto the equatorial domain (Archibald, Logsdon, and Doolittle 2000; Archibald, Blouin, and Doolittle 2001).
Here we demonstrate that functional divergence occurred between the different CCT subunits after each gene duplication event during the early evolution of eukaryotes. This divergence is apparent at the protein level due to the fixation of amino acid replacements in sites involved in ATP binding and in protein binding. In this study, we also demonstrate that CCT subunits that bind actin and those that bind tubulin were subjected to different selective constraints. These evolutionary results integrate with biochemical and structural results to support the model proposed for the interaction of CCT chaperonins with actin and tubulin (Llorca et al. 2001).
![]() |
Material and Methods |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
|
|
Testing the Constancy of Substitution Rates in the Branches Leading to Each CCT Subunit Cluster
To know whether significant amino acid changes occurred in CCT genes after duplication events, the constancy of substitution rates among lineages was tested using the two-cluster test implemented in the LINTREE program (Takezaki, Rzhetski, and Nei 1995). The two-cluster test examines the equality of the average substitution rates for two clusters linked by a node on the phylogenetic tree, using one or several outgroup sequences. The root of the phylogenetic tree for the two-cluster test was established using a subunit sequences from Methanococcus thermolithotrophicus, Thermoplasma acidophilum, and Sulfolobus sulfotaricus.
Detection of Positive Selection in the Different Branches of the Eukaryotic CCT Phylogenetic Tree
To test the hypothesis of variable selective pressures among the different branches of the CCT phylogenetic tree, the free-ratio model was compared with the Goldman and Yang model by the likelihood-ratio test (LRT) (Huelsenbeck and Crandall 1997). This test is based on the fact that the log-likelihood values of two nested models can be compared since twice the log-likelihood difference among the nested models follows a 2 distribution, with the degrees of freedom being the difference between the numbers of free parameters between the models compared. These tests were implemented using the program CODEML from the PAML package version 3.0 (Yang 2000).
The Goldman and Yang (1994) model assumes a single value for the whole phylogenetic tree along the complete sequence alignment, whereas the free-ratio model (Yang 1998) estimates a log-likelihood value assuming a different
value for each branch of the phylogenetic tree. These two models are nested, and, hence, their likelihood values can be compared using the LRT, the number of degrees of freedom being the difference in the number of
values freely estimated between the two models compared. Therefore, for the comparison between the model of Goldman and Yang and the free-ratio model. the number of degrees of freedom is N1, where N is the number of branches in the tree.
Examining Functional Divergence After CCT Gene Duplication
CCT sequence duplication events were tested for type I functional divergence (Wang and Gu 2001) using the method developed by Gu (1999). To implement this procedure, we used the program Diverge, version 1.04 (Gu and Vander Velden 2002; http://xgu1.zool.iastate.edu/cgi-bin/download.cgi). This method uses a maximum-likelihood procedure to estimate whether there has been a significant change in the rate of evolution after the emergence of two paralogs. This is done by calculating a coefficient of functional divergence () and determining whether the value of the coefficient is large enough to reject the null hypothesis of no functional differentiation. If the null hypothesis is rejected, the program calculates a posterior probability for functional divergence for each position in the alignment. We established a cutoff value, according to the effect that the elimination of the sets of amino acids having a posterior probability higher than this cutoff value had on the
value test (see Wang and Gu 2001). To detect the amino acids responsible for significant functional divergence after each gene duplication event, we compared subunits or well-supported groups of subunits to each other and determined the cutoff value above which the difference between the subunits becomes significant.
![]() |
Results |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
|
|
|
The estimation of values for six branches of the phylogenetic tree revealed multiple episodes of positive selection distributed among the different branches leading to several subunits (table 4 and fig. 1). Values of
significantly greater than 1 were obtained for the branch leading to
,
,
, the ß-
group, and the
-
-ß group (table 4).
|
Posterior probabilities were used to identify the most likely codon changes in the branches detected under positive selection. Figure 3A shows the location in the three-dimensional structure of the mouse CCT subunit of amino acid sites that are important for ATP binding and hydrolysis as well as for protein substrate binding. Interestingly, among the amino acid substitutions detected with high posterior probabilities in those branches subject to positive selection, several are positioned in ATP-binding sites and substrate-binding sites (fig. 3B). Some of the substitutions are in sites previously proposed as ATP-binding sites (amino acid positions 31 to 35, 45 to 53, 89 to 91, and 114 to 117 [Kim, Willison, and Horwich 1994]), and others are located in conserved motifs proposed to be involved in protein binding (table 4).
|
To test the significance of the distribution of amino acid substitutions, we conducted a 2 test comparing the observed number of substitutions in ATP-binding sites and substrate-binding sites with the expected number for each branch where positive selection was detected. The Bonferroni corrected probabilities of the observed amino acid substitutions in these sites gave values of 7.11 x 1027, 1.24 x 1015, and 1.52 x 1023, for the branches leading to CCT subunits
,
, and
-
-ß, respectively. Here, we only considered those amino acid substitutions with posterior probabilities higher than 0.90. This result indicates that subunits
,
, and
-
-ß, have acquired new functions or specialized its role by the fixation of amino acid substitutions in regions involved in substrate binding as well as ATP binding. On the other hand, we might expect that if saturation of synonymous sites had occurred, it would be randomly distributed in the gene sequence. This could result in the artifactual discovery of sites that appear to be under positive selection, but these sites should be at random locations. The amino acid positions where positive selection was detected were, however, significantly concentrated in sites involved in ATP and substrate binding.
Detection of Critical Amino Acids for Altered Functional Constraints on CCT Subunits
Functional divergence between genes results from changes in the functional constraints on one of the genes, resulting in high sequence conservation of one paralog in different species, while the other paralog evolves more freely. We analyzed functional divergence using the method of Gu (1999). The maximum-likelihood estimation of the coefficient of functional divergence (), its standard error and its significance for CCT subunit pairwise comparisons are shown in table 5. Significant
values were obtained for the pairwise subunit comparisons as well as for comparisons among different well-supported groups of subunits (table 5), implying that functional divergence between the different subunits is significantly supported by the data. Notably, functional divergence was detected after the duplications that gave CCT subunits ß and
that bind the C-terminal domains of actin and tubulin with the highest affinity compared with the remaining CCT subunits. Critical amino acids for functional divergence were detected by estimating the posterior probability of belonging to an S1 class (see Wang and Gu 2001) for each amino acid in the alignment in each comparison. To detect critical amino acids for type I functional divergence, different posterior-probability cutoff values were used, depending on the subunits or group of subunits compared (table 5). When critical amino acids (amino acids with probabilities higher than the cutoff value) were removed from the alignment, the
value was not significantly different from 0, ranging between 0 and 3.730 (P = 1 and P = 0.053, respectively).
|
Because the scheme of binding C-terminal domains by CCT subunits is more complex than that regarding the binding of the N-terminal domains, we expect functional divergence also between CCT subunits binding different protein domains. To test this hypothesis, we analyzed the functional divergence between the two types of subunits (for example, we compared CCT subunit ß with subunit ). Among the critical amino acids causing functional divergence between actin/tubulin-C-terminalbinding CCT subunits and actin/tubulin-N-terminalbinding CCT subunits, many (amino acid positions 31, 33 to 35, 48, 415, and 516) are identified as involved in ATP binding or in substrate binding (amino acid positions 222, 223, 244, 298, 316 to 318, and 358) (fig. 3C), also detected by the likelihood-based free-ratio model (fig. 3B).
The pairwise comparison of CCT subunits as well as the comparison between subunits able to bind either the N-terminal domains or the C-terminal domains of actin and tubulin show that functional divergence has occurred at amino acid sites important for both substrate binding and ATP binding.
![]() |
Discussion |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
The obvious question that arises here is whether these duplication events meant the acquisition of new functions (neofunctionalization) by each CCT subunit (for example to provide a broader specificity of substrate recognition) or whether a coevolutionary process occurred between several CCT subunits to accommodate a unique function in substrate binding while each of the others subunits maintained its old function (subfunctionalization). In the former case, we might expect to see functional divergence between the different subunits and no correlation in the amino acid sites at which positive selection is detected. In the latter case, however, although functional divergence might also be detected between CCT subunits, a correlation might be expected in the selective constraints on subunits involved in the same function, as was seen here. It is straightforward to hypothesize that, given the close physical contact between the different CCT subunits in each ring, all the subunits may have to coevolve to optimize substrate binding.
The significant acceleration in the rates of amino acid replacements detected by the two-cluster test in the lineages leading to the -ß-
group and in the lineage leading to subunit
suggests functional divergence after the duplications that gave rise to these subunits. The detection of positive selection in branches leading to different CCT subunits after many gene duplication events also suggests functional divergence.
Our detection of positive selection in different lineages agrees with CCT subunit-substrate interaction model suggested by Llorca et al. (2001). In fact, we have shown that positive selection has occurred in the branches leading to CCT subunits involved exclusively in tubulin binding (,
, and
) but not in those also involved in actin binding (
and
). This suggests that the initial capability of CCT to bind proteins was restricted to a very simple model and that the duplication events gave rise to CCT subunits able to bind tubulin in a more complex and specialized way. In addition, functional divergence was detected between CCT subunits proposed to bind the N-terminal domain of actin and tubulin and those that bind the C-terminal domains of the proteins. These results agree with biochemical studies that corroborated the similarity of the domains of actin and tubulin involved in binding to specific CCT subunits (Hynes and Willison 2000; Llorca et al. 2000; Ritco-Vonsovici and Willison 2000).
Two main evolutionary scenarios can be drawn from the results obtained in this work. The first result implies a specialization of CCT subunits in binding a specific protein by the fixation of amino acid substitutions by positive selection in the CCT subunit binding tubulin. On the other hand, the functional divergence between subunits involved in binding differentially N-terminal and C-terminal domain indicates a subfunctionalization of the different CCT subunits.
When amino acid substitutions were examined in those branches found to be under positive selection, we found that amino acid positions under positive selection coincided between the branches leading to CCT subunits involved in binding tubulin (fig. 3A and B), suggesting functional convergence in the amino acid composition of these subunit regions. Interestingly, amino acid residues involved in substrate binding or ATP hydrolysis are highly hydrophilic (nine amino acid changes [see Results]) in all the branches in which positive selection was detected, except in the branch (branch D) leading to the CCT subunit, which showed a higher fixation of hydrophobic amino acids in different regions of the apical domain without significant concentration in substrate-binding sites or ATP-binding sites. These results suggest that the interaction between CCT subunits and their substrates is through hydrophilic amino acids, which is in agreement with structural analysis of the apo-CCT
-actin complexes, which raised the possibility that CCT may not be using amino acids located in the hydrophobic groove of the apical domain to bind to its substrates (Llorca et al. 1999a). Archibald et al. (2001) also highlighted the fact that many conserved amino acid motifs in the apical domain are mainly composed of charged residues. Their conclusions, together with our results, put forward the conclusion that CCTs interact with their protein substrates through a different mechanism than does GroEL chaperonin in prokaryotic cells. Interestingly, many of the amino acid residues detected under positive selection are located in or close to regions involved in ATP binding or hydrolysis. As noted by Archibald, Blouin, and Doolittle (2001), ATP hydrolysis or binding motifs include amino acid signatures that distinguish CCT subunit groups from one another. Therefore, these amino acid sites are very likely involved in the functional divergence among the different CCT subunits.
The analysis of functional divergence between the different subunits demonstrate that amino acids that are critical for functional divergence between subunits are also involved in ATP as well as substrate binding (fig. 3C). Additionally, when subunit pairwise comparisons were carried out between subunits involved in binding the N-terminal and those involved in binding the C-terminal domains of actin and tubulin, several but not all of the amino acids involved in substrate binding were also detected to be critical for the functional divergence between these CCT subunits. We would expect that strong functional constraints on the amino acid sites involved in ATP binding and substrate binding occurred as noted by Archibald, Blouin, and Doolittle (2001). Therefore, amino acid replacements in these sites might imply an optimization of the function, a neofunctionalization or, alternatively, a subfunctionalization. The high convergence in the selective constraints between CCT subunits involved in binding tubulin and the C-terminal domains gives support to the hypothesis of subfunctionalization after the CCT duplication events and agrees with the model proposed by Llorca et al. (2001) for substrate binding by CCT chaperonins.
![]() |
Acknowledgements |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
![]() |
Footnotes |
---|
![]() |
Literature Cited |
---|
![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
---|
Akashi, H. 1999. Within- and between-species DNA sequence variation and the "footprint" of natural selection. Gene 238:39-51.[CrossRef][ISI][Medline]
Archibald, J. M., C. Blouin, and W. F. Doolittle. 2001. Gene duplication and the evolution of group II chaperonins: implications for structure and function. J. Struct. Biol. 135:157-169.[CrossRef][ISI][Medline]
Archibald, J. M., J. M. Logsdon, and W. F. Doolittle. 2000. Origin and evolution of eukaryotic chaperonins: phylogenetic evidence for ancient duplications in CCT genes. Mol. Biol. Evol. 17:1456-1466.
Bukau, B., and A. L. Horwich. 1998. The hsp70 and hsp60 chaperone machines. Cell 92:351-366.[ISI][Medline]
Crandall, K. A., C. R. Kelsey, H. Imanichi, H. C. Lane, and N. P. Salzman. 1999. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol. Biol. Evol. 16:372-382.[Abstract]
Ditzel, L., J. Lowe, D. Stock, K. O. Stetter, H. Huber, and R. Huber. 1998. Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT. Cell 93:125-138.[ISI][Medline]
Ellis, R. J., and F. U. Hartl. 1999. Principles of protein folding in the cellular environment. Curr. Opin. Struct. Biol. 9:102-110.[CrossRef][Medline]
Farr, G. W., E. C. Scharl, R. J. Schumacher, S. Sondek, and A. L. Horwich. 1997. Chaperonin-mediated folding in the eukaryotic cytosol proceeds through rounds of release of native and nonnative forms. Cell 89:927-937.[ISI][Medline]
Feldman, D. E., V. Thulasiraman, R. G. Ferreyra, and J. Frydman. 1999. Formation of the VHL-elongin BC tumor suppressor complex is mediated by the chaperonin TRiC. Mol. Cell 4:1051-1061.[ISI][Medline]
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.[ISI][Medline]
Felsenstein, J. 1993. PHYLIP (phylogeny inference package). Version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle.
Feng, D. F., and R. F. Doolittle. 1997. Converting amino acid alignment scores into measures of evolutionary time: a simulation study of various relationships. J. Mol. Evol. 44:361-370.[ISI][Medline]
Fenton, W. A., Y. Kashi, K. Frutak, and A. L. Horwich. 1994. Residues in chaperonin GroEL required for polypeptide binding and release. Nature 371:614-619.[CrossRef][ISI][Medline]
Fitch, W. M. 1971. Towards defining the course of evolution: minimum change for a specific tree topology. Syst. Zool. 20:406-416.[ISI]
Frydman, J., E. Nimmesgern, K. Ohtsuka, and F. U. Hartl. 1994. Folding of nascent polypeptide chains in a high molecular mass assembly with molecular chaperones. Nature 370:111-117.[CrossRef][ISI][Medline]
Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
Grantham, J., O. Llorca, J. M. Valpuesta, and K. R. Willison. 2000. Partial occlusion of both cavities of the eukaryotic chaperonin with antibody has no effect upon the rates of beta-actin or alpha-tubulin folding. J. Biol. Chem. 275:4587-4591.
Gu, X. 1999. Statistical methods for testing functional divergence after gene duplication. Mol. Biol. Evol. 16:1664-1674.
Gu, X., and K. Vander Velden. 2002. Diverge: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 18:500-501.
Gu, X., and J. Zhang. 1997. A simple method for estimating the parameter of substitution rate variation among sites. Mol. Biol. Evol. 14:1106-1113.[Abstract]
Gutsche, I., L. O. Essen, and W. Baumeister. 1999. Group II chaperonins: new TRIC(k)s and turns of a protein folding machine. J. Mol. Biol. 293:295-312.[CrossRef][ISI][Medline]
Gutsche, I., O. Mihalache, R. Hegerl, D. Typke, and W. Baumeister. 2000. ATPase cycle controls the conformation of an archaeal chaperonin as visualized by cryo-electron microscopy. FEBS Lett. 477:278-282.[CrossRef][ISI][Medline]
Huelsenbeck, J. P., and K. A. Crandall. 1997. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu. Rev. Ecol. Syst. 28:437-466.[CrossRef][ISI]
Hynes, G., J. E. Celis, V. A. Lewis, A. U. S. Carne, J. B. Lauridsen, and K. R. Willison. 1996. Analysis of chaperonin-containing TCP-1 subunits in the human keratinocyte two-dimensional protein database: further characterisation of antibodies to individual subunits. Electrophoresis 17:1720-1727.[ISI][Medline]
Hynes, G. M., and K. R. Willison. 2000. Individual subunits of the eukaryotic cytosolic chaperonin mediate interactions with binding sites located on subdomains of ß-actin. J. Biol. Chem. 275:18985-18994.
Kashuba, E., K. Pokrovskaja, G. Klein, and L. Szekely. 1999. Epstein-Barr virus-encoded nuclear protein EBNA-3 interacts with the epsilon-subunit of the T-complex protein 1 chaperonin complex. J. Hum. Virol. 2:33-37.[ISI][Medline]
Kim, S., K. R. Willison, and A. L. Horwich. 1994. Cystosolic chaperonin subunits have a conserved ATPase domain but diverged polypeptide-binding domains. Trends Biochem. Sci. 19:543-548.[CrossRef][ISI][Medline]
Klumpp, M., W. Baumeister, and L. O. Essen. 1997. Structure of the substrate binding domain of the thermosome, an archaeal group II chaperonin. Cell 91:263-270.[ISI][Medline]
Kubota, H., G. Hynes, A. Carne, A. Ashworth, and K. Willison. 1994. Identification of six Tcp-1-related genes encoding divergent subunits of the TCP-1-containing chaperonin. Curr. Biol. 4:89-99.[ISI][Medline]
Kubota, H., G. Hynes, and K. Willison. 1995. The chaperonin containing t-complex polypeptide 1 (TCP-1): multisubunit machinery assisting in protein folding and assembly in the eukaryotic cytosol. Eur. J. Biochem. 230:3-16.[Abstract]
Kumar, S., K. Tamura, and M. Nei. 1993. MEGA (molecular evolutionary genetics analysis). Version 1.01. Distributed by the authors, The Pennsylvania State University, University Park.
Lewis, S. A., G. Tian, I. E. Vainberg, and N. J. Cowan. 1996. Chaperonin-mediated folding of actin and tubulin. J. Cell Biol. 132:1-4.[ISI][Medline]
Li, W.-H., Z. Gu, H. Wang, and A. Nekrutenko. 2001. Evolutionary analyses of the human genome. Nature 409:847-849.[CrossRef][ISI][Medline]
Lingappa, J. R., R. L. Martin, M. L. Wong, D. Ganem, W. J. Welch, and V. R. Lingappa. 1994. A eukaryotic cytosolic chaperonin is associated with a high molecular weight intermediate in the assembly of hepatitis B virus capsid, a multimeric particle. J. Cell Biol. 125:99-111.[Abstract]
Liou, A. K., and K. R. Willison. 1997. Elucidation of the subunit orientation in CCT (chaperonin containing TCP1) from the subunit composition of CCT micro-complexes. EMBO J. 16:4311-4316.
Llorca, O., J. Martin-Benito, J. Grantham, M. Ritco-Vonsovici, K. R. Willison, J. L. Carrascosa, and J. M. Valpuesta. 2001. The sequential allosteric ring mechanism in the eukaryotic chaperonin-assisted folding of actin and tubulin. EMBO J. 20:4065-4075.
Llorca, O., J. Martin-Benito, M. Ritco-Vonsovici, J. Grantham, G. M. Hynes, K. R. Willison, J. L. Carrascosa, and J. M. Valpuesta. 2000. Eukaryotic chaperonin CCT stabilizes actin and tubulin folding intermediates in open quasi-native conformations. EMBO J. 19:5971-5979.
Llorca, O., E. A. McCormack, G. Hynes, J. Grantham, J. Cordell, J. L. Carrascosa, K. R. Willison, J. J. Fernandez, and J. M. Valpuesta. 1999a. Eukaryotic type II chaperonin CCT interacts with actin through specific subunits. Nature 402:693-696.[CrossRef][ISI][Medline]
Llorca, O., M. G. Smyth, J. L. Carrascosa, K. R. Willison, M. Radermacher, S. Steinbacher, and J. M. Valpuesta. 1999b. 3D reconstruction of the ATP-bound form of CCT reveals the asymmetric folding conformation of a type II chaperonin. Nat. Struct. Biol. 6:639-642.[CrossRef][ISI][Medline]
Llorca, O., M. G. Smyth, S. Marco, J. L. Carrascosa, K. R. Willison, and J. M. Valpuesta. 1998. ATP binding induces large conformational changes in the apical and equatorial domains of the eukaryotic chaperonin containing TCP-1 complex. J. Biol. Chem. 273:10091-10094.
Lynch, M., and J. S. Conery. 2000. The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
McCormack, E. A., M. J. Rohman, and K. R. Willison. 2001. Mutational screen identifies critical amino acid residues of beta-actin mediating interaction between its folding intermediates and eukaryotic cytosolic chaperonin CCT. J. Struct. Biol. 135:185-197.[CrossRef][ISI][Medline]
Nicholas, K. B., and H. B. Nicholas. 1997. GENEDOC. Distributed by the author (www.cris.com/ketchup/genedoc.shtml).
Nitsch, M., J. Walz, D. Typke, M. Klumpp, L. O. Essen, and W. Baumeister. 1998. Group II chaperonin in an open conformation examined by electron tomography. Nat. Struct. Biol. 5:855-857.[CrossRef][ISI][Medline]
Pappenberger G., J. A. Wilsher, S. M. Roe, D. J. Counsell, K. R. Willison, and L. H. Pearl. 2002. Crystal structure of the CCT apical domain: implications for substrate binding to the eukaryotic cytosolic chaperonin. J. Mol. Biol. 318:1367-1379.[CrossRef][ISI][Medline]
Ritco-Vonsovici, M., and K. R. Willison. 2000. Defining the eukaryotic cytosolic chaperonin-binding sites in human tubulins. J. Mol. Biol. 304:81-98.[CrossRef][ISI][Medline]
Saitou, N., and M. Nei. 1987. The Neighbor-Joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.[Abstract]
Schoehn, G., M. Hynes, M. Cliff, A. R. Clark, and H. R. Saibil. 2000a. Domain rotations between open, closed and bullet-shaped forms of the thermosome, an archaeal chaperonin. J. Mol. Biol. 301:323-332.[CrossRef][ISI][Medline]
Schoehn, G., E. Quaite-Randall, J. L. Jimenez, A. Joachimiak, and H. R. Saibil. 2000b. Three conformations of an archaeal chaperonin, TF55 from Sulfolobus shibatae. J. Mol. Biol. 296:813-819.[CrossRef][ISI][Medline]
Sharp, P. M. 1997. In search of molecular Darwinism. Nature 385:111-112.[Medline]
Srikakulam, R., and D. A. Winkelmann. 1999. Myosin II folding is mediated by a molecular chaperonin. J. Biol. Chem. 274:27265-27273.
Sternlicht, H., G. W. Farr, M. L. Sternlicht, J. K. Driscoll, and K. Willison. 1993. The t-complex polypeptide 1 complex is a chaperonin for tubulin and actin in vivo. Proc. Natl. Acad. Sci. USA 90:9422-9426.[Abstract]
Takezaki, N., A. Rzhetsky, and M. Nei. 1995. Phylogenetic test of the molecular clock and linearized tree. Mol. Biol. Evol. 12:823-833.[Abstract]
Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.[Abstract]
Thulasiraman, V., C. F. Yang, and J. Frydman. 1999. In vivo newly translated polypeptides are sequestered in a protected folding environment. EMBO J. 18:85-95.
Wang, Y., and X. Gu. 2001. Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction. Genetics 158:1311-1320.
Willison, K. R. 1999. Molecular chaperones and folding catalysts: composition and function of the eukaryotic cytosolic chaperonin containing TCP1. Pp. 555571 in B. Bukau, ed. Regulation, cellular functions and mechanisms. Harwood Academic Publishers, Amsterdam.
Won, K. A., R. J. Schumacher, G. W. Farr, A. L. Horwich, and S. I. Reed. 1998. Maturation of human cyclin E requires the function of eukaryotic chaperonin CCT. Mol. Cell Biol. 18:7584-7589.
Yang, Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15:568-573.[Abstract]
Yang, Z. 2000. Phylogenetic analysis by maximum likelihood (PAML). Version 3. University College London. London.
Zhang, J., H. F. Rosenberg, and M. Nei. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. USA 95:3708-3713.