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PubMed2003

Intimate evolution of proteins. Proteome atomic content correlates with genome base composition.

Discerning the significant relations that exist within and among genome sequences is a major step toward the modeling of biopolymer evolution. Here we report the systematic analysis of the atomic composition of proteins encoded by organisms representative of each kingdoms. Protein atomic contents are shown to vary largely among species, the larger variations being observed for the main architectural component of proteins, the carbon atom. These variations apply to the bulk proteins as well as to subsets of ortholog proteins. A pronounced correlation between proteome carbon content and genome base composition is further evidenced, with high G+C genome content being related to low protein carbon content. The generation of random proteomes and the examination of the canonical genetic code provide arguments for the hypothesis that natural selection might have driven genome base composition.

Animals↗
PubMed2000

Adaptive evolution of relish, a Drosophila NF-kappaB/IkappaB protein.

NF-kappaB and IkappaB proteins have central roles in regulation of inflammation and innate immunity in mammals. Homologues of these proteins also play an important role in regulation of the Drosophila immune response. Here we present a molecular population genetic analysis of Relish, a Drosophila NF-kappaB/IkappaB protein, in Drosophila simulans and D. melanogaster. We find strong evidence for adaptive protein evolution in D. simulans, but not in D. melanogaster. The adaptive evolution appears to be restricted to the IkappaB domain. A possible explanation for these results is that Relish is a site of evolutionary conflict between flies and their microbial pathogens.

Adaptation, Biological↗
PubMed1999

Evolution of protein sequences and structures.

The relationship between sequence similarity and structural similarity has been examined in 36 protein families with five or more diverse members whose structures are known. The structural similarity within a family (as determined with the DALI structure comparison program) is linearly related to sequence similarity (as determined by a Smith-Waterman search of the protein sequences in the structure database). The correlation between structural similarity and sequence similarity is very high; 18 of the 36 families had linear correlation coefficients r>/=0.878, and only nine had correlation coefficients r</=0.815. Inclusion of higher-order terms in the structure/sequence relationship improved the fit by less than 7% in 27 of the 36 families. Differences in sequence/structure correlations are distributed evenly among the four protein structural classes, alpha, beta, alpha/beta, and alpha+beta. While most protein families show high correlations between sequence similarity and structural similarity, the amount of structural change per sequence change, i.e. the structural mutation sensitivity, varies almost fourfold. Protein families with high and low structural mutation sensitivity are distributed evenly among protein structure classes. In addition, we did not detect strong correlations between structural mutation sensitivity and either protein family mutation rates or protein size. Our results are more consistent with models of protein structure that encode a protein family's fold throughout the protein sequence, and not just in a few critical residues.

Amino Acid Sequence↗
PubMed2003

More than the sum of their parts: on the evolution of proteins from peptides.

Despite their seemingly endless diversity, proteins adopt a limited number of structural forms. It has been estimated that 80% of proteins will be found to adopt one of only about 400 folds, most of which are already known. These folds are largely formed by a limited 'vocabulary' of recurring supersecondary structure elements, often by repetition of the same element and, increasingly, elements similar in both structure and sequence are discovered. This suggests that modern proteins evolved by fusion and recombination from a more ancient peptide world and that many of the core folds observed today may contain homologous building blocks. The peptides forming these building blocks would not in themselves have had the ability to fold, but would have emerged as cofactors supporting RNA-based replication and catalysis (the 'RNA world'). Their association into larger structures and eventual fusion into polypeptide chains would have allowed them to become independent of their RNA scaffold, leading to the evolution of a novel type of macromolecule: the folded protein.

Animals↗
PubMed1976

The origin and evolution of protein superfamilies.

The organization of proteins into superfamilies based primarily on their sequences is introduced: examples are given of the methods used to cluster the related sequences and to elucidate the evolutionary history of the corresponding genes within each superfamily. Within the framework of this organization, the amount of sequence information currently and potentially available in all living forms can be discussed. The 116 superfamilies already sampled reflect possibly 10% of the total number. There are related proteins from many species in all of these superfamilies, suggesting that the origin of a new superfamily is rare indeed. The proteins so far sequenced are so rigorously conserved by the evolutionary process that we would expect to recognize as related descendants of any protein found in the ancestral vertebrate. The evolutionary history of the thyrotropin-gonadotropin beta chain superfamily is discussed in detail as an example. Some proteins are so constrained in structure that related forms can be recognized in prokaryotes and eukaryotes. Evolution in these superfamilies can be traced back close to the origin of life itself. From the evolutionary tree of the c-type cytochromes the identity of the prokaryote types involved in the symbiotic origin of mitochondria and chloroplasts begins to emerge.

Amino Acid Sequence↗
PubMed2000

The proteins of linked genes evolve at similar rates.

Much more variation in the rate of protein evolution occurs than is expected by chance. But why some proteins evolve rapidly but others slowly is poorly resolved. It was proposed, for example, that essential genes might evolve slower than dispensable ones, but this is not the case; and despite earlier claims, rates of evolution do not correlate with amino-acid composition. A few patterns have been found: proteins involved in antagonistic co-evolution (for example, immune genes, parasite antigens and reproductive conflict genes) tend to be rapidly evolving, and there is a correlation between the rate of protein evolution and the mutation rate of the gene. Here we report a new highly statistically significant predictor of a protein's rate of evolution, and show that linked genes have similar rates of protein evolution. There is also a weaker similarity of rates of silent site evolution (see ref. 13), which appears to be, in part, a consequence of the similarity in rates of protein evolution. The similarity in rates of protein evolution is not a consequence of underlying mutational patterns. A pronounced negative correlation between the rate of protein evolution and a covariant of the recombination rate indicates that rates of protein evolution possibly reflect, in part, the local strength of stabilizing selection.

Animals↗
PubMed2002

Evolution of protein structures and functions.

Within the ever-expanding repertoire of known protein sequences and structures, many examples of evolving three-dimensional structures are emerging that illustrate the plasticity and robustness of protein folds. The mechanisms by which protein folds change often include the fusion of duplicated domains, followed by divergence through mutation. Such changes reflect both the stability of protein folds and the requirements of protein function.

Amino Acid Motifs↗
PubMed2006

Protein superfamily evolution and the last universal common ancestor (LUCA).

By exploiting three-dimensional structure comparison, which is more sensitive than conventional sequence-based methods for detecting remote homology, we have identified a set of 140 ancestral protein domains using very restrictive criteria to minimize the potential error introduced by horizontal gene transfer. These domains are highly likely to have been present in the Last Universal Common Ancestor (LUCA) based on their universality in almost all of 114 completed prokaryotic (Bacteria and Archaea) and eukaryotic genomes. Functional analysis of these ancestral domains reveals a genetically complex LUCA with practically all the essential functional systems present in extant organisms, supporting the theory that life achieved its modern cellular status much before the main kingdom separation (Doolittle 2000). In addition, we have calculated different estimations of the genetic and functional versatility of all the superfamilies and functional groups in the prokaryote subsample. These estimations reveal that some ancestral superfamilies have been more versatile than others during evolution allowing more genetic and functional variation. Furthermore, the differences in genetic versatility between protein families are more attributable to their functional nature rather than the time that they have been evolving. These differences in tolerance to mutation suggest that some protein families have eroded their phylogenetic signal faster than others, hiding in many cases, their ancestral origin and suggesting that the calculation of 140 ancestral domains is probably an underestimate.

Evolution, Molecular↗
PubMed2002

Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates.

An improved understanding of the evolution of gene function at the molecular level may provide significant insights into the origin of biological novelty and adaptation. With the approach of ancestral protein reconstruction, we here address the question of how a dramatically enhanced ribonucleolytic activity and the related antiviral activity evolved in a recently duplicated ribonuclease (eosinophil-derived neurotoxin) gene of higher primates. We show that the mother gene of the duplicated genes had already possessed a weak antiviral activity before duplication. After duplication, substitutions at two interacting sites (Arg-64-->Ser and Thr-132-->Arg) resulted in a 13-fold enhancement of the ribonucleolytic activity of eosinophil-derived neurotoxin. These substitutions are also necessary for the potent antiviral activity, with contributions from additional amino acid changes at interacting sites. Our observation that a change in eosinophil-derived neurotoxin function occurs only when both interacting sites are altered indicates the importance of complementary substitutions in protein evolution. Thus, neutral substitutions are not simply "noises" in protein evolution, as many have thought. They may play constructive roles by setting the intramolecular microenvironment for further complementary advantageous substitutions, which can lead to improved or altered function. Overall, our study illustrates the power of the "paleomolecular biochemistry" approach in delineating the complex interplays of amino acid substitutions in evolution and in identifying the molecular basis of biological innovation.

Adaptation, Biological↗
PubMed1994

Microbial systems and directed evolution of protein activities.

Recent advances in recombinant DNA methodology have had an important impact on the capacity to manipulate protein-coding sequences. The appearance of new, powerful screening systems completes a scenario for conducting directed evolution experiments. We review here some of the latest developments in experimental approaches to directed evolution, utilizing microbial systems. These include phage display, surface display, operator-repressor systems, and novel mutagenesis approaches. We also highlight the achievements and limitations of current methodologies. We present strategies used by our own group that permitted isolation of specificity mutants of beta-lactamase. Possible improvements for the future of the variation-selection approach to the study and manipulation of proteins are presented.

Bacteria↗
PubMed1999

Evolution of protein function, from a structural perspective.

The recent growth in structural data, and ensuing analyses, have revealed the structural and functional versatility of protein families. With respect to enzymes, local active-site mutations, variations in surface loops and recruitment of additional domains accommodate the diverse substrate specificities and catalytic activities observed within several superfamilies. Conversely, some functions have more than one structural solution, having evolved independently several times during evolution. Combined with the existence of multi-functional genes, which have arisen by gene recruitment, these phenomena must be considered in the process of genome annotation.

Animals↗