ABSTRACT
Almost a century ago, Wittgenstein pointed out that theory in science is intricately connected to language. This connection is not a frequent topic in the genomics literature. But a case can be made that functional genomics is today hindered by the paradoxes that Wittgenstein identified. If this is true, until these paradoxes are recognized and addressed, functional genomics will continue to be limited in its ability to extrapolate information from genomic sequences.
Subject(s)
Computational Biology/methods , Evolution, Molecular , Proteins/chemistry , Proteins/metabolism , Amino Acid Sequence , Animals , Genomics , Humans , Linguistics , Molecular Sequence Data , Phylogeny , Proteins/genetics , Sequence Alignment , Substrate SpecificityABSTRACT
The divergent evolution of protein sequences from genomic databases can be analyzed by the use of different mathematical models. The most common treat all sites in a protein sequence as equally variable. More sophisticated models acknowledge the fact that purifying selection generally tolerates variable amounts of amino acid replacement at different positions in a protein sequence. In their "stationary" versions, such models assume that the replacement rate at individual positions remains constant throughout evolutionary history. "Nonstationary" covarion versions, however, allow the replacement rate at a position to vary in different branches of the evolutionary tree. Recently, statistical methods have been developed that highlight this type of variation in replacement rates. Here, we show how positions that have variable rates of divergence in different regions of a tree ("covarion behavior"), coupled with analyses of experimental three-dimensional structures, can provide experimentally testable hypotheses that relate individual amino acid residues to specific functional differences in those branches. We illustrate this in the elongation factor family of proteins as a paradigm for applications of this type of analysis in functional genomics generally.
Subject(s)
Evolution, Molecular , Peptide Elongation Factor 1/physiology , Peptide Elongation Factor Tu/physiology , Amino Acid Sequence , Animals , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/physiology , Binding Sites , Computer Simulation , Fungal Proteins/chemistry , Fungal Proteins/genetics , Fungal Proteins/physiology , Humans , Insect Proteins/chemistry , Insect Proteins/genetics , Insect Proteins/physiology , Models, Genetic , Models, Molecular , Molecular Sequence Data , Peptide Elongation Factor 1/chemistry , Peptide Elongation Factor 1/genetics , Peptide Elongation Factor Tu/chemistry , Peptide Elongation Factor Tu/genetics , Phylogeny , Plant Proteins/chemistry , Plant Proteins/genetics , Plant Proteins/physiology , Protein Conformation , Protozoan Proteins/chemistry , Protozoan Proteins/genetics , Protozoan Proteins/physiology , Sequence Alignment , Sequence Homology, Amino Acid , Species Specificity , Structure-Activity RelationshipABSTRACT
The soybean genome hosts a family of several hundred, relatively homogeneous copies of a large, copia/Ty1-like retroelement designated SIRE-1. A copy of this element has been recovered from a Glycine max genomic library. DNA sequence analysis of two SIRE-1 subclones revealed that SIRE-1 contains a long, uninterrupted, ORF between the 3' end of the pol ORF and the 3' long terminal repeat (LTR), a region that harbors the env gene in retroviral genomes. Conceptual translation of this second ORF produces a 70-kDa protein. Computer analyses of the amino acid sequence predicted patterns of transmembrane domains, alpha-helices, and coiled coils strikingly similar to those found in mammalian retroviral envelope proteins. In addition, a 65-residue, proline-rich domain is characterized by a strong amino acid compositional bias virtually identical to that of the 60-amino acid, proline-rich neutralization domain of the feline leukemia virus surface protein. The assignment of SIRE-1 to the copia/Ty1 family was confirmed by comparison of the conceptual translation of its reverse transcriptase-like domain with those of other retroelements. This finding suggests the presence of a proretrovirus in a plant genome and is the strongest evidence to date for the existence of a retrovirus-like genome closely related to copia/Ty1 retrotransposons.
