Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

An efficient means for generating mutation data matrices from large numbers of protein sequences is presented here. By means of an approximate peptide-based sequence comparison algorithm, the set sequences are clustered at the 85% identity level. The closest relating pairs of sequences are aligned, and observed amino acid exchanges tallied in a matrix. The raw mutation frequency matrix is processed in a similar way to that described by Dayhoff et al. (1978), and so the resulting matrices may be easily used in current sequence analysis applications, in place of the standard mutation data matrices, which have not been updated for 13 years. The method is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fast enough to generate a matrix from a specific family or class of proteins in minutes. Differences observed between our 250 PAM mutation data matrix and the matrix calculated by Dayhoff et al. are briefly discussed.

The rapid generation of mutation data matrices from protein sequences

Hidden markov models in computational biology: applications to protein modeling

With the polymerase chain reaction (PCR) and versatile primers that amplify the whole cytochrome b gene (approximately 1140 bp), we obtained 17 complete gene sequences representing three orders of hoofed mammals (ungulates) and dolphins (cetaceans). The fossil record of some ungulate lineages allowed estimation of the evolutionary rates for various components of the cytochrome b DNA and amino acid sequences. The relative rates of substitution at first, second, and third positions within codons are in the ratio 10 to 1 to at least 33. For deep divergences (greater than 5 million years) it appears that both replacements and silent transversions in this mitochondrial gene can be used for phylogenetic inference. Phylogenetic findings include the association of (1) cetaceans, artiodactyls, and perissodactyls to the exclusion of elephants and humans, (2) pronghorn and fallow deer to the exclusion of bovids (i.e., cow, sheep, and goat), (3) sheep and goat to the exclusion of other pecorans (i.e., cow, giraffe, deer, and pronghorn), and (4) advanced ruminants to the exclusion of the chevrotain and other artiodactyls. Comparisons of these cytochrome b sequences support current structure-function models for this membrane-spanning protein. That part of the outer surface which includes the Qo redox center is more constrained than the remainder of the molecule, namely, the transmembrane segments and the surface that protrudes into the mitochondrial matrix. Many of the amino acid replacements within the transmembrane segments are exchanges between hydrophobic residues (especially leucine, isoleucine, and valine). Replacement changes at first and second positions of codons approximate a negative binomial distribution, similar to other protein-coding sequences. At four-fold degenerate positions of codons, the nucleotide substitutions approximate a Poisson distribution, implying that the underlying mutational spectrum is random with respect to position.

Evolution of the cytochrome b gene of mammals.

G protein-coupled receptor kinases (GRKs) constitute a family of six mammalian serine/threonine protein kinases that phosphorylate agonist-bound, or activated, G protein-coupled receptors (GPCRs) as their primary substrates. GRK-mediated receptor phosphorylation rapidly initiates profound impairment of receptor signaling, or desensitization. This review focuses on the regulation of GRK activity by a variety of allosteric and other factors: agonist-stimulated GPCRs, beta gamma subunits of heterotrimeric GTP-binding proteins, phospholipid cofactors, the calcium-binding proteins calmodulin and recoverin, posttranslational isoprenylation and palmitoylation, autophosphorylation, and protein kinase C-mediated GRK phosphorylation. Studies employing recombinant, purified proteins, cell culture, and transgenic animal models attest to the general importance of GRKs in regulating a vast array of GPCRs both in vitro and in vivo.

G protein-coupled receptor kinases.

The relationships among 153 EF-hand (calcium-modulated) proteins of known amino acid sequence were determined using the method of maximum parsimony. These proteins can be ordered into 12 distinct subfamilies--calmodulin, troponin C, essential light chain of myosin, regulatory light chain, sarcoplasmic calcium binding protein, calpain, aequorin, Stronglyocentrotus purpuratus ectodermal protein, calbindin 28 kd, parvalbumin, alpha-actinin, and S100/intestinal calcium-binding protein. Eight individual proteins--calcineurin B from Bos, troponin C from Astacus, calcium vector protein from Branchiostoma, caltractin from Chlamydomonas, cell-division-cycle 31 gene product from Saccharomyces, 10-kd calcium-binding protein from Tetrahymena, LPS1 eight-domain protein from Lytechinus, and calcium-binding protein from Streptomyces--are tentatively identified as unique; that is, each may be the sole representative of another subfamily. We present dendrograms showing the relationships among the subfamilies and uniques as well as dendrograms showing relationships within each subfamily. The EF-hand proteins have been characterized from a broad range of organismal sources, and they have an enormous range of function. This is reflected in the complexity of the dendrograms. At this time we urge caution in assigning a simple scheme of gene duplications to account for the evolution of the 600 EF-hand domains of known sequence.

Evolution of EF-hand calcium-modulated proteins. I. Relationships based on amino acid sequences

The EF-hand family of calcium-modulated proteins.

In the first report in this series we described the relationships and evolution of 152 individual proteins of the EF-hand subfamilies. Here we add 66 additional proteins and define eight (CDC, TPNV, CLNB, LPS, DGK, 1F8, VIS, TCBP) new subfamilies and seven (CAL, SQUD, CDPK, EFH5, TPP, LAV, CRGP) new unique proteins, which we assume represent new subfamilies. The main focus of this study is the classification of individual EF-hand domains. Five subfamilies--calmodulin, troponin C, essential light chain, regulatory light chain, CDC31/caltractin--and three uniques--call, squidulin, and calcium-dependent protein kinase--are congruent in that all evolved from a common four-domain precursor. In contrast calpain and sarcoplasmic calcium-binding protein (SARC) each evolved from its own one-domain precursor. The remaining 19 subfamilies and uniques appear to have evolved by translocation and splicing of genes encoding the EF-hand domains that were precursors to the congruent eight and to calpain and to SARC. The rates of evolution of the EF-hand domains are slower following formation of the subfamilies and establishment of their functions. Subfamilies are not readily classified by patterns of calcium coordination, interdomain linker stability, and glycine and proline distribution. There are many homoplasies indicating that similar variants of the EF-hand evolved by independent pathways.

Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories.

Nuclear receptor proteins regulate transcription under the influence of hormones or other small ligands. These proteins bind to specific DNA sequences, termed hormone response elements (HREs), that reside close to hormone-responsive genes (reviewed in Ref. 1). This signal transduction process involves three discernible domains in the nuclear receptor proteins (reviewed in Refs. 2, 3)-the N-terminus, the central DNA-binding domain comprised of two zinc finger motifs, and the Cterminal ligand-binding domain; only the N-terminus is not well conserved. In general, virtually nothing is known about the origin of transcriptional regulatory factors. With respect to the nuclear receptor proteins in particular, two evolutionary histories have bean proposed. The first assumes independent origins for the different domains. By this view, ligand-binding segments with functions in bioenergetics and intermediary metabolism became fused to a DNAbinding motif to produce transcription factors, and the cell acquired the ability to respond at the transcriptional level to fluctuations in its physiological state (1). The second model implicates a single, multi-domain precursor that initially mediated a simple signal transduction mechanism (perhaps similar to that employed by the modem thyroid receptors) and subsequently acquired

The origin of nuclear receptor proteins: a single precursor distinct from other transcription factors.

Publisher Summary This chapter describes the significance of maximum parsimony approach to the construction of evolutionary trees from aligned homologous sequences. A maximum parsimony tree accounts for the evolutionary descent or related sequences by the fewest possible genie changes. Such a tree maximizes the genetic likenesses associated with common ancestry while minimizing the incidence of convergent mutations. Calculation of tree length is simplified by removing the root from the tree. Such an unrooted tree or network still retains the interior nodes and the exterior nodes (the OTUs).The maximum parsimony procedure can reconstruct ancestral sequences for each interior node of a tree but cannot determine which interior node or which pair of adjacent interior nodes is closest to the root. The problem of finding the maximum parsimony tree can be broken down into two parts. The first part proved to be easy and was solved by Fitch for homologous nucleotide sequences. The algorithm requires as input data both the OTUs, which are contemporary homologous nucleotide sequences already aligned against one another, and the instructions for a tree or dendrogram specifying any one of the possible dichotomous branching orders for the OTUs.

Nancy D. Moncrief

Papers

Evolution of EF-hand calcium-modulated proteins. I. Relationships based on amino acid sequences

The EF-hand family of calcium-modulated proteins.

Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories.

The origin of nuclear receptor proteins: a single precursor distinct from other transcription factors.

Maximum parsimony approach to construction of evolutionary trees from aligned homologous sequences.