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G B Golding

Publications and source records attributed to G B Golding.

At least 37 records · Page 2Linked to original sources
PubMed1994

Evidence for intron capture: an unusual path for the evolution of proteins.

Most new genes are thought to evolve from preexisting genes but duplications of entire genes or shuffling of preexisting exons provides only a limited repertoire of new sequences that can be presented to a cell. Only pieces that previously existed can be used in the construction and any further divergence depends on the slow accumulation of mutations. We show here the presence of a small, in-frame intron in a ciliate phosphoglycerate kinase gene and the insertion of an unusually random amino acid sequence at the same position in trypanosome phosphoglycerate kinase. The unusual sequences in trypanosomes were likely to have originally been introns that have been subsequently captured by the protein and have now been incorporated as part of the coding sequence. Via this path a truly unique sequence can be incorporated into an existing protein, leading in time to the evolution of a new, functionally distinct protein.

Amino Acid Sequence↗
PubMed1993

Evolution of allosteric control in glycogen phosphorylase.

In relation to the primary sequence and three-dimensional structure of rabbit muscle glycogen phosphorylase, we have carried out a comparative sequence analysis of phosphorylases from human, rat, Dictyostelium, yeast, potato and Escherichia coli. Based on sequence similarity, a large region of the protein is shared by these enzymes extending from alpha-helix-1 to the last alpha-helix-33. Conserved residues are equally distributed between the N and C-terminal domains and occur primarily in buried residues. Phylogenetic analysis indicates that the two isozymes within either E. coli, potato or Dictyostelium are more closely related to each other than they are to other phosphorylases. Yeast phosphorylase is most closely related to the Dictyostelium isozymes. Mammalian muscle and brain isozymes are more closely related to each other than to the liver isozyme and the muscle isozyme is evolving at the slowest rate. All phosphorylases exhibit high conservation of active site and pyridoxal phosphate binding residues. Most phosphorylases also exhibit high conservation of sugar binding residues in the glycogen storage site. Phosphorylation and AMP binding site residues are poorly conserved in non-mammalian phosphorylases. In contrast, glucose-6-P binding residues are highly conserved in four of the seven non-mammalian enzymes. Analysis of interacting pairs of dimer contact residues indicates that they can be grouped into three relatively independent networks. One network contains phosphorylation and AMP binding residues and is poorly conserved in non-mammalian enzymes. A second network contains glucose-6-P binding residues and is highly conserved in enzymes containing a conserved glucose-6-P binding site. A third, conserved network contains residues within the tower helix and gate loop. A model for the evolution of allostery in phosphorylase is proposed, suggesting that glucose-6-P inhibition was an early control mechanism. The later creation of primarily distinct ligand binding sites for AMP/phosphorylation control may have allowed the establishment of a separate dimer contact network for propagating conformational changes leading to activation rather than inhibition of enzyme activity.

Allosteric Regulation↗
PubMed1993

Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes.

The 70-kDa heat-shock protein (HSP70) constitutes the most conserved protein present in all organisms that is known to date. Based on global alignment of HSP70 sequences from organisms representing all three domains, numerous sequence signatures that are specific for prokaryotic and eukaryotic homologs have been identified. HSP70s from the two archaebacterial species examined (viz., Halobacterium marismortui and Methanosarcina mazei) have been found to contain all eubacterial but no eukaryotic signature sequences. Based on several novel features of the HSP70 family of proteins (viz., presence of tandem repeats of a 9-amino-acid [a.a.] polypeptide sequence and structural similarity between the first and second quadrants of HSP70, homology of the N-terminal half of HSP70 to the bacterial MreB protein, presence of a conserved insert of 23-27 a.a. in all HSP70s except those from archaebacteria and gram-positive eubacteria) a model for the evolution of HSP70 gene from an early stage is proposed. The HSP70 homologs from archaebacteria and gram-positive bacteria lacking the insert in the N-terminal quadrants are indicated to be the ancestral form of the protein. Detailed phylogenetic analyses of HSP70 sequence data (viz., by bootstrap analyses, maximum parsimony, and maximum likelihood methods) provide evidence that archaebacteria are not monophyletic and show a close evolutionary linkage with the gram-positive eubacteria. These results do not support the traditional archaebacterial tree, where a close relationship between archaebacterial and eukaryotic homologs is observed. To explain the phylogenies based on HSP70 and other gene sequences, a model for the origin of eukaryotic cells involving fusion between archaebacteria and gram-negative eubacteria is proposed.

Amino Acid Sequence↗
PubMed1993

The rat adenine phosphoribosyltransferase sequence shows evolutionary rate variation among exons in rodents.

The complete genomic sequence of the rat APRT gene is described and compared with published mammalian sequences. The rat APRT gene organization is typical of other rodent APRTs with five exons, one large intron of 993 bp, and three smaller introns averaging 145 bp. Because complete sequences for mouse and Chinese hamster APRT are also known, it is possible to compare the evolutionary rates of change in the exons with those of the introns. The latter provide one possible estimate of underlying rates of change. It is shown that the APRT exons have differential rates of evolution in rodents and have had a recent and rapid burst of substitutions within the mouse lineage. Rates of change in the exons do not appear to be strongly correlated with the rates of change in the introns.

Adenine Phosphoribosyltransferase↗
PubMed1992

A phylogenetic analysis based on the gene encoding phosphoglycerate kinase.

We have determined the nucleotide sequence of both genomic and complementary DNA (cDNA) for the gene encoding the glycolytic enzyme phosphoglycerate kinase from the ciliated protozoan Tetrahymena thermophila. The amino acid sequence for the enzyme has also been derived from the cDNA sequence. The gene contains an open reading frame of 1260 nucleotides encoding 420 amino acids. Coding sequence in genomic DNA is interrupted by two introns at positions corresponding to introns 3 and 4 in mammalian phosphoglycerate kinase genes. The derived amino acid sequence was used to prepare a phylogeny by aligning the Tetrahymena sequence with 25 other phosphoglycerate kinase amino acid sequences. The Tetrahymena sequence is a typical eukaryotic sequence. There is recognizable and clear homology across species that cover nearly the complete range of life forms. The phylogenetic reconstruction of these sequences generally supports the conclusions that have been reached using rRNA sequences.

Amino Acid Sequence↗
PubMed1988

A sampling theory of selectively neutral alleles in a subdivided population.

Ewens' sampling distribution is investigated for a structured population. Samples are assumed to be taken from a single subpopulation that exchanges migrants with other subpopulations. A complete description of the probability distribution for such samples is not a practical possibility but an equilibrium approximation can be found. This approximation extracts the information necessary for constructing a continuous approximation to the complete distribution using known values of the distribution and its derivatives in randomly mating populations. It is shown that this approximation is as complete a description of a single biologically realistic subpopulation as is possible given standard uncertainties about the actual size of the migration rates, relative sizes of each of the subpopulations and other factors that might affect the genetic structure of a subpopulation. Any further information must be gained at the expense of generality. This approximation is used to investigate the effect of population subdivision on Watterson's test of neutrality. It is known that the infinite allele, sample distribution is independent of mutation rate when made conditional on the number of alleles in the sample. It is shown that the conditional, infinite allele, sample distribution from this approximation is also independent of population structure and hence Watterson's test is still approximately valid for subdivided populations.

Alleles↗
PubMed1988

Somatic immunoglobulin sequence divergence and its implications for studies of evolutionary divergence.

The divergence of immunoglobulin genes due to somatic mutation provides a natural example of DNA sequence divergence. This divergence was examined to gain insight into the processes of evolution and the determinants of the variance-to-mean ratio of sequence divergence. Normally, this ratio is found to be larger than expected (1.0 under Poisson assumptions) for the evolutionary divergence or most genes. Although not significantly less than one, all seven groups of immunoglobulin amino acid sequences have ratios smaller than expected, contrary to the evolutionary pattern generally observed. The substitutions in the immunoglobulin genes appear to be highly nonrandom and an excess of parallel changes (the major nonrandom feature of these mutations) is shown to cause smaller ratios. Because convergent or parallel mutations are often observed in the evolutionary divergence of genes, this suggests that forces causing the large observed ratios may actually have to be more powerful than previously expected. Further, since selection is one of the likely causes of parallel mutations, it should be noted that selection could significantly decrease the variance-to-mean ratio. The high frequency of parallel mutations and their resulting effects, as observed in the immunoglobulin genes, suggest that only poor inferences of sequence divergence can be made without actual knowledge of the ancestral sequence.

Amino Acid Sequence↗
PubMed1988

Studies on the expression and evolution of the glycogen phosphorylase gene family in the rat.

Muscle, liver, and brain glycogen phosphorylases in mammals comprise a family of closely related isozymes that are differentially expressed in a wide variety of cell types. Towards obtaining a better understanding of the mechanisms governing the tissue-specific control of expression of this isozyme family, we used an antibody generated against bovine liver phosphorylase to obtain quantitative estimates of the concentrations of the three isozymes in rat tissues by Western blot analysis. This analysis indicated that expression of these isozymes at the protein level, although widespread, was tissue-specific and each isozyme exhibited variations in expression throughout the tissues where it was produced. We also began a preliminary analysis of the evolution of the genes encoding these three isozymes. Towards this end, we isolated and sequenced a partial cDNA to the rat brain isozyme that encompassed the coding region from amino acids 569 to 729. Using known phosphorylase gene sequences, we reconstructed a phylogeny spanning three kingdoms. This phylogeny indicated that brain and muscle isozymes are more closely related to each other than to the liver isozyme and that gene duplications that give rise to the family predate the mammalian radiation. Differences in the relative rates of change of the three isozymes were observed and this may reflect different constraints on their evolution perhaps related to their functional roles and (or) tissue-specific expression.

Amino Acid Sequence↗
PubMed1987

Multiple substitutions create biased estimates of divergence times and small increases in the variance to mean ratio.

Analysis of mutational processes has demonstrated that mutations usually occur as non-random events with many factors that influence the fidelity of DNA replication. One such unusual pattern of mutation shows that some mutational events will create more than one sequence alteration. This possibility is not generally considered in estimates of sequence divergence and yet affects both the mean and variance of these estimates. Theoretical results and simulation results are presented to examine how extensive the effects of multiple alterations resulting from single mutational events may be on sequence divergence. It is shown that estimates of the divergence times are biased but that this bias is not large unless the number of sequence alterations per event are unrealistically large. The number of alterations per event required to achieve a given bias is determined. The variance is increased by multiple alterations above the variance expected for the same mean number of single alterations, but not up to the levels that are observed in nature. The resulting increase in the variance to mean ratio changes with the amount of divergence, from an initially high ratio followed by a slow decline to one.

Biological Evolution↗
PubMed1987

Patterns of somatic mutations in immunoglobulin variable genes.

The mechanism responsible for somatic mutation in the variable genes of antibodies is unknown and may differ from previously described mechanisms that produce mutation in DNA. We have analyzed 421 somatic mutations from the rearranged immunoglobulin variable genes of mice to determine if the nucleotide substitutions differ from those generated during meiosis and if the presence of nearby direct and inverted repeated sequences could template mutations around the variable gene. The results reveal a difference in the pattern of substitutions obtained from somatic mutations vs. meiotic mutations. An increased frequency of T:A to C:G transitions and a decreased frequency of mutations involving a G in the somatic mutants compared to the meiotic mutants is indicated. This suggests that the mutational processes responsible for somatic mutations in antibody genes differs from that responsible for mutation during meiosis. An analysis of the local DNA sequences revealed many direct repeats and palindromic sequences that were capable of templating some of the known mutations. Although additional factors may be involved in targeting mutations to the variable gene, mistemplating by nearby repeats may provide a mechanism for the enhancement of somatic mutation.

Animals↗
PubMed1986

Sequence evolution within populations under multiple types of mutation.

DNA sequence and restriction map data from natural populations can be used to estimate the phylogenetic history of observed sequences. Studies of this sort usually examine large regions of DNA where many evolutionary events have taken place. From such data, detailed phylogenies can be constructed and qualitatively different kinds of mutational and substitutional processes can be studied. The value of investigating more than one mutational type is in the power of comparing relative rates of these distinct substitutional processes. In this paper, we construct a neutral model to describe the frequencies of sequence haplotypes according to the haplotypes from which they arose. This theory of the frequency of haplotypes (incorporating their historical past) is applied to data from the alcohol dehydrogenase gene region of Drosophila melanogaster. The observed patterns of change associated with transposable elements around the Adh locus are not in accord with a neutral model. Values for the mutation rates cannot be found that will bring the observed data into agreement with a simple neutral model, but with the addition of mildly deleterious selection, the model can explain these patterns of change. These results suggest that transposable elements are deleterious to the organisms carrying them, but at levels only several times their rate of transpositional insertion. Similar analyses of small deletions in the Adh region suggest that they may experience mildly deleterious selection.

Animals↗
PubMed1986

Evidence for local DNA influences on patterns of substitutions in the human alpha-interferon gene family.

The evolutionary history of genes can be used to examine patterns of spontaneous mutation if the sequences are sufficiently extensive to provide reliable data. Many human alpha-interferon genes have been sequenced and they form a large multigene family including several pseudogenes. A phylogenetic history for 15 human interferon sequences was reconstructed and their ancestral sequences inferred using a maximum parsimony method. This evolutionary history provided a record of more than 738 spontaneous mutations that have occurred in man's recent evolution. Of these mutations, more than 267 base substitution and deletion-insertion events were analyzed to determine the possible effects of nearby DNA sequences. Many substitutions occur at the end of long runs of identical bases and some dinucleotide pairs may mutate more often than others. Because templating by local DNA sequences has been implicated in prokaryotic mutation, the sequences were also examined for nearby repeats that include the substituted nucleotide and hence are potentially capable of templating the substitution. The majority of sequence alterations examined have either a similar direct repeat or palindrome nearby. Often such templates can account for simultaneous multiple mutations. These results suggest that sequence-directed events may occur occasionally in eukaryotes and that neighbouring DNA sequences can influence both the occurrence and types of mutations in several different ways.

Base Sequence↗
PubMed1985

Sequence-directed mutagenesis: evidence from a phylogenetic history of human alpha-interferon genes.

We have studied the potential contribution of template-dependent events to genetic variation in mammals by examining the sequence alterations that have occurred in the recent evolution of human interferon genes. Fifteen members of the human alpha-interferon gene family were aligned, and a phylogenetic history was inferred. Many multiple events are inferred to have occurred in the evolution of the interferon genes and for the majority of these local DNA sequences were present that were capable of serving as templates for their occurrence. We conclude that the DNA sequence has the potential to explain many of the inferred spontaneous events and to explain complex alterations to sequences--i.e., the joint occurrence of base substitutions and insertions/deletions. Thus, such a mechanism would often cause multiple sequence changes as a result of a single mutational event and would provide additional genetic variation for evolution. Sequence-directed mutations would depend upon the local DNA sequences and, hence, would not be random at the DNA level.

Base Sequence↗
PubMed1984

The sampling distribution of linkage disequilibrium.

The probabilities of obtaining particular samples of gametes with two completely linked loci are derived. It is assumed that the population consists of N diploid, randomly mating individuals, that each of the two loci mutate according to the infinite allele model at a rate mu and that the population is at equilibrium. When 4N mu is small, the most probable samples of gametes are those that segregate only two alleles at either locus. The probabilities of various samples of gametes are discussed. The results show that most samples with completely linked loci have either a very small or a very large association between the alleles of each locus. This causes the distribution of linkage disequilibrium to be skewed and the distribution of the correlation coefficient to be bimodal. The correlation coefficient is commonly used as a test statistic with a chi square distribution and yet has a bimodal distribution when the loci are completely linked. Thus, such a test is not likely to be accurate unless the rate of recombination between the loci and/or the effective population size are sufficiently large enough so that the loci can be treated as unlinked.

Alleles↗