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G B Golding

Publications and source records attributed to G B Golding.

At least 19 recordsLinked to original sources
PubMed1998

Genome structure and gene content in protist mitochondrial DNAs.

Although the collection of completely sequenced mitochondrial genomes is expanding rapidly, only recently has a phylogenetically broad representation of mtDNA sequences from protists (mostly unicellular eukaryotes) become available. This review surveys the 23 complete protist mtDNA sequences that have been determined to date, commenting on such aspects as mitochondrial genome structure, gene content, ribosomal RNA, introns, transfer RNAs and the genetic code and phylogenetic implications. We also illustrate the utility of a comparative genomics approach to gene identification by providing evidence that orfB in plant and protist mtDNAs is the homolog of atp8 , the gene in animal and fungal mtDNA that encodes subunit 8 of the F0portion of mitochondrial ATP synthase. Although several protist mtDNAs, like those of animals and most fungi, are seen to be highly derived, others appear to be have retained a number of features of the ancestral, proto-mitochondrial genome. Some of these ancestral features are also shared with plant mtDNA, although the latter have evidently expanded considerably in size, if not in gene content, in the course of evolution. Comparative analysis of protist mtDNAs is providing a new perspective on mtDNA evolution: how the original mitochondrial genome was organized, what genes it contained, and in what ways it must have changed in different eukaryotic phyla.

Amino Acid Sequence↗
PubMed1998

Searching for substitution rate heterogeneity.

A permutation method for detecting regional substitution rate heterogeneity in DNA sequences is described. An estimated phylogeny for the sequences is required. The method is likelihood based and searches through all regions of a DNA sequence to find any regions that have an unusually large (or small) number of substitutions in comparison to an optimal substitution rate for the entire sequence. Likelihood ratio tests do not achieve proper statistical significance levels due to the large number of tests performed. Empirical corrections based on permutations are suggested and shown to give correct statistical accuracy. The ability of the method to detect rate heterogeneity is good even when the region is small and with less than twice the rate of evolution in the remainder of the sequence.

Algorithms↗
PubMed1998

The structural basis of molecular adaptation.

The study of molecular adaptation has long been fraught with difficulties, not the least of which is identifying out of hundreds of amino acid replacements those few directly responsible for major adaptations. Six studies are used to illustrate how phylogenies, site-directed mutagenesis, and a knowledge of protein structure combine to provide much deeper insights into the adaptive process than has hitherto been possible. Ancient genes can be reconstructed, and the phenotypes can be compared to modern proteins. Out of hundreds of amino acid replacements accumulated over billions of years those few responsible for discriminating between alternative substrates are identified. An amino acid replacement of modest effect at the molecular level causes a dramatic expansion in an ecological niche. These and other topics are creating the emerging field of "paleomolecular biochemistry."

Adaptation, Physiological↗
PubMed1998

The mosaic nature of the eukaryotic nucleus.

The phylogenies for each of the protein-coding genes from the Methanococcus jannaschii genome were surveyed to determine the history of the major groups of life. For each gene, homologous sequences from other archaea, eucarya, and Gram-positive and Gram-negative bacteria were collected and aligned, and a phylogeny was reconstructed with a maximum-likelihood algorithm. The majority of significant phylogenies favor the eucarya and the archaca as sister groups. A smaller, but still substantial, portion of these significant phylogenies favor an eucarya/Gram-negative clade. These results indicate that support for the early history of life is not unequivocal. A chimeric origin of eukaryotes or an ancient, massive horizontal transfer of genes from Gram-negative bacteria to eucarya can explain many of the observed phylogenies.

Alcohol Oxidoreductases↗
PubMed1997

An ancestral mitochondrial DNA resembling a eubacterial genome in miniature.

Mitochondria, organelles specialized in energy conservation reactions in eukaryotic cells, have evolved from eubacteria-like endosymbionts whose closest known relatives are the rickettsial group of alpha-proteobacteria. Because characterized mitochondrial genomes vary markedly in structure, it has been impossible to infer from them the initial form of the proto-mitochondrial genome. This would require the identification of minimally derived mitochondrial DNAs that better reflect the ancestral state. Here we describe such a primitive mitochondrial genome, in the freshwater protozoon Reclinomonas americana. This protist displays ultrastructural characteristics that ally it with the retortamonads, a protozoan group that lacks mitochondria. R. americana mtDNA (69,034 base pairs) contains the largest collection of genes (97) so far identified in any mtDNA, including genes for 5S ribosomal RNA, the RNA component of RNase P, and at least 18 proteins not previously known to be encoded in mitochondria. Most surprising are four genes specifying a multisubunit, eubacterial-type RNA polymerase. Features of gene content together with eubacterial characteristics of genome organization and expression not found before in mitochondrial genomes indicate that R. americana mtDNA more closely resembles the ancestral proto-mitochondrial genome than any other mtDNA investigated to date.

Animals↗
PubMed1997

Protein engineering reveals ancient adaptive replacements in isocitrate dehydrogenase.

Evolutionary analysis indicates that eubacterial NADP-dependent isocitrate dehydrogenases (EC 1.1.1.42) first evolved from an NAD-dependent precursor about 3.5 billion years ago. Selection in favor of utilizing NADP was probably a result of niche expansion during growth on acetate, where isocitrate dehydrogenase provides 90% of the NADPH necessary for biosynthesis. Amino acids responsible for differing coenzyme specificities were identified from x-ray crystallographic structures of Escherichia coli isocitrate dehydrogenase and the distantly related Thermus thermophilus NAD-dependent isopropylmalate dehydrogenase. Site-directed mutagenesis at sites lining the coenzyme binding pockets has been used to invert the coenzyme specificities of both enzymes. Reconstructed ancestral sequences indicate that these replacements are ancestral. Hence the adaptive history of molecular evolution is amenable to experimental investigation.

Amino Acid Sequence↗
PubMed1997

Substitution rate variation in closely related rodent species.

The existence of evolutionary rate variation has previously been demonstrated between different orders, different species and even between different regions of the same gene. To examine rate variation between closely related species of rodents we have sequenced the adenine phosphorybosyltransferase (APRT) gene from Mus spicilegus, Mus pahari, Mastomys hildebrandtii, Stochomys longicaudatus and Gerbillus campestris and compared these sequences with the previously published Mus musculus, Rattus norvegicus and Mesocricetus auratus APRT sequences. The alignment of these eight rodent APRT sequences reveals two large insertions within the introns: an insertion with sequence similar to a B1 repetitive element is found within Mastomys and an insertion with sequence similar to a B2 repetitive element is found within M. pahari. A phylogeny for the rodent APRTs agrees with the previously published rodent phylogeny based on other molecular and morphological data. The relative rate test which is often used to test for variation in rates of evolution in different lineages is shown here to be sensitive to the choice of outgroup and therefore should be used with great caution. This sensitivity is detectable only with closely related species and results from the prevalence of homoplastic substitutions. Rate variation is demonstrated within the APRT exons and introns and between the rodent species (with the most significant difference being a rate difference in M. spicilegus). In addition, some third codon positions are shown to be more prone to substitution than others. This clearly demonstrates that even between very closely related species there is ample evidence of major differences in rates of evolution among species, among regions of the gene and among different positions within the gene. We also demonstrate that standard methods of analysis might not detect this variation.

Adenine Phosphoribosyltransferase↗
PubMed1996

Evolutionary rate variation within Mus APRT.

Rodents are thought to have relatively high rates of evolution, twice as fast as the rates for mammals in other orders. However, the uniformly high rates of evolution inferred for the order Rodentia from Mus musculus and Rattus norvegicus are not consistently found for other rodent species. Using a maximum likelihood phylogenetic algorithm (DNAML), we show here that Mus spicilegus has a fivefold different rate of evolution in 1100 bp around the adenine phosphoribosyltransferase gene (APRT) since its divergence from a common ancestor with Mus musculus. A greater than threefold difference in rates is also found in a comparison of the number of evolutionary events directly detected from the APRT sequences of these two closely related Mus species. The evolutionary events can be directly detected, since M. spicilegus, M. musculus, and the four rodent outgroup species used to determine the ancestral sequence are so closely related. One of the major differences between M. spicilegus and M. musculus that might affect evolutionary rate is the degree of commensalism with man. The Mus species therefore provide a useful model for testing various hypotheses for the causes of rate variations between genes, and possibly, between lineages.

Adenine Phosphoribosyltransferase↗
PubMed1996

The origin of the eukaryotic cell.

Molecular sequence data are beginning to provide important insights into the evolutionary origin of eukaryotic cells. Global phylogenies of numerous protein sequences indicate that the eukaryotic cell nucleus is a chimera, which has received major contributions from both a Gram-negative eubacterium and an archaebacterium. Recent studies also indicate that the formation of the nuclear envelope and the endoplasmic reticulum was accompanied by duplication of genes for the molecular chaperone proteins (e.g. hsp70, hsp90), which facilitate protein transport across membranes. Based on these observations, it is suggested that the ancestral eukaryotic cell arose by a unique endosymbiotic event involving engulfment of an eocyte archaebacterium by a Gram-negative eubacterial host.

Amino Acid Sequence↗
PubMed1995

Protein-based phylogenies support a chimeric origin for the eukaryotic genome.

The phylogenetic position of the archaebacteria and the place of eukaryotes in the history of life remain a question of debate. Recent studies based on some protein-sequence data have obtained unusual phylogenies for these organisms. We therefore collected the protein sequences that were available with representatives from each of the major forms of life: the gram-negative bacteria, gram-positive bacteria, archaebacteria, and eukaryotes. Monophyletic, unrooted phylogenies based on these sequence data show that seven of 24 proteins yield a significant gram-positive-archaebacteria clade/gram-negative-eukaryotic clade. The phylogenies for these seven proteins cannot be explained by the traditional three-way split of the eukaryotes, archaebacteria, and eubacteria. Nine of the 24 proteins yield the traditional gram-positive-gram-negative clade/archaebacteria-eukaryotic clade. The remaining eight proteins give phylogenies that cannot be statistically distinguished. These results support the hypothesis of a chimeric origin for the eukaryotic cell nucleus formed from the fusion of an archaebacteria and a gram-negative bacteria.

Archaea↗
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↗