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K H Wolfe

Publications and source records attributed to K H Wolfe.

At least 37 records · Page 2Linked to original sources
PubMed1997

Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplasts.

The selective constraints influencing mRNA editing in plant organelles are largely unknown. To investigate these, we compared patterns of editing between monocot and dicot mitochondrial mRNA. On average, 24% of sites that are edited form C to U in one species have been substituted during evolution by a genomic T in the other: this is four times the rate of evolution seen at nonedited synonymously variable C residues. A similar, but weaker trend (not statistically significant) is seen at sites edited in chloroplast mRNA. The elevated substitution rate does not appear to be a consequence of a higher mutability of the trinucleotide motif (T-C-purine) associated with editing. nor to be a result of reverse transcription from mature mRNA. Selection to replace the genomic C with a T may account for the accelerated evolution, either due to elimination of inefficient transcripts and protein products or as a consequence of the prior loss of components outside the edit site which are necessary for editing; the latter hypothesis is supported by the frequent loss of editing without genomic mutation at third codon positions. Whatever the cause, the rapid rate of evolution indicates that editing confers little selective advantage at most sites.

Base Sequence↗
PubMed1996

Ebb and flow of the chloroplast inverted repeat.

The endpoints of the large inverted repeat (IR) of chloroplast DNA in flowering plants differ by small amounts between species. To quantify the extent of this movement and define a possible mechanism for IR expansion, DNA sequences across the IR-large single-copy (IR-LSC) junctions were compared among 13 Nicotiana species and other dicots. In most Nicotiana species the IR terminates just upstream of, or somewhere within, the 5' portion of the rps19 gene. The truncated copy of this gene, rps19', varies in length even between closely related species but is of constant size within a single species. In Nicotiana, six different rps19' structures were found. A phylogenetic tree of Nicotiana species based on restriction site data shows that the IR has both expanded and contracted during the evolution of this genus. Gene conversion is proposed to account for these small and apparently random IR expansions. A large IR expansion of over 12 kb has occurred in Nicotiana acuminata. The new IR-LSC junction in this species lies within intron 1 of the clpP gene. This rearrangement occurred via a double-strand DNA break and recombination between poly (A) tracts in clpP intron 1 and upstream of rps19. Nicotiana acuminata chloroplast DNA contains a "molecular fossil' of the IR-LSC junction that existed prior to this dramatic rearrangement.

Arabidopsis Proteins↗
PubMed1996

Sequence of 29 kb around the PDR10 locus on the right arm of Saccharomyces cerevisiae chromosome XV: similarity to part of chromosome I.

We report a 29,445 bp sequence from the right arm of yeast chromosome XV. It contains the genes MYO2, SNC2, PDR10, SCD5 (also called FTB1), MIP1, VMA4, MRS2, ALA1, KRE5, TEA1, and a homologue of YAL034c. Several discrepancies with previously published sequences were found. PDR10 encodes a protein highly similar to the pleiotropic drug resistance protein Pdr5p. This sequence contig forms part of a region of extended similarity to part of the left arm of chromosome I, which is a relic of an ancient duplicated chromosomal region.

ATP-Binding Cassette Transporters↗
PubMed1995

Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana.

Expression of the vestigial plastid genome of the nonphotosynthetic, parasitic flowering plant Epifagus virginiana was examined by northern analysis and by characterization of cDNAs. Probes for each of 12 plastid genes tested hybridized to all lanes of northern blots containing total RNA prepared from stems and fruits of Epifagus and from leaves of tobacco. Certain transcript patterns in Epifagus plastids are highly complex and similar to those of tobacco operons. In contrast, genes such as rps2, which have become orphaned in Epifagus as a result of evolutionary loss of formerly cotranscribed genes, show simpler transcript patterns in Epifagus than in tobacco. Sizing and sequencing of cDNAs generated by reverse transcriptase-PCR for three genes, rps12, rpl2, and clpP, show that their transcripts are properly cis- and/or trans-spliced at the same five group II intron insertion sites used in photosynthetic plants. A single, conventional C-->U edit in rps12 was found among the total of 1401 nucleotides of cDNA sequence that was determined for the three genes. An octanucleotide sequence identical to a putative guide RNA of plant organelles and perfectly complementary to the rps12 edit site itself was identified just 200 bp upstream of the edit site. These data, together with previous results from the complete sequencing of the Epifagus plastid genome, provide compelling evidence that this degenerate genome is nonetheless expressed and functional. Analysis of the putative maturase MatK, encoded by the group II intron of trnK in photosynthetic land plants but by a freestanding gene in Epifagus, leads us to hypothesize that it acts 'in trans' to assist the splicing of group II introns other than the one in which it is normally encoded.

Adenosine Triphosphatases↗
PubMed1994

Complete DNA sequence of yeast chromosome II.

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.

Base Composition↗
PubMed1994

Yeast homologue of mammalian Ran binding protein 1.

A Saccharomyces cerevisiae gene (HTN1) that encodes a homologue of mouse Ran binding protein 1 (RanBP1, also known as HTF9A) was identified, cloned and sequenced. The two proteins are 51% identical in sequence. The HTN1 protein may interact with yeast GSP1, GSP2, and PRP20 proteins in an intracellular signalling pathway equivalent to the mammalian RanBP1-Ran/TC4-RCC1 pathway. RanBP1 homologues also exist in worms and rice.

Amino Acid Sequence↗
PubMed1994

Sequence around the centromere of Saccharomyces cerevisiae chromosome II: similarity of CEN2 to CEN4.

We report the sequence of a 12 kilobase region spanning the centromere of Saccharomyces cerevisiae chromosome II. The sequence from the left arm includes genes for histones H2A and H2B. The sequence from the right arm includes a gene that probably encodes a novel trehalase, as well as the COQ1 gene (for an enzyme involved in coenzyme Q biosynthesis), and an open reading frame with significant similarity to bacterial genes of unknown function. The trehalase gene (YBR0106) on chromosome II is located beside the centromere and transcribed towards it. This is identical to the arrangement of the neutral trehalase gene (NTH1) beside the centromere of chromosome IV. The centromere regions of chromosomes II and IV may therefore have arisen through a duplication of the centromere region of an ancestral chromosome. The YBR0106 and NTH1 proteins are 77% identical in predicted amino acid sequence, but there is no pronounced sequence similarity between the two centromeres (CEN2 and CEN4) outside of the universally conserved CDE I and CDE III elements. The genes flanking the centromere and trehalase genes differ between the two chromosomes, so the similarity between chromosomes II and IV may be less extensive than that recently reported between chromosomes III and XIV.

Alkyl and Aryl Transferases↗
PubMed1994

Structure and evolution of the largest chloroplast gene (ORF2280): internal plasticity and multiple gene loss during angiosperm evolution.

We have determined the nucleotide sequence of the Pelargonium x hortorum ORF2280 homolog, the largest gene in the plastid genome of most land plants, and compared it to published homologs from Nicotiana tabacum, Epifagus virginiana, Spinacia oleracea, and Marchantia polymorpha. Multiple alignment of protein sequences requires an extraordinary number of gaps, indicating a very high frequency of insertion/deletion events during the evolution of the protein; however, the overall predicted size of the protein varies relatively little among the five species. At 2,109 codons, the Pelargonium gene is smaller than other land plant ORF2280 homologs and exhibits a rate of nucleotide substitution several times higher relative to Nicotiana, Epifagus, and Spinacia. Southern-blot and restriction-mapping studies were carried out to uncover length variation in ORF2280 homologs from 279 species (representing 111 families) of angiosperms. In many independent angiosperm lineages, this gene has sustained deletions ranging in size from 200 bp to almost 6 kb. Based on the severity of deletions, we postulate that the chloroplast homolog of ORF2280 has become nonfunctional in at least four independent lineages of angiosperms.

Amino Acid Sequence↗
PubMed1994

Similarity between putative ATP-binding sites in land plant plastid ORF2280 proteins and the FtsH/CDC48 family of ATPases.

Plastid ORF2280 proteins from five species of land plant are shown to have limited amino-acid sequence similarity to a family of proteins that includes the yeast CDC48, SEC18, PAS1 and SUG1 proteins, three subunits of the mammalian 26S protease, and the Escherichia coli FtsH protein. These proteins all contain one or two ATPase domains and many are involved in cell division, transport of proteins across membranes, or proteolysis. Similarity with the ORF2280 proteins is restricted to a single region of about 130 amino acids that contains: (1) sequences resembling a nucleotide binding site but lacking two normally conserved residues, and (2) a downstream conserved motif with the consensus sequence VIX2TX2PX3DPALX2P. Most of the rest of ORF2280 is very poorly conserved among land plants, even though other family members such as CDC48 have slow rates of protein sequence evolution. In contrast, a protein encoded by plastid DNA of the rhodophyte alga Porphyra purpurea is very similar to E. coli FtsH. Phylogenetic analysis suggests that the red and green plastid genes are not true homologues (orthologues) but distinct members of an ancient gene family.

ATP-Dependent Proteases↗
PubMed1993

Ninety extra nucleotide in ndhF gene of tobacco chloroplast DNA: a summary of revisions to the 1986 genome sequence.

Corrections to the published sequence of the tobacco chloroplast gene ndhF are presented, including a 90 bp Alu I restriction enzyme fragment internal to the gene that was apparently missed during the original sequencing effort. A summary of the corrections to the published tobacco chloroplast DNA that have come to light since its original publication is included.

Base Sequence↗
PubMed1993

Mammalian gene evolution: nucleotide sequence divergence between mouse and rat.

As a paradigm of mammalian gene evolution, the nature and extent of DNA sequence divergence between homologous protein-coding genes from mouse and rat have been investigated. The data set examined includes 363 genes totalling 411 kilobases, making this by far the largest comparison conducted between a single pair of species. Mouse and rat genes are on average 93.4% identical in nucleotide sequence and 93.9% identical in amino acid sequence. Individual genes vary substantially in the extent of nonsynonymous nucleotide substitution, as expected from protein evolution studies; here the variation is characterized. The extent of synonymous (or silent) substitution also varies considerably among genes, though the coefficient of variation is about four times smaller than for nonsynonymous substitutions. A small number of genes mapped to the X-chromosome have a slower rate of molecular evolution than average, as predicted if molecular evolution is "male-driven." Base composition at silent sites varies from 33% to 95% G+C in different genes; mouse and rat homologues differ on average by only 1.7% in silent-site G+C, but it is shown that this is not necessarily due to any selective constraint on their base composition. Synonymous substitution rates and silent site base composition appear to be related (genes at intermediate G+C have on average higher rates), but the relationship is not as strong as in our earlier analyses. Rates of synonymous and nonsynonymous substitution are correlated, apparently because of an excess of substitutions involving adjacent pairs of nucleotides. Several factors suggest that synonymous codon usage in rodent genes is not subject to selection.

Amino Acid Sequence↗
PubMed1992

Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant.

Complete nucleotide sequencing shows that the plastid genome of Epifagus virginiana, a nonphotosynthetic parasitic flowering plant, lacks all genes for photosynthesis and chlororespiration found in chloroplast genomes of green plants. The 70,028-base-pair genome contains only 42 genes, at least 38 of which specify components of the gene-expression apparatus of the plastid. Moreover, all chloroplast-encoded RNA polymerase genes and many tRNA and ribosomal protein genes have been lost. Since the genome is functional, nuclear gene products must compensate for some gene losses by means of previously unsuspected import mechanisms that may operate in all plastids. At least one of the four unassigned protein genes in Epifagus plastid DNA must have a nongenetic and nonbioenergetic function and, thereby, serve as the reason for the maintenance of an active genome. Many small insertions in the Epifagus plastid genome create tandem duplications and presumably arose by slippage mispairing during DNA replication. The extensive reduction in genome size in Epifagus reflects an intensification of the same processes of length mutation that govern the amount of noncoding DNA in chloroplast genomes. Remarkably, this massive pruning occurred with a virtual absence of gene order change.

Chromosomes↗
PubMed1992

Small single-copy region of plastid DNA in the non-photosynthetic angiosperm Epifagus virginiana contains only two genes. Differences among dicots, monocots and bryophytes in gene organization at a non-bioenergetic locus.

We have determined the nucleotide sequence of a 7 kb (1 kb = 10(3) base-pairs) region that includes the entire small single-copy region (SSC) of the plastid genome of Epifagus virginiana, a non-photosynthetic, parasitic flowering plant. The SSC (4.8 kb) is considerably smaller than those of photosynthetic plants due to the complete deletion of all photosynthetic, chlororespiratory and ribosomal protein genes. This leaves only two genes: a protein gene of 1738 codons whose product is unlikely to be involved in bioenergetic processes and a leucine tRNA gene (trn(LUAG)). Both genes span junctions between the inverted repeat and the SSC, with the consequence that the terminal 20 base-pairs of the repeat is transcribed in both directions and functions both as the 3' end of the tRNA gene and as an internal segment of orf1738. We find that the region of tobacco plastid DNA homologous to Epifagus orf1738 contains a single open reading frame (ORF) of 1901 codons rather than the three ORFs of 1244, 273 and 228 codons originally reported. However, we confirm that the equivalent region of the bryophyte Marchantia contains two genes (1068 and 464 codons) corresponding to the N and C-terminal portions of the dicot protein. In contrast, rice plastid DNA contains a severely truncated pseudogene at this locus.

Amino Acid Sequence↗
PubMed1992

Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: accelerated sequence evolution, altered promoter structure, and tRNA pseudogenes.

The nucleotide sequence of a 7.4 kb region containing the entire plastid ribosomal RNA operon of the nongreen parasitic plant Epifagus virginiana has been determined. Analysis of the sequence indicates that all four rRNA genes are intact and almost certainly functional. In contrast, the split genes for tRNA(Ile) and tRNA(Ala) present in the 16S-23S rRNA spacer region have become pseudogenes, and deletion upstream of the 16S rRNA gene has removed a tRNA(Val) gene and most of the promoter region for the rRNA operon. The rate of nucleotide substitution in 16S and 23S rRNAs is several times higher in Epifagus than in tobacco, a related photosynthetic plant. Possible reasons for this, including relaxed translational constraints, are discussed.

Base Sequence↗
PubMed1992

Rapid evolution of the plastid translational apparatus in a nonphotosynthetic plant: loss or accelerated sequence evolution of tRNA and ribosomal protein genes.

The vestigial plastid genome of Epifagus virginiana (beechdrops), a nonphotosynthetic parasitic flowering plant, is functional but lacks six ribosomal protein and 13 tRNA genes found in the chloroplast DNAs of photosynthetic flowering plants. Import of nuclear gene products is hypothesized to compensate for many of these losses. Codon usage and amino acid usage patterns in Epifagus plastic genes have not been affected by the tRNA gene losses, though a small shift in the base composition of the whole genome (toward A+T-richness) is apparent. The ribosomal protein and tRNA genes that remain have had a high rate of molecular evolution, perhaps due to relaxation of constraints on the translational apparatus. Despite the compactness and extensive gene loss, one translational gene (infA, encoding initiation factor 1) that is a pseudogene in tobacco has been maintained intact in Epifagus.

Amino Acid Sequence↗
PubMed1991

Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders.

Synonymous substitution rates have been estimated for 58 genes compared among primates, artiodactyls, and rodents. Although silent sites might be expected to be neutral, there is substantial rate variation among genes within each lineage. Some of the rate variation is associated with G + C content: genes with intermediate G + C values have the highest rates. Nevertheless, considerable heterogeneity remains after correcting for G + C content. Synonymous substitution rates also vary among lineages, but the relative rates of genes are well conserved in different lineages. Certain genes have also been sequenced in a fourth order (lagomorph or carnivore), and these data have been used to investigate mammalian phylogeny. Data on lagomorphs are consistent with a star phylogeny, but there is evidence that carnivores and artiodactyls are sister groups. Genes sequenced in both rat and mouse suggest that the increased substitution rate in rodents has occurred since the rat/mouse divergence.

Animals↗
PubMed1991

Mammalian DNA replication: mutation biases and the mutation rate.

Experimental studies have shown that the fidelity of DNA replication can be affected by the concentrations of free deoxyribonucleotides present in the cell. Replication of mammalian chromosomes is achieved using pools of newly-synthesized deoxyribonucleotides which fluctuate during the cell cycle. Since regions of mammalian chromosomes are replicated sequentially, there is the potential for differences among mammalian loci in both the relative and absolute frequencies of the various transitional and transversional mutations which may occur. Where these mutations are effectively neutral, at silent sites in genes and in non-coding sequences, this may result in different rates of evolution and in different base compositions, as have been observed in data from mammalian genes. A simple model of the DNA replication process is developed to describe how the mutation rate could be affected by the G + C contents of the deoxyribonucleotide pools and of the replicating DNA. Mutation rates are predicted to vary from locus to locus; only in the particular case of identical G + C contents in the DNA locus and the deoxyribonucleotide pools, and no proofreading, will the mutation rate be uniform over all loci.

Animals↗