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A F MacRae

Publications and source records attributed to A F MacRae.

8 recordsLinked to original sources
PubMed1999

Analysis of hexamer and pentamer motifs within a maize database: the presence of motif 'signatures' in functional gene categories.

Several transposable elements (TEs) have been reported in association with genes in maize and other plants. In this study we found, based on statistical analyses of 951 DNA sequences within a maize computer database, that short hexamer and pentamer DNA motifs from the Activator (Ac) and from the Tourist TEs, respectively, were also associated with maize genes. Moreover, these two short hexamer and pentamer TE motifs were nonrandomly and nearly nonrandomly distributed, respectively, with respect to particular biochemical functions of those maize genes. To determine whether this distribution may be unique to TE motifs, or may be more widespread among hexamers/pentamers in general, we similarly studied six additional hexamer or pentamer sequences not derived from TEs. These also showed nonrandom distribution with respect to functional gene categories in the maize database. However, each of the total of eight short sequence motifs we studied differed in its pattern of association with distinct sets of functional gene categories; that is, there was a unique 'signature' for each of the hexamers and pentameters tested. Potential biological hypotheses to explain these findings are discussed.

DNA Transposable Elements↗
PubMed1998

A pentamer-repeat-containing DNA sequence in Texas bluebonnet (Lupinus texensis Hook.)

A 654-bp EcoRI restriction fragment called Lup4 was shotgun cloned from Texas bluebonnet (Lupinus texensis Hook.) nuclear genomic DNA that had been extracted from plant leaves. Its sequence was determined on both strands. Southern blot analysis of EcoRI-digested Texas bluebonnet DNA revealed clone hybridization throughout the approximately 1.0 to > 23 kb size range; the darkest hybridization was in the high molecular weight range (approximately 6 to > 23 kb). Using dot blot analysis, the copy number of the 654-bp clone was estimated to be approximately 4.75 x 10(4) copies per haploid genome, and thus this repetitive sequence comprises 3.5-4.1% of the nuclear genome. Sequence analyses showed that this clone contains multiple repeats: mainly the ATTGG pentamer, but also derivative pentamers (e.g., GTTGG, TTTGG, ATAGG, and GGATT). Examination of DNA base occurrence revealed a strand bias in base composition. Data-base searches using the algorithm FASTA revealed no alignment with existing plant data base sequences, but showed sequence identity with several telomeric and satellite DNA sequences. The two highest-scoring alignments were with another pentamer-containing sequence from a telomeric region of the nematode Parascaris univalens.

Base Sequence↗
PubMed1995

Molecular evolution of the Ac/Ds transposable-element family in pearl millet and other grasses.

We report an Ac-like sequence from pearl millet (Pennisetum glaucum) and deletion derivative Ac-like sequences from pearl millet and another grass species, Bambusa multiplex. Sequence relationships between the pearl millet and maize Ac elements suggest that Ac/Ds transposable-element family is ancient. Further, the sequence identity between the Bambusa Ac-like sequence and maize Ac implies that the Ac/Ds transposable-element family has been in the grass family since its inception. The Ac-like sequences reported from pearl millet and maize Ac are statistically heterogeneous in pair-wise distance comparisons to each other. Yet, we are unable to discriminate between differential selection or ectopic exchange (recombination and conversion) between nonidentical transposable element homologues, as the cause of the heterogeneity. However, the more extreme heterogeneity exhibited between the previously described pearl millet element and maize Ac seems likely to derive from ectopic exchange between elements with different levels of divergence.

Base Sequence↗
PubMed1994

Molecular evolutionary characterization of an Activator (Ac)-like transposable element sequence from pearl millet (Pennisetum glaucum) (Poaceae).

We present data on the evolution of the Ac/Ds family of transposable elements in select grasses (Poaceae). A defective Ac-like element was cloned from a DNA library of the grass Pennisetum glaucum (pearl millet) and its entire 4531 bp sequence has been determined. When the pearl millet Ac-like sequence is aligned with the maize Ac sequence, it is found that there is approximately 70% DNA similarity in the central region spanning most of maize Ac exon II and all of exon III. In addition, there are two smaller regions of similarity at the Ac terminii. Besides these three major structural similarities, Pennisetum Ac has two large regions, one 5' and one 3', that show little similarity to Zea Ac. Furthermore, most of the sequences corresponding to intron II in maize Ac are absent in pearl millet Ac. Kimura's evolutionary distance between the central region of maize and pearl millet Ac sequences is estimated to be 0.429 +/- 0.020 nucleotide substitutions per site. This value is not significantly different from the average number of synonymous substitutions for coding regions of the Adh1 gene between maize and pearl millet, which is 0.395 +/- 0.051 nucleotide substitutions per site. If we assume Ac and Adh1 divergence times are equivalent between maize and pearl millet, then the above calculations suggest Ac-like sequences have probably not been strongly constrained by natural selection. Conserved DNA and amino acid sequence motifs are also examined. The level of DNA sequence divergence between maize and pearl millet Ac sequences, the estimated date when maize and pearl millet diverged (25-40 million years ago), coupled with their reproductive isolation/lack of current genetic exchange, all support the theory that Ac-like sequences have not been recently introduced into pearl millet from maize. Instead, Ac-like sequences were probably present in the progenitor of maize and pearl millet and have thus existed in the grasses for at least 25 million years.

Amino Acid Sequence↗
PubMed1992

Evolution of Ac and Dsl elements in select grasses (Poaceae).

We present data on evolution of the Ac/Ds family of transposable elements in select grasses (Poaceae). An Ac-like element was cloned from a DNA library of the grass Pennisetum glaucum (pearl millet) and 2387 bp of it have been sequenced. When the pearl millet Ac-like sequence is aligned with the corresponding region of the maize Ac sequence, it is found that all sequences corresponding to intron II in maize Ac are absent in pearl millet Ac. Kimura's evolutionary distance between maize and pearl millet Ac sequences is estimated to be 0.429 +/- 0.020 nucleotide substitutions per site. This value is not significantly different from the average number of synonymous substitutions for coding regions of the Adh1 gene between maize and pearl millet, which is 0.395 +/- 0.051 nucleotide substitutions per site. If we can assume Ac and Adh1 divergence times are equivalent between maize and pearl millet, then the above calculations suggest Ac-like sequences have probably not been strongly constrained by natural selection. The level of DNA sequence divergence between maize and pearl millet Ac sequences, the estimated date when maize and pearl millet diverged (25-40 million years ago), coupled with their reproductive isolation/lack of current genetic exchange, all support the theory that Ac-like sequences have not been recently introduced into pearl millet from maize. Instead, Ac-like sequences were probably present in the progenitor of maize and pearl millet, and have thus existed in the grasses for at least 25 million years. Ac-like sequences may be widely distributed among the grasses. We also present the first 2 Ds1 controlling element sequences from teosinte species: Zea luxurians and Zea perennis. A total of 10 Ds1 elements had previously been sequenced from maize and a distant maize relative, Tripsacum. When a maximum likelihood network of genetic relationships is constructed for all 12 sequenced Ds1 elements, the 2 teosinte Ds1 elements are as distant from most maize Ds1 elements and from each other, as the maize Ds1 elements are from one another. Our new teosinte sequence data support the previous conclusion that Ds1 elements have been accumulating mutations independently since maize and Tripsacum diverged. We present a scenario for the origin of Ds1 elements.

Amino Acid Sequence↗
PubMed1988

Evidence for non-neutrality of mitochondrial DNA haplotypes in Drosophila pseudoobscura.

Mitochondrial DNA (mtDNA) haplotypes usually are assumed to be neutral, unselected markers of evolving female lineages. This assumption was tested by monitoring haplotype frequencies in 12 experimental populations of Drosophila pseudoobscura which were polymorphic for mtDNA haplotypes. Populations were maintained for at least 10 generations, and in one case for 32 generations, while tests of mtDNA selective neutrality were conducted. In an initial population, formed from a mixture of two strains with different mitochondrial haplotypes, the frequency of the Bogota haplotype increased 46% in 3 generations, reaching an apparent equilibrium frequency of 82% after 32 generations. Perturbation of this equilibrium by addition of the less common haplotype resulted in a rapid, dramatic increase in frequency of the second haplotype, and a return to essentially the same equilibrium frequency as before perturbation. This behavior is not consistent with mtDNA neutrality, nor is the equilibrium consistent with a simple model of constant selection on the haploid mtDNAs. Replicate cage experiments with mtDNA haplotypes did not always generate the same result as the initial cage. Several lines of evidence, including manipulations of the nuclear genome, support the idea that both nuclear and mitochondrial genomes are involved in the dramatic mtDNA frequency changes. In another experiment, strong female viability selection was implicated via mtDNA frequency changes. Although the causes of the dramatic mtDNA frequency changes in our populations are not obvious, it is clear that Drosophila mitochondrial haplotypes are not always simply neutral markers. Our findings are relevant to the introduction of a novel mtDNA variant from one species or one population into another. Such introductions could be strongly favored by selection, even if it is sporadic.

Animals↗