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J F McDonald

Publications and source records attributed to J F McDonald.

At least 19 recordsLinked to original sources
PubMed1998

An enhancer region within the copia untranslated leader contains binding sites for Drosophila regulatory proteins.

The untranslated leader region (ULR) of the Drosophila LTR retrotransposon copia is known to be critical to the element's expression in a variety of species. Two copia ULR size variants are prevalent in natural populations. The more transcriptionally active full length variants contain within their ULRs two tandemly repeated copies of a 28-bp region of dyad symmetry with a sequence similarity to the core sequence of the SV40 enhancer. The region of dyad symmetry contains two inverted repeats of a 8-bp motif (TTGTGAAA) that occurs at three additional locations within the ULR. The less active ULR gap variants differ from full length variants in that they contain only one copy of the 28-bp sequence. We show that the full length copia ULR in either orientation but not the gap ULR can significantly enhance expression of a minimal hsp 70 promoter. We demonstrate by EMSA that the full length ULR, the gap ULR and the 28-bp sequence are each capable of binding the Drosophila CCAAT/enhancer binding protein (DmC/EBP) and another previously uncharacterized factor, copia binding factor-1 (CBF-1). Another Drosophila protein previously implicated in fat body specific expression of the alcohol dehydrogenase gene (Adh), the Box-B-binding factor-2 (BBF-2), is also shown to bind to the copia ULR.

Animals↗
PubMed1998

Evidence for the role of recombination in the regulatory evolution of Saccharomyces cerevisiae Ty elements.

The recent completion of the sequencing of the Saccharomyces cerevisiae genome provides a unique opportunity to analyze the evolutionary relationships existing among the entire complement of retrotransposons residing within a single genome. In this article we report the results of such an analysis of two closely related families of yeast long terminal repeat (LTR) retrotransposons, Ty1 and Ty2. In our study, we analyzed the molecular variation existing among the 32 Ty1 and 13 Ty2 elements present within the S. cerevisiae genome recently sequenced within the context of the yeast genome project. Our results indicate that while the Ty1 family is most likely ancestral to Ty2 elements, both families of elements are relatively recent components of the S. cerevisiae genome. Our results also indicate that both families of elements have been subject to purifying selection within their protein coding regions. Finally, and perhaps most interestingly, our results indicate that a relatively recent recombination event has occurred between Ty2 and a subclass of Ty1 elements involving the LTR regulatory region. We discuss the possible biological significance of these findings and, in particular, how they contribute to a better overall understanding of LTR retrotransposon evolution.

DNA, Fungal↗
PubMed1998

Interelement selection in the regulatory region of the copia retrotransposon.

We report the results of an analysis of naturally occurring cis-regulatory variation within and between two families of the copia Drosophila long terminal repeat (LTR) retrotransposon. The copia 5' LTR and adjacent untranslated leader region (ULR) consists of a number of well-characterized sequence motifs which play a role in regulating expression of the element. In order to understand the evolutionary forces which may be responsible for generating and maintaining copia regulatory sequence variation, we have quantified levels of naturally occurring copia LTR-ULR nucleotide variation and subjected the data to a series of tests of neutrality. Our analysis indicates that the copia LTR-ULR has been subject to negative purifying selection within families and positive adaptive selection between families. We discuss these findings with respect to the regulatory evolution of retrotransposons and the phenomenon of interelement selection.

5' Untranslated Regions↗
PubMed1998

Evolution of the copia retrotransposon in the Drosophila melanogaster species subgroup.

We report the results of a phylogenetic survey of the retrotransposon copia in the melanogaster subgroup of the Drosophila genus. The polymerase chain reaction was used to amplify the copia 5' long terminal repeat and the adjacent untranslated leader region from representative melanogaster subgroup species. Restriction and sequence analyses of this region reveal discrete classes of copia size variants within the melanogaster subgroup. Phylogenetic comparisons of copia sequence data indicate that the size variants represent different copia subfamilies which diverged prior to their distribution in the melanogaster subgroup. Our results also suggest that copia elements have been subject to horizontal and vertical transmission during their evolution.

Animals↗
PubMed1997

Ionic properties of membrane association by vitamin K-dependent proteins: the case for univalency.

Ionic properties of membrane interaction by prothrombin, protein Z, and other vitamin K-dependent proteins were studied to determine the relevance of a monovalent membrane contact mechanism between one phospholipid headgroup and a calcium-lined pore in the protein [McDonald, J. F., Shah, A. M., Schwalbe, R. A., Kisiel, W., Dahlback, B., and Nelsestuen, G. L. (1997) Biochemistry 36, 5120-5127]. For comparison, multivalent ionic interaction was illustrated by peptides of +3 to +5 net charge and by blood clotting factor V. As expected, the peptides were easily dissociated by salt and gave nominal charge-charge interactions (zazb values) of -13 to -17. Factor V showed much higher binding affinity despite nominal zazb values of about 9. Membrane-bound prothrombin and protein Z showed very low sensitivity to salt as long as calcium was at saturating levels (zazb values of approximately -1.3 to -1.4), appropriate for univalent ionic attraction. Prothrombin contains +3 charge groups (Lys-2, Lys-11, Arg-10) that are absent from the GLA domain (residues 1-35) of protein Z, while protein Z contains -4 charge groups (Gla-11, Asp-34, Asp-35) that are absent in prothrombin. Thus, similar zazb relationships indicated little role for these surface charges in direct membrane contact. Calcium-saturated protein Z bound to phosphatidylcholine (PC) in a manner which indicated the addition of one calcium ion, bringing the total calcium stoichiometry in the protein-membrane complex to at least 8. Protein Z bound to phosphatidic acid (PA) in a manner suggesting the need for a fully ionized phosphate headgroup, a property expected by ion pairing in an isolated environment. Electrostatic calculations showed that the proposed protein site for phosphate interaction was electropositive. The cluster of hydrophobic amino acids (Phe-5, Leu-6, and Val-9) on the surface of prothrombin was electronegative, suggesting a role in the electrostatic architecture of the GLA domain. Overall, membrane binding by vitamin K-dependent proteins appeared consistent with the formation of an ion pair in an isolated environment.

Amino Acid Sequence↗
PubMed1997

Potent inhibition of terminal complement assembly by clusterin: characterization of its impact on C9 polymerization.

The interactions of the heterodimeric apolipoprotein and complement inhibitor, clusterin (CL, 80 kDa), with actively assembling terminal complement proteins were characterized. Clusterin inhibited at three sites and by two modes of action. Clusterin inhibited C9 assembly on C5b-8 and C5b-9 and also bound to C5b-7 to prevent membrane attachment. The impact on C5b-9 assembly was the most potent. C9 assembly was monitored by assembly-induced fluorescence changes of C9 labeled with fluorescein isothiocyanate (FITC-C9). Assembly of monomeric FITC-C9 with C5b-8 or C5b-9(1) produced a substantial decrease in fluorescence intensity due to changes in the environment of the probe. Addition of the next subunit of unlabeled C9 produced a further small change. One equivalent of FITC-C9 bound to C5b-8 at low temperatures, but the fluorescence change and addition of more C9 did not occur until the temperaure was increased. Kinetic analysis of the fluorescence change suggested an irreversible, first-order process with an activation energy of 29 kcal/mol (k = 0.12 s(-1) at 25 degrees C). The kinetic properties differed for C9 addition to C5b-9(1) (0.27 s(-1) at 25 degrees C, 21 kcal/mol), indicating that C9 activation occurred at a different or altered site. Clusterin binding to C5b-8-(FITC-C9)1 caused fluorescence quenching similar to that of unlabeled C9, indicating that it bound to the C9 binding site. Clusterin binding to C5b-8 and C5b-9(1) was reversible with affinities that were 2 and 15 times that of C9 for the C5b-8 and C5b-9(1) complexes, respectively. The results suggested that the presence of <10% of the circulating clusterin in its heterodimeric, active form could reduce the rate of complement cytolysis of nucleated cells by 10-fold, and under some conditions by 100-fold or more. This would provide a high level of protection for certain cells and may allow time for action by other inhibitors of complement.

Clusterin↗
PubMed1997

Comparison of naturally occurring vitamin K-dependent proteins: correlation of amino acid sequences and membrane binding properties suggests a membrane contact site.

Membrane-binding properties of human and bovine forms of vitamin K-dependent proteins Z, S, and C were characterized. Each of these proteins showed unique properties and interspecies differences that correlated with specific amino acid sequence variations in the amino-terminal 45 residues. Protein Z showed 100-fold slower membrane binding and dissociation kinetics relative to other vitamin K-dependent proteins that have been tested. This property seemed to correlate with an extra gamma-carboxyglutamic acid (Gla) residue at position 11 of protein Z. The interspecies difference for protein Z consisted of a higher packing density for the bovine protein on the membrane and a 9-fold slower dissociation rate. Higher affinity correlated with Asp at position 34 of bovine protein Z, where the human protein contains Asn. While both protein S species showed high affinity for the membrane, it was significantly greater for the human protein versus bovine protein S. Again, higher affinity correlated with an Asp (vs Asn) at position 34. Protein C was characterized by binding affinities that were 100-1000-fold lower than the other proteins. Low affinity appeared to be related to loss of Gla-32 (homologous to Gla-33 of protein Z). Interspecies differences of protein C appeared to be related to proline at position 10 (homologous to position 11 of protein Z) of bovine protein C, which produced at least 10-fold lower affinity than the human protein. Comparable substitutions at positions homologous to 11, 33, and 34 of protein Z may also underlie membrane binding behaviors of other vitamin K-dependent proteins. The three-dimensional structure of strontium-prothrombin fragment 1 [Seshadri et al. (1994) Biochemistry 33, 1087] shows that these positions are clustered on the protein surface near strontium-8, another possible candidate for membrane contact. A membrane contact mechanism consisting of an isolated protein-lipid ion pair is proposed. Comparison of naturally occurring vitamin K-dependent proteins has provided possible bases for divergent membrane binding and suggested future approaches to determine biological function.

Amino Acid Sequence↗
PubMed1997

LTR retrotransposons and the evolution of eukaryotic enhancers.

Since LTR retrotransposons and retroviruses are especially prone to regional duplications and recombination events, these viral-like systems may be especially conducive to the evolution of closely spaced combinatorial regulatory motifs. Using the Drosophila copia LTR retrotransposon as a model, we show that a regulatory region contained within the element's untranslated leader region (ULR) consists of multiple copies of an 8 bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation in the number of these motifs is correlated with the enhancer strength of the ULR. Our results indicate that inter-element selection may favor the evolution of more active enhancers within permissive genetic backgrounds. We propose that LTR retroelements and perhaps other retrotransposons constitute drive mechanisms for the evolution of eukaryotic enhancers which can be subsequently distributed throughout host genomes to play a role in regulatory evolution.

Animals↗
PubMed1997

Molecular domestication of mobile elements.

Transposable elements are ubiquitous in all organisms and represent a dynamic component of their genomes, causing mutations and thereby genetic variation. Because of their independent and expansive replication strategy, these elements are called selfish and were thought to have no impact on the adaptive evolution of their host organisms. Although most TE-induced mutations seem to exert only negative effects on the fitness of their carrier, recent evidence indicates that in the course of evolution at least some TE-mediated changes have become established features of the host genome. For example, the insertion of TEs may provide novel cis-regulatory regions to preexisting host genes or TE-derived trans-acting factors may undergo a molecular transition into novel host genes through a process described as molecular domestication. The stationary P element related gene clusters of D. guanche, D. madeirensis and D. subobscura provide an excellent model system to study the evolutionary impact of TEs on genome evolution. Each cluster unit consists of a cis-regulating section composed of different insertion sequences followed by the first three exons of a P element that are coding for a 66 kDa 'repressor-like' protein.

Animals↗
PubMed1996

Naturally occurring variation in copia expression is due to both element (cis) and host (trans) regulatory variation.

Significant differences in levels of copia [Drosophila long terminal repeat (LTR) retrotransposon] expression exist among six species representing the Drosophila melanogaster species complex (D. melanogaster, Drosophila mauritiana, Drosophila simulans, Drosophila sechellia, Drosophila yakuba, and Drosophila erecta) and a more distantly related species (Drosophila willistoni). These differences in expression are correlated with major size variation mapping to putative regulatory regions of the copia 5' LTR and adjacent untranslated leader region (ULR). Sequence analysis indicates that these size variants were derived from a series of regional duplication events. The ability of the copia LTR-ULR size variants to drive expression of a bacterial chloramphenicol acetyltransferase reporter gene was tested in each of the seven species. The results indicate that both element-encoded (cis) and host-genome-encoded (trans) genetic differences are responsible for the variability in copia expression within and between Drosophila species. This finding indicates that models purporting to explain the dynamics and distribution of retrotransposons in natural populations must consider the potential impact of both element-encoded and host-genome-encoded regulatory variation to be valid. We propose that interelement selection among retrotransposons may provide a molecular drive mechanism for the evolution of eukaryotic enhancers which can be subsequently distributed throughout the genome by retrotransposition.

Animals↗
PubMed1996

Venous angiography is needed to interpret inferior petrosal sinus and cavernous sinus sampling data for lateralizing adrenocorticotropin-secreting adenomas.

Bilateral simultaneous venous sampling of ACTH from the inferior petrosal sinus is a reliable test for diagnosing Cushing's disease, but is not reliable for lateralizing ACTH-secreting pituitary adenomas. We reviewed 23 consecutive patients with Cushing's disease who underwent venous angiography of the cavernous and inferior petrosal sinuses followed by bilateral simultaneous venous sampling of ACTH in the inferior petrosal and cavernous sinuses. Venous drainage was bilaterally symmetric in 14 patients (61%) and asymmetric in 9 (39%). The most common asymmetric pattern (6 patients) was for blood from both cavernous sinuses to drain into the right inferior petrosal sinus, with no significant drainage into the left. Cavernous sinus sampling in 21 patients correctly lateralized the tumor in 12 cases of symmetric venous drainage, but in only 3 cases of asymmetric drainage. Inferior petrosal sinus sampling in all 23 patients correctly lateralized the tumor in 12 cases of symmetric drainage, but in only four cases of asymmetric drainage. Overall, venous sampling correctly lateralized 70% of the tumors. Incorrect lateralization in cases of asymmetric venous drainage is probably attributable to shunting of blood toward the side of dominant venous drainage. Our findings illustrate the need for venography in all patients undergoing venous sampling of ACTH because an understanding of the venous drainage patterns is essential to correctly interpret venous sampling data and warn physicians that the lateralization data may be incorrect or unreliable.

Adenoma↗
PubMed1995

Analysis of copia sequence variation within and between Drosophila species.

The sequences of the 5' long-terminal repeat (LTR) and adjacent leader regions of 27 full-length copia elements isolated from natural populations of Drosophila melanogaster, D. simulans, and D. mauritiana are presented. Phylogenetic analyses indicate that although D. melanogaster copia elements are distinct from those of D. simulans and D. mauritiana, the elements of these latter two species are not distinguishable from one another. LTRs and adjacent 5' leader regions of elements isolated from D. simulans and D. mauritiana are structurally similar to one another and carry substantial deletional variation mapping to regions previously identified as being of potential importance for copia expression.

Animals↗
PubMed1993

Evolution and consequences of transposable elements.

Recent studies on transposable elements (TEs) have shed light on the mechanisms that have shaped their evolution. In addition to accumulating nucleotide substitutions over evolutionary time, TEs appear to be especially prone to genetic rearrangements and vertical transmissions across even distantly related species. As a consequence of replicating in host genomes, TEs have a significant mutational effect on their hosts. Although most TE-insertion mutations seem to exert a negative effect on host fitness, a growing body of evidence indicates that some TE-mediated genetic changes have become established features of host species genomes indicating that TEs can contribute significantly to organismic evolution.

Animals↗
PubMed1991

Phosphoramidon blocks the pressor activity of porcine big endothelin-1-(1-39) in vivo and conversion of big endothelin-1-(1-39) to endothelin-1-(1-21) in vitro.

In porcine aortic endothelial cells, the 21-amino acid peptide endothelin-1 (ET-1) is formed from a 39-amino acid intermediate called "big endothelin-1" (big ET-1) by a putative ET-converting enzyme (ECE) that cleaves the 39-mer at the bond between Trp-21 and Val-22. Since big ET-1 has only 1/100-1/150th the contractile activity of ET-1, inhibition of ECE should effectively block the biological effects of ET-1. Big ET-1 injected intravenously into anesthetized rats produces a sustained pressor response that presumably is due to conversion of big ET-1 into ET-1 by ECE. We determined the type of protease activity responsible for this conversion by evaluating the effectiveness of protease inhibitors in blocking the pressor response to big ET-1 in ganglion-blocked anesthetized rats. The serine protease inhibitor leupeptin, the cysteinyl protease inhibitor E-64, and the metalloprotease inhibitors captopril and kelatorphan were all ineffective at blocking the pressor response to big ET-1. However, the metalloprotease inhibitors phosphoramidon and thiorphan dose-dependently inhibited the pressor response to big ET-1, although phosphoramidon was substantially more potent than thiorphan. None of the inhibitors blocked the pressor response to ET-1 and none had any effect on mean arterial pressure when administered alone. In a rabbit lung membrane preparation, ECE activity was identified that was blocked by the metalloprotease inhibitors phosphoramidon and 1,10-phenanthroline in a concentration-dependent manner. This enzyme converted big ET-1 to a species of ET that comigrated on HPLC with ET-1 and produced an ET-like contraction in isolated rat aortic rings. Our results suggest that the physiologically relevant ECE is a metalloprotease.

Animals↗
PubMed1991

Tissue specific expression of the Drosophila Adh gene: a comparison of in situ hybridization and immunocytochemistry.

The tissue specific patterns for Drosophila melanogaster alcohol dehydrogenase (Adh) mRNA and protein expression were determined using in situ hybridization and immunocytochemical techniques. Alcohol dehydrogenase mRNAs were localized in thin sections of frozen tissue using the hybridization of single stranded RNA probes. Alcohol dehydrogenase protein was identified in frozen tissue samples using ADH antisera, a biotinylated secondary antibody, and streptavidin conjugated to horseradish peroxidase. In tissues such as fat body, gastric caeca, and adult cardiac valve, the patterns of expression for ADH protein and mRNA were identical. Other tissues such as oocytes, nurse cells, imaginal disks, and brain show levels of Adh mRNA that are lower than or equivalent to those observed in the previously mentioned tissues, but they exhibit little or no ADH protein. The lack of concordance between Adh mRNA and ADH protein expression in oocytes and nurse cells may reflect the packaging of maternal mRNAs (but not ADH protein) for use in early development. The reason(s) for the other discrepancies in protein and mRNA expression are not known at this time but may be due to post-transcriptional regulation in these specific tissues.

Alcohol Dehydrogenase↗
PubMed1991

Evaluation of recurrent macrodactyly with three-dimensional imaging.

Macrodactyly is a deformity that may progress beyond initial surgical resection. Three-dimensional computed tomography imaging may aid in the surgical planning, given the osseous irregularities that may exist. The objective in revisional surgery of this type is to provide the most functional and cosmetic result. In this case, the hallux was saved when the patient previously had requested an amputation. The case also illustrates that when earlier surgery has been performed, the classic approaches to macrodactyly advocated in the literature may not be feasible. The surgeon must then approach the deformity with some flexibility, and three-dimensional imaging may be a useful tool.

Adult↗
PubMed1990

Inhibition of Escherichia coli glutamine synthetase by alpha- and gamma-substituted phosphinothricins.

We have investigated the inhibition of Escherichia coli glutamine synthetase (GS) with alpha- and gamma-substituted analogues of phosphinothricin [L-2-amino-4-(hydroxymethylphosphinyl)butanoic acid (PPT)], a naturally occurring inhibitor of GS. These compounds display inhibition of bacterial GS that is competitive vs L-glutamate, with Ki values in the low micromolar range. At concentrations greater than Ki the phosphinothricins caused time-dependent loss of enzyme activity, while dilution after enzyme inactivation resulted in recovery of enzyme activity. ATP was required for inactivation; the nonhydrolyzable ATP analogue AMP-PCP failed to support inhibition of GS by the phosphinothricins. The binding of these inhibitors to the enzyme was also characterized by measurement of changes in protein fluorescence, which provided similar inactivation rate constants k1 and k2 for the entire series of compounds. Rate constants koff for recovery were also determined by fluorescence measurement and were comparable for both PPT and the gamma-hydroxylated analogue GHPPT and significantly greater for the alpha- and gamma-alkyl-substituted compounds. Electron paramagnetic resonance spectra provided information on the interaction of the phosphinothricins with the manganese form of the enzyme in the absence of ATP, and significant binding was observed for PPT and GHPPT. 31P NMR experiments confirmed that enzyme inactivation is accompanied by hydrolysis of ATP, although phosphorylated phosphinothricins could not be detected in solution. The kinetic behavior of these compounds is consistent with a mechanism involving inhibitor phosphorylation, followed by release from the active site and simultaneous hydrolysis to form Pi and free inhibitor.

Adenosine Triphosphate↗