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E M Prager

Publications and source records attributed to E M Prager.

At least 37 records · Page 2Linked to original sources
PubMed1987

Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila.

Sequence comparisons were made for up to 667 bp of DNA cloned from 14 kinds of Hawaiian Drosophila and five other dipteran species. These sequences include parts of the genes for NADH dehydrogenase (subunits 1, 2, and 5) and rRNA (from the large ribosomal subunit). Because the times of divergence among these species are known approximately, the sequence comparisons give insight into the evolutionary dynamics of this molecule. Transitions account for nearly all of the differences between sequences that have diverged by less than 2%: for these sequences the mean rate of divergence appears to be about 2%/Myr. In comparisons involving greater divergence times and greater sequence divergence, relatively more of the sequence differences are due to transversions. Specifically, the fraction of these differences that are counted as transversions rises from an initial value of less than 0.1 to a plateau value of nearly 0.6. The time required to reach half of the plateau value, about 10 Myr, is similar to that for mammalian mtDNA. The mtDNAs of flies and mammals are also alike in the shape of the curve relating the percentage of positions at which there are differences in protein-coding regions to the time of divergence. For both groups of animals, the curve has a steep initial slope ascribable to fast accumulation of synonymous substitutions and a shallow final slope resulting from the slow accumulation of substitutions causing amino acid replacements. However, the percentage of all sites that can experience a high rate of substitution appears to be only about 8% for fly mtDNA compared to about 20% for mammalian mtDNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1984

Stomach lysozymes of ruminants. I. Distribution and catalytic properties.

A major regulatory shift affecting the expression of lysozyme c may have been involved in the origin of two groups of mammals whose nutrition depends on foregut bacteria. A survey of 23 mammalian species reveals that the lysozyme c activity per g of stomach mucosa is many times higher for ruminants and a leaf-eating monkey than for animals lacking a foregut. The implication is that stomach lysozyme c functions as a major digestive enzyme in ruminant-like mammals, helping to make those bacterial which enter the stomach from the foregut available for hydrolysis by conventional digestive enzymes. The high level of stomach lysozyme is due to more enzyme molecules rather than to an increase in the activity of each molecule. This was shown for the cow by purifying the three, non-allelic lysozymes c that account for the lysozyme activity in gastric mucosa and measuring their specific activities and for other foregut fermenters by immunological titration. Lysozyme appears in the stomach mucosa before birth and reaches adult levels before weaning. Other tissues tested from cattle lack lysozyme c and may instead have low levels of another lysozyme that could belong to the g class, the first indication that lysozyme g may be present in mammals. The lysozymes of eight ruminants, four Old World monkeys, and 12 other animals were compared as regards the ability to lyse bacterial cells under various conditions and to resist inactivation by pepsin. There are differences among these species in the dependence of the rate of bacterial lysis on time, pH, and ionic strength. Although not every lysozyme was tested in all of these catalytic respects, there were no exceptions to the following generalizations. First, at ionic strengths above 0.1 and pH values above 5, the rate of lysis by ruminant and monkey lysozymes c rose with the time of reaction, whereas the rate was more nearly constant for the other animal lysozymes. Second, the lytic activity at neutral pH is lower than at pH 5 for the ruminant and monkey lysozymes c when the ionic strength is over 0.1; by contrast, for other lysozymes c under these conditions the activity at neutral pH is about as high as at pH 5. This latter property, which may be viewed as an adaptation for functioning as a digestive enzyme in the stomach, can be explained in part by differences in electrostatic interactions between lysozyme and the substrate due to the relatively non-basic nature of ruminant and monkey lysozymes compared to other lysozymes c.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1984

Stomach lysozymes of ruminants. II. Amino acid sequence of cow lysozyme 2 and immunological comparisons with other lysozymes.

The complete sequence of 129 amino acids has been determined for one of three closely related lysozymes c purified from cow stomach mucosa. The sequence differs from those known for 17 other lysozymes c at 39-60 positions, at one of which there has been a deletion of 1 amino acid. The glutamate replacement at position 101 and the deletion of proline at position 102 eliminate the aspartyl-prolyl bond that is present between these positions in all other mammalian lysozymes c tested. This bond appears to be the most acid-sensitive one in such lysozymes at physiological temperature. Of the 40 positions previously found to be invariant among lysozymes c, only one has undergone substitution in the cow lineage. This modest number of changes at novel positions is consistent with the inference, based on tree analysis and antigenic comparisons, that the tempo of evolutionary change in the cow lysozyme lineage has not been radically different from that in other lysozyme c lineages. The mutations responsible for the distinctive catalytic properties and stability of cow lysozyme c could be a minor fraction of the total that have been fixed in the cow lineage.

Amino Acid Sequence↗
PubMed1983

Unusual type of mitochondrial DNA in mice lacking a maternally transmitted antigen.

Mice that lack a maternally transmitted antigen (Mta) on the cell surface share a distinctive type of mitochondrial DNA. This is evident from restriction analyses of mitochondrial DNAs from 25 strains of mice whose antigenic state is known. One hundred sixty-eight cleavage sites have been mapped in the mitochondrial DNA of Mta- mice. Detailed maps for the 8 other types of mitochondrial DNA detected in the survey have also been prepared. The Mta- mice are estimated to differ from those expressing the antigen by 108 to 141 base substitutions at widely scattered points in the mitochondrial genome.

Animals↗
PubMed1983

Mitochondrial DNA evolution in mice.

This study extends knowledge of mitochondrial DNA (mtDNA) diversity in mice to include 208 animals belonging to eight species in the subgenus Mus. Highly purified mtDNA from each has been subjected to high-resolution restriction mapping with respect to the known sequence of one mouse mtDNA. Variation attributed to base substitutions was encountered at about 200 of the 300 cleavage sites examined, and a length mutation was located in or near the displacement loop. The variability of different functional regions in this genome was as follows, from least to most: ribosomal RNA, transfer RNA, known proteins, displacement loop and unidentified reading frames. --Phylogenetic analysis confirmed the utility of the Sage and Marshall revision of mouse classification, according to which there are at least four species of commensal mice and three species of aboriginal mice in the complex that was formerly considered to be one species. The most thoroughly studied of these species is Mus domesticus, the house mouse of Western Europe and the Mediterranean region, which is the mitochondrial source of all 50 of the laboratory strains examined and of the representatives of wild house mice introduced by Europeans to North and South America during the past few hundred years. --The level of mtDNA variation among wild representatives of M. domesticus is similar to that for the Eastern European house mouse (M. musculus) and several other mammalian species. By contrast, among the many laboratory strains that are known or suspected to stem from the pet mouse trade, there is little interstrain variation, most strains having the "old inbred" type of domesticus mtDNA, whose frequency in the 145 wild mice examined is low, about 0.04. Also notable is the apparent homogeneity of mtDNA in domesticus races that have fixed six or more fused chromosomes and the close relationship of some of these mtDNAs to those of karyotypically normal mice. --In addition, this paper discusses fossil and other evidence for the view that in mice, as in many other mammals, the average rate of point mutational divergence in mtDNA is 2-4% per million years. From this, it is estimated that the commensal association between mice and our ancestors began more than a million years ago, i.e., at an early stage in the evolution of Homo erectus.

Animals↗
PubMed1982

Mitochondrial DNA sequences of primates: tempo and mode of evolution.

We cloned and sequenced a segment of mitochondrial DNA from human, chimpanzee, gorilla, orangutan, and gibbon. This segment is 896 bp in length, contains the genes for three transfer RNAs and parts of two proteins, and is homologous in all 5 primates. The 5 sequences differ from one another by base substitutions at 283 positions and by a deletion of one base pair. The sequence differences range from 9 to 19% among species, in agreement with estimates from cleavage map comparisons, thus confirming that the rate of mtDNA evolution in primates is 5 to 10 times higher than in nuclear DNA. The most striking new finding to emerge from these comparisons is that transitions greatly outnumber transversions. Ninety-two percent of the differences among the most closely related species (human, chimpanzee, and gorilla) are transitions. For pairs of species with longer divergence times, the observed percentage of transitions falls until, in the case of comparisons between primates and non-primates, it reaches a value of 45. The time dependence is probably due to obliteration of the record of transitions by multiple substitutions at the same nucleotide site. This finding illustrates the importance of choosing closely related species for analysis of evolutionary process. The remarkable bias toward transitions in mtDNA evolution necessitates the revision of equations that correct for multiple substitutions at the same site. With revised equations, we calculated the incidence of silent and replacement substitutions in the two protein-coding genes. The silent substitution rate is 4 to 6 times higher than the replacement rate, indicating strong functional constraints at replacement sites. Moreover, the silent rate for these two genes is about 10% per million years, a value 10 times higher than the silent rate for the nuclear genes studied so far. In addition, the mean substitution rate in the three mitochondrial tRNA genes is at least 100 times higher than in nuclear tRNA genes. Finally, genealogical analysis of the sequence differences supports the view that the human lineage branched off only slightly before the gorilla and chimpanzee lineages diverged and strengthens the hypothesis that humans are more related to gorillas and chimpanzees than is the orangutan.

Animals↗
PubMed1982

Mapping the antigenic epitope for a monoclonal antibody against lysozyme.

A monoclonal antibody (HyHEL-5), prepared to chicken lysozyme c by the method of Köhler and Milstein, identified an antigenic site (epitope) that was shared by the lysozymes of seven different species of galliform birds. The lysozymes of two galliform species, bobwhite quail and chachalaca, shared only partial antigenic identity with the epitope defined by this antibody. Duck lysozyme did not react with the antibody at all. Amino acids that determined the epitope structure were tentatively identified by comparing the amino acid sequences of these lysozymes and assuming the antigenic changes produced by evolutionary substitutions are not due to long-range conformational changes. Arg 68 was identified as a determining amino acid. Arg 68 is hydrogen-bonded to Arg 45, and together these two amino acids form a basic cluster that may be a subsite of the epitope. The antibody inhibited lysis of Micrococcus lysodeikticus by chicken lysozyme. Additionally, Biebrich Scarlet, a dye that binds to the catalytic site, inhibited antibody binding to this lysozyme, which indicates that the epitope extends into the cleft region between Arg 45 and Arg 114. The epitope was hypothesized to involve a region measuring at least 13 x 6 x 15 A including the Arg 68-Arg 45 complex that borders the enzymatic catalytic site. Four other monoclonal antibodies to lysozyme have been partially characterized; each had a distinct pattern of binding specificity for various species of bird lysozymes.

Animals↗
PubMed1980

Mammoth albumin.

Serum albumin was detected immunologically in muscle from a mammoth that died about 40,000 years ago. Rabbits injected with ground mammoth muscle produced antibodies that react strongly with elephant albumin, weakly with sea cow albumin, and still more weakly or not at all with other mammalian albumins. Since elephant albumin elicited antibodies with the same specificity, some of the surviving mammoth albumin molecules evidently have antigenic sites identical to those on native elephant albumin. Much of the mammoth albumin has, however, undergone postmortem change. The small amount of soluble albumin extractable from mammoth muscle is heterogeneous in size, charge, and antigenic properties.

Animals↗
PubMed1979

Amino acid sequence of California quail lysozyme. Effect of evolutionary substitutions on the antigenic structure of lysozyme.

To examine the effect of amino acid substitutions in lysozyme on the binding of antibodies to lysozyme, we purified lysozyme from the egg whites of California quail and Gambel quail. Tryptic peptides were isolated from digests of the reduced and carboxymethylated lysozymes and subjected to quantitative analysis of their amino acid compositions. The two proteins were identical by this criterion. Each peptide from the California quail lysozyme was then sequenced by quantitative Edman degradation, and the peptides were ordered by homology with other bird lysozymes. California quail lysozyme is most similar in amino acid sequence to bobwhite quail lysozyme, from which it differs by two substitutions: arginine for lysine at position 68 and histidine for glutamine at position 121. California and bobwhite quail lysozymes were antigenically distinct from each other in quantitative microcomplement fixation tests, indicating that substitutions at one or both of these positions can alter the antigenic structure of lysozyme. Yet neither of these positions is among those claimed to account for the precise and entire antigenic structure of lysozyme [Atassi, M. Z., & Lee, C.-L. (1978) Biochem. J. 171, 429--434]. Two possible explanations for this discrepancy are discussed.

Amino Acid Sequence↗
PubMed1978

Construction of phylogenetic trees for proteins and nucleic acids: empirical evaluation of alternative matrix methods.

The methods of Fitch and Margoliash and of Farris for the construction of phylogenetic trees were compared. A phenetic clustering technique--the UPGMA method--was also considered. The three methods were applied to difference matrices obtained from comparison of macromolecules by immunological, DNA hybridization, electrophoretic, and amino acid sequencing techniques. To evaluate the results, we used the goodness-of-fit criterion. In some instances, the F-M and Farris methods gave a comparably good fit of the output to the input data, though in most cases the F-M procedure gave a much better fit. By the fit criterion, the UPGMA procedure was on the average better than the Farris method but not as good as the F-M procedure. On the basis of the results given in this report and the goodness-of-fit criterion, it is suggested that where input data are likely to include overestimates as well as true estimates and underestimates of the actual distances between taxonomic units, the F-M method is the most reasonable to use for constructing phylogenies from distance matrices. Immunological, DNA hybridization, and electrophoretic data fall into this category. By contrast, where it is known that each input datum is indeed either a true estimate or an underestimate of the actual distance between 2 taxonomic units, the Farris procedure appears, on theoretical grounds, to be the matrix method of choice. Amino acid and nucleotide sequence data are in this category.

Animals↗
PubMed1978

Comparison of various immunological methods for distinguishing among mammalian pancreatic ribonucleases of known amino acid sequence.

Fourteen mammalian pancreatic ribonucleases of known amino acid sequence were compared by 1 or more of 3 different immunological methods: standard quantitative micro-complement fixation, spot-plate micro-complement fixation, and inhibition of phage inactivation. It was found that, while the results obtained by the 3 techniques were correlated with one another, the standard micro-complement fixation procedure was most versatile, economical of materials, and easiest to execute. The standard MC'F technique was more sensitive than the spot-plate technique to differences in amino acid sequence. The inhibition of phage inactivation method was more sensitive than the standard method for measuring differences among closely related RNases but proved impractical for amino acid differences over 15%; the MC'F method could be extended to at least 30% sequence differences. The standard method, moreover, readily detected the single amino acid difference between dromedary and camel RNases. A linear relationship was found between immunological distance (y) in the MC'F test and percent sequence difference (x) which fit the equation y = 7x. The strength of the correlation between immunological distance and percent sequence difference is consistent with the proposal that a large fraction of the evolutionary substitutions of amino acids in ribonuclease are immunologically detectable. This could be explained either by a multideterminant hypothesis or by a pauci-determinant hypothesis which says that substitutions occurring outside determinants produce small conformational changes influencing determinant reactivity.

Amino Acid Sequence↗
PubMed1976

Congruency of phylogenies derived from different proteins. A molecular analysis of the phylogenetic position of cracid birds.

This communication examines the question of phylogenetic congruency--i.e., whether or not the branching order of evolutionary trees is independent of the protein studied. It was found that trees constructed for birds on the basis of immunological comparison of their transferrins, albumins, and ovalbumins agree approximately with a published tree based on the amino acid sequences of their lysozymes c. This congruency is especially noteworthy with respect to the phylogenetic position of the chachalaca, a Mexican bird classified on morphological grounds in the family Cracidae of the order Galliformes. At the protein level, this species differs as much from non-cracid galliform birds as does the duck, which belongs to another order. Despite the organismal similarity between cracid and non-cracid galliform birds, the molecular relationship is remote. If this contrast between organismal and molecular results had been based on comparative studies with only lysozyme, one could have ascribed the contrast to the possibility that chachalaca lysozyme was paralogous, rather than orthologous, to the other bird lysozymes c. Examination of several proteins is thus desirable in cases of possible paralogy.

Amino Acids↗