Variation in Activities of Amylase Allozymes Associated with Chromosome Inversions in DROSOPHILA PSEUDOOBSCURA, D. PERSIMILIS and D. MIRANDA

Different electrophoretic alleles of amylase show associations with particular chromosome 3 inversions in D. pseudoobscura and D. persimilis. Relative adult amylase activities were compared in 37, 37 and 10 strains of D. pseudoobscura, D. persimilis and D. miranda, respectively. Strains carrying the same electrophoretic allele were compared by crossing these lines individually to a reference strain carrying a different electrophoretic mobility allele. This procedure allows comparisons among species, inversions, electromorphs and strains for genetic variation in amylase activity. F2 analysis established that the activity variation co-segregates with the structural amylase locus. This type of variation could be due to either structural gene differences or differences in closely linked, cis-acting regulatory regions. Variation has been detected among and within electrophoretic mobility classes. Moreover, this variation is clearly nonrandom and reveals more of the genetic structure associated with the chromosomal inversion phylogeny of D. pseudoobscura and D. persimilis. ----Some of the findings are: (1) Similar electromorphs in D. pseudoobscura and D. persimilis usually show different activities. These species show nearly complete differentiation of amylase alleles, based on activities. (2) D. persimilis has the broadest range of variation in amylase activity, about four-fold between the highest and lowest alleles. D. pseudoobscura and D. miranda are also polymorphic for activity, but have more constrained ranges of variation. D. miranda alleles show on the average about four times the activity of D. pseudoobscura alleles. (3) Some association of electrophoretic mobility and activity has been found. Alleles 1.09 of D. persimilis, as well as 1.43 and 1.55 of D. miranda, have relatively high activity. It may be that these high activity alleles are part of an adaptation to cooler habitats. (4) Within electrophoretic classes, associations of activities with inversions have been found. These are especially strong in D. persimilis. The 1.00 alleles in the ST, KL, MD and WT inversions, the 0.92 allele in the ST and MD inversions and the 1.09 allele in the WT and KL inversions have levels of activities that depend upon the arrangement in which they are located. These results demonstrate that suppression of recombination in inversion heterokaryotypes can result in extensive genic divergence between inversions.     

Distinctions among Allelic Variants Associated with Chromosome 3 Inversions in DROSOPHILA PSEUDOOBSCURA and DROSOPHILA PERSIMILIS

Efforts were made to discriminate new genetic variants among electrophoretic alleles that are associated with chromosome 3 inversions of Drosophila pseudoobscura and D. persimilis. Apparent genetic similarities for electrophoretic alleles between these two species and among the common inversions they carry were reexamined by altering gel concentration and buffer pH. At the amylase locus, the 1.09 electrophoretic allele could be further separated into two allelic classes that differentiated the WT and KL arrangements. Similarly, the 0.84 electrophoretic allele was divided into two allelic classes, one characteristic of the Santa Cruz phylad arrangements, TL and SC, and the other found in strains of the Standard phylad arrangements and CH. Uncommon amylase alleles proved to be different alleles in the two species. No new allelic variants, however, could be found among strains with the amylase 1.00 allele, the commonest allele in the Standard phylad of both species. No major new allelic variation was detected for acid phosphatase-3 and larval protein-10 that revealed any further differentiation among species or inversions. Variation at all three loci in strains of the Bogota population remained genetically similar to variation in strains of mainland D. pseudoobscura.     

Balancing Selection on Electrophoretic Variation of Phosphoglucose Isomerase in Two Species of Field Cricket: Gryllus Veletis and G. Pennsylvanicus

Two species of crickets, Gryllus veletis and G. pennsylvanicus, share six electrophoretic mobility classes for the enzyme phosphoglucose isomerase (PGI), despite evidence from other genetic markers that the two species are not closely related within eastern North American field crickets. Moreover, the frequencies of the two most common PGI electrophoretic classes (PGI-100 and PGI-65) covary in sympatric populations of these species in the eastern United States, suggesting that PGI may be subject to trans-specific balancing selection. To determine the molecular basis of the electrophoretic variation, we characterized the DNA sequence of the Pgi gene from 29 crickets (15 G. veletis and 14 G. pennsylvanicus). Amino acid substitutions that distinguish the electrophoretic classes are not the same in the two species, and there is no evidence that specific replacement substitutions represent trans-specific polymorphism. In particular, the amino acids that diagnose the PGI-65 allele relative to the PGI-100 allele differ both between G. veletis and G. pennsylvanicus and within G. pennsylvanicus. The heterogeneity among electrophoretic classes that covary in sympatric populations coupled with analysis of patterns of nucleotide variation suggest that Pgi is not evolving neutrally. Instead, the data are consistent with balancing selection operating on an emergent property of the PGI protein.     

Homopolymer length variation in the Drosophila gene mastermind

Runs of identical amino acids encoded by triplet repeats (homopolymers) are components of numerous proteins, yet their role is poorly understood. Large numbers of homopolymers are present in the Drosophila melanogaster mastermind (mam) protein surrounding several unique charged amino acid clusters. Comparison of mam sequences from D. virilis and D. melanogaster reveals a high level of amino acid conservation in the charged clusters. In contrast, significant divergence is found in repetitive regions resulting from numerous amino acid replacements and large insertions and deletions. It appears that repetitive regions are under less selective pressure than unique regions, consistent with the idea that homopolymers act as flexible spacers separating functional domains in proteins. Notwithstanding extensive length variation in intervening homopolymers, there is extreme conservation of the amino acid spacing of specific charge clusters. The results support a model where homopolymer length variability is constrained by natural selection.Correspondence to: B. Yedvobnick     

Species identification in protozoa: Glucosephosphate isomerase variation in the Paramecium aurelia group

Results are presented for intra- and interspecies variation in electrophoretic mobility of the enzyme glucosephosphate isomerase in the Paramecium aurelia species complex. Three new observations have been made: (1) the hitherto indistinguishable species 1 and 5 can be distinguished on the basis of GPI electrophoretic mobility, (2) the degree of intraspecies variation is much higher for GPI than for the previously studied mitochondrial dehydrogenases and esterases, and (3) several of the enzymatic variants observed in one species are apparently indistinguishable from some found in other species. The intraspecies variants found have been shown to be allelic, and, on the basis of the enzyme patterns of the heterozygotes, it is proposed that GPI is a dimeric enzyme determined by two loci. In view of the use of enzyme variation as a means of species identification in protozoa, these results suggest that the use of such methods can lead to underestimating the number of species and possibly to misclassification. The implications of these findings together with the results obtained with Tetrahymena are discussed.     

A study on the crystalline style of the freshwater mussel,parreysia corrugata

The crystalline style of Parreysia corrugata is a flexible, gelatinous rod of glyco-protein, protrudes from the style sac and impinges on the gastric shield. The style is insoluble in glycerine, alcohol, acetic acid and other dilute acids but it dissolves in distilled water and has a pH 7.0. It contains twelve free amino acids and fourteen protein-bound amino acids. The enzyme amylase was found to be present.     

Hindered migration of amino acids toward their isoelectric positions in gel electrofocusing, and facilitation of the migration at high ionic strength

Amino acids with a largepI -pK_p difference are known to be poor carrier ampholytes in electrofocusing, exhibiting isoelectric zones with poor conductivity across as many as 4 pH units. Accordingly, radioactive amino acids of this type, e.g., glycine, are found to be distributed over the entire pH gradient formed by Ampholine in electrofocusing gels, while radioactive amino acids like histidine or glutamic acid with small pI - pK_p differences form single peaks at or near their pI's. When poor carrier ampholyte amino acids are subjected to gel electrofocusing in 0.1 KCl, their distribution sharpens into single peaks, at or near the pI, indistinguishable from those of the good carrier ampholyte amino acids. At an intermediate stage of peak coalescence of the original broad distributions of poor carrier ampholyte amino acids, in 0.01 KCl, acidic and basic peaks of amino acid can be observed, possibly analogous to acidie and basic distributions previously observed with labeled Ampholine. The rate of peak coalescence of anionic amino acids seems higher than that of the cationic species. The mechanism by which high ionic strength facilitates the condensation of poor carrier ampholyte amino acids at their pI remains unknown. Possibly, the current within zones of poor carrier ampholyte amino acids is insufficient, or poor carrier ampholyte amino acids are not sufficiently charged, to allow for electrophoretic migration of the bulk of loaded amino acid to its isoelectric position, unless the current density is increased by electrofocusing at high ionic strength. Alternatively, 0.1 KCl may interfere with electrovalent interactions between amino acids and isoelectric carrier ampholyte zones, analogous to the action of urea in preventing the interaction between polyanions and carrier ampholytes.     

NONRIBOSOMAL INCORPORATION OF AMINO ACIDS INTO THE TROPONIN-LIKE PROTEIN FROM SYNAPTOSOMES

A preparation of synaptosomal cytoplasm was isolated from forebrain of young rats and incubated with various amino acids in vitro. Incorporation of amino acids into protein was observed. This incorporation did not occur by ribosomal protein synthesis. The amino acid incorporating system was not stimulated by ATP and was inhibited by calcium. The system incorporated amino acids enzymatically. An electrophoretic analysis of the synaptosomal preparation, following incubation in the presence of radioactive amino acids, showed only three labelled protein species (molecular weights 37,000, 26,000 and 20,000). This incorporation of amino acids was found to have a high degree of specificity for three protein species. Migration of the three protein species was found to be nearly identical to that of rabbit muscle troponin. The proteins incorporating amino acids were also found to have other characteristics of the troponin subunits. A possible role of troponin modification is discussed.     

Electrophoretic seed albumin patterns inVicia species of sectt.Hypechusa andPeregrinae (Fabaceae)

This work is a continuation of electrophoretic investigations aimed at revealing a wild relative ofVicia faba. Electrophoretic analysis (PAGE) of seed albumins covered 52 accessions representing eightVicia species of sect.Hypechusa and two species of sect.Peregrinae. Most of the examined species showed an intraspecific variation due to differences between accessions and/or individual variation within accessions. In spite of the intraspecific variation, marked interspecific differences were recorded. However, none of the investigated species displayed electrophoretic seed albumin patterns similar to those reported earlier forV. faba. Contribution of the obtained results to characterization of the examined taxa is discussed.     

Amino acids as determinants of host preference for the xylem feeding leafhopper,Homalodisca coagulata (Homoptera: Cicadellidae)

Summary Homalodisca coagulata is a highly polyphagous xylem feeder with distinct seasonal patterns in it's selection of host plants. These patterns were examined in relation to the amino acid content of the xylem for four common host species; Lagerstroemia indica, Baccharis halimifolia, Prunus persica, and Prunus salicina. Xylem fluid was collected from each host species at times when numbers of feeding leafhoppers were both low and high. In each case, concentrations of amino acids were greatest when numbers were high. Similarly, comparisons between host species at given times showed that concentrations of amino acids were positively correlated with host selection. In a second study, amino acids of xylem were manipulated by budding scions of a non-preferred host (P. persica) on rootstocks of preferred (P. salinica) and non-preferred (P. persica) hosts. Morphology and phenology of the budded trees were similar to that of the scion species yet the xylem composition of amino acids was primarily dependent on the rootstock. Concentrations of amino acids and the preference of leafhoppers were roughly two-fold greater for scions of the preferred than the non-preferred rootstock. In both studies, amides (glutamine plus asparagine) were the amino acids most highly correlated with host selection. These compounds are the predominant amino acids in xylem fluid, have high nitrogen to carbon ratios, and account for a high percentage of the caloric value in xylem fluid. Many of the less abundant amino acids were positively correlated with host preference, but the correlations were less consistent and correlation coefficients were generally lower.Florida Agricultural Experiment Station Journal Series No. 9672     

THE COMPARATIVE EXTENT OF VARIATION OF FREE AMINO ACIDS AND CERTAIN “SECONDARY” SUBSTANCES AMONG CASSIA SPECIES

Alston , R. E. (U. Texas, Austin), and H. S. Irwin . The comparative extent of variation of free amino acids and certain “secondary” substances among Cassia species. Amer. Jour. Bot. 48(1): 35–39. Illus. 1961.—Five species of Cassia, selected to include 4 sections of the genus, were examined by chromatographic methods for free amino acids and for substances visible in ultraviolet light, visible light and after spraying with a general reagent for phenols. The latter, representing a heterogeneous group, are referred to as “secondary” substances (implying that they are not intimately involved in basic energy transfer or assimilative activity of all tissues). Among the species examined there was definite but only moderate variation in the free amino acids present, and differences were predominantly quantitative. In contrast, a minimum of 25 “secondary” substances appeared on the chromatograms when viewed in ultraviolet light and ammonia vapor, with no more than 9 of the spots present in a single species. While free amino acid patterns may be useful in themselves, it seems that patterns of variation of “secondary” substances offer a greater potential in taxonomic work.     

Ecological factors affecting gene flow in the Brachionus plicatilis complex (Rotifera)

We investigated how adaptation to salinity and temperature acts as reproductive barriers in three sympatric species from the Brachionus plicatilis species complex. These species co-occur in a salt marsh in Spain, and a previous electrophoretic study of variation revealed no hybrids between them. A factorial experiment was designed to test for differences in population growth rates and patterns of bisexual reproduction. The design combined representative strains from each species in different salinity and temperature conditions, representing the range over which these rotifers are found in their natural environment. We found differences in the growth response of the three species to both factors and in the pattern of bisexual reproduction. These differences help to explain patterns of succession observed in the field. We conclude that these ecological factors, together with mate recognition systems, account for the absence of gene flow in these sympatric species. Received: 22 July 1996 / Accepted: 14 March 1997     

A common RNA recognition motif identified within a defined U1 RNA binding domain of the 70K U1 snRNP protein

We have defined the RNA binding domain of the 70K protein component of the U1 small nuclear ribonucleoprotein to a region of 111 amino acids. This domain encompasses an octamer sequence that has been observed in other proteins associated with RNA, but has not previously been shown to bind directly to a specific RNA sequence. Within the U1 RNA binding domain, an 80 amino acid consensus sequence that is conserved in many presumed RNA binding proteins was discerned. This sequence pattern appears to represent an RNA recognition motif (RRM) characteristic of a distinct family of proteins. By site-directed mutagenesis, we determined that the 70K protein consists of 437 amino acids (52 kd), and found that its aberrant electrophoretic migration is due to a carboxy-terminal charged domain structurally similar to two Drosophila proteins (su(wa) and tra) that may regulate alternative pre-messenger RNA splicing.     

Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins

We studied the amino acid frequency and substitution patterns between homologues of prokaryotic species adapted to temperatures in the range 0–102°C, and found a significant temperature-dependent difference in frequency for many of the amino acids. This was particularly clear when we analysed the surface and core residues separately. The difference between the surface and the core is getting more pronounced in proteins adapted to warmer environments, with a more hydrophobic core, and more charged and long-chained amino acids on the surface of the proteins. We also see that mesophiles have a more similar amino acid composition to psychrophiles than to thermophiles, and that archea appears to have a slightly different pattern of substitutions than bacteria. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Characterization, expression in Streptomyces lividans, and processing of the amylase of Streptomyces griseus IMRU 3570: two different amylases are derived from the same gene by an intracellular processing mechanism.

Extracellular amylase in Streptomyces lividans was undetectable in starch-supplemented medium. However, S. lividans produced fivefold-higher levels of amylase than Streptomyces griseus IMRU 3570 when transformed with the S. griseus amy gene. Two major proteins of 57 and 50 kDa with amylase activity accumulated in the culture broths of the donor S. griseus and S. lividans transformed with the amy gene. Both proteins were also present in protoplast lysates in the same relative proportion; they gave a positive reaction with antibodies against the 57-kDa amylase. They did not differ in substrate specificity or enzyme kinetics. The two amylases were purified to homogeneity by a two-step procedure. Both proteins showed the same amino-terminal sequence of amino acids, suggesting that both proteins are derived from the same gene. The deduced signal peptide has 28 amino acids with two positively charged arginines near the amino-terminal end. When an internal NcoI fragment was removed from the amy gene, the resulting S. lividans transformants did not synthesize any of the two amylase proteins and showed no reaction in immunoblotting. Formation of the 50-kDa protein was observed when pure 57-kDa amylase was treated with supernatants of protoplast lysates but not when it was treated with membrane preparations, indicating that the native 57-kDa amylase could be processed intracellularly.     

Cloning and characterization of a maltotriose-producing α-amylase gene from <Emphasis Type="Italic">Thermobifida fusca</Emphasis>

The gene (tfa), encoding a maltotriose-producing α-amylase from Thermobifida fusca NTU22, was cloned, sequenced and expressed in Escherichia coli. The gene consists of 1,815 base pairs and encodes a protein of 605 amino acids. The base composition of the tfa coding sequence is 69% G+C and the protein has a predicted pI value of 5.5. The deduced amino acid sequence of the tfa amylase exhibited a high degree of similarity with amylases from Thermomonospora curvata and Streptomyces amylases. The purified amylase could be detected as a single band of about 65 kDa by SDS-polyacrylamide gel electrophoresis and this agrees with the predicted size based on the nucleotide sequence. The optimal pH and temperature of the purified amylase were 7.0 and 60°C, respectively. The properties of purified amylase from the E. coli transformant are similar to that of an amylase purified from the original T. fusca NTU22.     

Comparative characterization of random‐sequence proteins consisting of 5, 12, and 20 kinds of amino acids

Screening of functional proteins from a random‐sequence library has been used to evolve novel proteins in the field of evolutionary protein engineering. However, random‐sequence proteins consisting of the 20 natural amino acids tend to aggregate, and the occurrence rate of functional proteins in a random‐sequence library is low. From the viewpoint of the origin of life, it has been proposed that primordial proteins consisted of a limited set of amino acids that could have been abundantly formed early during chemical evolution. We have previously found that members of a random‐sequence protein library constructed with five primitive amino acids show high solubility (Doi et al., Protein Eng Des Sel 2005;18:279–284). Although such a library is expected to be appropriate for finding functional proteins, the functionality may be limited, because they have no positively charged amino acid. Here, we constructed three libraries of 120‐amino acid, random‐sequence proteins using alphabets of 5, 12, and 20 amino acids by preselection using mRNA display (to eliminate sequences containing stop codons and frameshifts) and characterized and compared the structural properties of random‐sequence proteins arbitrarily chosen from these libraries. We found that random‐sequence proteins constructed with the 12‐member alphabet (including five primitive amino acids and positively charged amino acids) have higher solubility than those constructed with the 20‐member alphabet, though other biophysical properties are very similar in the two libraries. Thus, a library of moderate complexity constructed from 12 amino acids may be a more appropriate resource for functional screening than one constructed from 20 amino acids.     

Random sampling, abundance–extinction dynamics and niche-filtering immigration constraints explain the generation of species richness gradients

Aim  The paradigm that species' patterns of distribution, abundance and coexistence are the result of adaptations of the species to their niches has recently been challenged by evidence that similar patterns may be generated by simple random processes. We argue here that a better understanding of macroecological patterns requires an integration of both ecological and neutral stochastic approaches. We demonstrate the utility of such an integrative approach by testing the sampling hypothesis in a species–energy relationship of forest bird species.
Location  A Mediterranean biome in Catalonia, Spain.
Methods  To test the sampling hypothesis we designed a metacommunity model that reproduces the stochastic sampling from a regional pool to predict local species richness variation. Four conceptually different sampling procedures were evaluated.
Results  We showed that stochastic sampling processes predicted a substantial part (over 40%) of the observed variation in species richness, but left considerable variation unexplained. This remaining variation in species richness may be better understood as the result of alternative ecological processes. First, the sampling model explained more variation in species richness when the probability that a species colonises a new locality was assumed to increase with its niche width, suggesting that ecological differences between species matter when it comes to explaining macroecological patterns. Second, extinction risk was significantly lower for species inhabiting high-energy regions, suggesting that abundance–extinction processes play a significant role in shaping species richness patterns.
Main conclusions  We conclude that species–energy relationships may not simply be understood as a result of either ecological or random sampling processes, but more likely as a combination of both.     

Amylase protein inhibitors and the role of Aegilops species in polyploid wheat speciation

Protein inhibitors extracted with water from seeds of Triticum and genetically related species were characterized according to their apparent molecular weights, electrophoretic mobilities and their specificities in inhibiting α-amylases from human saliva and Tenebrio molitor L. larvae. No detectable amylase inhibition activity was found in extracts from diploid wheats, whereas in all tetraploid and hexaploid wheats as well as in the Aegilops species tested we found several amylase inhibitor groups of different molecular weights. In each group, several inhibitor components slightly different in their electrophoretic mobilities, but identical in their inhibition behaviour toward amylases from different origins have been shown. Both from the qualitative and quantitative standpoints, amylase protein inhibitors from hexaploid wheats were the summation of those from tetraploid wheats plus the ones from Aegilops squarrosa. Amylase inhibitors from Aegilops speltoides largely differed from those extracted from tetraploid wheats as well as from all the amylase inhibitors described in plant seeds up to now. These results indicate a relevant homology between the amylase inhibitor coding genes of the D wheat genome and those of the D Aegilops genome and confirm that Ae. squarrosa is the donor of the whole D genome to hexaploid wheats. They also suggest that Ae. speltoides is not the donor of the B genome to polyploid wheats, although a not yet identified Aegilops species might be such a donor.