Structural and antigenic polymorphism of the 35- to 48-kilodalton merozoite surface antigen (MSA-2) of the malaria parasite Plasmodium falciparum.

Merozoite surface antigen MSA-2 of the human parasite Plasmodium falciparum is being considered for the development of a malaria vaccine. The antigen is polymorphic, and specific monoclonal antibodies differentiate five serological variants of MSA-2 among 25 parasite isolates. The variants are grouped into two major serogroups, A and B. Genes encoding two different variants from serogroup A have been sequenced, and their DNA together with deduced amino acid sequences were compared with sequences encoded by other alleles. The comparison shows that the serological classification reflects differences in DNA sequences and deduced primary structure of MSA-2 variants and serogroups. Thus, the overall homologies of DNA and amino acid sequences are over 95% among variants in the same serogroup. In contrast, similarities between the group A variants and a group B variant are only 70 and 64% for DNA and amino acid sequences, respectively. We propose that the MSA-2 protein is encoded by two highly divergent groups of alleles, with limited additional polymorphism displayed within each group.     

Genetic polymorphism of plasma α1B-glycoprotein and transferrin in arctic and silver foxes

Plasma samples of 235 foxes from 38 complete families (14 of arctic foxes, 21 of silver foxes and 3 with arctic x silver fox hybrid offspring) were analysed by one-dimensional horizontal polyacrylamide gel electrophoresis (PAGE) pH 9.0 followed by general-protein staining of gels. A major postalbumin of fox plasma was identified as alpha 1B-glycoprotein (alpha 1B) by using immunoblotting with antiser m specific to human or pig plasma alpha 1B. Four codominant, autosomal alleles of alpha 1B were found in arctic foxes. Two transferrin (TF) alleles (TfF, TfS) were observed in arctic foxes and two (TfD, Tff) in silver foxes; the TF F type of both of the fox species showed identical electrophoretic mobilities. The arctic foxes showed a high degree of polymorphism for both TF and alpha 1B. The silver foxes showed a scarce polymorphism of TF and were monomorphic for alpha 1B. The arctic fox, silver fox and their hybrids could be clearly differentiated from one another by their plasma protein patterns obtained by the PAGE method.     

Molecular and structural analysis of electrophoretic variants of soybean seed storage proteins

Soybean (Glycine max L.) storage proteins are composed mainly of two major components, beta-conglycinin and glycinin. Electrophoretic variants of the beta subunit of beta-conglycinin and the A3 polypeptide of glycinin were detected on SDS-PAGE, and designated them as beta* and A3*, respectively. beta* and A3* exhibited higher and lower mobilities, respectively, than the common beta subunit and A3 polypeptide. The N-terminal nine and 10 amino acid sequences of beta* and A3* were completely identical to the previously reported sequences of the beta subunit and the A3 polypeptide, respectively. Analysis using concanavalin A-horseradish peroxidase and treatment with N-glycosidase indicated that glycans were not responsible for the difference in electrophoretic mobility of beta* or A3*. Furthermore, five clones of beta* or beta and three clones of A3*, respectively, were sequenced but we could not detect deletions and insertions except for a single or a few amino acid substitutions as compared with the common beta subunit and A3 polypeptide. These results indicate that a single or a few amino acid substitution affects the electrophoretic mobilities of beta* and A3*.     

中华菊头蝠MHCⅡ-DRB 基因遗传多态性及进化

采样自云南同一种群的中华菊头蝠共16 个个体,用于DRB 基因的分子进化和多态性研究。利用翼膜组织提取DNA 基因组,并PCR 克隆测序分析。获得了相差3 bp 的两种不同长度序列类型,A 序列类型263 bp,在研究群体中有15 个等位基因;B 序列类型260 bp,在研究群体中有8 个等位基因。在分析的74 个氨基酸变异位点上检测到12 个正向选择位点。在9 个个体中检测到分布频率最高的等位基因,也有多个等位基因只存在一个个体中。单个个体中最多存在6 个等位基因。遗传多态性分析表明中华菊头蝠DRB 基因具有较高的多态性。中华菊头蝠DRB 基因可能至少存在3 个重复座位。利用已发表的翼手目DRB 第二外显子序列构建的系统进化树表明中华菊头蝠MHCⅡ-DRB 基因处于独立进化支。     

Polymorphism of Δ3,5-Δ2,4-dienoyl-coenzyme A isomerase (the ECH1 gene product protein) in human striated muscle tissue

Two polymorphic variants of the ECH1 gene product protein (delta3,5-delta2,4-dienoyl-coenzyme A isomerase) have been revealed by proteomics methods in samples of human striated muscle tissue. These variants are identical in molecular weight (29.7 kD) but different in pI values (6.57 and 6.75) and in amino acid substitution (41 E-->A) confirmed by mass spectrometry. The same type of polymorphism has been detected in samples of different tissues of the same person, so these variants are considered (also based on other data) to be allelic. The rates of these alleles in two representative cohorts of Moscow and Minsk residents are similar.     

De Novo mutation-like events observed at the 6PGD locus of the Japanese quail,and the principle of polymorphism breeding more polymorphism

In our stock of Japanese quail, four alleles which specify electrophoretic variants A, B, C, and D of an enzyme, 6PGD, are maintained. Analysis of the progeny from a mating which should have produced only known types of heterozygotes enabled us to detect a great variety of mutation-like events which affected the germ cells of the parents. A total of 1011 progeny from 26 such matings were typed for their 6PGD phenotype. Eleven showed unexpected phenotypes, some of which were apparent products of deletions or duplications. Thus, it appeared that the spontaneous rate of occurrence of all the mutation-like events per 6PGD locus per generation approaches 1×10^–2 in Japanese quail. All 11 mutation-like events occurred in the heterozygous parents. Furthermore, 8 of the 11 parents were A/D heterozygotes. A and D show the greatest difference in their electrophoretic mobility, which suggests that two variant subunits differ by several amino acid substitutions rather than by a single amino acid substitution. Of the 11 unexpected progeny, three received new, hitherto nonexistent electrophoretic variants from one of the parents. Perhaps there is a principle that mutation-like events are more likely to occur in germ cells of the parent which is heterozygous for extremely different alleles. This would imply that the new electrophoretic variants presently observed were produced by intracistronic recombination.This work was supported in part by a grant (CA 05138) from the National Cancer Institute, U.S. Public Health Service.     

Genetic polymorphism of human plasma apolipoprotein A-IV is due to nucleotide substitutions in the apolipoprotein A-IV gene

Genetic polymorphism of human plasma apolipoprotein A-IV has been detected by isoelectric focusing techniques followed by immunoblotting. The molecular basis for this apoA-IV polymorphism has been elucidated. Analysis of the protein coding sequences of the apoA-IV alleles 1 and 2 revealed a single G to T substitution in the apoA-IV-2 allele. The point mutation, occurring in a region highly conserved among the mouse, rat, and human A-IV apolipoproteins, converts the glutamine at position 360 of the mature protein to a histidine. This amino acid substitution adds one positive charge unit to the apoA-IV-1 isoprotein (pI 4.97) thus creating the more basic apoA-IV-2 isoprotein (pI 5.02). Computer analysis of the apoA-IV-2 allele revealed that the single G to T substitution results in the loss of a BbvI and a Fnu4HI restriction enzyme site and in the formation of a new restriction site for the enzyme SfaNI. Protein primary and secondary structure predictions were largely unaffected by this amino acid exchange. These results on the structure of the apoA-IV-1 and apoA-IV-2 alleles suggest that the three other rare isoproteins (apoA-IV-0, apoA-IV-3, and apoA-IV-4) are also due to nucleotide and subsequent amino acid substitutions in the apoA-IV sequence.     

Affinity differences for vitamin D metabolites associated with the genetic isoforms of the human serum carrier protein (DBP)

Human vitamin D binding protein (DBP) displays considerable polymorphism with 120 described alleles. Among these, three alleles are frequently observed, Gc 1F (pI 4.94–4.84), Gc 1S (pI 4.95–4.85) and Gc 2 (pI 5.1). Differences between these genetic forms of the protein in affinity for vitamin D metabolites have been detected by electrophoretic methods. The constant affinity (Ka) values determined in this study confirm these differences. The affinities of six rare variants were also examine. Those of the DBP genetic forms to the vitamin D derivatives 25-OH-D₃ and 1,25-(OH)₂-D₃ seem to be related to the isoelectric point of the proteins: a high affinity corresponding to a low isoelectric point. The Gc 1A9 and 1A11 mutants were associated with higher affinity for the vitamin D derivatives and the Gc 1C1 and 1C21 mutants were deficient.     

Transferrin variants in Japan and New Zealand. Report of an unusually sialyzed TF variant

The genetic polymorphism of transferrin (TF) was studied in 2,167 Japanese individuals and in 448 New Zealanders. The three TF C subtypes were identified, but TF C3 was absent from Japanese populations. In addition, three TF B and six TF D variants were observed, each of which occurred either in Japanese or in New Zealanders. Stepwise removal of N-acetyl-neuraminic acid (NANA) with neuraminidase revealed that the most cathodal variant TF DShinnanyo found in a Japanese family was characterized by having only two NANA residues.     

A new allele, DNASE1*6, of human deoxyribonuclease I polymorphism encodes an Arg to Cys substitution responsible for its instability.

A new allele, DNASE1*6, of human deoxyribonuclease I (DNase I) has been discovered by isoelectric focusing: its gene product has the most cathodic pI of the six electrophoretic variants. Results of DNA sequencing, mismatched PCR-restriction fragment length polymorphism, and transient transfection of the variant construct showed that the mutant was caused by a C-T transition at nucleotide position 1826, resulting in an Arg to Cys substitution at amino acid position 185 of the mature enzyme. The variant isoenzyme, expressed in COS-7 cells, was more labile than the other types. Instability and an increase in the pI value of the variant suggest that a structural alteration, perhaps due to aberrant formation of a disulfide bond, could occur in the enzyme.     

Analysis of coding sequences for tissue inhibitor of metalloproteinases 1 (TIMP1) and 2 (TIMP2) in patients with aneurysms.

Aneurysms are characterized by dilation, i.e. expansion and thinning of all the arterial wall layers, which is accompanied by remodeling of the connective tissue. Genes involved in the regulation of tissue remodeling are therefore candidate genes. We analyzed TIMP1 and TIMP2 coding sequences in 12 individuals with abdominal aortic aneurysms (AAA), one individual with AAA and intracranial aneurysms (IA), four individuals with IA and two clinically unaffected individuals. We identified two nucleotide variants in both the TIMP1 and the TIMP2 coding sequences. All differences occurred in the third base positions of codons and were neutral polymorphisms. A significant difference was observed in the frequency of TIMP2 nt 573 polymorphism between 168 alleles from AAA patients and 102 control alleles.     

Partial nucleotide sequences, and routine typing by polymerase chain reaction-restriction fragment length polymorphism, of the brown trout (Salmo trutta) lactate dehydrogenase, LDH-C1*90 and *100 alleles

The cDNA nucleotide sequences of the lactate dehydrogenase alleles LDH-C1*90 and *100 of brown trout (Salmo trutta) were found to differ at position 308 where an A is present in the *100 allele but a G is present in the *90 allele. This base substitution results in an amino acid change from aspartic acid at position 82 in the LDH-C1 100 allozyme to a glycine in the 90 allozyme. Since aspartic acid has a net negative charge whilst glycine is uncharged, this is consistent with the electrophoretic observation that the LDH-C1 100 allozyme has a more anodal mobility relative to the LDH-C1 90 allozyme. Based on alignment of the cDNA sequence with the mouse genomic sequence, a local primer set was designed, incorporating the variable position, and was found to give very good amplification with brown trout genomic DNA. Sequencing of this fragment confirmed the difference in both homozygous and heterozygous individuals. Digestion of the polymerase chain reaction products with BslI, a restriction enzyme specific for the site difference, gave one, two and three fragments for the two homozygotes and the heterozygote, respectively, following electrophoretic separation. This provides a DNA-based means of routine screening of the highly informative LDH-C1* polymorphism in brown trout population genetic studies. Primer sets presented could be used to sequence cDNA of other LDH* genes of brown trout and other species.     

Possible Polyphyletic Origin of Major Histocompatibility Complex Class I Chain-Related Gene A (MICA) Alleles

Phylogenetic relationships among 23 nonhuman primate (NHP) major histocompatibility complex class I chain-related gene (MIC) sequences, 54 confirmed human MICA alleles, and 16 human MICE alleles were constructed with methods of sequence analysis. Topology of the phylogenetic tree showed separation between NHP MICs and human MICs. For human MICs, the topology indicated monophyly for the MICB alleles, while MICA alleles were separated into two lineages, LI and LII. Of these, LI MICA alleles shared a common ancestry with gorilla (Ggo) MIC. One conservative amino acid difference and two nonconservative amino acid differences in the 3 domain were found between the MICA lineages. The nonconservative amino acid differences might imply structural and functional differences. Transmembrane (TM) trinucleotide-repeat variants were found to be specific to the MICA lineages such as A4, A9, and A10 to LI and A5 to LII. Variants such as A5.1 and A6 were commonly found in both MICA lineages. Based on these analyses, we postulate a polyphyletic origin for MICA alleles and their division into two lineages, LI and LII. As such, there would be 30 alleles in LI and 24 alleles in LII, thereby reducing the current level of polymorphism that exists, based on a presumed monophyletic origin. The lower degree of polymorphism in MICA would then be in line with the rest of the human major histocompatibility complex nonclassical class I genes.     

Isoallele Frequencies in Very Large Populations

The frequencies of electrophoretically distinguishable allelic forms of enzymes may be very different from the corresponding frequencies of structurally distinct forms, because many sequence variants may have identical electrophoretic charge. In large populations such frequencies will be determined largely by the number of amino acid sites that are free to vary. The number of distinguishable electrophoretic variants will remain fairly small. Beyond some limiting size, no further effect of population size on allele frequencies is expected, so isolated large populations will have closely similar allele frequencies if polymorphism is due largely to mutation and drift. The most common electrophoretic alleles are expected to be flanked by the next most common, with the rarer alleles increasingly distal. Neither strong selection nor mutation/drift interpretations of enzyme polymorphism are yet disproven, nor is any point between these extremes.     

Identification of base substitutions in ten types of rare variants of phosphoglucomutase-1 (PGM1) encountered in Japanese.

In a previous starch-gel electrophoresis study of erythrocyte phosphoglucomutase-1 (PGM1) in 23,095 Japanese from Hiroshima and Nagasaki, we detected 14 types of rare variant alleles. To determine sequence differences in these rare alleles, cell lines were established from peripheral B-lymphocytes from 24 unrelated individuals in whom nine types of rare variants are presumed to exist on the basis of earlier electrophoresis studies. cDNAs reverse transcribed from mRNAs extracted from these cell lines were amplified by polymerase chain reaction and sequences determined. Amino acid substitution types were deduced from each cDNA sequence. Although two individuals were reported to have an identical electromorph (PGM1 4HR3), sequence analysis revealed that alleles encoding these electromorphs possessed different base substitutions, and one was renamed PGM1 4HR4. As the amino acid substitution of ten different variants could be deduced by cDNA sequence in this study, the effect of each amino acid substitution on enzyme activity could be precisely simulated. The secondary structure of each variant predicted by computer simulations revealed that very decreased activity observed on PGM1 4HR2 protein was caused by significant secondary structure change introduced by the amino acid substitution. On the basis of the crystal structure, the amino acid substitutions of the ten types of rare variants seem to be outside the active center of this enzyme.     

Haemopexin in sheep,mouflon and goat: genetic polymorphism,heterogeneity and partial characterization*

Benzidine staining of starch gels after electrophoresis of sera to which haematin was added revealed polymorphism of haemopexin in sheep, mouflon and goat. In sheep three phenotypes were observed, Hpx A, Hpx AB and Hpx B. Pedigree data support the hypothesis of codominant inheritance from a single locus by two alleles, Hpx^A and Hpx^B. Neuraminidase treatment of haemopexin preparations showed that Hpx B covered two variants, B1 and B2, thus indicating genetic control by three alleles (Hpx^A, Hpx^B1 and Hpx^B2). In sheep populations the frequency of Hpx^B is low. In mouflon, in addition to the two variants that are like those of sheep, absence of haemopexin was observed in some animals, by using starch gel electrophoresis as well as immunoelectrophoresis. In goat, three phenotypes were detected, Hpx A, Hpx AB and Hpx B, differing in migration from those of sheep. Haemopexins of the studied species are heterogeneous. Sialic acid is responsible for electrophoretic heterogeneity of sheep haemopexin. Chemical. composition (amino acid and carbohydrate), molecular weight (56 060) and N-terminal sequence (Leu-Pro-Pro-) of sheep haemopexin were also determined.     

Genetic variation of haemoglobin alpha- and beta-chains in rabbits detected by isoelectric focusing and reversed-phase chromatography

Previous studies on the amino acid sequences and on the amino acid composition of peptides revealed genetic polymorphism both of the haemoglobin alpha-chain (Hb alpha) and beta-chain (Hb beta) in rabbits. In this study, rabbit haemolysates were analysed by isoelectric focusing in a narrow pH range (6.7-7.7) and by reversed-phase chromatography. Two variants were found for both Hb alpha and Hb beta. The two methods detected the same variants in this material. Inheritance data were consistent with the hypothesis that the observed Hb alpha and Hb beta variants were each controlled by two codominant, autosomal alleles. Haemoglobin polymorphism appears to be frequent in domestic rabbits since both variants of each chain were observed in all the three breeds studied.     

Tracing the history of an enzyme polymorphism: the case of alcohol dehydrogenase-2 (Adh-2) of the olive fruit fly Bactrocera oleae

In the olive fruit fly Bactrocera oleae, previous studies have described a one-locus three-allele electrophoretic polymorphism of the enzyme alcohol dehydrogenase and provided evidence that the polymorphism is under the influence of selection. A recent study has shown that this species carries a two-locus duplication for alcohol dehydrogenase. Here, we show that the polymorphism maps at one of the duplicated loci, Adh2, and identify the nucleotide and, therefore, the inferred amino acid differences among the three allozymes. At the amino acid level, the polymorphism is of the simplest possible form: there is no intra-allozyme variation, and interallozyme differences are restricted to one amino acid for two pairs of alleles and to two amino acids for the third pair. Consideration of the amino acid residues at the sites that segregate in B. oleae in four congeneric species and the phylogenetic trees produced from the nucleotide sequences of the Adh2 gene of these species point to the same allozyme as the ancestral form of the polymorphism. Interestingly, this allozyme comprises less than 1% of the gene pool of present-day natural populations of B. oleae, where the other two allozymes appear to form a stable polymorphism. Previous studies have shown that the frequency of the rare allozyme rises rapidly in laboratory colonies maintained on artificial diet and declines again when the artificial diet is replaced with olive fruit, the natural substrate of B. oleae. The geographical distribution of several congeneric species suggests that B. oleae originated in the Indian subcontinent, where the olive tree is practically absent. The poor performance of the ancestral allele on the olive fruit suggests the possibility that the decline of this allele and the concomitant rise of the presently common alleles might be associated with the expansion of the insect's geographical distribution to areas where the olive tree has become its main and perhaps sole host. The estimated age of the polymorphism is compatible with this hypothesis, but firmer support could be difficult to obtain.