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PubMed2005

Differential evolution of repetitive sequences in Cryptosporidium parvum and Cryptosporidium hominis.

Cryptosporidium parvum and Cryptosporidium hominis are two morphologically identical species of Apicomplexan protozoa infecting humans. Although the genomes of these species are 97% identical, their host range is strikingly different. C. parvum infects humans and animals and is primarily a zoonotic infection, whereas C. hominis is typically not detected in animals. The extent of genetic polymorphism in both species has been surveyed locally, but not on a larger geographical scale. Herein, a collection of unrelated C. parvum and C. hominis isolates was genotyped using multiple, randomly distributed micro- and minisatellites. In average, minisatellites, consisting of tandemly repeated sequence motifs of 6-24 basepair, were more polymorphic than microsatellites. When the average number of micro- and minisatellite alleles per locus was used as a measure of heterogeneity, no difference between C. parvum and C. hominis was found. However, the frequency distribution of alleles in both species was significantly different and in 6 of the 14 loci the size of the C. parvum and C. hominis repeats did not overlap. Assuming that C. parvum and C. hominis evolved from a common ancestor, these observations suggest a differential evolution of repeat length at these loci.

Alleles↗
PubMed1987

L1 repeat elements in the human epsilon-G gamma-globin gene intergenic region: sequence analysis and concerted evolution within this family.

We have deduced the sequence of a composite long interspersed repeated DNA in primates and herein describe its relationship to a complex repeat element (L1Heg) located in the interval linking the human epsilon- and G gamma-globin genes. The main element of L1Heg is 3' truncated and interrupted by the insertion of the 3' end of a second L1 element. Transposition of L1Heg into this intergenic locus generated a 62-bp duplication of flanking sequences. In contrast, insertion of the second repeat may have been mediated by homology between donor and target sequences. The main repeat represents a novel class of abundant elements whose sequences have diverged from other rodent and primate LINES approximately 1.3 kb downstream from the 5' terminus of L1Heg. Comparison of L1Heg with the sequences of two other related L1 members revealed a complex set of rearrangements confined within a region that resembles the long terminal repeats of other types of retroposons. The boundaries of conversion-like events were defined on the basis of the clustering of nucleotide sequence variants common to two or more nonallelic 3' L1H elements. Several of these events are apparently initiated or resolved within a common 150-bp region that coincides with the 3' terminus of a pan-mammalian open reading frame. This analysis showed that concerted genetic interactions and random drift both contribute appreciably to sequence variation within this set of L1H members.

Animals↗
PubMed1980

Evolution of DNA sequences has been retarded in Malagasy primates.

It is generally accepted that there are six major groups of living primates: (1) lemurs (including all the primates of Madagascar), (2) lorises (including galago and potto), (3) tarsiers, (4) New World monkeys, (5) Old World monkeys and (6) apes (including man). Tree shrews, once considered to be primates, are now generally recognized as not significantly more closely related to the six groups than other mammals. The first surviving primate lines to diverge from the common primate ancestor are believed to have given rise to one or more of the first three groups. However, the fossil record is insufficient to determine their relative branching order. Furthermore, neither morphological considerations nor studies of protein evolution produce unanimity as to whether tarsiers are more closely related to the prosimians (the lemurs plus lorises) or the simians (the monkeys and apes). In an attempt to resolve these discrepancies, we have measured the DNA sequence difference between several primates. We report here that the evolution of DNA of primates from Madagascar is significantly less than that of all other groups of living primates. This is not expected in the simplest form of the theory of neutral selection and may be important for our understanding of evolution at the molecular level.

Animals↗
PubMed2004

Short variable sequence acquired in evolution enables selective inhibition of various inward-rectifier K+ channels.

Tertiapin (TPN), a small protein toxin originally isolated from honey bee venom, inhibits only certain eukaryotic inward-rectifier K(+) (Kir) channels with high affinity. We found that a short ( approximately 10 residues) sequence in Kir channels, located in the N-terminal part of the linker between the two transmembrane segments, is essential for high-affinity inhibition by TPN and that variability in the region underlies the great variation of TPN affinities among eukaryotic Kir channels. This short variable region is however not present in a bacterial Kir channel (KirBac1.1) or in many other types of prokaryotic and eukaryotic K(+) channels. Thus, the acquisition in evolution of the variable region in eukaryotic Kir channels has created the opportunity to selectively target the numerous types of Kir channel that play important physiological roles. We also show that TPN sensitivity can be readily conferred onto some Kir channels that currently have no known inhibitors by replacing their variable region with that from a TPN-sensitive channel. In heterologous expression systems, such acquired toxin sensitivity will allow currents carried by mutant channels to be readily isolated from interfering background currents. Finally we show that, in the heteromeric GIRK1/4 channels, the GIRK4 and not GIRK1 subunit confers the high affinity for TPN.

Amino Acid Sequence↗
PubMed1983

Evolution of the nucleotide sequence of influenza virus RNA segment 7 during drift of the H3N2 subtype.

The complete genetic information contained in the influenza virus RNA segment 7 of the A/Bangkok/1/79 (H3N2) strain has been cloned by in vitro synthesis of the complementary dsDNA and its insertion into plasmid pBR322. The nucleotide sequence of the viral RNA segment has been determined from the cDNA insert. It is 1027 nucleotides long, and contains two open reading frames, as shown for other influenza virus strains. When compared with the previously published sequence for the A/Udorn/72 (H3N2) strain, 15 nucleotide exchanges are observed, most of them silent mutations, and only two causing amino acid changes in each of the M1 and M2 protein sequences.

Amino Acid Sequence↗
PubMed1985

Polymorphism and evolution of Alu sequences in the human low density lipoprotein receptor gene.

Two clusters of Alu sequences in the human low density lipoprotein (LDL) receptor gene have been analyzed in detail. One Alu cluster is present within the intron separating exons 15 and 16 of the gene and contains a polymorphic Pvu II site. The presence or absence of this site gives rise to two allelic fragments of 14 and 16.5 kilobases, respectively, in genomic Southern blots using cloned cDNA probes. This DNA polymorphic site is caused by a single adenine to guanine transition within an Alu repetitive element. The second cluster of Alu sequences is located in exon 18 of the LDL receptor gene. Southern blotting of primate DNAs suggests that this cluster became associated with the gene about 30 million years ago. Comparison of bovine DNA sequences, which lack this Alu cluster, with those of the human indicates that the Alu sequences inserted in exon 18 in two independent events.

Adult↗
PubMed1993

Overrepresentation of chromosome 12p sequences and karyotypic evolution in i(12p)-negative testicular germ-cell tumors revealed by fluorescence in situ hybridization.

Human testicular germ-cell tumors (TGCTs) comprise a heterogeneous group of solid neoplasms. These tumors are characterized by the presence of a highly specific chromosomal abnormality, i.e., an isochromosome of the short arm of chromosome 12. At present, this i(12p) chromosome is found in more than 80% of TGCTs. Isochromosome 12p has also been observed in some ovarian and extragonadal germ cell tumors. In the remaining so-called i(12p)-negative TGCTs other abnormalities involving chromosome 12, mainly 12p, can be found. In order to establish whether 12p abnormalities other than i(12p) are a common phenomenon in TGCTs, a panel of 11 i(12p)-negative tumors was investigated using multicolor fluorescence in situ hybridization. All TGCTs examined appeared to contain chromosomal abnormalities involving 12p, resulting in a distinct overrepresentation of short arm sequences. In addition, indications were obtained for a clonal evolution in one of the tumors. Our data suggest that the occurrence of 12p abnormalities is a common phenomenon in i(12p)-negative TGCTs and that these abnormalities, analogous to i(12p), may contribute to the process of tumor development.

Chromosome Aberrations↗
PubMed2006

Evolution of short sequence repeats in Mycobacterium tuberculosis.

Whole genome comparison has revealed the presence of short sequence repeats (also called mycobacterial interspersed repeat units and variable number tandem repeat units) used for genotyping schemes. In this study, we have used deletion analysis, single nucleotide polymorphism data and spoligotype taken from published data from others to investigate the evolution of selected repeats that form the common denominators of the majority of established schemes. Analysis of the number of repeats per locus from over 400 isolates revealed that the general trend globally appears to be loss of repeats in modern strains compared with ancestral strains.

DNA, Bacterial↗
PubMed1983

Nucleotide sequences of complementary deoxyribonucleic acids for the pro alpha 1 chain of human type I procollagen. Statistical evaluation of structures that are conserved during evolution.

Nucleotide sequences were determined for two cloned cDNAs encoding for over three-fourths of the pro alpha 1 (I) chain of type I procollagen from man. Comparison with previously published data on amino acid sequences of the alpha 1 (I) chain of type I collagen made it possible to examine mutations in the transcribed products of the gene which have occurred during the evolution of man, calf, rat, mouse, and chick. Comparison of the nucleotide sequences with the corresponding sequences of cDNAs from chick [Fuller, F., & Boedtker, H. (1981) Biochemistry 20, 996] and with cDNAs for the pro alpha 2(I) chain from man [Bernard, M.P., Myers, J. C., Chu, M.-L., Ramirez, F., Eikenberry, E. F., & Prockop, D. J. (1983) Biochemistry 22, 1139] demonstrated that selective pressure during evolution for 250 million or more years acted more strongly on the structure of the pro alpha 1 (I) chain than on the pro alpha 2(I) chain. To improve the reliability of the comparison, the nucleotide sequences were examined with a modification of previous procedures for evaluating mutations in replacement sites and silent sites. The corrected divergence for replacement sites between the alpha 1 (I) chains was 6 +/- 0.8% whereas it was 15 +/- 1.9% for the alpha 2(I) chains. The C-propeptide domain of the pro alpha 1 (I) chain was also highly conserved with a corrected divergence at replacement sites of 5 +/- 0.9%, a value that was not distinguishable from the value previously found for the C-propeptide of the pro alpha 2(I) chain. Therefore, a large part of the structure of both C-propeptides appears to be under selective pressure. Inspection of changes in the C-propeptide of the pro alpha 1 (I) chain suggested that there was a highly conserved region around the carbohydrate attachment site similar to the highly conserved region of 37 amino acids previously found in the C-propeptide of the pro alpha 2(I) chain. Two statistical tests, however, were unable to confirm nonrandom distribution of changes in the C-propeptide of the pro alpha 1(I) chain. The same tests established the presence of a nonrandom distribution in nucleotide changes of the C-propeptide of the pro alpha 2(I) chain. The 3'-noncoding region of the cDNA for pro alpha 1(I) of human type I procollagen showed no homology with the same region in the chick.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed2003

Sequence diversity and evolution of the malaria vaccine candidate merozoite surface protein-1 (MSP-1) of Plasmodium falciparum.

The merozoite surface protein-1 (MSP-1) of the malaria parasite Plasmodium falciparum is a major blood-stage antigen containing highly polymorphic tripeptide repeats in the domain known as block 2 and several non-repetitive domains that are essentially dimorphic. We have analyzed sequence variation in block 2 repeats and in non-repetitive block 17, as well as other polymorphisms within the MSP-1 gene, in clinical isolates of P. falciparum. Repeat haplotypes were defined as unique combinations of repeat motifs within block 2, whereas block 17 haplotypes were defined as unique combinations of single nucleotide replacements in this domain. A new block 17 haplotype, E-TNG-L, was found in one isolate from Vietnam. MSP-1 alleles, defined as unique combinations of haplotypes in blocks 2 and 17 and other polymorphisms within the molecule, were characterized in 60 isolates from hypoendemic Brazil and 37 isolates from mesoendemic Vietnam. Extensive diversity has been created in block 2 and elsewhere in the molecule, while maintaining significant linkage disequilibrium between polymorphisms across the non-telomeric MSP-1 locus separated by a map distance of more than 4 kb, suggesting that low meiotic recombination rates occur in both parasite populations. These results indicate a role for non-homologous recombination, such as strand-slippage mispairing during mitosis and gene conversion, in creating variation in a malarial antigen under strong diversifying selection.

Alleles↗
PubMed2005

Evolution of the longitudinal magnetization for pulse sequences using a fast spin-echo readout: application to fluid-attenuated inversion-recovery and double inversion-recovery sequences.

The fast spin-echo (FSE) sequence is frequently used as a fast data-readout technique in conjunction with other pulse sequence elements, such as in fluid-attenuated inversion-recovery (FLAIR) and double inversion-recovery (DIR) sequences. In order to implement those pulse sequences, an understanding is required of how the longitudinal magnetization evolves during the FSE part of the sequence. This evolution has been addressed to a certain extent by previous publications, but the DIR literature in particular appears to be replete with approximations to the exact expression for the longitudinal magnetization, and several papers contain errors. Equations are therefore presented here for the evolution of the longitudinal magnetization for a FSE readout. These are then applied to calculate the magnetization available immediately prior to the 90 degrees imaging pulse for the FLAIR-FSE and DIR-FSE pulse sequences.

Animals↗
PubMed1994

Sequences of four splits of HLA-A10 group. Implications for serologic cross-reactivities and their evolution.

Nucleotide sequences of alleles encoding four serologically defined splits of the HLA-A10 group, A26.1, A26.3, A26.4, and A10SA, were determined. It was confirmed that the alleles coding for A26.1 and A26.3 are identical with A*2602 and A*2601, respectively. On the other hand, alleles for A26.4 and A10SA are thus far undescribed. A26.4 (A*2603) was different from the other A26 splits at three positions: 74 histidine, 76 valine, and 77 aspartate. A10SA (A*2604) was different from A26.3 (A*2601) by a single substitution of arginine by leucine at position 163. A comparison of amino acid sequences of HLA-A10 cross-reacting antigens revealed that all of the A10 group antigens share specific amino acids: 142 isoleucine, 144 glutamine, 145 arginine, 149 threonine, and 152 glutamate. Moreover, A26.1, A26.3, A10SA, and A43 share 76 alanine and 77 asparagine, which is consistent with the reported serologic cross-reactivity. The close relationship between the alleles for the A10 cross-reacting group was supported by a phylogenetic tree analysis for the HLA-A alleles.

Alleles↗
PubMed1997

Sequence, structure and evolution of the ecdysone-inducible Lsp-2 gene of Drosophila melanogaster.

The Lsp-2 gene encodes a major larval serum protein (hexamerin) of Drosophila melanogaster. Transcription of Lsp-2 is controlled by 20-hydroxyecdysone. Here we report the analysis of the structure of the Lsp-2 gene including the adjacent 5' and 3' sequences. In contrast to all other known hexamerin genes, Lsp-2 does not contain an intron. The Lsp-2 mRNA measures 2312 bases, as deduced from experimental determination of the transcription-start and stop sites and conceptual translation results in a 718 amino acid hexamerin subunit, including a 21-amino-acid signal peptide. While the calculated molecular mass of the native 697-amino-acid subunit is 83.5 kDa, mass spectrometry gave a value of 74.5 kDa. We detected in the Lsp-2 gene a 2052-bp antisense ORF that probably does not code for any protein. An unusual accumulation of rarely used codon triplets was found at the 5' and 3' ends of the Lsp-2 ORF. The calculated secondary structure matches well with that of arthropod hemocyanins. Electron micrographs show for LSP-2 hexamers a cubic shape, which can not be easily reconciled with its hexameric structure. Phylogenetic analysis revealed that LSP-2 diverged from the LSP-1 like hexamerins after separation of the Diptera from other insect orders.

Amino Acid Sequence↗
PubMed1996

Monkey Clara cell 10 kDa protein (CC10): a characterization of the amino acid sequence with an evolutional comparison with humans, rabbits, rats, and mice.

Monkey Clara cell 10 kDa protein (CC10) was purified from monkey lung lavage. This protein showed an apparent molecular weight of about 10 kDa and 5 kDa under non-reducing and reducing conditions, respectively, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. From the amino acid sequence data, monkey CC10 protein consisted of two identical 70-amino-acid polypeptide chains joined by two cystine residues, and possessed sequence identities of 78.6%, 52.9%, 52.9%, and 44.3% with human CC10, rat CC10 (PCB binding protein), rabbit uteroglobin, and mouse CC10, respectively. When monkey CC10 was compared with rabbit uteroglobin (progesterone binding protein), two polar residues of Tyr-21 and Thr-60, important for progesterone binding specificity, were substituted for Phe-21 and Met-60, and thus monkey CC10 may not have a binding capacity with progesterone. Monkey CC10 also possessed a surface homology with lipocortin I (anti-inflammatory peptide), thus suggesting that monkey CC10 plays a role in the anti-inflammatory process at the air-liquid interface over the bronchio-bronchiolar epithelium.

Amino Acids↗
PubMed2001

Elements of thermodynamics in RNA evolution.

The paper presents some aspects correlating thermal stability of RNA folding and the occurrence of structural motifs in natural ribonucleic acids. Particularly, the thermodynamic stability of 2'-5' and 3'-5' linked RNA and the contribution of unpaired terminal nucleotides (dangling ends) in secondary (2D) and tertiary (3D) structures of RNA are discussed. Both examples suggest that during evolution nature selected sequences and structures of RNA which are the most thermally stable and efficient for their biological function.

Base Sequence↗