Alternative alignments from comparison of protein structures

Comparison of two protein structures often results in not only a global alignment but also a number of distinct local alignments; the latter, referred to as alternative alignments, are however usually ignored in existing protein structure comparison analyses. Here, we used a novel method of protein structure comparison to extensively identify and characterize the alternative alignments obtained for structure pairs of a fold classification database. We showed that all alternative alignments can be classified into one of just a few types, and with which illustrated the potential of using alternative alignments to identify recurring protein substructures, including the internal structural repeats of a protein. Furthermore, we showed that among the alternative alignments obtained, permuted alignments, which included both circular and scrambled permutations, are as prevalent as topological alignments. These results demonstrated that the so far largely unattended alternative alignments of protein structures have implications and applications for research of protein classification and evolution.     

SadA,a novel adhesion receptor in Dictyostelium

Little is known about cell-substrate adhesion and how motile and adhesive forces work together in moving cells. The ability to rapidly screen a large number of insertional mutants prompted us to perform a genetic screen in Dictyostelium to isolate adhesion-deficient mutants. The resulting substrate adhesion-deficient (sad) mutants grew in plastic dishes without attaching to the substrate. The cells were often larger than their wild-type parents and displayed a rough surface with many apparent blebs. One of these mutants, sadA-, completely lacked substrate adhesion in growth medium. The sadA- mutant also showed slightly impaired cytokinesis, an aberrant F-actin organization, and a phagocytosis defect. Deletion of the sadA gene by homologous recombination recreated the original mutant phenotype. Expression of sadA-GFP in sadA-null cells restored the wild-type phenotype. In sadA-GFP-rescued mutant cells, sadA-GFP localized to the cell surface, appropriate for an adhesion molecule. SadA contains nine putative transmembrane domains and three conserved EGF-like repeats in a predicted extracellular domain. The EGF repeats are similar to corresponding regions in proteins known to be involved in adhesion, such as tenascins and integrins. Our data combined suggest that sadA is the first substrate adhesion receptor to be identified in Dictyostelium.     

Length and Sequence Variability in Mitochondrial Control Region of the Milkfish, <Emphasis Type="BoldItalic">Chanos chanos</Emphasis>

Extensive length variability was observed in the mitochondrial control region of the milkfish, Chanos chanos. The nucleotide sequence of the control region and flanking regions was determined. Length variability and heteroplasmy was due to the presence of varying numbers of a 41-bp tandemly repeated sequence and a 48-bp insertion/deletion (indel). The structure and organization of the milkfish control region is similar to that of other teleost fish and vertebrates. However, extensive variation in the copy number of tandem repeats (4–20 copies) and the presence of a relatively large (48-bp) indel, are apparently uncommon in teleost fish control region sequences reported to date. High sequence variability of control region peripheral domains indicates the potential utility of selected regions as markers for population-level studies. Received March 14, 2001; accepted June 29, 2001     

Individual Identification and Paternity Determination in Chimpanzees (Pan troglodytes) Using Human Short Tandem Repeat (STR) Markers

We studied 155 human short tandem repeat (STR) DNA markers in chimpanzees (Pan troglodytes) via the polymerase chain reaction (PCR). There is no difference in number of alleles per locus among STRs of different motif length (di-, tri-, or tetranucleotide repeats). We investigated 42 of the most informative STRs in greater detail using DNA isolated from a panel of 41 African-born, captive-housed chimpanzees. They reveal a wealth of genetic variability in chimpanzees, with an average of six alleles and 70.6% heterozygosity. The average paternity exclusion probability is 51.6%, and the best three STRs jointly provide >95% mean exclusion probability. Used in combination to define a multiple-locus genotype, the five most informative focal STRs can potentially uniquely identify every chimpanzee alive in the world. Although the subjects are of unknown geographical origin, homozygosity tests indicate little evidence for population subdivision. These markers represent the basis of a powerful battery of genetic tests, including individual identification, e.g., in poaching, paternity testing, or reconstruction of pedigrees among captive and wild chimpanzee breeding populations.     

Analysis of the genomic organisation of a small chromosome of Leishmania braziliensis M2903 reveals two genes encoding GTP-binding proteins, one of which belongs to a new G-protein family and is an antigen

Leishmania braziliensis M2903 contains a highly amplified small chromosome. This work is aimed at resolving its structural organization and determining whether this unusual chromosome contains specific genes encoding proteins with important functions in disease pathology or drug resistance. Our results show that the M2903 250-kb small chromosome contains LD1 sequences and has an inverted repeat structure. The LD1 sequences and two cDNAs (cDNA2 and cDNA53) were mapped on a cosmid contig, and the two cDNAs and the corresponding genomic fragments from the small chromosome were sequenced. The gene encoding cDNA2 predicts a putative GTP-binding protein with homology to other GTP-binding proteins only in the G-1 domain region; however, four other conserved motifs can be recognized. Sequence similarity to cDNA53 is located in at least five chromosomes, and its small chromosome copy is a pseudogene. An open reading frame downstream of the cDNA53 pseudogene predicts another GTP-binding protein that belongs to a new G-protein family with an unusual conserved GTP-binding domain and a newly characterized conserved sequence motif. A portion of this GTP-binding protein gene was studied previously in L. aethiopica as a recombinant antigen that reacts with human antibodies.     

Similarity of Structural Features and Evolution of Satellite DNAs from Palorus subdepressus (Coleoptera) and Related Species

A novel highly abundant satellite DNA comprising 20% of the genome has been characterized in Palorus subdepressus (Insecta, Coleoptera). The 72-bp-long monomer sequence is composed of two copies of T₂A₅T octanucleotide alternating with 22-nucleotide-long elements of an inverted repeat. Phylogenetic analysis revealed clustering of monomer sequence variants into two clades. Two types of variants are prevalently organized in an alternating pattern, thus showing a tendency to generate a new complex repeating unit 144 bp in length. Fluorescent in situ hybridization revealed even distribution of the satellite in the region of pericentric heterochromatin of all 20 chromosomes. P. subdepressus satellite sequence is clearly species specific, lacking similarity even with the satellite from congeneric species P. ratzeburgii. However, on the basis of similarity in predicted tertiary structure induced by intrinsic DNA curvature and in repeat length, P. subdepressus satellite can be classified into the same group with satellites from related tenebrionid species P. ratzeburgii, Tenebrio molitor, and T. obscurus. It can be reasonably inferred that repetitive sequences of different origin evolve under constraints to adopt and conserve particular features. Obtained results suggest that the higher-order structure and repeat length, but not the nucleotide sequence itself, are maintained through evolution of these species. Received: 23 April 1997 / Accepted: 11 July 1997     

Population database of STRs in West Africa: a genetic study of TPOX, HUMVWA31/A, HUMTH01, and CYP19

Four tetrameric STRs (TPOX, HUMVWA31/A, HUMTH01, and CYP19) were analysed in a West African population (Cabo Verde). No significant deviations from Hardy–Weinberg proportions were observed, either in conventional or exact tests. Pairwise comparisons confirmed allelic independence for all the combinations of loci. Data is provided for the first time about CYP19 in Black populations. In comparisons between African and Afro‐American populations, significant frequency differences for several alleles at the TH01 and VWA31/A loci were observed. The allele frequencies provided in this study contribute to a better knowledge of the variability of these markers among the main human groups, especially in the context of Subsaharan African populations. This revised version was published online in July 2006 with corrections to the Cover Date.     

Length polymorphism and allele structure of trinucleotide microsatellites in natural accessions of Arabidopsis thaliana

 The objective of this work was to assess the degree of trinucleotide microsatellite length polymorphism in the selfing species Arabidopsis thaliana. PCR amplifications of 12 microsatellite loci among 49 natural populations revealed between one to eight length variants (alleles) for each locus. The average number of alleles per locus was four and the average genetic diversity index was 0.43. Divergence between length variants was investigated at the nucleotide level. Several observations emerge from the sequence data: (1) for most loci, length polymorphism results only from variations in the number of trinucleotide repeats; (2) for a few others, some variability was noted in the flanking sequences; (3) for compound and interrupted loci containing two arrays of trinucleotide repeats, length variations preferentially affect the longest one. Five of the Arabidopsis thaliana accessions were clearly composed of two sublines. In 2 other accessions, some heterozygous individual plants, probably resulting from recent outcrosses, were found. A phylogenetic tree constructed on the basis of trinucleotide microsatellite allelic diversity shows that genetic relationships among the accessions are not correlated with their geographic origin. Received: 4 November 1997 / Accepted: 3 March 1998