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At least 433 records · Page 24Linked to original sources
PubMed1998

Spermatozoa as phylogenetic characters for the Eucestoda.

Spermatozoon ultrastructure and spermiogenesis are significant characters for phylogenetic inference. Sperm ultrastructure is reviewed from the literature in 56 species of Eucestoda. Data are available for 11 of the 12 orders of Eucestoda (Lecanicephalidea excepted), but in some orders data are scarce and often limited to a single species. Spermiogenesis and sperm ultrastructure in the Eucestoda is compared to that of other parasitic Platyhelminthes, with emphasis on structures of phylogenetic interest. Not only the descriptions of sperm structure, but those of the process of spermiogenesis, are necessary to define characters. Synapomorphies based on sperm ultrastructure for the Eucestoda include the absence of a mitochondrion in mature sperm and the presence of a crested body. A proposed synapomorphy for the Cyclophyllidea + Tetrabothriidea is the twisting of the peripheral microtubules; the absence of intercentriolar body and the absence of striated roots in the spermatid may constitute additional synapomorphies for this assemblage. Absence of flagellar rotation during spermiogenesis is synapomorphic for the Cyclophyllidea, and absence of proximodistal fusion could be synapomorphic for a part of the Cyclophyllidea. Several other characters could be useful for understanding phylogeny within the Eucestoda. The polarity of these characters could in several cases be determined, but diagnoses for taxa or relationships based on synapomorphies cannot be specified unequivocally due to putative convergence. Such characters and their putative polarity include: (1) the number of axonemes in mature spermatozoon (plesiomorphic=2; apomorphic=1); (2) size and number of crested bodies (p=1; a=several); and (3) angle of twisted microtubules; shape of nucleus (p=compact cord; a=crescent and annulus). Additional apomorphic attributes include (1) presence of a periaxonemal sheath (a putative synapomorphy for the Cyclophyllidea + Tetrabothriidea if reversals are postulated in certain cyclophyllideans); (2) presence of proteinaceous transverse walls; (3) presence of dense granules; and (4) shape of apical cones and posterior structures. Studies of sperm structure in the poorly known orders and additional comparative studies in the Cyclophyllidea are expected to provide new information for elucidation of phylogenetic relationships.

Animals↗
PubMed2002

Phylogenetic relationships among Spanish Barbus species (Pisces, Cyprinidae) shown by RAPD markers.

Random amplified polymorphic DNA (RAPD) markers were used to estimate the population structure and phylogenetic relationships among the eight species of the genus Barbus that inhabit the Iberian Peninsula. Ten random oligodecamers were used to amplify DNA from 232 fish sampled from 15 populations. A total of 270 markers were detected that revealed low levels of genetic variability. The conclusions of cluster analysis indicate two main branches and three well-differentiated groups: north-eastern, Mediterranean and Atlantic. This clustering mainly reflects the evolutionary history of the genus, which is closely related to the paleogeography of the Iberian Peninsula. The contribution and application of these results to the conservation of the species, to their taxonomic status and to the process of colonization of the Iberian Peninsula by the genus Barbus are discussed.

Animals↗
PubMed2006

The Parkinson disease gene LRRK2: evolutionary and structural insights.

Mutations in the human leucine-rich repeat kinase 2 (LRRK2) gene are associated with both familial and sporadic Parkinson disease (PD). LRRK2 belongs to a gene family known as Roco. Roco genes encode for large proteins with several protein domains. Particularly, all Roco proteins have a characteristic GTPase domain, named Roc, plus a domain of unknown function called COR. In addition, LRRK2 and several other Roco proteins also contain a protein kinase domain. In this study, I use a combination of phylogenetic and structural analyses of the COR, Roc, and kinase domains present in Roco proteins to describe the origin and evolutionary history of LRRK2. Phylogenetic analyses using these domains demonstrate that LRRK2 emerged from a duplication that occurred after the protostome-deuterostome split. The duplication was followed by the acquisition by LRRK2 proteins of a specific type of N-terminal repeat, described here for the first time. This repeat is absent in the proteins encoded by the paralogs of LRRK2, called LRRK1 or in protostome LRRK proteins. These results suggest that Drosophila or Caenorhabditis LRRK genes may not be good models to understand human LRRK2 function. Genes in the slime mold Dictyostelium discoideum with structures very similar to those found in animal LRRK genes, including the protein kinase domain, have been described. However, phylogenetic analyses suggest that this structural similarity is due to independent acquisitions of distantly related protein kinase domains. Finally, I confirm in an extensive sequence analysis that the Roc GTPase domain is related but still substantially different from small GTPases, such as Rab, Ras, or Rho. Modeling based on known kinase structures suggests that mutations in LRRK2 that cause familiar PD may alter the local 3-dimensional folding of the LRRK2 protein without affecting its overall structure.

Amino Acid Sequence↗
PubMed2001

Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation.

Automatic identification of sub-structures in multi-aligned sequences is of great importance for effective and objective structural/functional domain annotation, phylogenetic treeing and other molecular analyses. We present a segmentation algorithm that optimally partitions a given multi-alignment into a set of potentially biologically significant blocks, or segments. This algorithm applies dynamic programming and progressive optimization to the statistical profile of a multi-alignment in order to optimally demarcate relatively homogenous sub-regions. Using this algorithm, a large multi-alignment of eukaryotic 16S rRNA was analyzed. Three types of sequence patterns were identified automatically and efficiently: shared conserved domain; shared variable motif; and rare signature sequence. Results were consistent with the patterns identified through independent phylogenetic and structural approaches. This algorithm facilitates the automation of sequence-based molecular structural and evolutionary analyses through statistical modeling and high performance computation.

Algorithms↗
PubMed1991

Molecular studies of corticosteroid binding globulin structure, biosynthesis and function.

Phylogenetic comparisons of the primary structure of corticosteroid binding globulin (CBG) have revealed several conserved domains that include sites for N-glycosylation and a region which probably represents a portion of the steroid binding site. The major site of CBG biosynthesis in adults is clearly the liver, and the human CBG gene promoter contains sequence elements that interact with liver-specific transcription factors. Low levels of CBG gene expression have been detected in other tissues, and these may be important for fetal development during late gestation when hepatic CBG mRNA levels are low. Studies of the ontogeny of CBG biosynthesis in the rat have also indicated that plasma CBG levels may be influenced by a more rapid clearance of the protein during pubertal development. Analyses of the structural organization and chromosomal location of the human CBG gene have further confirmed its close relationship with the serine proteinase inhibitors, and suggests that CBG, alpha 1-proteinase inhibitor and alpha 1-antichymotrypsin evolved relatively recently by gene duplication. The functional significance of this relationship has been examined and our studies suggest that a specific interaction between CBG and elastase on the surface of neutrophils may represent a physiologically important event that promotes the delivery of glucocorticoids to these cells at sites of inflammation.

Amino Acid Sequence↗
PubMed1992

Nucleotide sequence of the 3' terminal region of belladonna mottle virus-Iowa (renamed Physalis mottle virus) RNA and an analysis of the relationships of tymoviral coat proteins.

The 3' terminal 1255 nt sequence of Physalis mottle virus (PhMV) genomic RNA has been determined from a set of overlapping cDNA clones. The open reading frame (ORF) at the 3' terminus corresponds to the amino acid sequence of the coat protein (CP) determined earlier except for the absence of the dipeptide, Lys-Leu, at position 110-111. In addition, the sequence upstream of the CP gene contains the message coding for 178 amino acid residues of the C-terminus of the putative replicase protein (RP). The sequence downstream of the CP gene contains an untranslated region whose terminal 80 nucleotides can be folded into a characteristic tRNA-like structure. A phylogenetic tree constructed after aligning separately the sequence of the CP, the replicase protein (RP) and the tRNA-like structure determined in this study with the corresponding sequences of other tymoviruses shows that PhMV wrongly named belladonna mottle virus [BDMV(I)] is a separate tymovirus and not another strain of BDMV(E) as originally envisaged. The phylogenetic tree in all the three cases is identical showing that any subset of genomic sequence of sufficient length can be used for establishing evolutionary relationships among tymoviruses.

Amino Acid Sequence↗
PubMed2006

[Molecular characterization of O-antigen gene cluster of Escherichia coli O23 reference strain and identification of UDP-N-acetylglucosamine 4-epimerase].

Lipopolysaccharide (LPS) is one of the major components of the outer membrane of gram-negative bacteria. It is an amphipathic molecule composing of lipid A, a core oligosaccharide and an O-specific antigen. O-antigen, which is a repeat unit polysaccharide, is a major contribution to the antigenic variability of the bacterial cell surface. Genes involved in O-antigen biosynthesis are generally found to be clustered between the housekeeping genes galF and gnd on the chromosome of E. coli. E. coli O23 is one of the enterotoxigenic E. coli causing pediatric diarrhea in the developing world. The O-antigen gene cluster of E. coli O23 type strain was amplified by long-range PCR using primers based on galF and gnd and then sequenced. Except for galF and gnd, seven open reading frames were identified and assigned functions on the basis of their similarity to those from available databases. The seven genes include a UDP-N-acetylglucosamine 4-epimerase gene (gne), the O-antigen polymerase gene (wzy), the O-antigen transferase gene (wzx) and four glycosyltransferase genes (orf2, orf4, orf5, orf6). The UDP-N-acetylglucosamine 4-epimerase (Gne) was identified by mutation and complementation complement tests. The structure of Gne was predicted by the homology modeling method, and the active sites were also analyzed. The phylogenetic and structural analysis showed that the Gne derived from the common ancestor with E. coli O23 Gne were UDP-GlcNAc/UDP-GalNAc epimerases. The specific DNA used for rapid molecular genotyping for E. coli O23 was also identified.

Base Sequence↗
PubMed2002

Phylogenetic analysis of the genus Plasmodium based on the gene encoding adenylosuccinate lyase.

Phylogenetic studies of the genus Plasmodium have been performed using sequences of the nuclear, mitochondrial and plastid genes. Here we have analyzed the adenylosuccinate lyase (ASL) gene, which encodes an enzyme involved in the salvage of host purines needed by malaria parasites for DNA synthesis. The ASL gene is present in several eukaryotic as well as prokaryotic organisms and does not have repeat regions, which facilitates the accuracy of the alignment. Furthermore, it has been shown that ASL is not subject to positive natural selection. We have sequenced the ASL gene of several different Plasmodium species infecting humans, rodents, monkeys and birds and used the obtained sequences along with the previously known P. falciparum ASL sequence, for structural and phylogenetic analysis of the genus Plasmodium. The genetic divergence of ASL is comparable with that observed in other nuclear genes such as cysteine proteinase, although ASL cannot be considered conserved when compared to aldolase or superoxide dismutase, which exhibit a slower rate of evolution. Nevertheless, a protein like ASL has a rate of evolution that provides enough information for elucidating evolutionary relationships. We modeled 3D structures of the ASL protein based on sequences used in the phylogenetic analysis and obtained a consistent structure for four different species despite the divergence observed. Such models would facilitate alignment in further studies with a greater number of plasmodial species or other Apicomplexa.

Adenylosuccinate Lyase↗
PubMed1998

Distinct functions of the closely related tandem RNA-recognition motifs of hnRNP A1.

hnRNP A1 regulates alternative splicing by antagonizing SR proteins. It consists of two closely related, tandem RNA-recognition motifs (RRMs), followed by a glycine-rich domain. Analysis of variant proteins with duplications, deletions, or swaps of the RRMs showed that although both RRMs are required for alternative splicing function, each RRM plays distinct roles, and their relative position is important. Surprisingly, RRM2 but not RRM1 could support this function when duplicated, despite their very similar structure. Specific RNA binding and annealing are not sufficient for hnRNP A1 alternative splicing function. These observations, together with phylogenetic and structural data, suggest that the two RRMs are quasi-symmetric but functionally nonequivalent modules that evolved as components of a single bipartite domain.

Alternative Splicing↗
PubMed2004

Phylogenetic clusters of rhizobia revealed by genome structures.

Rhizobia, bacteria that fix atmospheric nitrogen, are important agricultural resources. In order to establish the evolutionary relationships among rhizobia isolated from different geographic regions and different plant hosts for systematic studies, we evaluated the use of physical structure of the rhizobial genomes as a phylogenetic marker to categorize these bacteria. In this work, we analyzed the features of genome structures of 64 rhizobial strains. These rhizobial strains were divided into 21 phylogenetic clusters according to the features of genome structures evaluated by the endonuclease I-CeuI. These clusters were supported by 16S rRNA comparisons and genomic sequences of four rhizobial strains, but they are largely different from those based on the current taxonomic scheme (except 16S rRNA).

Genome, Bacterial↗
PubMed1997

Isolation of several human axonemal dynein heavy chain genes: genomic structure of the catalytic site, phylogenetic analysis and chromosomal assignment.

Dynein heavy chains (DHCs) are the main components of multisubunit motor ATPase complexes called dyneins. Axonemal dyneins provide the driving force for ciliary and flagellar motility. Recent molecular studies demonstrated that multiple DHC isoforms are produced by separate genes. We describe the isolation of five human axonemal DHC genes. Analysis of the human genomic clones revealed the existence of intronic sequences that were used to demonstrate that human axonemal DHC genes are located on different chromosomes. The cloned human DHC sequences were integrated into an evolutionary approach based on phylogenetic analysis. Tissue expression studies showed that these human axonemal DHCs are expressed in testis and/or trachea, two tissues with axonemal structures that can be altered in primary ciliary dyskinesia, making DHC genes strong candidates in the genesis of these human diseases.

Amino Acid Sequence↗
PubMed2003

An unusual receptor tyrosine kinase of Schistosoma mansoni contains a Venus Flytrap module.

Previous studies have suggested that successful development of the parasitic helminth Schistosoma mansoni must be dependent on an adaptative molecular dialogue with its hosts and on the existence of receptors for growth factors and hormones. Attempts to identify a homolog of the insulin receptor (IR) have led us to characterize a new receptor tyrosine kinase (RTK) molecule in S. mansoni. SmRTK-1 is an integral membrane protein with a single membrane-spanning sequence separating an extracellular ligand-binding domain and a cytoplasmic TK domain. Structural and phylogenetic analyses of the kinase domain of SmRTK-1 confirmed its similarity to IR catalytic domains. However, sequence analysis of the extracellular domain of SmRTK-1 revealed similarity with various proteins (such as drug receptors) that share a structure known as the Venus Flytrap (VFT) module. Alignment with other VFT modules for which the structure has been solved was used to generate a 3D model of the putative VFT module of SmRTK-1. Phylogenetic analysis indicated that the SmRTK-1 VFT module was closer to that of the GABA(B) receptor. Numerous RTK genes recently discovered in vertebrate and invertebrate species code for large families of modular proteins with diverse structures and ligand-binding specificities. SmRTK-1 probably represents a new class of RTK whose function remains to be determined. RTKs are present in all metazoans and associated with the control of metabolism, growth and development. The preferential localization of SmRTK-1 in sporocyst germinal cells and ovocytes could be in favor of its function in schistosome growth and differentiation.

Amino Acid Sequence↗
PubMed1998

The comparison of microglia maturation in different structures of the human nervous system.

The aim of the study was to find out whether differences in morphology and time-sequence of microglia appearance in course of development of the phylogenetically different structures of the central nervous system (CNS) in normal human fetus do exist. An attempt was also made to evaluate quantitatively the development of microglial cells in comparison to astroglia, taking into account their role in the structural and immunological maturation of the CNS. The study was performed on CNS tissue of frontal lobes, mesencephalon and cerebellum from 72 fetuses between 8 and 22 week of gestation (GW). Histochemical and immunohistochemical reactions were used as basic study methods. A quantitative evaluation of developing microglia and astroglia in all investigated structures was performed by counting the mean number of cells per 1 mm2. Morphological and ultrastructural patterns of the three basic types of microglia; ameboid, ramified active and ramified resting, were characterized. It was indicated that they emerge at the same time in all structures under study, except the ameboid microglia arising earlier in the mesencephalon. A quantitative evaluation revealed that the number of ameboid microglial cells decreased slightly in an early stage of fetal development. The number of ramified microglial cells between 11 and 22 GW increased in all structures. The highest values of ramified microglia were found in mesencephalon, and the lowest in white matter of cerebellum. The number of astroglial cells exceeded the increase in ramified microglia by several times in all structures.

Brain↗
PubMed1999

Evolutionary genetics of Trypanosoma and Leishmania.

We review recent advances in the study of population structure and phylogenetic diversity of parasites belonging to the genera Trypanosoma and Leishmania. In all species properly analyzed, these parasites exhibit a basically clonal population structure, with occasional bouts of genetic exchange or hybridization, and a strong structuration of their populations into discrete evolutionary lineages. On an evolutionary scale, the impact of sex appears to be greater in African than in American trypanosomes. The taxonomic status of some Leishmania 'species' is questionable.

Animals↗
PubMed1997

bilbo, a non-LTR retrotransposon of Drosophila subobscura: a clue to the evolution of LINE-like elements in Drosophila.

We used the repetitive character of transposable elements to isolate a non-LTR retrotransposon in Drosophila subobscura. bilbo, as we have called it, has homology to TRIM and LOA elements. Sequence analysis showed a 5' untranslated region (UTR), an open reading frame (ORF) with no RNA-binding domains, a downstream ORF that had structural homology to that of the I factor, and, finally, a 3' UTR which ended in several 5-nt repeats. The results of our phylogenetic and structural analyses shed light on the evolution of Drosophila non-LTR retrotransposons and support the hypothesis that an ancestor of these elements was structurally complex.

Amino Acid Sequence↗
PubMed2026

Molecular Cloning, Recombinant Expression, and In Silico Structural Analysis of Cu/Zn-Superoxide Dismutase from Trachyspermum ammi.

Superoxide dismutase (SOD) is an essential antioxidant metalloenzyme that is critical for the cellular defense against oxidative damage, as it scavenges superoxide radicals and maintains the redox status. Cytosolic Cu/Zn-SOD is particularly important in the regulation of oxidative stress among different isoforms in higher plants. While Cu/Zn-SODs from several plant species have been characterized, molecular information is limited for Trachyspermum ammi, a medicinally important member of a family Apiaceae with antioxidant potential.In the present study, an integrated molecular and in silico approach has been taken to clone and analyze a Cu/Zn type SOD gene from T. ammi to get insight into its structural and evolutionary characteristics. PCR amplification yielded an open reading frame of 456 bp encoding a protein of 152 amino acids. Sequence analysis showed that plant Cu/Zn-SODs, especially those from Daucus carota, were highly similar to one another (about 90-95%).Multiple sequence alignment confirmed the presence of conserved catalytic motifs and metal-binding histidine residues, both of which are crucial for enzymatic function. Physicochemical analysis predicted the protein to be stable, hydrophilic and compatible with cytosolic localization. The analysis of secondary structure indicated a predominance of β-strands, consistent with the conserved β-barrel architecture of plant Cu/Zn-SODs.The three-dimensional structure was built by homology modeling using a closely related plant Cu/Zn-SOD template with high sequence identity. Structural validation demonstrated an acceptable stereochemical quality with 86.3% residues in the favored region of Ramachandran plot, satisfactory ERRAT and Verify3D scores, and a low RMSD value of 0.104 Å on structural superimposition. Phylogenetic analysis placed the enzyme in the Apiaceae lineage, suggesting evolutionary conservation among related plant species. In conclusion, this study presents the first molecular and structural characterization of Cu/Zn-SOD from T. ammi and confirms the existence of a conserved structural framework typical of plant Cu/Zn-SODs. These results provide a basis for further studies concerning recombinant expression, enzymatic validation and potential relevance in antioxidant and plant stress biology.

Cloning, Molecular↗
PubMed2003

Integration of related sequences with protein three-dimensional structural families in an updated version of PALI database.

The database of Phylogeny and ALIgnment of homologous protein structures (PALI) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of protein domains in various families. The latest updated version (Release 2.1) comprises of 844 families of homologous proteins involving 3863 protein domain structures with each of these families having at least two members. Each member in a family has been structurally aligned with every other member in the same family using two proteins at a time. In addition, an alignment of multiple structures has also been performed using all the members in a family. Every family with at least three members is associated with two dendrograms, one based on a structural dissimilarity metric and the other based on similarity of topologically equivalenced residues for every pairwise alignment. Apart from these multi-member families, there are 817 single member families in the updated version of PALI. A new feature in the current release of PALI is the integration, with 3-D structural families, of sequences of homologues from the sequence databases. Alignments between homologous proteins of known 3-D structure and those without an experimentally derived structure are also provided for every family in the enhanced version of PALI. The database with several web interfaced utilities can be accessed at: http://pauling.mbu.iisc.ernet.in/~pali.

Animals↗
PubMed2003

The marsupial placenta: a phylogenetic analysis.

The structure, physiology, and endocrinology of the yolk sac placenta of different marsupial groups is compared and phylogenetically analyzed to provide information on placental characters in the marsupial stem species. We conclude that the marsupial stem species possessed a functional yolk sac placenta. Histotrophic nutrition by uterine secretion decreased during late pregnancy and at least half of the yolk sac was vascularized at the time of shell coat rupture. Due to yolk sac fusion, the larger part of the avascular, bilaminar yolk sac could not serve as a placenta at late gestation in the polyovular marsupial stem species. The bilaminar yolk sac gained a relatively greater importance for nutrition in monovular australidelphians. In macropodids a greater proportion of the yolk sac remained bilaminar at the time of shell coat rupture than in the stem species. Another derived feature of macropodids is the sustained plasma progesterone synthesis that is in turn responsible for an extended secretory phase of the uterus and a lengthened gestation. The placenta of the marsupial stem species was probably capable of metabolising histo- and hemotrophes. Recognition of pregnancy during early stages of development is a derived character of macropodids that we suggest did not occur in the marsupial stem species. However, birth and birth behaviour were apparently induced by prostaglandins in the marsupial stem species. Although the yolk sac formed the definitive placenta, it is likely that the allantois provided a supplementary placental function in the marsupial stem species, but that the role of the allantois became progressively less important during the evolution of marsupial placentation.

Animals↗