Molecular evolution of satellite DNA CLsat in lizards of the Darevskia species (Sauria: Lacertidae): correlation with species diversity

The structure and evolution of a satellite DNA family was examined in lizards from the genus Darevskia (family Lacertidae). Comparison of tandem units of repeated DNA (satDNA), CLsat, in all species from the genus Darevskia has shown that their variability is largely based on single-nucleotide substitutions, which constitute about 50 diagnostic positions underlying classification of the family into three subfamilies. Maximum differences between the subfamilies reached 25%. At this level of tandem unit divergence between the subfamilies, no cross-hybridization between them was observed (at 65 degrees C). The individual variability of one subfamily within the species was on average 5% while the variability between species consensuses within a subfamily was 10%. The presence of highly conserved regions in all monomers and some features of their organization show that satellites of all Darevskia species belong to one satDNA family. The organization of unit sequences of satellites CLsat and Agi also detected by us in another lizard genus, Lacerts s. str. was compared. Similarity that was found between these satellites suggests their relatedness and common origin. A possible pathway of evolution of these two satDNA families is proposed. The distribution and content of CLsat repeat subfamilies in all species of the genus was examined by Southern blotting hybridization. Seven species had mainly CLsatI (83 to 96%); three species, approximately equal amounts of CLsatI and CLsatIII (the admixture of CLsatII was 2-3%); and five species, a combination of all three subfamilies in highly varying proportions. Based on these results as well as on zoogeographic views on phylogeny and taxonomy of the Darevskia species, hypotheses on the evolution of molecular-genetic relationships within this genus are advanced.     

The human HERC family of ubiquitin ligases: novel members, genomic organization, expression profiling, and evolutionary aspects

The HERC family of ubiquitin ligases is characterized by the presence of a HECT domain and one or more RCC1-like domains. We report the identification of two novel members, HERC4 and HERC6, and subdivide the family into one group of two large and one group of four small members according to protein size and domain structure. The small members share a similar genomic organization, three of them mapping to chromosomal region 4q22, indicating strong evolutionary cohesions. Phylogenetic analysis reveals that the HERC ancestor emerged in nematodes and that the family expanded throughout evolution. The mRNA expression pattern of the small human members was found to be diverse in selected tissues and cells; overexpressed proteins display a similar cytosolic distribution. These data indicate that the HERC family members exhibit similarities in many aspects, but also sufficient differences indicating functional diversity.     

Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues

Subtilisin-like serine proteases (subtilases) are a very diverse family of serine proteases with low sequence homology, often limited to regions surrounding the three catalytic residues. Starting with different Hidden Markov Models (HMM), based on sequence alignments around the catalytic residues of the S8 family (subtilisins) and S53 family (sedolisins), we iteratively searched all ORFs in the complete genomes of 313 eubacteria and archaea. In 164 genomes we identified a total of 567 ORFs with one or more of the conserved regions with a catalytic residue. The large majority of these contained all three regions around the "classical" catalytic residues of the S8 family (Asp-His-Ser), while 63 proteins were identified as S53 (sedolisin) family members (Glu-Asp-Ser). More than 30 proteins were found to belong to two novel subsets with other evolutionary variations in catalytic residues, and new HMMs were generated to search for them. In one subset the catalytic Asp is replaced by an equivalent Glu (i.e. Glu-His-Ser family). The other subset resembles sedolisins, but the conserved catalytic Asp is not located on the same helix as the nucleophile Glu, but rather on a beta-sheet strand in a topologically similar position, as suggested by homology modeling. The Prokaryotic Subtilase Database (www.cmbi.ru.nl/subtilases) provides access to all information on the identified subtilases, the conserved sequence regions, the proposed family subdivision, and the appropriate HMMs to search for them. Over 100 proteins were predicted to be subtilases for the first time by our improved searching methods, thereby improving genome annotation.     

The constitution of the order centrospermae: rRNA-DNA hybridization studies among betalain- and anthocyanin-producing families

Ribosomal RNA homologies and the thermal stabilities of rRNA/DNA hybrids among ten species of the Centrospermae (including three from the family Caryophyllaceae and seven from five betalain-producing families), three other angiosperms, and one fern, suggest that the betalain-producing families are phylogenetically closer to each other than to the anthocyanin-producing families which are examined.     

Molecular systematics of the deep-sea hydrothermal vent endemic Brachyuran family Bythograeidae: a comparison of three Bayesian species tree methods

Brachyuran crabs of the family Bythograeidae are endemic to deep-sea hydrothermal vents and represent one of the most successful groups of macroinvertebrates that have colonized this extreme environment. Occurring worldwide, the family includes six genera (Allograea, Austinograea, Bythograea, Cyanagraea, Gandalfus, and Segonzacia) and fourteen formally described species. To investigate their evolutionary relationships, we conducted Maximum Likelihood and Bayesian molecular phylogenetic analyses, based on DNA sequences from fragments of three mitochondrial genes (16S rDNA, Cytochrome oxidase I, and Cytochrome b) and three nuclear genes (28S rDNA, the sodium-potassium ATPase a-subunit 'NaK', and Histone H3A). We employed traditional concatenated (i.e., supermatrix) phylogenetic methods, as well as three recently developed Bayesian multilocus methods aimed at inferring species trees from potentially discordant gene trees. We found strong support for two main clades within Bythograeidae: one comprising the members of the genus Bythograea; and the other comprising the remaining genera. Relationships within each of these two clades were partially resolved. We compare our results with an earlier hypothesis on the phylogenetic relationships among bythograeid genera based on morphology. We also discuss the biogeography of the family in the light of our results. Our species tree analyses reveal differences in how each of the three methods weighs conflicting phylogenetic signal from different gene partitions and how limits on the number of outgroup taxa may affect the results.     

Molecular evolution of voltage-sensitive ion channel genes: on the origins of electrical excitability

We have analyzed nucleic acid and amino acid sequence alignments of a variety of voltage-sensitive ion channels, using several methods for phylogenetic tree reconstruction. Ancient duplications within this family gave rise to three distantly related groups, one consisting of the Na+ and Ca++ channels, another the K+ channels, and a third including the cyclic nucleotide-binding channels. A series of gene duplications produced at least seven mammalian homologues of the Drosophila Shaker K+ channel; clones of only three of these genes are available from all three mammalian species examined (mouse, rat, and human), pointing to specific genes that have yet to be recovered in one or another of these species. The Shaw-related K+ channels and the Na+ channel family have also undergone considerable expansion in mammals, relative to flies. These expansions presumably reflect the needs of the high degree of physiological and neuronal complexity of mammals. Analysis of the separate domains of the four-domain channels (Ca++ and Na+) supports their having evolved by two sequential gene duplications and implies the historical existence of a functional two-domain channel.      

Phylogenetic systematic evaluation of a classification of the Zoogonidae Odhner, 1902 (Cercomeria: Trematoda: Digenea: Plagiorchiiformes)

A recent systematic study of the digenean family Zoogonidae presented a series of cladograms, which are the product of phylogenetic systematic, or cladistic, analysis. However, one of the two subfamilies and nine of the 21 genera recognised in that study lacked putative synapomorphies, a requirement for phylogenetic systematic studies. This study presents a re-analysis of the database for the zoogonids, based on rigorous application of phylogenetic systematic methods. A new phylogenetic tree is presented, which better fits the original data than the published tree (with a consistency index of 52.3% vs. 46.3%). Four subfamilies, three monophyletic and one of uncertain status, and 10 genera could be recognised phylogenetically. This would affect the nomenclatorial status of one-third (26) of the species in the family. However, it is recommended that another analysis, based on more characters, be carried out before nomenclatorial changes are proposed.     

The phylogenetic placement of Hollandichthys Eigenmann 1909 (Teleostei: Characidae) and related genera

The phylogenetic relationships among characids are complex with many genera remaining of uncertain systematic position inside the family. The genus Hollandichthys is one of these problematic genera. It has been considered as incertae sedis inside this family until two recently published phylogenies, one morphological and one molecular, arrived at alternative hypothesizes as to the relationships of Hollandichthys with Pseudochalceus or Rachoviscus, respectively. In this paper, we infer the phylogenetic relations of these taxa based on five genes (three mitochondrial - COI, ND2 and 16S; and two nuclear - Sia and Trop), totaling up to 2719 bp. The 41 analyzed species in the Characidae include four incertae sedis characid taxa once hypothesized as related to Hollandichthys, but never analyzed in a single phylogeny (Rachoviscus, Pseudochalceus, Nematocharax and Hyphessobrycon uruguayensis). Here we propose Rachoviscus as the sister-group of Hollandichthys, grouped in the large clade C previously defined, along with the remaining incertae sedis taxa studied here. In addition, we support the evidence that insemination evolved independently at least three times in the Characidae.     

Evolution of the Alx homeobox gene family: parallel retention and independent loss of the vertebrate Alx3 gene

The Alx gene family is implicated in craniofacial development and comprises two to four homeobox genes in each vertebrate genome analyzed. Using phylogenetics and comparative genomics, we show that the common ancestor of jawed vertebrates had three Alx genes descendent from the two-round genome duplications (Alx1, Alx3, Alx4), compared with a single amphioxus gene. Later in evolution one of the paralogues, Alx3, was lost independently from at least three different vertebrate lineages, whereas Alx1 and Alx4 were consistently retained. Comparison of spatial gene expression patterns reveals that the three mouse genes have equivalent craniofacial expression to the two chick and frog genes, suggesting that redundancy compensated for gene loss. We suggest that multiple independent loss of one Alx gene was predisposed by extensive and persistent overlap in gene expression between Alx paralogues. Even so, it is unclear whether it was coincidence or evolutionary bias that resulted in the same Alx gene being lost on each occasion, rather than different members of the gene family.     

New members of the neurexin superfamily: multiple rodent homologues of the human CASPR5 gene

Proteins of the Caspr family are involved in cell contacts and communication in the nervous system. We identified and, by in silico reconstruction, compiled three orthologues of the human CASPR5 gene from the mouse genome, four from the rat genome, and one each from the chimpanzee, dog, opossum, and chicken genomes. Obviously, Caspr5 gene duplications have taken place during evolution of the rodent lineage. In the rat, the four paralogues are located in one chromosome arm, Chr 13p. In the mouse, however, the three Caspr5 genes are located in two chromosomes, Chr 1 and Chr 17. RT-PCR shows that all three mouse paralogues are being expressed. Common expression is found in brain tissue but different expression patterns are seen in other organs during fetal development and in the adult stage. Tissue specificity of expression has diverged during evolution of this young rodent gene family.     

Toxoplasma gondii: identification of a developmentally regulated family of genes related to SAG2

Previous studies have shown the surface of Toxoplasma gondii to be dominated by a family of proteins closely related to SAG1. In this study, we report the existence of a second family of genes defined by homology to SAG2. The predicted amino acid sequences of these three new proteins suggests that they are all glycosylphosphatidylinositol-linked surface antigens. All three also contain N-linked glycosylation sites, although their use has yet to be demonstrated. One of these SAG2-related antigens, SAG2B, is expressed in tachyzoites with an apparent size of 23 kDa. It is distinct, however, from the previously identified P23. In contrast to SAG2B, SAG2C and SAG2D appear to be expressed exclusively on the surface of bradyzoites. Analysis of the SAG2 family shows it to have weak but significant homology to the SAG1 family. Thus, all of the sequenced surface antigens of tachyzoites and many of those of bradyzoites fall into one large superfamily that can be divided into two subgroups defined by the prototypic and highly immunogenic SAG1 and SAG2, respectively.     

Phylogeny of Malpighiaceae: evidence from chloroplast ndhF and trnl-F nucleotide sequences

The Malpighiaceae are a family of ～1250 species of predominantly New World tropical flowering plants. Infrafamilial classification has long been based on fruit characters. Phylogenetic analyses of chloroplast DNA nucleotide sequences were analyzed to help resolve the phylogeny of Malpighiaceae. A total of 79 species, representing 58 of the 65 currently recognized genera, were studied. The 3' region of the gene ndhF was sequenced for 77 species and the noncoding intergenic spacer region trnL-F was sequenced for 65 species; both sequences were obtained for the outgroup, Humiria (Humiriaceae). Phylogenetic relationships inferred from these data sets are largely congruent with one another and with results from combined analyses. The family is divided into two major clades, recognized here as the subfamilies Byrsonimoideae (New World only) and Malpighioideae (New World and Old World). Niedenzu's tribes are all polyphyletic, suggesting extensive convergence on similar fruit types; only de Jussieu's tribe Gaudichaudieae and Anderson's tribes Acmanthereae and Galphimieae are monophyletic. Fleshy fruits evolved three times in the family and bristly fruits at least three times. Among the wing-fruited vines, which constitute more than half the diversity in the family, genera with dorsal-winged samaras are fairly well resolved, while the resolution of taxa with lateral-winged samaras is poor. The trees suggest a shift from radially symmetrical pollen arrangement to globally symmetrical pollen at the base of one of the clades within the Malpighioideae. The Old World taxa fall into at least six and as many as nine clades.     

Sequence and phylogenetic analyses of the twin-arginine targeting (Tat) protein export system

Twin-arginine targeting (Tat) protein secretion systems consist of two protein types, members of the TatA and TatC families. Homologues of these proteins are found in many archaea, bacteria, chloroplasts and mitochondria. Every prokaryotic organism with a fully sequenced genome exhibits either neither family member, or between one and three paralogues of these two family members. The Arabidopsis thaliana genome encodes three of each. Although many mitochondrially encoded TatC homologues have been identified, corresponding TatA homologues have not been found in this organelle. Phylogenetic analyses reveal that most prokaryotic Tat systems consist of one TatC homologue and two sequence-divergent TatA homologues (TatA and TatB). When only one TatA homologue is present, TatB is missing, and when three TatA homologues are present, the third one arose by duplication of TatA, not TatB. Further, homologues most resembling TatB are more sequence-divergent than those more closely resembling TatA. In contrast to the TatA family, the TatC family shows phylogenetic clustering in strict accordance with organismal type. These results are discussed in terms of their probable structural, functional and evolutionary significance.     

Sulcus vocalis: evidence for autosomal dominant inheritance

We found evidence of autosomal dominant hereditary transmission of sulcus vocalis. Four dysphonic patients from three generations of the same family were submitted to videolaryngoscopic examination (three patients) and to direct laryngoscopy (one patient) to diagnose the hoarseness. Sulcus vocalis was diagnosed in all four patients. The finding of four affected individuals in three generations, with vertical transmission affecting man and women, is more consistent with autosomal dominant inheritance pattern; it is an etiological model that we propose for the sulcus vocalis in this pedigree.     

Multiple endocrine neoplasia,type II: a combined surgical and genetic approach to treatment.

A family with multiple endocrine neoplasia, type II living in southeastern Ontario is described. Twenty individuals are known to have had medullary carcinoma of the thyroid, pheochromocytoma or both, the diagnosis of multiple endocrine neoplasia. type II is strongly suspected in five other individuals in the earlier generations. In this family the diseases seems to be transmitted by an autosomal dominant gene. A screening program set up for the family in 1977 has in 2 years identified four asymptomatic individuals (three with medullary carcinoma of the thyroid and one with this carcinoma and a pheochromocytoma). The family background, clinical picture, treatment and some of the problems of the screening program are described.     

The ubiquitin-encoding multigene family of flax, Linum usitatissimum.

Ubiquitin (Ubq), a 76-amino acid (aa) protein, is found in all eukaryotic organisms and is one of the most conserved proteins so far studied. It is implicated in many cellular processes. The Ubq-encoding genes (ubq) are generally present as a multigene family. In flax, we have estimated that this multigene family contains at the most ten members. The initial flax ubq sequences were isolated from a flax genomic library in lambda EMBL4 using a heterologous Arabidopsis thaliana ubq probe. An 916-bp fragment from one of the phage clones was subcloned and sequenced. The aa sequence derived from the nucleotide sequence of this fragment is identical to that of other plant Ubqs. This fragment was then used to isolate additional flax ubq clones. In all, eleven phage lambda clones, which represent six members of the gene family, were restriction-mapped and characterized. These six members are represented as three monomers, three poly-Ubqs, one hexamer and two tetramers. They can be present at either a single locus (two of the monomers and one of the poly-Ubqs) or at two loci (the remaining three genes). The other four members of the family are yet to be cloned and characterized.     

Familial Clustering of Hepatitis B Antigen: A Study in Relatives of Patients with Liver Diseases and Hepatitis B Antigenaemia

Twelve of the 100 family contacts of 29 patients with transient and persistent hepatitis B antigenaemia were found to be positive for hepatitis B antigen (HBAg). No relation was found between familial clustering and the nature of liver disease or the duration of antigenaemia in the index cases.Eight affected relatives were apparently healthy carriers of HBAG, one had cirrhosis, and three (in the same family) developed acute viral hepatitis.The absence of parenteral exposure in the HBA,-positive family contacts and the identity in antigenic determinants d or y with those of the index cases, suggest a non-parenteral spread of HBAg in families of patients with HBAg-associated liver diseases.     

Solution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A

Plant cell wall hydrolases generally have a modular structure consisting of a catalytic domain linked to one or more noncatalytic carbohydrate-binding modules (CBMs), whose common function is to attach the enzyme to the polymeric substrate. Xylanase A from Pseudomonas fluorescens subsp. cellulosa (Pf Xyn10A) consists of a family 10 catalytic domain, an N-terminal family IIa cellulose-binding module, and an internal family 10 cellulose-binding module. The structure of the 45-residue family 10 CBM has been determined in solution using NMR. It consists of two antiparallel beta-sheets, one with two strands and one with three, with a short alpha-helix across one face of the three-stranded sheet. There is a high density of aromatic residues on one side of the protein, including three aromatic residues (Tyr8, Trp22, and Trp24), which are exposed and form a flat surface on one face, in a classical polysaccharide-binding arrangement. The fold is closely similar to that of the oligonucleotide/oligosaccharide-binding (OB) fold, but appears to have arisen by convergent evolution, because there is no sequence similarity, and the presumed binding sites are on different faces.     

The repertoire of solute carriers of family 6: identification of new human and rodent genes

Tremendous amount of primary sequence information has been made available from the genome sequencing projects, although a complete annotation and identification of all genes is still far from being complete. Here, we present the identification of two new human genes from the pharmacologically important family of transporter proteins, solute carriers family 6 (SLC6). These were named SLC6A17 and SLC6A18 by HUGO. The human repertoire of SLC6 proteins now consists of 19 functional members and four pseudogenes. We also identified the corresponding orthologues and additional genes from mouse and rat genomes. Detailed phylogenetic analysis of the entire family of SLC6 proteins in mammals shows that this family can be divided into four subgroups. We used Hidden Markov Models for these subgroups and identified in total 430 unique SLC6 proteins from 10 animal, one plant, two fungi, and 196 bacterial genomes. It is evident that SLC6 proteins are present in both animals and bacteria, and that three of the four subfamilies of mammalian SLC6 proteins are present in Caenorhabditis elegans, showing that these subfamilies are evolutionary very ancient. Moreover, we performed tissue localization studies on the entire family of SLC6 proteins on a panel of 15 rat tissues and further, the expression of three of the new genes was studied using quantitative real-time PCR showing expression in multiple central and peripheral tissues. This paper presents an overall overview of the gene repertoire of the SLC6 gene family and its expression profile in rats.     

The comparative leaf anatomy of Agave, Beschorneria, Doryanthes and Furcraea species (Agavaceae: Agaveae)

The leaf anatomy is compared of 35 ppecies and one variety of Agave , three species of Furcraea , one species of Beschorneria and one species of Doryanrhes , four genera assigned to the tribe Agaveae by Hutchinson in his classification of the family Agavaceae. The genera can be readily differentiated by leaf anatomy. There are close similarities between Agave, Beschorneria and Furcraea , but Doryanthes differs widely from these genera. Sufficient anatomical differences exist to differentiate the Agave species examined.