DNA content variation in monilophytes and lycophytes: large genomes that are not endopolyploid

Less than 1% of known monilophytes and lycophytes have a genome size estimate, and substantially less is known about the presence and prevalence of endopolyploid nuclei in these groups. Thirty-one monilophyte species (including three horsetails) and six lycophyte species were collected in Ontario, Canada. Using flow cytometry, genome size and degree of endopolyploidy were estimated for 37 species. Across the five orders covered, 1Cx-values averaged 4.2 pg in the Lycopodiales, 18.1 pg for the Equisetales, 5.06 pg for a single representative of the Ophioglossales, 14.3 pg for the Osmundales, and 7.06 pg for the Polypodiales. There was no indication of endoreduplication in any of the leaf, stem, or root tissue analyzed. This information is essential to our understanding of DNA content evolution in land plants.     

Transforming growth factor-beta-related proteins: an ancestral and widespread superfamily of cytokines in metazoans

Members of the transforming growth factor beta (TGF-beta) superfamily of cell signalling polypeptides have attracted much attention because of their ability, from nematodes to mammals, to control cellular functions that in turn, regulate embryo development and tissue homeostasis. On the basis of structure similarities, the TGF-beta members (ligands, receptors and Smads) are subdivided into TGF-beta sensu stricto, bone morphogenetic proteins (BMP) and activins. Although BMP is the best characterized pathway in metazoans, recent findings in molluscs and non-bilateria as well as the analysis of nematode and arthropod genomes, demonstrate the early origin of these distinct subfamilies of ligands, receptors and Smads. This report analyses the large diversity of ligands, receptors and Smads in metazoans from cnidarians and molluscs to mammals. The contribution of new data, mainly from the lophochotrozoan Crassostrea gigas and other organisms on the fringe of the 'branded model organisms', will help us to demonstrate that TGF-betas are probably the most ancestral active cytokines characterized at the molecular level in both Protostome and Deuterostome lineages.     

Highly conserved linkage homology between birds and turtles: Bird and turtle chromosomes are precise counterparts of each other

The karyotypes of birds, turtles and snakes are characterized by two distinct chromosomal components, macrochromosomes and microchromosomes. This close karyological relationship between birds and reptiles has long been a topic of speculation among cytogeneticists and evolutionary biologists; however, there is scarcely any evidence for orthology at the molecular level. To define the conserved chromosome synteny among humans, chickens and reptiles and the process of genome evolution in the amniotes, we constructed comparative cytogenetic maps of the Chinese soft-shelled turtle (Pelodiscus sinensis) and the Japanese four-striped rat snake (Elaphe quadrivirgata) using cDNA clones of reptile functional genes. Homology between the turtle and chicken chromosomes is highly conserved, with the six largest chromosomes being almost equivalent to each other. On the other hand, homology to chicken chromosomes is lower in the snake than in the turtle. Turtle chromosome 6q and snake chromosome 2p represent conserved synteny with the chicken Z chromosome. These results suggest that the avian and turtle genomes have been well conserved during the evolution of the Arcosauria. The avian and snake sex Z chromosomes were derived from different autosomes in a common ancestor, indicating that the causative genes of sex determination may be different between birds and snakes.Matsuda and Nishida-Umehara contributed equally to this work.     

Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery

Among the most numerous objects in the biosphere, phages show enormous diversity in morphology and genetic content. We have sequenced 7 T4-like phages and compared their genome architecture. All seven phages share a core genome with T4 that is interrupted by several hyperplastic regions (HPRs) where most of their divergence occurs. The core primarily includes homologues of essential T4 genes, such as the virion structure and DNA replication genes. In contrast, the HPRs contain mostly novel genes of unknown function and origin. A few of the HPR genes that can be assigned putative functions, such as a series of novel Internal Proteins, are implicated in phage adaptation to the host. Thus, the T4-like genome appears to be partitioned into discrete segments that fulfil different functions and behave differently in evolution. Such partitioning may be critical for these large and complex phages to maintain their flexibility, while simultaneously allowing them to conserve their highly successful virion design and mode of replication.     

Identification of a family of effectors secreted by the type III secretion system that are conserved in pathogenic Chlamydiae

Chlamydiae are Gram-negative, obligate intracellular pathogens that replicate within a membrane-bounded compartment termed an inclusion. Throughout their development, they actively modify the eukaryotic environment. The type III secretion (TTS) system is the main process by which the bacteria translocate effector proteins into the inclusion membrane and the host cell cytoplasm. Here we describe a family of type III secreted effectors that are present in all pathogenic chlamydiae and absent in the environment-related species. It is defined by a common domain of unknown function, DUF582, that is present in four or five proteins in each Chlamydiaceae species. We show that the amino-terminal extremity of DUF582 proteins functions as a TTS signal. DUF582 proteins from C. trachomatis CT620, CT621, and CT711 are expressed at the middle and late phases of the infectious cycle. Immunolocalization further revealed that CT620 and CT621 are secreted into the host cell cytoplasm, as well as within the lumen of the inclusion, where they do not associate with bacterial markers. Finally, we show that DUF582 proteins are present in nuclei of infected cells, suggesting that members of the DUF582 family of effector proteins may target nuclear cell functions. The expansion of this family of proteins in pathogenic chlamydiae and their conservation among the different species suggest that they play important roles in the infectious cycle.     

Evidence that the 32, 38 and 20 kilodalton surface antigens of schistosomula and schistosomes are a family of conserved proteins

The structures of the 38, 32 and 20 kDa surface antigens isolated from schistosomula and adult worms of Schistosoma mansoni were compared by two-dimensional peptide mapping, by immunological analysis and by one- and two-dimensional electrophoresis. Peptide mapping showed a high degree of similarity between the isolated antigens from both parasite stages. The NIMP/M47 monoclonal antibody showed cross-reactivity between the 32 and the 20 kDa antigens under denaturating and non-denaturating conditions, as demonstrated by immunoprecipitation and Western blotting. It is concluded that these antigens constitute a homologous family of surface antigens.     

Extensive gene order differences within regions of conserved synteny between the Fugu and human genomes: implications for chromosomal evolution and the cloning of disease genes.

The suitability of the Fugu genome to facilitate the identification of candidate human disease genes using comparative positional cloning is dependent upon the extent to which synteny and gene order are conserved between the two species. We have cloned seven Fugu genes which are closely linked to Surfeit genes in two regions of the Fugu genome and have mapped and ordered their human homologues both by PCR analysis of the Genebridge 4 panel of radiation hybrids and by fluorescence in situ hybridization. All seven human genes map to a 3 Mb region of chromosome band 9q34.1, approximately 2-4 Mb proximal to the human Surfeit genes. Although both Fugu regions are syntenic with human chromosome band 9q34, the relative order of the genes differs greatly in the two species. Indeed, some of the genes that are adjacent in the Fugu genome are separated by at least 2-4 Mb in the human genome. This suggests that intra-chromosomal rearrangements, most probably inversions, have been common during the 900 million years of divergent evolution separating Fugu and human. The utility of Fugu to facilitate human disease gene identification by comparative positional cloning is questioned in light of these results.     

Human immunoglobulin D segments: isolation of a new D segment and polymorphic deletion of the D1 segment

We have isolated and identified a new human germline D segment which is not physically linked to the known D cluster. The nucleotide sequence of the new D segment was highly homologous with the known D segments. Frequent polymorphic deletion of the D1 segment was found in the Japanese population. Nucleotide sequences surrounding the deletion indicate that homologous recombination is likely to be responsible for the deletion of the D1 segment.     

Rapidly evolving repetitive DNAs in a conservative genome: A test of factors that affect chromosomal evolution

The hypothesis that tandemly repeated DNA sequences may facilitate chromosomal rearrangements was tested by comparing a conservatively evolving karyotype of a bat species (Macrotus waterhousii) with data published for a rapidly evolving karyotype of an equid species (Equus zebra). Empirical data generated from the phylogenetic screening of rapidly evolving repetitive DNAs from approximately 0.1% of theM. waterhousii genome showed only one sequence that was repetitive inM. waterhousii but low in copy number or absent from the outgroupArtibeus jamaicensis. This compares to 34 such clones containing sequences which were repetitive inE. zebra but were low in copy number or absent from the outgroupCeratotherium simum. The bat sequence represents a single family of repeated sequences, whereas six families of sequences were identified inE. zebra. Southern blot analysis suggested that the sequence fromM. waterhousii is interspersed rather than tandemly repeated, as are the sequences inE. zebra. These data support the above hypothesis and suggest that species with conservatively evolving karyotypes have fewer numbers and families of rapidly evolving DNA sequences than do species such as the equids that possess a karyotype that is considered to have undergone rapid karyotypic evolution.     

Molecular cytogenetics of Alstroemeria: identification of parental genomes in interspecific hybrids and characterization of repetitive DNA families in constitutive heterochromatin

The genus Alstroemeria consists of diploid(2n=2x=16) species originating mainly from Chile and Brazil. Most cultivars are triploid or tetraploid interspecific hybrids. C-banding of eight species revealed obvious differentiation of constitutive heterochromatin within the genus. The present study focused on the molecular (cyto)genetic background of this differentiation. Genomic slot-blot analysis demonstrated strong conservation of major parts of the genomes among six species. The chromosomes of A. aurea and A. ligtu, species with pronounced interstitial C-bands, were found to contain large amounts of highly repetitive and species-specific DNA. The variation in size,number and intensity of strongly probed bands of major repetitive DNA families observed in genomic Southern blots of Sau3A, HaeIII, and MseI digests indicated a strong correlation between variation in genomic DNA composition and different C-banding patterns among Alstroemeria species. Genomic in situ hybridization (GISH)revealed a clear distinction between parental chromosomes in the hybrids between Chilean and Brazilian species and also between Chilean species, as long as at least one of the parental species possessed prominent C-banding. Regarding the latter, discriminative hybridization resulted from highly repetitive species specific DNA in the heterochromatic chromosome regions of A. aurea and A. ligtu, and caused GISH banding patterns that coincided with the C-banding patterns. This revised version was published online in August 2006 with corrections to the Cover Date.     

A new microsporidium Fibrillaspora daphniae g. n. sp. n. infecting Daphnia magna (Crustacea: Cladocera) in Siberia and its taxonomic placing within a new family Fibrillasporidae and new superfamily Tubulinosematoidea (Opisthosporidia: Microsporidia)

Parasitology Research - Infection with a new microsporidium, Fibrillaspora daphniae g. n. sp. n., was found in a local Daphnia magna population in Tomsk region (Western Siberia, Russia) at the...     

PPE protein (Rv3873) from DNA segment RD1 of Mycobacterium tuberculosis: strong recognition of both specific T-cell epitopes and epitopes conserved within the PPE family

Proteins encoded by DNA segment RD1 of Mycobacterium tuberculosis have recently been demonstrated to play important roles in bacterial virulence, vaccine development, and diagnostic reagent design. Previously, we characterized two immunodominant T-cell antigens, the early secreted antigen target (ESAT-6) and the 10-kDa culture filtrate protein (CFP10), which are encoded by the esx-lhp operon in this region. In the present study we characterized a third putative open reading frame in this region, rv3873, which encodes a PPE protein. We found that the rv3873 gene is expressed in M. tuberculosis H37Rv and that the native protein, Rv3873, is predominantly associated with the mycobacterial cell or wall. When tested as a His-tagged recombinant protein, Rv3873 stimulated high levels of gamma interferon secretion in peripheral blood mononuclear cells isolated from tuberculosis (TB) patients, as well as from healthy tuberculin purified protein derivative-positive donors. In contrast to other RD1-encoded antigens, Rv3873 was also found to be recognized by a significant proportion of Mycobacterium bovis BCG-vaccinated donors. Epitope mapping performed with overlapping peptides revealed a broad pattern of T-cell recognition comprising both TB-specific epitopes and epitopes also recognized by BCG-vaccinated donors. The immunodominant epitope (residues 118 to 135) for both TB patients and BCG-vaccinated individuals was found to be highly conserved among a large number of PPE family members.     

Familial translocation with partial trisomy of 13 and 22: evidence that specific regions of chromosomes 13 and 22 are responsible for the phenotype of each trisomy.

A newborn infant with clinical and pathological findings typical trisomy 13 and 22 syndromes had an extra chromosome which was a derivative chromosome from maternal balanced translocation affecting Nos. 13 and 22; 47,XY,+der(22),t(13:22)(q22:q12)Mat. The presence of extra specific euchromatic regions of No. 13(13q22 and/or 13q34) and No. 22 (22q11) seem to be responsible for the trisomy 13 and 22 syndromes.