Molecular organization and chromosomal localization of 5S rDNA in Amazonian Engystomops (Anura, Leiuperidae)

<p>Abstract</p> <p>Background</p> <p>For anurans, knowledge of 5S rDNA is scarce. For <it>Engystomops </it>species, chromosomal homeologies are difficult to recognize due to the high level of inter- and intraspecific cytogenetic variation. In an attempt to better compare the karyotypes of the Amazonian species <it>Engystomops freibergi </it>and <it>Engystomops petersi</it>, and to extend the knowledge of 5S rDNA organization in anurans, the 5S rDNA sequences of Amazonian <it>Engystomops </it>species were isolated, characterized, and mapped.</p> <p>Results</p> <p>Two types of 5S rDNA, which were readily differentiated by their NTS (non-transcribed spacer) sizes and compositions, were isolated from specimens of <it>E. freibergi </it>from Brazil and <it>E. petersi </it>from two Ecuadorian localities (Puyo and Yasuní). In the <it>E. freibergi </it>karyotypes, the entire type I 5S rDNA repeating unit hybridized to the pericentromeric region of 3p, whereas the entire type II 5S rDNA repeating unit mapped to the distal region of 6q, suggesting a differential localization of these sequences. The type I NTS probe clearly detected the 3p pericentromeric region in the karyotypes of <it>E. freibergi </it>and <it>E. petersi </it>from Puyo and the 5p pericentromeric region in the karyotype of <it>E. petersi </it>from Yasuní, but no distal or interstitial signals were observed. Interestingly, this probe also detected many centromeric regions in the three karyotypes, suggesting the presence of a satellite DNA family derived from 5S rDNA. The type II NTS probe detected only distal 6q regions in the three karyotypes, corroborating the differential distribution of the two types of 5S rDNA.</p> <p>Conclusions</p> <p>Because the 5S rDNA types found in <it>Engystomops </it>are related to those of <it>Physalaemus </it>with respect to their nucleotide sequences and chromosomal locations, their origin likely preceded the evolutionary divergence of these genera. In addition, our data indicated homeology between Chromosome 5 in <it>E. petersi </it>from Yasuní and Chromosomes 3 in <it>E. freibergi </it>and <it>E. petersi </it>from Puyo. In addition, the chromosomal location of the type II 5S rDNA corroborates the hypothesis that the Chromosomes 6 of <it>E. petersi </it>and <it>E. freibergi </it>are homeologous despite the great differences observed between the karyotypes of the Yasuní specimens and the others.</p

Genomic organization of nucleolin gene in carp fish: Evidence for several genes

http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602006000200017&lng=es&nrm=isoThe protein nucleolin, functionally involved in the main steps of ribosome biogenesis, is codified by a single copy gene in mammals. Here we report that at least three different genes codify for this protein in carp fish (Cyprinus carpio). This is the first description of the genomic organization of nucleolin in a teleost. The carp nucleolin gene includes 8.8 kb and contains 16 exons. Promoter cis regulatory elements are similar to constitutive genes, i.e., a putative TATA box, three G/C boxes, and three pyrimidine-rich boxes. As in other species, carp nucleolin gene introns host three snoRNA codifying sequences: U23 from the H/ACA family and two C/D box snoRNAs, U20 and U82. Both U20 and U82 span a complementary sequence with carp 18S rRNA. Additionally, we identified two cDNAs coding for nucleolin, confirming the existence of several nucleolin genes in carp. Amino acidderived sequence from carp cDNAs differ from mammal protein because they span additional acidic domains at the amino end, whose functional significance remains unclear. We performed amino acid sequence comparison and phylogenetic analyses showing that the three isoforms of carp nucleolin, which we describe herein, cluster in two groups. cNUC1 probably diverges from cNUC2 and cNUC3 as result of ancestral fish-specific genome duplication, indeed C. carpio is a tetraploid fish

Xenopus laevis as a Model Organism

Model organisms are often assumed to be representative of some more inclusive taxon of which the species is a part. This assumption leads to mistaken generalizations about the evolutionary and comparative significance of the data gathered. This paper reviews com? parative and evolutionary studies of Xenopus laevis and its relatives. Phylogenetic analysis of data from DNA sequences and morphology indicate that Xenopus is monophyletic and that Silurana is its sister group. The most basal lineages of Pipidae diverged prior to the breakup of Gondwana. The bizarre morphology of Xenopus is in part due to changes in the mode of meta? morphosis. Speciation in Xenopus is unique among Anura in being associated with various levels of polyploidy owing to allopolyploidy. Several kinds of molecular studies indicate substantial divergence between Xenopus and Silurana. The contribution of data from model studies of Xenopus would be greatly enhanced if comparable data were available from a more basally placed lineage such as Bombina. [Xenopus; Silurana; Pipidae; model organisms; morphology; historical biogeog- raphy; fossils; molecular systematics; ribosomal DNA; mitochondrial DNA; phylogeny; devel? opment; heterochrony; caenogenesis; functional anatomy; behavior; polyploidy; karyotypes; molecular biology.

On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons.

Ribosome assembly occurs mainly in the nucleolus, yet recent studies have revealed robust enrichment and translation of mRNAs encoding many ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Here, we report a physical and functional interaction between locally synthesized RPs and ribosomes in the axon. We show that axonal RP translation is regulated through a sequence motif, CUIC, that forms an RNA-loop structure in the region immediately upstream of the initiation codon. Using imaging and subcellular proteomics techniques, we show that RPs synthesized in axons join axonal ribosomes in a nucleolus-independent fashion. Inhibition of axonal CUIC-regulated RP translation decreases local translation activity and reduces axon branching in the developing brain, revealing the physiological relevance of axonal RP synthesis in vivo. These results suggest that axonal translation supplies cytoplasmic RPs to maintain/modify local ribosomal function far from the nucleolus in neurons.This work was supported by Wellcome Trust Grants (085314/Z/08/Z and 203249/Z/16/Z) to C.E.H. and (100329/Z/12/Z) to W.A.H., European Research Council Advanced Grant (322817) to C.E.H., Champalimaud Vision Award to C.E.H. and by the Netherlands Organization for Scientific Research (NWO Rubicon 019.161LW.033) to M.K. CFK acknowledges funding from the UK Engineering and Physical Sciences Research Council, EPSRC (grants EP/L015889/1 and EP/H018301/1), the Wellcome Trust (grants 3-3249/Z/16/Z and 089703/Z/09/Z) and the UK Medical Research Council, MRC (grants MR/K015850/1 and MR/K02292X/1) and Infinitus (China) Ltd

Transcriptome analysis for novel peptide in breeding gland of Hymenochirus boettgeri

The primary goal of the project was to find nucleotide sequences potentially encoding a pheromone from the breeding gland of Hymenochirus boettgeri. The reasons in searching for the sequence of a pheromone were to better understand the organism and to use the information for application in reproduction of other species. Due to climate change and rampant deforestation, such as in Africa’s Congo Basin, many amphibian species are being threatened. With these increasing threats, a viable option for the future may be breeding in captivity for the amphibian species. Pheromone characterization from the breeding gland of Hymenochirus boettgeri may help with better understanding of reproduction in other species. Overall, five candidate signaling peptides that have the potential to be a pheromone from the breeding gland were found with transcriptome assembly and annotation of the breeding gland. The project focused on obtaining transcriptome data for the breeding gland by 1) RNA sequencing 2) de novo transcriptome assembly and 3) transcriptome annotation. The transcriptome of the breeding gland is now available for future proteomic studies

A second base pair interaction between U3 small nucleolar RNA and the 5′-ETS region is required for early cleavage of the yeast pre-ribosomal RNA

In eukaryotes, U3 snoRNA is essential for pre-rRNA maturation. Its 5′-domain was found to form base pair interactions with the 18S and 5′-ETS parts of the pre-rRNA. In Xenopus laevis, two segments of U3 snoRNA form base-pair interactions with the 5′-ETS region and only one of them is essential to the maturation process. In Saccharomyces cerevisiae, two similar U3 snoRNA–5′ ETS interactions are possible; but, the functional importance of only one of them had been tested. Surprisingly, this interaction, which corresponds to the non-essential one in X. laevis, is essential for cell growth and pre-rRNA maturation in yeast. In parallel with [Dutca et al. (2011) The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Research, 39, 5164–5180], here we show, that the second possible 11-bp long interaction between the 5′ domain of S. cerevisiae U3 snoRNA and the pre-rRNA 5′-ETS region (helix VI) is also essential for pre-rRNA processing and cell growth. Compensatory mutations in one-half of helix VI fully restored cell growth. Only a partial restoration of growth was obtained upon extension of compensatory mutations to the entire helix VI, suggesting sequence requirement for binding of specific proteins. Accordingly, we got strong evidences for a role of segment VI in the association of proteins Mpp10, Imp4 and Imp3

Mammalian ribosomal protein S3a genes and intron-encoded small nucleolar RNAs U73 and U82

http://www.ester.ee/record=b4330778~S58*es

The 5S rDNA of the bivalve Cerastoderma edule: nucleotide sequence of the repeat unit and chromosomal location relative to 18S–28S rDNA

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