Genomic Organization and Control of the Grb7 Gene Family

Grb7 and their related family members Grb10 and Grb14 are adaptor proteins, which participate in the functionality of multiple signal transduction pathways under the control of a variety of activated tyrosine kinase receptors and other tyrosine-phosphorylated proteins. They are involved in the modulation of important cellular and organismal functions such as cell migration, cell proliferation, apoptosis, gene expression, protein degradation, protein phosphorylation, angiogenesis, embryonic development and metabolic control. In this short review we shall describe the organization of the genes encoding the Grb7 protein family, their transcriptional products and the regulatory mechanisms implicated in the control of their expression. Finally, the alterations found in these genes and the mechanisms affecting their expression under pathological conditions such as cancer, diabetes and some congenital disorders will be highlighted

Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination

<p>Abstract</p> <p>Background</p> <p>Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle".</p> <p>Results</p> <p>Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, <it>Aceros waldeni </it>and <it>Penelopides panini</it>. The mt genomes are characterized by a tandemly duplicated region encompassing part of <it>cytochrome b</it>, 3 tRNAs, <it>NADH6</it>, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (<it>A. waldeni</it>) and 22,737 bp (<it>P. panini</it>), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i.e., in every generation.</p> <p>Conclusions</p> <p>The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.</p

Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: The giant moas of New Zealand

The tempo and mode of evolution of the extinct giant moas of New Zealand remain obscure because the number of lineages and their divergence times cannot be estimated reliably by using fossil bone characters only. We therefore extracted ancient DNA from 125 specimens and genetically typed them for a 658-bp mtDNA control region sequence. The sequences detected 14 monophyletic lineages, 9 of which correspond to currently recognized species. One of the newly detected lineages was a genetically divergent form of Megalapteryx originally described as a separate species, two more were lineages of Pachyornis in southern and northeastern New Zealand, and two were basal lineages of South Island Dinornis. When results from genetic typing and previous molecular sexing were combined, at least 33.6% of the specimens were incorrectly classified. We used longer sequences of the control region and nine other mtDNA genes totaling 2,814 base pairs to derive a strongly supported phylogeny of the 14 moa lineages. Molecular dating estimated the most recent common ancestor of moas existed after the Oligocene drowning of New Zealand. However, a cycle of lineage-splitting occurred ≈4–10 million years ago, when the landmass was fragmented by tectonic and mountain-building events and general cooling of the climate. These events resulted in the geographic isolation of lineages and ecological specialization. The spectacular radiation of moa lineages involved significant changes in body size, shape, and mass and provides another example of the general influence of large-scale paleoenvironmental changes on vertebrate evolutionary history

DNA barcoding a relict avifauna: an important tool for systematics and conservation management

BACKGROUND: DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds. RESULTS: We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods. CONCLUSIONS: DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds

Single nucleotide +1 frameshifts in an apparently functional mitochondrial cytochrome b gene in ants of the genus Polyrhachis

Twelve of 30 species examined in the ant genus Polyrhachis carry single nucleotide insertions at one or two positions within the mitochondrial cytochrome b (cytb) gene. Two of the sites are present in more than one species. Nucleotide substitutions in taxa carrying insertions show the strong codon position bias expected of functional protein coding genes, with substitutions concentrated in the third positions of the original reading frame. This pattern of evolution of the sequences strongly suggests that they are functional cytb sequences. This result is not the first report of +1 frameshift insertions in animal mitochondrial genes. A similar site was discovered in vertebrates, where single nucleotide frameshift insertions in many birds and a turtle were reported by Mindell et al. (Mol Biol Evol 15:1568, 1998). They hypothesized that the genes are correctly decoded by a programmed frameshift during translation. The discovery of four additional sites gives us the opportunity to look for common features that may explain how programmed frameshifts can arise. The common feature appears to be the presence of two consecutive rare codons at the insertion site. We hypothesize that the second of these codons is not efficiently translated, causing a pause in the translation process. During the stall the weak wobble pairing of the tRNA bound in the peptidyl site of the ribosome, together with an exact Watson–Crick codon–anticodon pairing in the +1 position, allows translation to continue in the +1 reading frame. The result of these events is an adequate level of translation of a full-length and fully functional protein. A model is presented for decoding of these mitochondrial genes, consistent with known features of programmed translational frameshifting in the yeast TY1 and TY3 retrotransposons