Molecular cloning and expression pattern of 11 genes involved in lipid metabolism in yellow catfish Pelteobagrus fulvidraco

11 genes involved in lipid metabolism were cloned from liver of yellow catfish Pelteobagrus fulvidraco, including CPT 1A, CPT 1B, PPARα, PPARγ, SREBP-1, G6PD, 6PGD, FAS, acetyl-CoA ACCa, ACCb, and LPL. Phylogenetic analysis further identified these genes, and confirmed the classification and evolutionary status of yellow catfish. mRNA of all eleven genes was present in liver, muscle, mesenteric adipose, ovary and heart, but at varying levels. The present study will facilitate further studies on the regulation of lipid metabolism at the molecular level for the fish species.     

Evolutionary aspects of a unique internal mitochondrial targeting signal in nuclear-migrated rps19 of sugar beet (Beta vulgaris L.)

The endosymbiotic theory postulates that many genes migrated from endosymbionts to the nuclear genomes of their hosts. Some migrated genes lack presequences directing proteins to mitochondria, and their mitochondrial targeting signals appear to be inscribed in the core coding regions as internal targeting signals (ITSs). ITSs may have evolved after sequence transfer to nuclei or ITSs may have pre-existed before sequence transfer. Here, we report the molecular cloning of a sugar beet gene for ribosomal protein S19 (Rps19; the first letter is capitalized when the gene is a nuclear gene). We show that sugar beet Rps19 (BvRps19) is an ITS-type gene. Based on amino-acid sequence comparison, dicotyledonous rps19s (the first letter is lower-cased when the gene is a mitochondrial gene), such as tobacco rps19 (Ntrps19), resemble an ancestral form of BvRps19. We investigated whether differences in amino-acid sequences between BvRps19 and Ntrps19 were involved in ITS evolution. Analyses of the intracellular localization of chimaeric GFP-fusion proteins that were transiently expressed in Welsh onion cells showed that Ntrps19-gfp was not localized in mitochondria. When several BvRps19-type amino acid substitutions, none of which was seen in any other angiosperm rps19, were introduced into Ntrps19-gfp, the modified Ntrps19-gfp became localized in mitochondria, supporting the notion that an ITS in BvRps19 evolved following sequence transfer to nuclei. Not all of these substitutions were seen in other ITS-type Rps19s, suggesting that the ITSs of Rps19 are diverse.     

Binding of LARP6 to the Conserved 5′ Stem-Loop Regulates Translation of mRNAs Encoding Type I Collagen

Type I collagen is the most abundant protein in the human body, produced by folding of two α1(I) polypeptides and one α2(I) polypeptide into the triple helix. A conserved stem-loop structure is found in the 5′ untranslated region of collagen mRNAs, encompassing the translation start codon. We cloned La ribonucleoprotein domain family member 6 (LARP6) as the protein that binds the collagen 5′ stem-loop in a sequence-specific manner. LARP6 has a distinctive bipartite RNA binding domain not found in other members of the La superfamily. LARP6 interacts with the two single-stranded regions of the 5′ stem-loop. The K_d for binding of LARP6 to the 5′ stem-loop is 1.4 nM. LARP6 binds the 5′ stem-loop in both the nucleus and the cytoplasm. In the cytoplasm, LARP6 does not associate with polysomes; however, overexpression of LARP6 blocks ribosomal loading on collagen mRNAs. Knocking down LARP6 by small interfering RNA also decreased polysomal loading of collagen mRNAs, suggesting that it regulates translation. Collagen protein is synthesized at discrete regions of the endoplasmic reticulum. Using collagen-GFP (green fluorescent protein) reporter protein, we could reproduce this focal pattern of synthesis, but only when the reporter was encoded by mRNA with the 5′ stem-loop and in the presence of LARP6. When the reporter was encoded by mRNA without the 5′ stem-loop, or in the absence of LARP6, it accumulated diffusely throughout the endoplasmic reticulum. This indicates that LARP6 activity is needed for focal synthesis of collagen polypeptides. We postulate that the LARP6-dependent mechanism increases local concentration of collagen polypeptides for more efficient folding of the collagen heterotrimer.     

Functional analysis of the yeast genome

The release of the complete genome sequence of the yeast Saccharomyces cerevisiae has ushered in a new phase of genome research in which sequence function will be assigned. The goal is to determine the biological function of each of the >6,000 open reading frames in the yeast genome. Innovative approaches have been developed that exploit the sequence data and yield information about gene expression levels, protein levels, subcellular localization and gene function for the entire genome.     

Limusaurus inextricabilis (Theropoda: Ceratosauria) gives a hand to evolutionary teratology: a complementary view on avian manual digits identities

It is widely accepted that birds are rooted within theropod dinosaurs. However, there is controversy between palaeontological and developmental data regarding manual digit identities of birds and their tetanuran ancestors (I, II and III vs. II, III and IV). To resolve this conflict, the principle of a frame‐shift has been considered. Identities of digits I–III would develop on condensations 2–4. Nevertheless, the discovery of the basal Ceratosauria Limusaurus inextricabilis has been used as a reference to define the digital identity of Tetanurae as II–IV. The new concept of evolutionary teratology states that certain anatomical structures identified in evolutionary lineages are viable developmental anomalies (‘adaptive’ or not), becoming part of the considered groups. The features of Limusaurus' forelimb match teratological characterization. This diagnosis, associated with the variations previously identified in derived Ceratosauria taxa (Carnotaurinae), underline an anatomical and developmental independence (regarding evolutionary conserved mechanisms) compared with Tetanurae and therefore birds. Consequently, Limusaurus should not be used as a reference concerning the identity of avian manuals digits. Evolutionary teratology supports identities I, II and III of the tetanuran manus via a frame‐shift that did not occur in the Ceratosauria lineage. © 2016 The Linnean Society of London