A 460-kb DNA Sequence of the Escherichia coli K-12 Genome Corresponding to the 40.1-50.0 min Region on the Linkage Map

The 465,813 base pair sequence corresponding to the 40.1–50.0min region on the genetic map of Escherichia coli K-12 (W3110)was determined. Analysis of the sequence revealed that thisregion contained at least 466 potential open reading frames,of which 187 (40%) were previously reported, 105 (23%) werehomologous to other known genes, 103 (22%) were identical orsimilar to hypothetical genes registered in databases, and theremaining 71 (15%) did not show a significant similarity toany other gene. At the 45.2–46.0 min region, we founda very large cluster of about 30 genes, whose functions areinvolved in the biosynthesis of polysaccharides as the componentsof outer membranes. In addition, we identified anew asn-tRNAgene, designated asnW, between the asnT and asnU genes and anew lysogenic phage attachment site as the cis-element.     

The 2005 version of the chloroplast DNA sequence from tobacco (Nicotiana tabacum)

The complete nucleotide sequence of tobacco chloroplast DNA was first determined in 1986, and then its updated gene map was reported in 1998. During the course of sequencing the chloroplast DNA ofNicotiana sylvestris, the female progenitor of tobacco, we found some sequence errors and amended the 1998 version. The tobacco chloroplast DNA comprises 155,943 bp, 4 bp longer than the 1998 version.     

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.     

The FUS gene is dual‐coding with both proteins contributing to FUS‐mediated toxicity

Novel functional coding sequences (altORFs) are camouflaged within annotated ones (CDS) in a different reading frame. We show here that an altORF is nested in the FUS CDS, encoding a conserved 170 amino acid protein, altFUS. AltFUS is endogenously expressed in human tissues, notably in the motor cortex and motor neurons. Over‐expression of wild‐type FUS and/or amyotrophic lateral sclerosis‐linked FUS mutants is known to trigger toxic mechanisms in different models. These include inhibition of autophagy, loss of mitochondrial potential and accumulation of cytoplasmic aggregates. We find that altFUS, not FUS, is responsible for the inhibition of autophagy, and pivotal in mitochondrial potential loss and accumulation of cytoplasmic aggregates. Suppression of altFUS expression in a Drosophila model of FUS‐related toxicity protects against neurodegeneration. Some mutations found in ALS patients are overlooked because of their synonymous effect on the FUS protein. Yet, we show they exert a deleterious effect causing missense mutations in the overlapping altFUS protein. These findings demonstrate that FUS is a bicistronic gene and suggests that both proteins, FUS and altFUS, cooperate in toxic mechanisms.     

A transcription factor atlas of directed differentiation

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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.