bluuebunny/crossref_metadata_2025_split huggingface dataset:
amiB, a novel gene required for the growth/differentiation transition in Dictyostelium
Authors: Kon Takahide , Adachi Hiroyuki , Sutoh Kazuo 
Published: March 2003

BackgroundThe differentiation programme of Dictyostelium discoideum is initiated by starvation. Nutrient depletion triggers the differentiation of Dictyostelium cells through the transcriptional inactivation of some growth‐phase genes, as well as through the transcriptional activation of essential genes required for the aggregation of the cells. The adenylyl cyclase (ACA) gene, acaA, is one of the earliest genes expressed following starvation. ACA produces intracellular and extracellular cAMP that drives further differentiation by inducing chemotaxis, developmental gene expression and morphogenesis of Dictyostelium cells. Although several genes have been identified as being essential for the initiation of differentiation process, such as the transcriptional activation of ACA expression, the molecular mechanisms of the growth/differentiation transition remain to be explored.ResultsUsing insertional mutagenesis, we have isolated a mutant that does not aggregate upon starvation. The disrupted gene, amiB (aggregation minus B), is predicted to encode a novel protein of 298.9 kDa. When starved, amiB− cells produced an undetectable level of cAMP. Analyses of gene expression showed that amiB− cells fail to turn off the expression of one of the growth‐phase genes, cprD, and to turn on the expression of ACA following starvation. The ectopic expression of ACA from a constitutive promoter rescued the differentiation and morphogenesis of amiB− mutants. Furthermore, the ectopic expression of a putative transcriptional factor DdMyb2 or a catalytic subunit of cAMP‐dependent protein kinase (PKA‐C), both of which are thought to be involved in ACA expression pathway(s), also rescued the starvation‐induced ACA expression and further differentiation of the amiB− mutant.ConclusionThese results suggest that AmiB plays a role at the start of Dictyostelium differentiation through induction of the ACA expression which is essential for cAMP signalling.
A human homologue of yeast anti‐silencing factor has histone chaperone activity
Authors: Munakata Tsubasa , Adachi Nobuaki , Yokoyama Natsuko , Kuzuhara Takashi , Horikoshi Masami 
Published: March 2003

BackgroundStructural changes in chromatin play essential roles in regulating eukaryotic gene expression. Silencing, potent repression of transcription in Saccharomyces cerevisiae, occurs near telomeres and at the silent mating‐type loci, as well as at rDNA loci. This type of repression relates to the condensation of chromatin that occurs in the heterochromatin of multicellular organisms. Anti‐silencing is a reaction by which silenced loci are de‐repressed. Genetic studies revealed that several factors participate in the anti‐silencing reaction. However, actions of factors and molecular mechanisms underlying anti‐silencing remain unknown.ResultsHere we report the functional activity of a highly evolutionarily conserved human factor termed CIA (CCG1‐interacting factor A), whose budding yeast homologue ASF1 has anti‐silencing activity. Using yeast two‐hybrid screening, we isolated histone H3 as an interacting factor of CIA. We also showed that CIA binds to histones H3/H4 in vitro, and that the interacting region of histone H3 is located in the C‐terminal helices. Considering the functional role of CIA as a histone‐interacting protein, we found that CIA forms a nucleosome‐like structure with DNA and histones.ConclusionsThese results show that human CIA, whose yeast homologue ASF1 is an anti‐silencing factor, possesses histone chaperone activity. This leads to a better understanding of the relationship between chromatin structural changes and anti‐silencing processes.
Identification of an imprinted gene, Meg3/Gtl2 and its human homologue MEG3, first mapped on mouse distal chromosome 12 and human chromosome 14q
Authors: Miyoshi Naoki , Wagatsuma Hirotaka , Wakana Shigeharu , Shiroishi Toshihiko , Nomura Masashi , Aisaka Kohzoh , Kohda Takashi , Surani M. Azim , Kaneko‐Ishino Tomoko , Ishino Fumitoshi 
Published: March 2003

BackgroundThe paternal duplication of mouse distal chromosome 12 leads to late embryonal/neonatal lethality and growth promotion, whereas maternal duplication leads to late embryonal lethality and growth retardation. Human paternal or maternal uniparental disomies of chromosome 14q that are syntenic to mouse distal chromosome 12 have also been reported to show some imprinting effects on growth, mental activity and musculoskeletal morphology. For the isolation of imprinted genes in this region, a systematic screen of maternally expressed genes (Megs) was carried out by our subtraction‐hybridization method using androgenetic and normally fertilized embryos.ResultsWe have isolated seven candidate clones of the mouse Meg gene. Among them, we identified a novel maternally expressed imprinted gene, Meg3, on mouse distal chromosome 12 and showed that it was identical to the Gtl2 gene. We also found that the human homologue MEG3 on chromosome 14q was also monoallelically expressed.ConclusionsThis is the first identification of the imprinting gene, both on mouse distal chromosome 12 and on human chromosome 14q, respectively. Because there are no obvious open reading frames in either the mouse Meg3/Gtl2 or human MEG3, the function of these genes remains unclear. However, this result will provide a good basis for the further investigation of several important imprinted genes in this chromosomal region.
Genes involved in the determination of the rate of inversions at short inverted repeats
Authors: Slupska Malgorzata M. , Chiang Ju‐Huei , Luther Wendy M. , Stewart Jean Lee , Amii Lisa , Conrad Alexis , Miller Jeffrey H. 
Published: March 2003

BackgroundNot all of the enzymatic pathways involved in genetic rearrangements have been elucidated. While some rearrangements occur by recombination at areas of high homology, others are mediated by short, often interrupted homologies. We have previously constructed an Escherichia coli strain that allows us to examine inversions at microhomologies, and have shown that inversions can occur at short inverted repeats in a recB,C‐dependent fashion.ResultsHere, we report on the use of this strain to define genetic loci involved in limiting rearrangements on an F′ plasmid carrying the lac genes. Employing mini‐Tn10 derivatives to generate insertions near or into genes of interest, we detected three loci (rmuA,B,C) that, when mutated, increase inversions. We have mapped, cloned and sequenced these mutator loci. In one case, inactivation of the sbcC gene leads to an increase in rearrangements, and in another, insertions near the recE gene lead to an even larger increase. The third gene involved in limiting inversions, rmuC, has been mapped at 86 min on the E. coli chromosome and encodes a protein of unknown function with a limited homology to myosins, and some of the SMC (structural maintenance of chromosomes) proteins.ConclusionsThis work presents the first example of an anti‐mutator role of the sbcC,D genes, and defines a new gene (rmuC) involved in DNA recombination.
Mis3 with a conserved RNA binding motif is essential for ribosome biogenesis and implicated in the start of cell growth and S phase checkpoint
Authors: Kondoh Hiroshi , Yuasa Tatsuro , Yanagida Mitsuhiro 
Published: March 2003

BackgroundIn normal somatic cell cycle, growth and cell cycle are properly coupled. Although CDK (cyclin‐dependent kinase) activity is known to be essential for cell cycle control, the mechanism to ensure the coupling has been little understood.ResultsWe here show that fission yeast Mis3, a novel evolutionarily highly conserved protein with the RNA‐interacting KH motif, is essential for ribosome RNA processing, and implicated in initiating the cell growth. Growth arrest of mis3‐224, a temperature sensitive mutant at the restrictive temperature, coincides with the early G2 block in the complete medium or the G1/S block in the release from nitrogen starvation, reflecting coupling of cell growth and division. Genetic interactions indicated that Mis3 shares functions with cell cycle regulators and RNA processing proteins, and is under the control of Dsk1 kinase and PP1 phosphatase. Mis3 is needed for the formation of 18S ribosome RNA, and may hence direct the level of proteins required for the coupling. One such candidate is Mik1 kinase. mis3‐224 is sensitive to hydroxyurea, and the level of Mik1 protein increases during replication checkpoint in a manner dependent upon the presence of Mis3 and Cds1.ConclusionsMis3 is essential for ribosome biogenesis, supports S phase checkpoint, and is needed for the coupling between growth and cell cycle. Whether Mis3 interacts solely with ribosomal precursor RNA remains to be determined.
Requirement of transfer‐messenger RNA for the growth of Bacillus subtilis under stresses
Authors: Muto Akira , Fujihara Ai , Ito Ken‐ichi , Matsuno Jun , Ushida Chisato , Himeno Hyouta 
Published: March 2003

BackgroundBacterial transfer‐messenger RNA (tmRNA, 10Sa RNA) is involved in a trans‐translation reaction which contributes to the degradation of incompletely synthesized peptides and to the recycling of stalled ribosomes. However, its physiological role in the cell remains elusive. In this study, an efficient system for controlling the expression of the gene for tmRNA (ssrA), as well as a tmRNA gene‐defective strain (ssrA::cat), were constructed in Bacillus subtilis. The effects of tmRNA on the growth of the cells were investigated under various physiological culture conditions using these strains.ResultsThe cells were viable in the absence of ssrA expression under the usual culture conditions. However, the growth rate of cells without tmRNA expression, relative to that of the expressed cells, decreased with elevating temperature (> 45 °C), and at 52 °C, the highest temperature for growth of the wild‐type, cells grew depending on the expression level of tmRNA. Furthermore, the transcription level of the ssrA from the authentic promoter at a high temperature (51 °C) was about 10‐fold higher than that at a lower temperature (37 °C). tmRNA‐dependent growth and an increase in tmRNA amount were also observed in cells under other stresses, such as high concentrations of ethanol or cadmium chloride. It is also shown that alanylated tmRNA rather than tmRNA‐mediated proteolysis is required for growth at high temperature.ConclusionThe expression of tmRNA gene (ssrA) is required for the efficient growth of B. subtilis under several strong stresses. The transcription of ssrA increases under several stressful conditions, suggesting that it is a stress‐response gene. Alanyl‐tmRNA, probably via its ability of recycling stalled ribosomes via trans‐translation, is involved in the stress tolerance of bacteria.
Involvement of fatty acid synthase in axonal development in mouse embryos
Authors: Ueno Kohji 
Published: March 2003

BackgroundDynamic protein palmitoylation of signalling proteins is thought to be an important step in the regulation of signal transduction in eukaryotic cells. The enzyme responsible for protein palmitoylation in vertebrates, however, has not been identified. I have previously reported that p260/270, which is expressed in embryos of the silkworm Bombyx mori, has protein palmitoylase activity.ResultsA homologue of Bombyx p260/270, mouse fatty‐acid synthase (FAS), was shown to be expressed specifically throughout most of the central and peripheral nervous system in mouse embryos. Mouse FAS was expressed specifically in cultured primary neurones in which growth‐associated protein (GAP)‐43 was expressed. GAP‐43, by protein palmitoylation, regulates Go signal transduction and neural axonal growth. In a cell‐free system, purified FAS from mouse embryos transferred palmitate to GAP‐43 through cysteine residues. Furthermore, cerulenin, an inhibitor of FAS, reduced axonal growth and in vivo palmitoylation of GAP‐43 in cultured neurones.ConclusionsMouse FAS was hypothesized to be responsible for the palmitoylation of GAP‐43 and subsequent regulation of axonal growth in mouse embryos.
Interaction of ribosome recycling factor and elongation factor EF‐G with E. coli ribosomes studied by the surface plasmon resonance technique
Authors: Ishino Tetsuya , Atarashi Kenji , Uchiyama Susumu , Yamami Tohru , Saihara Yukari , Yoshida Toshio , Hara Hiroto , Yokose Kazuteru , Kobayashi Yuji , Nakamura Yoshikazu 
Published: March 2003

Ribosome recycling factor (RRF), in concert with elongation factor EF‐G, is required for disassembly of the post‐termination complex of a ribosome after the release of polypeptides. How RRF dissociates the complex has long been puzzling. Crystal structures of RRF molecules have been solved recently and shown to mimic a transfer RNA (tRNA) shape, which prompted us to examine whether RRF binds to the ribosome as tRNA does.The formation of ribosome complexes on the surface‐coupled RRF and elongation factor EF‐G of Escherichia coli was monitored in real time with a BIACORE 2000 instrument based on the surface plasmon resonance technique. RRF interacted with 70S ribosomes as well as 50S and 30S subunits, although it interacted preferentially with 50S subunits, which was clearly seen under high but physiological ionic conditions. This 50S interaction was diminished by a single amino acid substitutions for Arg132 of RRF, which did not appreciably affect the protein folding but nullified the activity in vivo and in vitro. Moreover, a set of antibiotics that inhibited the RRF−50S interaction were also inhibitory to the polysome breakdown activity of RRF in vitro. The BIACORE technique also worked very well in demonstrating the action of the antibiotics thiostrepton and fusidic acid, which are inhibitory to the RRF function by freezing the pre‐ and post‐translocation intermediates catalysed by EF‐G.These results suggest that the preferential interplay of RRF with the 50S subunit may be of biological significance, probably reflecting the mode of RRF action. The BIACORE technique proved useful for real‐time monitoring of the interaction between the ribosome and translation factors, as well as for screening of potential inhibitors for ribosome recycling factor.
Hes7: a bHLH‐type repressor gene regulated by Notch and expressed in the presomitic mesoderm
Authors: Bessho Yasumasa , Miyoshi Goichi , Sakata Ryoichi , Kageyama Ryoichiro 
Published: March 2003

Background:Whereas Notch signalling is essential for somitogenesis, mice deficient for the basic helix‐loop‐helix (bHLH) genes Hes1 and Hes5, downstream Notch effectors, display normal somite formation, indicating that there may be an as‐yet unidentified Hes1‐related bHLH gene.Results:We identified a novel bHLH gene, designated Hes7, from mouse embryos. Hes7 has a conserved bHLH domain in the amino‐terminal region and the WRPW domain at the carboxy‐terminal end, like Hes1. The mouse Hes7 gene is located next to Aloxe3, which is mapped to a position 37.0 cM from the centromere on chromosome 11. In a transfection analysis, Hes7 represses transcription from the N box‐ and E box‐containing promoters. In addition, Hes7 suppresses the E47‐induced transcriptional activation. Promoter analysis indicated that Hes7 expression is controlled by Notch signalling. Strikingly, Hes7 is specifically expressed in the presomitic mesoderm in a dynamic manner. We also identified two related bHLH genes from human: one is closely related to mouse Hes7 and therefore designated hHes7 and the other designated hHes4.Conclusion:The structure, transcriptional activity and expression pattern in the presomitic mesoderm of Hes7 are very similar to those of Hes1, suggesting that Hes7, together with Hes1, may play a role in somite formation under the control of Notch signalling.
The Drosophila UBC9 homologue lesswright mediates the disjunction of homologues in meiosis I
Authors: Apionishev Sergey , Malhotra Deepak , Raghavachari Seshasayee , Tanda Soichi , Rasooly Rebekah S. 
Published: March 2003

BackgroundIn Saccharomyces cerevisiae and other organisms, the UBC9 (ubiquitin‐conjugating 9) protein modifies the function of many different target proteins through covalent attachment of the ubiquitin‐like protein SMT‐3/SUMO.ResultsUsing a second‐site suppression screen of a mutation in the nod locus with a variable meiotic phenotype, we have identified mutations in the Drosophila melanogaster UBC9 homologue, encoded by the gene lesswright (lwr). lwr mutations dominantly suppress the nondisjunction and cytological defects of female meiotic mutations that affect spindle formation. The lwr lethal phenotype is rescued by a Drosophila UBC9/lwr transgene.ConclusionsWe suggest that LWR mediates the dissociation of heterochromatic regions of homologues at the end of meiotic prophase I. Our model proposes that when there is less LWR protein, homologues remain together longer, allowing for more normal spindle formation in mutant backgrounds and therefore more accurate meiotic chromosome segregation.
Coronin forms a stable dimer through its C‐terminal coiled coil region: an implicated role in its localization to cell periphery
Authors: Asano Shiro , Mishima Masanori , Nishida Eisuke 
Published: March 2003

BackgroundCoronin is an actin‐binding protein, which contains WD (Trp‐Asp) repeats and a coiled‐coil motif, and plays a role in regulating organization of the actin cytoskeletal network. Coronin localizes to the cell periphery, is involved in lamellipodium extension, and has an implicated role in cytokinesis, cell motility and phagocytosis.ResultsOur experiments with two different tagged forms of Xenopus coronin (Xcoronin) have shown that Xcoronin forms an oligomer. This oligomer complex is stable, resistant to 2.4 m NaCl, 0.6 m KI or 2 m urea. Physiochemical analysis of endogenous Xcoronin and the protein expressed in COS7 cells or in bacteria has revealed that the oligomer complex is an Xcoronin dimer. A C‐terminal coiled‐coil motif of Xcoronin is necessary and sufficient for the dimerization. Mutations in the coiled‐coil motif generated dimerization deficient mutants of Xcoronin. Moreover, these mutant forms of Xcoronin failed to localize to the cell periphery, suggesting that dimerization is important for the proper subcellular localization of Xcoronin.ConclusionXcoronin forms a stable dimer via its C‐terminal coiled‐coil region. We propose that coronin dimerization is necessary for its proper subcellular localization and function.
p48 subunit of mouse PTF1 binds to RBP‐Jκ/CBF‐1, the intracellular mediator of Notch signalling, and is expressed in the neural tube of early stage embryos
Authors: Obata Junko , Yano Masato , Mimura Hideki , Goto Tomokazu , Nakayama Rika , Mibu Yuko , Oka Chio , Kawaichi Masashi 
Published: March 2003

BackgroundDevelopment of the pancreas and the nervous tissues is regulated by common transcription factors. A basic helix‐loop‐helix protein, p48 of pancreas transcription factor 1 (PTF1), is essential for differentiation of the exocrine acinar cells.ResultsWe isolated PTF1 p48 from 9.5‐day mouse embryos as a binding protein of RBP‐Jκ, a mediator of Notch signalling. p48 bound to RBP‐Jκ more strongly than and in a distinct way from Notch1. In 9.5–12.5 day embryos, p48 was expressed in the dorsal part of the neural tube as well as in the pancreatic buds. Two lines of evidence suggested functions of p48 in neurogenesis: (i) expression of p48 was induced in P19 cells when they committed to neural fate upon retinoic acid treatment, and (ii) p48 over‐expressed in Xenopus embryos repressed the development of neuronal precursors. p48 inhibited the MASH1‐activated transcription from the E‐box, while p48 stimulated transcription from the PTF1 motif synergistically with E47. The p48/E47‐activated transcription from the PTF1 motif was stimulated further by RBP‐Jκ and RBP‐Jκ derivatives that mimicked the active RBP‐Jκ/Notch complex.ConclusionsIn developing embryos, p48 is expressed in both the nervous system and the pancreas. p48 inhibits neuronal differentiation. We propose possible mechanisms for this inhibition.
A single nucleotide polymorphism at the splice donor site of the human MYH base excision repair gene results in reduced translation efficiency of its transcripts
Authors: Yamaguchi Satoru , Shinmura Kazuya , Saitoh Takayuki , Takenoshita Seiichi , Kuwano Hiroyuki , Yokota Jun 
Published: March 2003

AbstractBackground: Adenine paired with 8‐hydroxyguanine, a major oxidatively damaged DNA lesion, is excised by mutY homologue (MYH) base excision repair protein in human cells. Since genetic polymorphisms of DNA repair genes associated with the activities and the expression levels of their products may modulate cancer susceptibility of individuals, we investigated the effect of a single nucleotide polymorphism (SNP) in the MYH gene on the difference in the expression levels of its products.Results: An aberrant size of the β type nuclear form transcript was detected in a lung cancer cell line, VMRC‐LCD, by reverse transcriptase‐polymerase chain reaction (RT‐PCR) analysis. The transcript contained the intron 1 sequence, and it was due to alternative splicing resulting from IVS1+5G/C SNP. The presence of the upstream open reading frame (ORF) on the 5′‐side of the native ORF in the β type transcript from the IVS1+5C allele could reduce the translation efficiency of the transcript into the nuclear form protein. Thus, expression vectors bearing the 5′‐untranslated region sequence of either the IVS1+5G or 5C allele were constructed. In vitro translation analysis, as well as Western blot and quantitative RT‐PCR analyses of the H1299 lung cancer cell line transfected with these vectors, revealed that the translation efficiency of the IVS1+5C transcript into MYH protein was much lower (≈ 30%) than that of the IVS1+5G transcript.Conclusions: The SNP at the splice donor site of the MYH gene resulted in reduced translation efficiency of its transcripts. This is the fourth case of single nucleotide variations that cause alterations in translation initiation sites and translation efficiencies in human cells.
The Cpx stress response system of Escherichia coli senses plasma membrane proteins and controls HtpX, a membrane protease with a cytosolic active site
Authors: Shimohata Nobuyuki , Chiba Shinobu , Saikawa Naoya , Ito Koreaki , Akiyama Yoshinori 
Published: March 2003

AbstractBackground: The abnormal accumulation of misfolded proteins outside the plasma (cytoplasmic or inner) membrane up‐regulates the synthesis of a class of envelope‐localized catalysts of protein folding and degradation. The pathway for this transmembrane signalling is mediated by the CpxR‐CpxA two‐component phospho‐relay mechanism.Results: We now show that an abnormality in the plasma membrane proteins, due either to the impairment of FtsH, a protease acting against integral membrane proteins, or to the overproduction of a substrate membrane protein of FtsH, activates this stress response pathway. Under such conditions, the cpxR gene function becomes essential for cell growth. We further show that the expression of a putative protease, HtpX, in the plasma membrane, is under the control of CpxR. Synthetic growth inhibition was observed when the ftsH and htpX disruption mutations had been combined, suggesting that these gene products have some complementary or overlapping proteolytic functions. Topology analyses indicated that the metalloproteinase active site of HtpX is located on the cytosolic side of the membrane.Conclusions: Taken together, these results suggest that the Cpx ‘extracytoplasmic’ stress response system controls the quality of the plasma membrane, even on its cytoplasmic side.