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PubMed2003

Truncated product of the bifunctional DLST gene involved in biogenesis of the respiratory chain.

Dihydrolipoamide succinyltransferase (DLST) is a subunit enzyme of the alpha-ketoglutarate dehydrogenase complex of the Krebs cycle. While studying how the DLST genotype contributes to the pathogenesis of Alzheimer's disease (AD), we found a novel mRNA that is transcribed starting from intron 7 in the DLST gene. The novel mRNA level in the brain of AD patients was significantly lower than that of controls. The truncated gene product (designated MIRTD) localized to the intermembrane space of mitochondria. To investigate the function of MIRTD, we established human neuroblastoma SH-SY5Y cells expressing a maxizyme, a kind of ribozyme, that specifically digests the MIRTD mRNA. The expression of the maxizyme specifically eliminated the MIRTD protein and the resultant MIRTD-deficient cells exhibited a marked decrease in the amounts of subunits of complexes I and IV of the mitochondrial respiratory chain, resulting in a decline of activity. A pulse-label experiment revealed that the loss of the subunits is a post-translational event. Thus, the DLST gene is bifunctional and MIRTD transcribed from the gene contributes to the biogenesis of the mitochondrial respiratory complexes.

Acyltransferases↗
PubMed1999

Positive selection of novel peroxisome biogenesis-defective mutants of the yeast Pichia pastoris.

We have developed two novel schemes for the direct selection of peroxisome-biogenesis-defective (pex) mutants of the methylotrophic yeast Pichia pastoris. Both schemes take advantage of our observation that methanol-induced pex mutants contain little or no alcohol oxidase (AOX) activity. AOX is a peroxisomal matrix enzyme that catalyzes the first step in the methanol-utilization pathway. One scheme utilizes allyl alcohol, a compound that is not toxic to cells but is oxidized by AOX to acrolein, a compound that is toxic. Exposure of mutagenized populations of AOX-induced cells to allyl alcohol selectively kills AOX-containing cells. However, pex mutants without AOX are able to grow. The second scheme utilizes a P. pastoris strain that is defective in formaldehyde dehydrogenase (FLD), a methanol pathway enzyme required to metabolize formaldehyde, the product of AOX. AOX-induced cells of fld1 strains are sensitive to methanol because of the accumulation of formaldehyde. However, fld1 pex mutants, with little active AOX, do not efficiently oxidize methanol to formaldehyde and therefore are not sensitive to methanol. Using these selections, new pex mutant alleles in previously identified PEX genes have been isolated along with mutants in three previously unidentified PEX groups.

Alcohol Oxidoreductases↗
PubMed2000

Defective pigment granule biogenesis and aberrant behavior caused by mutations in the Drosophila AP-3beta adaptin gene ruby.

Lysosomal protein trafficking is a fundamental process conserved from yeast to humans. This conservation extends to lysosome-like organelles such as mammalian melanosomes and insect eye pigment granules. Recently, eye and coat color mutations in mouse (mocha and pearl) and Drosophila (garnet and carmine) were shown to affect subunits of the heterotetrameric adaptor protein complex AP-3 involved in vesicle trafficking. Here we demonstrate that the Drosophila eye color mutant ruby is defective in the AP-3beta subunit gene. ruby expression was found in retinal pigment and photoreceptor cells and in the developing central nervous system. ruby mutations lead to a decreased number and altered size of pigment granules in various cell types in and adjacent to the retina. Humans with lesions in the related AP-3betaA gene suffer from Hermansky-Pudlak syndrome, which is caused by defects in a number of lysosome-related organelles. Hermansky-Pudlak patients have a reduced skin pigmentation and suffer from internal bleeding, pulmonary fibrosis, and visual system malfunction. The Drosophila AP-3beta adaptin also appears to be involved in processes other than eye pigment granule biogenesis because all ruby allele combinations tested exhibited defective behavior in a visual fixation paradigm.

Adaptor Protein Complex alpha Subunits↗
PubMed2001

Sphingolipid activator proteins: proteins with complex functions in lipid degradation and skin biogenesis.

Sphingolipid activator proteins (SAPs or saposins) are essential cofactors for the lysosomal degradation of membrane-anchored sphingolipids. Four of the five known proteins of this class, SAPs A--D, derive from a single precursor protein and show high homology, whereas the fifth protein, GM2AP, is larger and displays a different secondary structure. Although the main function of all five proteins is assumed to lie in the activation of lipid degradation, their specificities and modes of action seem to differ considerably. It has recently been demonstrated that the action of the proteins is highly enhanced by the presence of acidic lipids in the target membranes. These results have some interesting implications for the topology of lysosomal degradation of lipids and may provide new insights into the function of these interesting proteins, which are ubiquitously expressed in the different tissues of the body. Recent studies indicated that the SAPs play an important role in the biogenesis of the epidermal water barrier, which has been demonstrated by the analysis of the skin phenotype displayed by SAP-knockout mice. The results obtained so far have led to some new insights into the formation of the epidermal water permeability barrier and may lead to a better understanding of this complex process.

Epidermis↗
PubMed1999

Nonsense and temperature-sensitive mutations in PEX13 are the cause of complementation group H of peroxisome biogenesis disorders.

Peroxisome biogenesis disorders, including Zellweger syndrome (ZS), neonatal adrenoleukodystrophy (NALD) and infantile Refsum disease, are lethal hereditary diseases caused by abnormalities in peroxisomal assembly. To date, 12 genotypes have been identified. We now have evidence that the complete human cDNA encoding Pex13p, an SH3 protein of a docking factor for the peroxisome targeting signal 1 receptor (Pex5p), rescues peroxisomal matrix protein import and its assembly in fibroblasts from PBD patients of complementation group H. In addition, we detected mutations on the human PEX13 cDNA in two patients of group H. A severe phenotype of a ZS patient (H-02) was homozygous for a nonsense mutation, W234ter, which results in the loss of not only the SH3 domain but also the putative transmembrane domain of Pex13p. A more mildly affected NALD patient (H-01), whose fibroblasts showed the temperature-sensitive (TS) phenotype, was homozygous for a missense mutation in the SH3 domain of Pex13p, I326T. This mutant PEX13 cDNA expression in a PEX13-defective CHO mutant showed I326T to be a TS mutation and thus suggested that Pex13p with the I326T mutation in the SH3 domain is stable at 30 degrees C but is somewhat unstable at 37 degrees C.

Amino Acid Sequence↗
PubMed2006

Parkin enhances mitochondrial biogenesis in proliferating cells.

We describe a novel function of parkin, a RING protein, which is elaborately involved in mitochondrial biogenesis. Parkin was located within the mitochondrial organelle of proliferating cells. Anti-proliferative treatments released parkin from mitochondria to cytosol. Results of pharmacological treatments indicate that parkin was released from mitochondria when permeability transition pore was opened. The extra-mitochondrial localization was also observed in differentiated cells. In proliferating cells, transcription and replication of mitochondrial DNA was enhanced by parkin overexpression and attenuated by parkin suppression with siRNA. Parkin was associated with mitochondrial transcription factor A (TFAM) and enhanced TFAM-mediated mitochondrial transcription. These results indicate that parkin is involved in the regulation of mitochondrial transcription/replication other than the ubiquitin-mediated protein degradation system in proliferating cells.

Animals↗
PubMed2006

The mitochondrial ATP-binding cassette transporter Abcb7 is essential in mice and participates in cytosolic iron-sulfur cluster biogenesis.

Proteins with iron-sulfur (Fe-S) clusters participate in multiple metabolic pathways throughout the cell. The mitochondrial ABC half-transporter Abcb7, which is mutated in X-linked sideroblastic anemia with ataxia in humans, is a functional ortholog of yeast Atm1p and is predicted to export a mitochondrially derived metabolite required for cytosolic Fe-S cluster assembly. Using an inducible Cre/loxP system to delete exons 9 and 10 of the Abcb7 gene, we examined the phenotype of mice deficient in Abcb7. We found that Abcb7 was essential in extra-embryonic tissues early in gestation and that the mutant allele exhibits an X-linked parent-of-origin lethality effect. Furthermore, using X-chromosome inactivation assays and tissue-specific deletions, Abcb7 was found to be essential for the development and function of numerous other cell types and tissues. A notable exception to this was liver, where loss of Abcb7 impaired cytosolic Fe-S cluster assembly but was not lethal. In this situation, control of iron regulatory protein 1, a key cytosolic modulator of iron metabolism, which is responsive to the availability of cytosolic Fe-S clusters, was impaired and contributed to the dysregulation of hepatocyte iron metabolism. Altogether, these studies demonstrate the essential nature of Abcb7 in mammals and further substantiate a central role for mitochondria in the biogenesis of cytosolic Fe-S proteins.

ATP-Binding Cassette Transporters↗
PubMed1999

Analysis of the early biogenesis of CD1b: involvement of the chaperones calnexin and calreticulin, the proteasome and beta(2)-microglobulin.

beta(2)-Microglobulin (beta(2)m)-associated human CD1b proteins present lipid and glycolipid antigens, which are loaded on CD1b in endosomal compartments. In contrast, the related MHC class I molecules acquire antigenic peptides in the endoplasmic reticulum. Here, we investigated the biogenesis of CD1b before beta(2)m binding in comparison to MHC class I. In beta(2)m-deficient FO-1 cells, we found CD1b heavy chains (HC) complexed with the chaperones calnexin and calreticulin, while MHC class I HC associated only with calnexin. Despite this difference, both CD1b HC and MHC class I HC were degraded when the chaperone interactions were prevented by the glucosidase inhibitor castanospermine. The degradation of both molecules included the proteasome and mannosidases. Chaperone-unassociated CD1b could be rescued from degradation by supplementing FO-1 cells with beta(2)m. Finally, prevention of chaperone interaction significantly reduced neoexpression of CD1b upon differentiation of monocytes to dendritic cells, underlining the importance of chaperones for proper expression of CD1b under physiological conditions.

Antigens, CD↗
PubMedDate not supplied

The yellow variegated mutant of Arabidopsis is plastid autonomous and delayed in chloroplast biogenesis.

The yellow variegated mutant of Arabidopsis thaliana is characterized by bright-yellow true leaves that turn green- and white-sectored as leaf development proceeds. Variegation is due to the action of a nuclear recessive gene. Whereas cells in the green sectors contain morphologically normal chloroplasts, cells in the yellow and white sectors are heteroplastidic and contain plastids with rudimentary lamellar structures, as well as some normal-appearing chloroplasts. This indicates that plastids in yellow variegated are affected differently by the nuclear mutation (the mutant is "plastid autonomous"). Genetic analyses have revealed that yellow variegated is an allele of the var2 locus, and that defective plastids are not maternally inherited. The traits of plastid autonomy and lack of maternal inheritance of the plastid defect set var2 apart from other nuclear gene-induced variegations and define a novel class of variegation mutant. The primary lesion in var2 probably does not involve a blockage in the pathways of pigment biosynthesis. Under high temperatures or low light conditions, plant growth is retarded and mutant plants are nearly all-green. Considered together, our data suggest that var2 is delayed in chloroplast biogenesis. We suggest that the stochastic pattern of variegation in the mutant may be due to an interplay of factors that regulate var2 gene expression and factors that mediate rates of cell and plastid division. Plastids with a critical threshold of the partially functional var2 protein are green, while plastids containing less than the threshold of var2 activity are white.

Alleles↗
PubMed2003

Gene expression regulating epithelial intercellular junction biogenesis during human blastocyst development in vitro.

We investigated gene expression associated with trophectoderm epithelial intercellular junction formation in single human embryos at different stages of cleavage using RT-PCR methods based upon magnetic bead separation of polyA+ RNA. Trophectoderm tight junction (TJ) and desmosome biogenesis contribute to intercellular sealing and tissue integrity, critical for vectorial transport and blastocoel cavity formation. Expression of the various genes throughout human preimplantation development showed differing levels of sensitivity of detection; these genes included claudin-1, occludin (TM4+ and TM4 isoforms), ZO-1 (ZO-1alpha+ and ZO-1alpha- isoforms), ZO-2 and JAM (junction adhesion molecule), and the desmosome junction gene, DSC2 (desmocollin 2). Some transcripts appeared to be expressed throughout preimplantation development (claudin-1, JAM, occludin TM4+ and TM4, ZO-1alpha- isoform) while others tended to be expressed preferentially in later cleavage and associated with blastocyst formation (ZO-2, ZO-1alpha+ isoform, DSC-2), illustrating an expression pattern broadly similar to mouse cleavage stages. Human embryo transcript detection was significantly decreased when reverse transcription was performed in solid phase to generate a bead/cDNA transient library rather than after mRNA elution from beads. Transcript detection tended to be positively correlated with embryo morphological grade using the solid phase method. In blastocysts, occludin TM4-, ZO-1alpha+ and DSC2 transcripts were the most susceptible to failure of detection, indicative of low levels of expression which may impact on trophectoderm differentiation competence. Immunoconfocal microscopy analysis of selected adhesion and TJ proteins in human embryos indicated poor membrane assembly compared with mouse blastocysts, which may further affect embryo viability.

Blastocyst↗
PubMed1987

Two novel genes, fanA and fanB, involved in the biogenesis of K99 fimbriae.

The nucleotide sequence of the region located transcriptionally upstream of the K99 fimbrial subunit gene (fanC) was determined. Several putative transcription signals and two open reading frames, designated fanA and fanB, became apparent. Frameshift mutations in fanA and fanB reduced K99 fimbriae expression 8-fold and 16-fold, respectively. Complementation of the mutants in trans restored the K99 expression to about 75% of the wild type level, indicating that fanA and fanB code for transacting polypeptides involved in the biogenesis of K99 fimbriae. The fanA and fanB gene products FanA and FanB were not detectable in minicell preparations, indicating that both polypeptides are synthesized in very small amounts. However, in an in vitro DNA directed translation system FanA and FanB could be identified. The deduced amino acid sequences of FanA and FanB showed that both polypeptides contain no signal peptides, indicating a cytoplasmic location. Furthermore, the polypeptides are very hydrophilic, mainly basic, and exhibit remarkable homology to each other and to a regulatory protein (papB) encoded by the pap-operon (1). Some of these features are characteristics of nucleic acid binding proteins, which suggests that FanA and FanB have a regulatory function in the synthesis of FanC and the auxiliary polypeptides FanD-H.

Base Sequence↗
PubMed1999

MitBASE pilot: a database on nuclear genes involved in mitochondrial biogenesis and its regulation in Saccharomyces cerevisiae.

In the framework of the EU BIOTECH PROGRAM and within the 'MITBASE: a comprehensive and integrated database on mtDNA' project, we have prepared a pilot database (MitBASE Pilot) on nuclear genes involved in mitochondrial biogenesis and its regulation in Saccharomyces cerevisiae. MitBASE Pilot includes nuclear genes encoding mitochondrial proteins as well as nuclear genes encoding products which are localised in other sub-cellular compartments but nevertheless interact with mitochondrial functions. Genes have been classified on the basis of the mitochondrial process in which they participate and the mitochondrial phenotype of the gene knockout. The structure of the MitBASE Pilot database has been conceived for a flexible organisation of the information. An intuitive visual query system has been developed which allows users to select information in different combinations, both in the query and the output format, according to their needs. MitBASE Pilot is a relational database, is maintained at the EMBL-European Bioinformatics Institute (EBI) and is available at the World Wide Web site http://www3.ebi.ac. uk/Research/Mitbase/mitbiog.pl

Cell Nucleus↗
PubMed2000

Myc induces the nucleolin and BN51 genes: possible implications in ribosome biogenesis.

The c-Myc oncoprotein and its dimerization partner Max bind the DNA core consensus sequence CACGTG (E-box) and activate gene transcription. However, the low levels of induction have hindered the identification of novel Myc target genes by differential screening techniques. Here, we describe a computer-based pre-selection of candidate Myc/Max target genes, based on two restrictive criteria: an extended E-box consensus sequence for Myc/Max binding and the occurrence of this sequence within a potential genomic CpG island. Candidate genes selected by these criteria were evaluated experimentally for their response to Myc. Two Myc target genes are characterized here in detail. These encode nucleolin, an abundant nucleolar protein, and BN51, a co-factor of RNA polymerase III. Myc activates transcription of both genes via E-boxes located in their first introns, as seen for several well-characterized Myc targets. For both genes, mutation of the E-boxes abolishes transcriptional activation by Myc as well as repression by Mad1. In addition, the BN51 promoter is selectively activated by Myc and not by USF, another E-box-binding factor. Both nucleolin and BN51 are implicated in the maturation of ribosomal RNAs, albeit in different ways. We propose that Myc, via regulation of these and probably many other transcriptional targets, may be an important regulator of ribosome biogenesis.

Cell Cycle Proteins↗
PubMed1995

Biogenesis of novel quinone coenzymes.

Recently, two novel quinonoid coenzymes, 2,4,5-trihydroxyphenylalanine quinone (topa quinone; TPQ) and tryptophan tryptophylquinone (TTQ), were identified in copper-containing amine oxidase and methylamine dehydrogenase, respectively. Unlike the formerly known quinonoid coenzyme, pyrroloquinoline quinone (PQQ), which is non-covalently bound to several prokaryotic dehydrogenases and produced through its own biosynthetic pathway, each of TPQ and TTQ is bound covalently to the polypeptide chain as an integral amino acid residue and encoded by a codon for a normal (unmodified) amino acid in the gene. Thus, these coenzymes must be generated through post-translational modification of the precursor amino acid; for TPQ, oxidation of a specific tyrosine occurring in the consensus Asn-Tyr-Asp/Glu sequence, and for TTQ, oxidation of a specific tryptophan and cross-linking with another tryptophan separated by 50 residues in the same polypeptide chain. We recently demonstrated that, using the inactive precursor forms of bacterial copper amine oxidases, TPQ is generated through self-processing of the protein with the participation of the bound copper ions. On the other hand, the absence of a prosthetic metal ion in methylamine dehydrogenase as well as its existence in the periplasm renders TTQ biogenesis more complicated, likely requiring an external enzymatic system(s).

Amine Oxidase (Copper-Containing)↗
PubMed1985

Biogenesis of microsomal aldehyde dehydrogenase in rat liver.

The biogenesis of a microsomal NAD(P)+-dependent aldehyde dehydrogenase (AlDH) in rat liver was studied using specific antibody raised against the purified enzyme prepared by the method of Nakayasu et al. (Nakayasu, H., Mihara, K., & Sato, R. (1978) Biochem. Biophys. Res. Commun. 83, 697-703). The antibody raised against purified AlDH inhibited the activity of microsome-bound AlDH as effectively as that of the detergent-solubilized enzyme, suggesting that AlDH molecules are present on the outer surface of microsomal vesicles and that a major portion of each molecule, including the active site, is exposed. The cell-free translation of RNA preparations extracted from free and membrane-bound polysomes showed that AlDH was exclusively synthesized on free polysomes. The in vitro synthesized AlDH had the same molecular weight as the authentic enzyme. When a single intravenous injection of [3H]leucine was given to rats, there was no detectable difference in the specific radioactivities of AlDH in rough and smooth microsomes even at the shortest time point, suggesting random incorporation of newly synthesized AlDH molecules into rough and smooth endoplasmic reticulum.

Aldehyde Oxidoreductases↗
PubMed1997

Biogenesis of eukaryotic 20S proteasomes: the complex maturation pathway of a complex enzyme.

Eukaryotic 20S proteasomes harbor a remarkably complex architecture and unique proteolytic properties. Its catalytic mechanism places this enzyme in a new kind of protease family. The recently solved crystal structure of the yeast 20S complex, along with elucidation of the maturation pathway of human proteasomes, has allowed insight into structure/function relationships. Although not all of the unusual enzymatic properties such as broad substrate specificity, predominant generation of peptides with a specific size, or susceptibility to activating complexes can be explained in detail, knowledge of the structure provides important hints for an explanation of underlying mechanisms. Except for ribosome biogenesis, the complexity of eukaryotic proteasome maturation is without precedence. It is a slow process that involves a series of precisely ordered events. Proteasome structure formation is characterized by an initial cooperative formation of an alpha ring matrix, providing docking sites for a defined subset of beta subunits. Subsequent structural rearrangement allows the residual subunits to bind, followed by dimerization of two half-proteasomes. The prosequences of beta subunits exert specific functions during this process and are removed by cis- and trans-autocatalysis, most likely in the completely assembled proteasome cylinder.

Animals↗
PubMed1999

Participation of dynamin in the biogenesis of cytoplasmic vesicles.

Dynamin is a 100-kDa GTPase that has been implicated in endocytosis. To extend our understanding of its cellular functions, we have microinjected specific affinity-purified anti-dynamin antibodies into cultured mammalian epithelial cells. Using this approach, dynamin function can be inhibited specifically and rapidly in single cells. Effects of microinjected inhibitory antibodies on distinct endocytic processes and plasmalemmal morphology were then assayed by fluorescence microscopy (FM) and ultrastructural analysis. Micro-injected antibodies inhibit the clathrin-mediated endocytosis of fluorophore-labeled transferrin and cause a marked invagination of the plasma membrane. Many of these long plasmalemmal invaginations had clathrin-coated pits along their cytoplasmic surface. A number of distinct noncoated pits resembling plasmalemmal caveolae also accumulated in anti-dynamin antibody-injected cells. Further, the cellular uptake of cholera toxin B, which normally occurs by the internalization of caveolae, was inhibited in these cells. In support of these observations, immunoisolation techniques, double-label immuno-FM, and immunoelectron microscopy (immuno-EM) provided biochemical and morphological evidence that dynamin associates with plasmalemmal caveolae. Together, these observations indicate that dynamin mediates scission from the plasma membrane of both clathrin-coated pits and caveolae during distinct endocytic processes. These results demonstrate that dynamin isoforms are involved in an additional endocytic process that is distinct from clathrin-mediated endocytosis and provide significant insights into the molecular mechanisms governing the GTP-mediated internalization of caveolae. Evidence is provided demonstrating that dynamin isoforms have a differential distribution in mammalian cells. Targeting information for these isoforms is provided at least in part by regions of alternative splicing. Thus, the different dynamin isoforms may be localized to distinct cellular compartments but provide a similar scission function during the biogenesis of nascent cytoplasmic vesicles.

Animals↗
PubMed1994

Hexosamine and cell wall biogenesis in the aquatic fungus Blastocladiella emersonii.

Chitin, a beta-(1-->4) polymer of N-acetyl-glucosamine, is an important constituent of fungal cell walls. This polymer is synthesized by the incorporation of N-acetyl-D-glucosamine units from the precursor UDP-N-acetyl-D-glucosamine (UDP-GlcNAc) in a reaction catalyzed by chitin synthase. In the aquatic fungus Blastocladiella emersonii, chitin, the major component of the cell wall, is synthesized and incorporated in the cell surface of the free-swimming zoospore during the abrupt transition from this wall-less cell to the sessile, wall-containing cyst. Studies with cycloheximide indicate that chitin synthesis occurs in the apparent absence of protein synthesis, and thus posttranslational controls presumably regulate the cell wall biogenesis during encystment. Glutamine: fructose 6-phosphate amidotransferase, first enzyme of the hexosamine biosynthetic pathway, was found to play a central role in the regulation of chitin synthesis in this fungus. This enzyme exists in two forms, which are interconvertible by phosphorylation or dephosphorylation of serine residues. It is allosterically inhibited in the phosphorylated form, as it is in the zoospore, by UDP-GlcNAc. In addition, UDP-GlcNAc inhibits the dephosphorylation of amidotransferase catalyzed by protein phosphatases 2A and 2C. Thus, UDP-GlcNAc plays a dual role in hexosamine and chitin synthesis in zoospore: it not only inhibits the phosphorylated form of the enzyme but also prevents its dephosphorylation. The available data suggest that substrate availability plays a role in the control of chitin synthesis during zoospore differentiation.

Blastocladiella↗