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PubMed2003

Parallel analysis of tagged deletion mutants efficiently identifies genes involved in endoplasmic reticulum biogenesis.

Increased levels of HMG-CoA reductase induce cell type- and isozyme-specific proliferation of the endoplasmic reticulum. In yeast, the ER proliferations induced by Hmg1p consist of nuclear-associated stacks of smooth ER membranes known as karmellae. To identify genes required for karmellae assembly, we compared the composition of populations of homozygous diploid S. cerevisiae deletion mutants following 20 generations of growth with and without karmellae. Using an initial population of 1,557 deletion mutants, 120 potential mutants were identified as a result of three independent experiments. Each experiment produced a largely non-overlapping set of potential mutants, suggesting that differences in specific growth conditions could be used to maximize the comprehensiveness of similar parallel analysis screens. Only two genes, UBC7 and YAL011W, were identified in all three experiments. Subsequent analysis of individual mutant strains confirmed that each experiment was identifying valid mutations, based on the mutant's sensitivity to elevated HMG-CoA reductase and inability to assemble normal karmellae. The largest class of HMG-CoA reductase-sensitive mutations was a subset of genes that are involved in chromatin structure and transcriptional regulation, suggesting that karmellae assembly requires changes in transcription or that the presence of karmellae may interfere with normal transcriptional regulation.

DNA, Fungal↗
PubMed1996

Thyromimetic action of the peroxisome proliferators clofibrate, perfluorooctanoic acid, and acetylsalicylic acid includes changes in mRNA levels for certain genes involved in mitochondrial biogenesis.

The effects of three peroxisome proliferators on the mRNA levels for some mitochondrial inner-membrane proteins in rat liver were investigated. Clofibrate, perfluorooctanoic acid, and acetylsalicylic acid all increased the mRNA levels for the mitochondrial-encoded respiratory-chain components cytochrome c oxidase subunit I and NADH dehydrogenase subunit I. Mitochondrial 16S rRNA was also induced by clofibrate. The mRNA levels for the nuclear-encoded mitochondrial inner-membrane proteins adenine nucleotide translocator and cytochrome c1 were selectively induced by the different peroxisome proliferators. Malic enzyme, which is induced by thyroid hormone, was also induced by the three peroxisome proliferators tested. These effects are in some ways similar to those obtained with thyroid hormone.

Animals↗
PubMed1996

Biogenesis and metabolic fate of docosahexaenoic and arachidonic acids in rat uterine stromal cells in culture.

To gain some insight into the mechanisms involved in the opposing effects of arachidonic acid and docosahexaenoic acid on the growth of rat uterine stromal cells (UIII cells), the dynamics of the uptake, conversion, and incorporation of labeled 18:2(n-6), 18:3(n-3), 20:4(n-6), 20:5(n-3), and 22:6(n-3) into lipid pools and phospholipid subclasses were examined. A very active and time-dependent conversion of [14C]18:3(n-3) to higher homologs was observed; 64.7 +/- 0.7 and 11.5 +/- 0.4% of the [14C] radioactivity incorporated in cellular lipids was recovered as 22:5(n-3) and 22:6(n-3) after 72 h incubation, respectively. The distribution of labeled fatty acids obtained after 72 h incubation with [3H]20:5(n-3) was not significantly different from that observed with 18:3(n-3). Arachidonic acid was the major fatty acid formed from [14C]18:2(n-6) and only trace amounts of 22:5(n-6) were detected. When cells were incubated for 72 h with 20:4(n-6), more than 75% of the radioactivity was recovered as arachidonate and slightly higher amounts of 22:4(n-6) and 22:5(n-6) were formed compared to those obtained after incubation with 18:2(n-6). Using both [14C]- and [3H]22:6(n-3), no significant retroconversion of labeled 22:6(n-3) occurred in the cells. More than 90% of labeled 20:4(n-6) and 22:6(n-3) taken up by the cells were esterified into phospholipids, but significant differences in their distribution among phospholipid classes and subclasses were observed. Docosahexaenoic acid was more rapidly and efficiently incorporated into phosphatidylethanolamine than 20:4(n-6) and was principally recovered in plasmalogens. Arachidonic acid was mainly incorporated in the diacyl subclasses of phosphatidylcholine and phosphatidylethanolamine and in phosphatidylinositol. The divergent profiles of these two fatty acids within the phospholipid compartments provide some information for the mechanisms of their opposite effects on UIII cell growth.

Animals↗
PubMed2001

Biogenesis of volatile aldehydes from fatty acid hydroperoxides: molecular cloning of a hydroperoxide lyase (CYP74C) with specificity for both the 9- and 13-hydroperoxides of linoleic and linolenic acids.

A novel member of the plant cytochrome P450 CYP74 family of fatty acid hydroperoxide metabolizing enzymes has been cloned from melon fruit (Cucumis melo). The cDNA is comprised of 1,446 nucleotides encoding a protein of 481 amino acids. The homology at the amino acid level to other members of the CYP74 family is 35-50%, the closest relatives being allene oxide synthases. The cDNA was expressed in Escherichia coli, and the corresponding protein was purified by affinity column chromatography. The native enzyme showed a main Soret band at 418 nm, indicative of a low spin ferric cytochrome P450, and a 447-nm peak appeared in the CO-difference spectrum. Using [U-14C]radiolabeled substrate, HPLC, UV, and GC-MS, the products of conversion of 9S-hydroperoxy-linoleic acid were identified as 9-oxo-nonanic acid and 3Z-nonenal. Kinetic analysis of this hydroperoxide lyase showed the highest rate of reaction with 9-hydroperoxy-linolenic acid followed by 9-hydroperoxy-linoleic acid and then the corresponding 13-hydroperoxides. Overall, the newly characterized cytochrome P450 enzyme is a fatty acid hydroperoxide lyase with a preference, but not absolute specificity for the 9-positional hydroperoxides of linoleic and linolenic acids.

Aldehyde-Lyases↗
PubMed2002

The role of heme and iron-sulfur clusters in mitochondrial biogenesis, maintenance, and decay with age.

Mitochondria decay with age from oxidative damage and loss of protective mechanisms. Resistance, repair, and replacement mechanisms are essential for mitochondrial preservation and maintenance. Iron plays an essential role in the maintenance of mitochondria, through its two major functional forms: heme and iron-sulfur clusters. Both iron-based cofactors are formed and utilized in the mitochondria and then distributed throughout the cell. This is an important function of mitochondria that is not directly related to the production of ATP. Heme and iron-sulfur clusters are important for the normal assembly and for the optimal activity of the electron transfer complexes. Loss of mitochondrial cytochrome c oxidase (complex IV), integrity of mtDNA, and function can result from abnormal homeostasis of iron. We review the physiological role of iron-sulfur clusters and heme in the integrity of the mitochondria and the generation of oxidants.

Heme↗
PubMed1995

Chloroplast biogenesis 72: a [4-vinyl]chlorophyllide a reductase assay using divinyl chlorophyllide a as an exogenous substrate.

[4-Vinyl]Chlorophyllide alpha reductase (4VCR) catalyzes the conversion of 2,4-divinyl chlorophyllide alpha (DV Chlide alpha) to 2-vinyl,4-ethyl chlorophyllide alpha (MV Chlide alpha) via an NAPDH- dependent reaction. MV Childe alpha is the immediate precursor of monovinyl chlorophyll alpha in plants. In etiolated cucumber (Cucumis sativus L.) cotyledons, 4VCR is a plastidic membrane-bound enzyme. Further research on this enzyme required the development of an assay that utilizes DV Childe alpha as an exogenous substrate. Such an assay is now described. It involves conversion of exogenous DV Chlide alpha to MV Chlide alpha at high rates by etioplast membranes of cucumber, corn (Zea mays L.), and barley (Hordum vulgare L.). 4VCR exhibits high activity between 30 and 40C and in the pH range of 6.3 to 7.0. Activity is quasilinear for the first 60 s of incubation.

Chlorophyllides↗
PubMed2001

Chloroplast biogenesis 84: solubilization and partial purification of membrane-bound [4-vinyl]chlorophyllide a reductase from etiolated barley leaves.

[4-Vinyl] chlorophyllide a reductase (4VCR) is a key enzyme of the chlorophyll (Chl) biosynthetic pathway. It catalyzes the conversion of divinyl chlorophyllide (Chlide) a to monovinyl Chlide a by reduction of the vinyl group at position 4 of the macrocycle to ethyl. 4VCR is a membrane-bound enzyme, embedded in etioplast and etiochloroplast membranes. A study of the regulation and properties of this enzyme is mandatory for a comprehensive understanding of the biosynthetic heterogeneity of Chl biosynthesis. Solubilization and partial purification of 4VCR are described for the first time. The enzyme was solubilized with 5 mM Chaps and was partially purified by chromatography on DEAE-Sephacel and Cibacron Blue 3GA-1000 agarose. An overall 20-fold purification was achieved. The partially purified enzyme was stable for several months at -80 degrees C.

Cell Membrane↗
PubMed1997

Role of the carboxy-terminal phenylalanine in the biogenesis of outer membrane protein PhoE of Escherichia coli K-12.

Most bacterial outer membrane proteins contain a phenylalanine at their C terminus. It has been shown that this residue has an important role in the efficient and correct assembly of PhoE protein into the Escherichia coli outer membrane, since its substitution or deletion resulted in the accumulation of trypsin-sensitive monomers of this normally trimeric protein. Here, the role of the C-terminal Phe in the assembly of PhoE was studied in further detail. Immunocytochemical labelling on ultrathin cryosections revealed that a mutant PhoE protein that lacks the C-terminal Phe accumulates in the periplasm. However, when the expression levels of the altered species were reduced, the efficiency of outer membrane incorporation was increased and the lethal effects were alleviated. The role of the C-terminal Phe in protein folding, trimerization and outer membrane incorporation was further studied in vitro. Deletion of this residue interfered with the efficiency of the formation of an assembly-competent folded monomer, and the stability of this PhoE form was affected. The in vitro trimerization and insertion into outer membranes were not affected by the mutation.

Bacterial Proteins↗
PubMed1999

A reductase/isomerase subunit of mitochondrial NADH:ubiquinone oxidoreductase (complex I) carries an NADPH and is involved in the biogenesis of the complex.

Respiratory chains of bacteria and mitochondria contain closely related forms of the proton-pumping NADH:ubiquinone oxidoreductase, or complex I. The bacterial complex I consists of 14 subunits, whereas the mitochondrial complex contains some 25 extra subunits in addition to the homologues of the bacterial subunits. One of these extra subunits with a molecular mass of 40 kDa belongs to a heterogeneous family of reductases/isomerases with a conserved nucleotide binding site. We deleted this subunit in Neurospora crassa by gene disruption. In the mutant nuo 40, a complex I lacking the 40 kDa subunit is assembled. The mutant complex I does not contain tightly bound NADPH present in wild-type complex I. This NADPH cofactor is not connected to the respiratory electron pathway of complex I. The mutant complex has normal NADH dehydrogenase activity and contains the redox groups known for wild-type complex I, one flavin mononucleotide and four iron-sulfur clusters detectable by electron paramagnetic resonance spectroscopy. In the mutant complex these groups are all readily reduced by NADH. However, the mutant complex is not capable of reducing ubiquinone. A recently described redox group identified in wild-type complex I by UV-visible spectroscopy is not detectable in the mutant complex. We propose that the reductase/isomerase subunit with its NADPH cofactor takes part in the biosynthesis of this new redox group.

Electron Spin Resonance Spectroscopy↗
PubMed2001

Biogenesis of the dicarboxylate carrier (DIC): translocation across the mitochondrial outer membrane and subsequent release from the TOM channel are membrane potential-independent.

The mitochondrial inner membrane of Saccharomyces cerevisiae contains a group of homologous carrier proteins that mediate the exchange of several metabolites. The members of this protein family are synthesized in the cytosol and reach their final topology after translocation across the mitochondrial outer membrane. Using the ADP/ATP carrier (AAC) as a model protein, previous studies have established four distinct steps of the import pathway (stages I-IV). In the absence of the mitochondrial membrane potential (deltapsi), the AAC accumulates at the inner surface of the outer membrane (stage IIIa) and remains bound to the outer membrane import channel. Only in the presence of the membrane potential, can a complex of small Tim proteins mediate transfer of the AAC to the inner membrane. In this study, we characterized the import pathway of the dicarboxylate carrier (DIC). Different from the AAC, the DIC showed complete deltapsi-independent translocation across the outer membrane, release from the import pore, and mainly accumulated in a soluble state in the intermembrane space, thus defining a new translocation intermediate (stage III*). The DIC should be a suitable model protein for the characterization of deltapsi-independent functions of the intermembrane space Tim proteins.

Carrier Proteins↗
PubMed1995

Comments on "Let there be life; thermodynamic reflections on biogenesis and evolution" by Avshalom C. Elitzur.

This comment is in response to a paper previously published in the Journal entitled "Let there be life", by A. C. Elitzur. Elitzur ascribes to Eigen the proposal that life began with the appearance of an autocatalytic (self-replicating) molecule. This was discussed by biologists and philosophers in the nineteenth century. Eigen's proposal is moot: there never was a primeval soup. The absence of evidence is evidence of absence. Elitzur also confuses thermodynamics with statistical mechanics. The statistical equation of Boltzmann and Planck for entropy appears in discussions of statistical mechanics, not in discussions of classical thermodynamics. Elitzur calls the Second Law of Thermodynamics an explanation of evolution. On the contrary, his mentor Eigen wrote: "In physics we know of principles which cannot be reduced to any more fundamental laws. As axioms, they are abstracted from experience, their predictions being consistent with the consequences that can be subjected to experimental test. "Typical examples are the first and second law of thermodynamics. Darwin's principle of natural selection does not fall into the category of first principles." The reader is invited to compare the material in Elitzur's paper with the discussion in Yockey's (1992) book, Information Theory and Molecular Biology, Cambridge, Cambridge University Press.

Animals↗
PubMed2000

The pathophysiology of mitochondrial biogenesis: towards four decades of mitochondrial DNA research.

Mitochondria are with very few exceptions ubiquitous organelles in eukaryotic cells where they are essential for cell life and death. Mitochondria play a central role not only in a variety of metabolic pathways including the supply of the bulk of cellular ATP through oxidative phosphorylation (OXPHOS), but also in complex processes such as development, apoptosis, and aging. Mitochondria contain their own genome that is replicated and expressed within the organelle. It encodes 13 polypeptides all of them components of the OXPHOS system, and thus, the integrity of the mitochondrial DNA (mtDNA) is critical for cellular energy supply. In the past 12 years more than 50 point mutations and around 100 rearrangements in the mtDNA have been associated with human diseases. Also in recent years, several mutations in nuclear genes that encode structural or regulatory factors of the OXPHOS system or the mtDNA metabolism have been described. The development of increasingly powerful techniques and the use of cellular and animal models are opening new avenues in the study of mitochondrial medicine. The detailed molecular characterization of the effects produced by different mutations that cause mitochondrial cytopathies will be critical for designing rational therapeutic strategies for this group of devastating diseases.

Animals↗
PubMed2000

The pilL and pilN genes of IncI1 plasmids R64 and ColIb-P9 encode outer membrane lipoproteins responsible for thin pilus biogenesis.

The predicted amino acid sequences of the pilL and pilN genes, required for the thin pilus formation of IncI1 plasmids R64 and ColIb-P9, contain N-terminal lipoprotein signal peptide motifs. The pilL and pilN products were labeled with [(3)H]palmitic acid as 38- and 57-kDa proteins, respectively, indicating that they are lipoproteins. Both PilL and PilN were localized to the outer membrane.

Amino Acid Sequence↗
PubMed2000

Trafficking/sorting and granule biogenesis in the beta-cell.

Proinsulin is packaged into nascent (immature, clathrin-coated) secretory granules in the trans-Golgi network (TGN) of the beta -cell along with other granular constituents including the proinsulin conversion enzymes. It is assumed that such packaging is dependent on an active sorting process, separating granular proteins from other secretory or membrane proteins, but the mechanism remains elusive. As granules mature, the clathrin coat is lost, the intragranular milieu is progressively acidified, and proinsulin is converted to insulin and C-peptide. Loss of clathrin is believed to arise by budding of clathrin-coated vesicles from maturing granules, carrying with them any inappropriate or unnecessary products and providing an additional means for refinement of granular content.

Animals↗
PubMed2006

Biogenesis of iron-sulfur cluster proteins in plastids.

Iron-sulfur (Fe-S) clusters are co-factors of proteins that perform a number of biological roles, including electron transfer, redox and non-redox catalysis, regulation of gene expression, and as sensors within all living organisms, prokaryotes and eukaryotes. These clusters are thought to be among the oldest structures found in biological cells. In chloroplasts, Fe-S clusters play a key role in photosynthetic electron transport as well as nitrogen and sulfur assimilation. The capacity of the Fe atom in Fe-S clusters to take up an electron reversibly provides the required electron carrier capacity in these pathways. Iron and sulfur limitation both affect plant primary production and growth. It has long been known that iron deficiency leads to defects in photosynthesis and bleaching in young leaves, phenomena that are closely linked to a defect in chloroplastic photosystem-I (PSI) accumulation, a major Fe-S containing protein complex in plants. Although the functional importance of Fe-S cluster proteins is evident and isolated chloroplasts have been shown to be able to synthesize their own Fe-S clusters, much is yet to be learned about the biosynthesis of Fe-S proteins in plastids. The recent discovery of a NifS-like protein in plastids has hinted to the existence of an assembly machinery related to bacterial Fe-S assembly systems. This chapter aims to summarize what we presently know about the assembly of Fe-S clusters in plants with an emphasis on green plastids.

Bacterial Proteins↗