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PubMed1984

Amino acid sequence of a new mitochondrially synthesized proteolipid of the ATP synthase of Saccharomyces cerevisiae.

The purification and the amino acid sequence of a proteolipid translated on ribosomes in yeast mitochondria is reported. This protein, which is a subunit of the ATP synthase, was purified by extraction with chloroform/methanol (2/1) and subsequent chromatography on phosphocellulose and reverse phase h.p.l.c. A mol. wt. of 5500 was estimated by chromatography on Bio-Gel P-30 in 80% formic acid. The complete amino acid sequence of this protein was determined by automated solid phase Edman degradation of the whole protein and of fragments obtained after cleavage with cyanogen bromide. The sequence analysis indicates a length of 48 amino acid residues. The calculated mol. wt. of 5870 corresponds to the value found by gel chromatography. This polypeptide contains three basic residues and no negatively charged side chain. The three basic residues are clustered at the C terminus. The primary structure of this protein is in full agreement with the predicted amino acid sequence of the putative polypeptide encoded by the mitochondrial aap1 gene recently discovered in Saccharomyces cerevisiae. Moreover, this protein shows 50% homology with the amino acid sequence of a putative polypeptide encoded by an unidentified reading frame also discovered near the mitochondrial ATPase subunit 6 gene in Aspergillus nidulans.

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PubMed2005

Angiostatin's molecular mechanism: aspects of specificity and regulation elucidated.

Tumor growth requires the development of new vessels that sprout from pre-existing normal vessels in a process known as "angiogenesis" [Folkman (1971) N Engl J Med 285:1182-1186]. These new vessels arise from local capillaries, arteries, and veins in response to the release of soluble growth factors from the tumor mass, enabling these tumors to grow beyond the diffusion-limited size of approximately 2 mm diameter. Angiostatin, a naturally occurring inhibitor of angiogenesis, was discovered based on its ability to block tumor growth in vivo by inhibiting the formation of new tumor blood vessels [O'Reilly et al. (1994a) Cold Spring Harb Symp Quant Biol 59:471-482]. Angiostatin is a proteolytically derived internal fragment of plasminogen and may contain various members of the five plasminogen "kringle" domains, depending on the exact sites of proteolysis. Different forms of angiostatin have measurably different activities, suggesting that much remains to be elucidated about angiostatin biology. A number of groups have sought to identify the native cell surface binding site(s) for angiostatin, resulting in at least five different binding sites proposed for angiostatin on the surface of endothelial cells (EC). This review will consider the data supporting all of the various reported angiostatin binding sites and will focus particular attention on the angiostatin binding protein identified by our group: F(1)F(O) ATP synthase. There have been several developments in the quest to elucidate the mechanism of action of angiostatin and the regulation of its receptor. The purpose of this review is to describe the highlights of research on the mechanism of action of angiostatin, its' interaction with ATP synthase on the EC surface, modulators of its activity, and issues that should be explored in future research related to angiostatin and other anti-angiogenic agents.

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PubMed2003

Aromatase inhibition affects testosterone-induced masculinization of song and the neural song system in female canaries.

Songbirds have a specialized steroid-sensitive network of brain nuclei, the song system, for controlling song. Most nuclei of the song system express androgen receptors, and the sensory-motor integration nucleus High Vocal Center (HVC) alone also expresses estrogen receptors. Apart from expressing estrogen receptors in the vocal control system, songbirds are unique among birds because they have high concentrations of the estrogen-synthesizing enzyme aromatase in the neostriatum surrounding HVC. However, the role of estrogen in controlling the development of the song structure has been scarcely investigated. In this work, we show that blocking the production of estrogen during testosterone-induced song motor development in adult female canaries alters the song pattern compared to control females treated with testosterone only. These effects were correlated with inhibition of the expression of estrogen-sensitive genes, such as brain-derived nerve growth factor, in HVC. The expression of the ATP-synthase gene, an indicator of cell activity, in HVC, and the size of HVC, were not affected by the treatment. Our results provide the first example of estrogen-sensitive mechanisms controlling the structural features of adult birdsong.

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PubMed2005

Inverted repeat of a large segment unveiled on the right arm of Saccharomyces cerevisiae chromosome II.

By means of gene disruption analyses, Saccharomyces cerevisiae strain YPH499 was shown to have two, and only two, copies of ATP3 that encodes the gamma-subunit of H+-dependent ATP synthase and locates on the right arm of chromosome II. Linkage analyses of the two distinguishably marked copies of ATP3 indicated that the distance between them was about 43 cM. Since YBR030W, an ORF proximal to ATP3 by a distance of 17 kbp, was also found to be duplicated, we marked them with two distinguishable nutritional markers, which were also distinguishable from those used for marking the two copies of ATP3, and achieved four-point linkage analyses; CEN2 marked with an appropriate nutritional marker gene was included as a reference point. And, the following linkage map was deduced: CEN2- [11 cM]-YBR030Wa- [8 cM]-ATP3a-[47 cM]-ATP3b- [55 cM]-YBR030Wb. From this map, we suspected that a segment spanning at least YBR030W-ATP3 would be inversely duplicated on the right arm of chromosome II. We then carried out chromosome fragmentation analyses, using several laboratory strains including YPH499, and obtained data in accord with our speculation for all strains, although the distance between the two copies of ATP3 varied from 48 kbp to 192 kbp among the strains examined.

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PubMed2002

Cysteine-reactive fluorescence probes of catalytic sites of ATP synthase.

We searched for new fluorescent probes of catalytic-site nucleotide binding in F(1)F(0)-ATP synthase by introducing Cys mutations at positions in or close to catalytic sites and then reacting Cys-mutant F(1) with thiol-reactive fluorescent probes. Four suitable mutant/probe combinations were identified. beta F410C labeled by 7-fluorobenz-2-oxa-1,3-diazole-4-sulfonamide (ABD-F) gave very large signal changes in response to nucleotide, allowing facile measurement of fluorescence and nucleotide-binding parameters, not only in F(1) but also in F(1)F(0). The results are consistent with the presence of three asymmetric catalytic sites of widely different affinities, with similar properties in both enzymes, and revealed a unique probe environment at the high-affinity site 1. beta Y331C F(1) labeled by ABD-F gave a large signal which monitored catalytic site polarity changes that occur along the ATP hydrolysis pathway. Two other mutant/probe combinations with significant nucleotide-responsive signals were beta Y331C labeled by 5-((((2-iodoacetyl)amino)ethyl)amino)naphthaline-1-sulfonic acid and alpha F291C labeled by 2-4'-(iodoacetamido)anilino)naphthalene-6-sulfonic acid. The signal of the latter responds differentially to nucleoside diphosphate versus triphosphate bound in catalytic sites.

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PubMed1999

Quantification of OXPHOS gene transcripts during muscle cell differentiation in patients with mitochondrial myopathies.

The transcript levels of nuclear and mitochondrial genes involved in oxidative phosphorylation were quantified in human myoblasts and myotubes cultured from biopsies of patients harboring either heteroplasmic point mutation or deletion of mitochondrial DNA. The transcript patterns were determined by two different methodologies, competitive reverse-transcription polymerase chain reaction and classical Northern blot analysis, both referred to the mitochondrial to nuclear DNA ratio. In myoblasts from the patients with MELAS (myopathy, encephalopathy, lactic acidosis, and stroke-like episodes) and KSS (Kearns-Sayre) syndromes, both methodologies revealed an increase of mtDNA transcript levels. A higher level of the nuclear ATP synthase beta transcript was observed in the MELAS patient cells and could be the consequence of a feedback effect of the mitochondrial DNA mutation. Moreover, the nuclear and mitochondrial transcript accumulation is more pronounced after myoblast differentiation. Thus, the OXPHOS expression is specifically altered in patients with mitochondrial diseases. The competitive RT-PCR, a rapid and sensitive technique, could be applied to investigation of mitochondrial myopathies.

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PubMed2000

Trypanosoma cruzi: a putative vacuolar ATP synthase subunit and a CAAX prenyl protease-encoding gene, as examples of gene identification in genome projects.

An international genome program has been initiated to increase the knowledge about the Trypanosoma cruzi genome and thereby find effective tools to treat Chagas' disease. We here report the molecular characterization of two novel genes found in the course of this project. Two of the open reading frames (ORF) identified in the sequencing of the third smallest chromosome of the CL Brener strain of T. cruzi were selected for further molecular characterization due to their similarity to genes with interesting functions in other organisms and their potential as targets to combat the parasite. The first ORF (402 bp) showed homology to a 14-kDa vacuolar ATP synthase subunit F from a variety of organisms, such as yeast, rat, bovine, human, and a number of prokaryotes. The second ORF (1188 bp) resembled a CAAX prenyl protease-encoding gene, identified in different organisms, including Homo sapiens, Saccharomyces cerevisiae, and Arabidopsis thaliana, as well as several prokaryotes. RT-PCR from T. cruzi total epimastigote RNA allowed us to isolate the complete transcripts of these genes. Furthermore, screening of an available normalized cDNA library derived from the same stage of the parasite confirmed that both genes are expressed at least in the epimastigote stage of T. cruzi. Comparison of the putative T. cruzi proteins to their counterparts in other organisms revealed significant protein sequence conservation over large evolutionary distances. Computer analysis revealed the presence of several motifs in both proteins, possibly related to the regulation and localization of these proteins in the parasite.

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PubMed1993

Complete sequence of a bovine alpha-lactalbumin pseudogene: the region homologous to the gene is flanked by two directly repeated LINE sequences.

A 3-kb fragment hybridizing with a bovine alpha-lactalbumin cDNA probe was isolated from a bovine genomic library and completely sequenced. An internal fragment beginning downstream from exon 2, as already reported for another pseudogene, but ending in the 3'-untranslated region of exon 4 shares 78% sequence similarity with the bovine alpha-lactalbumin gene. This region is flanked by two directly repeated LINE sequences. The 5' ends of the fragment and of the aforementioned pseudogene share a specific nucleotide stretch, which suggests that they might have had a common origin.

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PubMed2003

Molecular mechanisms of energy transduction in cells: engineering applications and biological implications.

The synthesis of ATP from ADP and inorganic phosphate by F1F0-ATP synthase, the universal enzyme in biological energy conversion, using the energy of a transmembrane gradient of ions, and the use of ATP by the myosin-actin system to cause muscular contraction are among the most fundamental processes in biology. Both the ATP synthase and the myosin-actin may be looked upon as molecular machines. A detailed analysis of the molecular mechanisms of energy transduction by these molecular machines has been carried out in order to understand the means by which living cells produce and consume energy. These mechanisms have been compared with each other and their biological implications have been discussed. The thermodynamics of energy coupling in the oxidative phosphorylation process has been developed and the consistency of the mechanisms with the thermodynamics has been explored. Novel engineering applications that can result have been discussed in detail and several directions for future work have been pointed out.

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PubMed1989

Bistability and control for ATP synthase and adenylate cyclase is obtained by the removal of substrate inhibition.

The thesis of this article is that the raison d'être of the electron transfer chain and the receptor system is to remove 'substrate inhibition' of the enzymes ATP synthase and adenylate cyclase respectively. Activation by energization or hormone is analogous and presents the features of ideal control system; bistability, hysteresis, sensitivity and amplification, and rapid transitions between resting and active states. In the first part of the article, the simplest nontrivial model conforming with the experimental results is put forward. After the system is described, nonlinear and linear models are developed. An important aspect captured by the model is that the enzyme is structurally asymmetric corresponding to the assumption of regulatory site(s) distinct from catalytic site(s). The structural distinction between a regulatory site and a catalytic site entails different binding and specificity properties of the two types of sites with respect to the nucleotides. In the second part, the experimental evidence for the theory is discussed. It is shown that energization and hormone indeed reduce 'substrate inhibition' and that the properties of time lag and criticality predicted by the theory are indeed verified in experiment and are in turn explained by the theory. The theory can explain and correlate various hitherto unexplained experimental phenomena such as the irreversibility of ATP synthesis and the functional role of the ATP synthase asymmetry. The property of hysteresis predicted by the nonlinear model, is indicated by postillumination ATP synthesis, and preactivation of chloroplasts with reduced dithiols indeed display 'hysteresis loops'. In Aplysia memory for short term sensitization may reside in the hysteretic prolonged elevation of cAMP in sensory neurons.

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PubMed1981

The nucleotide sequence of the atp genes coding for the F0 subunits a, b, c and the F1 subunit delta of the membrane bound ATP synthase of Escherichia coli.

The nucleotide sequence has been determined of a 2,500 base pair segment of the E. coli chromosome located between 3.75 and 6.25 kb counterclockwise of the origin of replication at 83.5 min. The sequence contains the atp genes coding for subunits a-, b-, c-, delta- and part of the alpha-subunit of the membrane bound ATP synthase. The precise start positions of the atpE (c), atpF (b), atpH (delta) and atpA (alpha) genes have been defined by comparison of the potential coding sequences with the known amino acid sequence of the c-subunit and the determined N-terminal amino acid sequences of the respective subunits. The genes are expressed in the counterclockwise direction. Their order (counterclockwise) is: atpB (a), atpE (c), atpF (b), atpH (delta) and atpA(alpha). The coding sequences for subunits b and delta yield polypeptides of 156 and 177 amino acids, respectively, in accordance with the established sizes of these subunits; the one for the c-subunit, the DCCD binding protein, fits perfectly with its known sequence of 79 amino acids. The a-subunit is comprised within a coding sequence yielding a polypeptide of 271 amino acids. It is suggested, however, that the a-subunit (atpB) contains only 201 amino acids, in accordance with its known size, starting from a translation initiation site within the larger coding sequence. The stoichiometry of the F0 sector subunits is discussed and a model is proposed for the functioning of the highly charged b-subunit of the F0 sector as the actual proton conductor.

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PubMed1982

Localized energy coupling during photophosphorylation by chromatophores of Rhodopseudomonas capsulata N22.

The principle of the dual inhibitor titration method for testing models of electron-transport phosphorylation is outlined, and the method is applied to the study of photophosphorylation in bacterial chromatophores. It is concluded that energy coupling is strictly localized in nature in this system, in the sense that free energy released by a particular electron-transport chain may be used only by a particular H+-ATP synthase. Dual inhibitor titrations using the uncoupler SF 6847 and the H+-ATP synthase inhibitor oligomycin indicate that uncouplers act by shuttling rapidly between the localized energy-coupling sites.

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PubMed1982

Topological and functional aspects of the proton conductor, F0, of the Escherichia coli ATP-synthase.

The isolated H+ conductor, F0, of the Escherichia coli ATP-synthase consists of three subunits, a, b, and c. H+-permeable liposomes can be reconstituted with F0 and lipids; addition of F1-ATPase reconstitutes a functional ATP-synthase. Mutants with altered or missing F0 subunits are defective in H+ conduction. Thus, all three subunits are necessary for the expression of H+ conduction. The subunits a and b contain binding sites for F1. Computer calculations, cross-links, membrane-permeating photo-reactive labels, and proteases were used to develop tentative structural models for the individual F0 subunits.

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PubMed1984

Mitochondrial oxidative phosphorylation and respiratory chain: review.

Basic events concerning oxidative phosphorylation, i.e. the synthesis of ATP at the expense of respired oxygen at the level of mitochondria are described. Our knowledge concerning the functioning of respiratory chain, its structure, organization and topology inside the inner membrane of mitochondria has considerably improved in recent years. A central question--how does the respiratory chain cooperate with ATP-synthetase, also embedded in the inner membrane, to bring about the oxidative phosphorylation of ADP to ATP--has been one of the most challenging and difficult problems in biochemical research. The chemiosmotic hypothesis proposed by the British biochemist Peter Mitchell appears best in describing the basic events of the recovery of the redox energy liberated along the respiratory chain to synthesize ATP through a membrane process. Moreover the chemiosmotic hypothesis is not restricted to mitochondrial oxidative phosphorylation but appears to provide a general explanation to the synthesis of ATP in all transducing membranes: inner mitochondrial membrane, bacterial plasma membrane, thylakoid membranes in chloroplasts of green plants.

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PubMed2005

Esophageal ATP synthase and keratinocyte growth factor gene expression changes after acid and bile-induced mucosal damage.

OBJECTIVE AND DESIGN: Intramural gene expression changes may be critically involved in tissue damage, defense and repair after esophageal regurgitation. The aims were to characterize the consequences of short-term exposure to luminal bile, acid, or bile mixed with acid on the beta-ATPase, keratinocyte growth factor 1 (KGF-1) and KGF receptor (KGF-R) expressions within the mucosa and the muscle layer in a large animal model. MATERIALS AND SUBJECTS: Esophageal segments of anesthetized dogs were exposed to saline (n = 3), diluted canine bile (n = 6), hydrochloric acid (n = 5) or bile + hydrochloric acid (n = 5), and tissue biopsies were taken at the end of the 180-min observation period. Semiquantitative reverse transcriptase polymerase chain reactions were carried out and the degree of histological damage was evaluated on the 0-16-grade Geisinger scoring scale. RESULTS: Acid exposure was followed by a significant decrease in the level of beta-ATPase expression in the mucosa, and parallel increases in KGF-1 and KGF-R expression. Corresponding changes in the muscle layer were not significant. Bile alone evoked more severe tissue damage, with significantly decreased beta-ATPase levels in both the mucosa and the muscle, whereas the KGF-1 expression did not change significantly. The bile + acid treatment induced an intermediate state, with significant beta-ATPase transcription level decreases in both layers, while the mucosal KGF-1 expression was lower than that following acid treatment alone. CONCLUSIONS: The acid-induced transcriptional level downregulation of mucosal beta-ATPase gene expression in the smooth muscle layer was exacerbated by bile, but the concomitant KGF and KGF-R gene expression changes may indicate the start of a consecutive repair process.

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