Endo.SK1: an inducible site-specific endonuclease from yeast mitochondria

Site-specific endonucleases have been found in various eukaryotic organelles such as mitochondria, chloroplasts and nuclei. These endonucleases initiate site-specific or homologous gene conversion in mitochondrial and nuclear DNA. Here, we report a new site-specific endonuclease activity, Endo.SK1, identified in mitochondria of strain SK1, a homothallic diploid strain ofSaccharomyces cerevisiae. Nucleotide sequences around the Endo.SK1-cleavage sites are different from those of known yeast site-specific endonucleases. The Endo.SK1 activity is, at least partly, specified by a gene in the SK1-derived mitochondria. A novel feature of the Endo.SK1 activity is its inducibility: the endonuclease activity was induced by ca. 40-fold by transfer of cells from a glucose medium into an acetate medium, and was then repressed. This transient induction was independent of the ploidy level of the cells, and coincided with induction of fumarase, a mitochondrial enzyme involved in the TCA cycle. Co-induction and co-repression of the mitochondrial site-specific endonuclease activity and a respiration-related enzyme indicate that the endonuclease activity is regulated in response to physiological conditions, and suggest a possible role for the endonuclease in mitochondrial DNA metabolism.     

A proenkephalin A-derived peptide analogous to bovine adrenal peptide E from frog brain: Purification, synthesis, and behavioral effects

A peptide derived from the posttranslational processing of proenkephalin A was isolated from an extract of the brain of the European green frog Rana ridibunda and its primary structure established as: Tyr-Gly-Gly-Phe-Met-Arg-Arg-Val-Gly-Arg¹⁰-Pro-Glu-Trp-Trp-Gln-Asp-Tyr-Gln-Lys-Arg²⁰-Tyr-Gly-Gly-Phe-Met. The structure was confirmed by chemical synthesis. The peptide represents an amphibian equivalent of bovine adrenal peptide E [preproenkephalin A (206–230)-peptide] but the sequence contains two amino acid substitutions (Met¹⁵ → Gln and Leu²⁵ → Met) compared with the mammalian peptide. The data support previous hypotheses that the Leu-enkephalin sequence is not present in preproenkephalin A of amphibians. Intracerebroventricular injections of frog peptide E (10 and 100 ng) in mice had no significant effect on horizontal locomotor activity. The peptide, in doses up to 1 μg, had no effect on latency of escape jumping in the hot plate test and the peptide (100 ng) did not modify responses (paw licking, rearing, and escape jumping) in morphine-treated mice.     

Characterization of the Stable Maintenance of theShigella flexneriPlasmid pHS-2

pHS-2 is a 3-kb plasmid originally isolated fromShigella flexneriinfections associated with reactive arthritis in humans. This plasmid is stably maintained in many clinical isolates ofShigella flexneri.The nucleotide sequence of this plasmid displays two closely linked regions that may play a role in the maintenance of this plasmid. One region consists of a 250-bp locus showing a significant homology to the ColE1cersite. The results indicate that thecer-like site of pHS-2, like the ColE1cersite, acts as arecA-independent, site-specific recombination site involved in the resolution of multimers, requiring the presence of the host-encoded factors ArgR, PepA, XerC, and XerD. The second region consists of a 36-kDa open reading frame involved in generating resistance to the bactericidal effect of complement, which confers a selective advantage to cells containing this sequence. The results also indicate that pHS-2 can replicate in another species of Enterobacteriaceae (Escherichia coli) and is mobilized by the F plasmid.     

The Quaternary eolian sequence of Madeira: stratigraphy, chronology, and paleoenvironmental interpretation

A thick (ca. 40 m) sequence of coastal eolian sediments occurs on a narrow peninsula on the eastern end of the island of Madeira, located in the Eastern Atlantic at 33°N latitude. The sediments consist of black volcanic sands (with or without bioclasts) as well as clay units up to 2 m thick. A series of inceptisols (Eutrochrepts) and one alfisol (a Hapludalf) are developed in these sediments. Land snail shells and secondary carbonates, in the form of well-developed rhizoliths, calcretes, fissure-fills, and soil nodules, are present in abundance. The chronology of the sequence was determined by ¹⁴C and U---Th analyses of land snail shells and secondary carbonates and amino acid epimerization analysis of land snail shells. All sediments, including the clay units, are originally of eolian origin, derived from the beach to the south of the deposit, but some have been redeposited by colluviation. Temporal variation in the lithology of the sediments relates to variations in sea-level, with black sands being deposited during lower sea level stands and clays at the lowest. It is suggested that fine marine sediments, exposed during low sea-level stands, may also be the dominant source of silty or clayey units in other coastal eolian deposits in the subtropical Atlantic and Mediterranean.

The sequence spans from 200,000–300,000 years ago up to the 20th century. Sedimentation was discontinuous and often rapid; erosional hiatuses are present. During the Holocene, eolian sands started accumulating at 8200 yr B.P. during a transgressive phase and stopped at 4500 yr B.P. as sea level approached its present height. Colluviation increased dramatically following the first human settlement of the island in the 15th century and continued up to the 20th century, as dated by amino acid epimerization analysis of land snails. Earlier periods of colluviation were identified from the age distribution of land snail shells redeposited in younger colluvium.

Paleoenvironmental reconstruction was based mainly on soil and sediment features (including rhizolith morphology) and land snail faunas but also on stable isotope variations (¹³C, ¹⁸O) in land snails and secondary carbonates, pollen (generally not well preserved), and phytoliths. Most of the portion of the Middle Pleistocene represented in the sequence was characterized by moderately dry conditions, in comparison to the late Pleistocene and Holocene. During the last interglacial, relatively wet conditions occurred, wetter than during the Holocene interglacial. Moderately moist conditions were present during the accumulation of the thick unit dating to ca. 80,000 yr B.P. As sea level fell subsequent to this period, conditions appear to have become drier. Starting ca. 50,000–55,000 yr B.P., conditions were especially wet, but prior to the last glacial maximum, markedly arid conditions ensued. Toward the end of the last glacial, wet conditions returned and produced the best-developed soil preserved in the sequence. Moderately moist conditions occurred during the early to middle Holocene but apparently become slightly drier after 4500 yr B.P. The impact of human settlement can be seen in the loss of woody vegetation and enhanced gullying and colluviation during the last ca. 500 years.     

Incorporation of Molecular Oxygen and Water during Enzymatic Oxidation of Cyanide by Pseudomonas fluorescens NCIMB 11764

Cell extracts (high-speed [150,000 x g] supernatants) from Pseudomonas fluorescens NCIMB 11764 catalyzed the oxidation of cyanide to CO(inf2) (and NH(inf3)). Conversion was both oxygen and NADH dependent, with 1 mol of each being consumed per mol of cyanide degraded. Analysis of (sup13)CO(inf2) by mass spectrometry indicated that one atom each of isotopically labelled oxygen 18 from molecular oxygen and water were incorporated during enzymatic conversion. The results confirm earlier reports of oxygenase-mediated cyanide conversion in this organism. A reaction pathway for cyanide oxidation involving initial monooxygenation followed by hydrolysis of a hypothetical oxygenated intermediate to CO(inf2) (and NH(inf3)) is proposed.     

Characterization of aminopeptidase N from Torpedo marmorata kidney

Summary— A major antigen of the brush border membrane of Torpedo marmorata kidney was identified and purified by immunoprecipitation. The sequence of its 18 N terminal amino acids was determined and found to be very similar to that of mammalian aminopeptidase N (EC 3.4.11.2). Indeed aminopeptidase N activity was efficiently immunoprecipitated by monoclonal antibody 180K1. The purified antigen gives a broad band at 180 kDa after SDS-gel electrophoresis, which, after treatment by endoglycosidase F, is converted to a thinner band at 140 kDa. This antigen is therefore heavily glycosylated. Depending on solubilization conditions, both the antigen and peptidase activity were recovered either as a broad peak with a sedimentation coefficient of 18S (2% CHAPS) or as a single peak of 7.8S (1% CHAPS plus 0.2 % C₁₂E₉), showing that Torpedo aminopeptidase N behaves as an oligomer stabilized by hydrophobic interactions, easily converted into a 160 kDa monomer. The antigen is highly concentrated in the apical membrane of proximal tubule epithelial cells (600 gold particles/μm² of brush border membrane) whereas no labeling could be detected in other cell types or in other membranes of the same cells (basolatéral membranes, vacuoles or vesicles). Monoclonal antibodies prepared here will be useful tools for further functional and structural studies of Torpedo kidney aminopeptidase N.     

Homologous, homeologous, and illegitimate repair of double-strand breaks during transformation of a wild-type strain and a rad52 mutant strain of Saccharomyces cerevisiae.

Different modes of in vivo repair of double-strand breaks (DSBs) have been described for various organisms: the recombinational DSB repair (DSBR) mode, the single-strand annealing (SSA) mode, and end-to-end joining. To investigate these modes of DSB repair in Saccharomyces cerevisiae, we have examined the fate of in vitro linearized replicative plasmids during transformation with respect to several parameters. We found that (i) the efficiencies of both intramolecular and intermolecular linear plasmid DSB repair are homology dependent (according to the amount of DNA used during transformation [100 ng or less], recombination between similar but not identical [homeologous] P450s sequences sharing 73% identity is 2- to 18-fold lower than recombination between identical sequences); (ii) the RAD52 gene product is not essential for intramolecular recombination between homologous and homeologous direct repeats (as in the wild-type strain, recombination occurs with respect to the overall alignment of the parental sequences); (iii) in contrast, the RAD52 gene product is required for intermolecular interactions (the rare transformants which are obtained contain plasmids resulting from deletion-forming intramolecular events involving little or no sequence homology); (iv) similarly, sequencing data revealed examples of intramolecular joining within the few terminal nucleotides of the transforming DNA upon transformation with a linear plasmid with no repeat in the wild-type strain. The recombinant junctions of the rare illegitimate events obtained with S. cerevisiae are very similar to those observed in the repair of DSB in mammalian cells. Together, these and previous results suggest the existence of alternative modes for DSB repair during transformation which differ in their efficiencies and in the structure of their products. We discuss the implications of these results with respect to the existence of alternative pathways and the role of the RAD52 gene product.     

The influence of the cytosolic oncotic pressure on the permeability of the mitochondrial outer membrane for ADP: implications for the kinetic properties of mitochondrial creatine kinase and for ADP channelling into the intermembrane space

Summary Cytosolic proteins as components of the physiological mitochondrial environment were substituted by dextrans added to media normally used for incubation of isolated mitochondria. Under these conditions the volume of the intermembrane space decreases and the contact sites between the both mitochondrial membranes increase drastically. These morphological changes are accompanied by a reduced permeability of the mitochondrial outer compartment for adenine nucleotides as it was shown by extensive kinetic studies of mitochondrial enzymes (oxidative phosphorylation, mi-creatine kinase, mi-adenylate kinase). The decreased permeability of the mitochondrial outer membrane causes increased rate dependent concentration gradients in the micromolar range for adenine nucleotides between the intermembrane space and the extramitochondrial space. Although all metabolites crossing the outer membrane exhibit the same concentration gradients, considerable compartmentations are detectable for ADP only due to its low extramitochondrial concentration. The consequences of ADP-compartmentation in the mitochondrial intermembrane space for ADP-channelling into the mitochondria are discussed.     

Autoradiographic Distribution and Characteristics of High- and Low-Affinity Polyamine-Sensitive [3H]Ifenprodil Sites in the Rat Brain: Possible Relationship to NMDAR2B Receptors and Calmodulin

Abstract: We have studied the regional distribution and characteristics of polyamine-sensitive [³H]ifenprodil binding sites by quantitative autoradiography in the rat brain. In forebrain areas ifenprodil displaced [³H]ifenprodil (40 nM) in a biphasic manner with IC₅₀ values ranging from 42 to 352 nM and 401 to 974 µM. In hindbrain regions, including the cerebellum, ifenprodil displacement curves were monophasic with IC₅₀ values in the high micromolar range. Wiping studies using forebrain slices (containing both high- and low-affinity sites) or cerebellar slices (containing only the low-affinity site) showed that high- and low-affinity ifenprodil sites are sensitive to spermine and spermidine, to the aminoglycoside antibiotics neomycin, gentamicin, and kanamycin, and to zinc. Two calmodulin antagonists, W7 and calmidazolium, also displaced [³H]ifenprodil from both sites. Other calmodulin antagonists, including trifluoperazine, prenylamine, and chlorpromazine, selectively displaced [³H]ifenprodil from its low-affinity site in hindbrain and forebrain regions. High-affinity [³H]ifenprodil sites, defined either by ifenprodil displacement curves or by [³H]ifenprodil binding in the presence of 1 mM trifluoperazine, were concentrated in the cortex, hippocampus, striatum, and thalamus with little or no labeling of hindbrain or cerebellar regions. This distribution matches that of NMDAR2B mRNA, supporting data showing that ifenprodil has a preferential action at NMDA receptors containing this subunit. Low-affinity [³H]ifenprodil sites have a more ubiquitous distribution but are especially concentrated in the molecular layer of the cerebellum. [³H]Ifenprodil was found to bind to calmodulin-agarose with very low affinity (IC₅₀ of ifenprodil = 516 µM). This binding was displaced by calmodulin antagonists and by polyamines, with a potency that matched their displacement of [³H]ifenprodil from its low-affinity site in brain sections. However, the localization of the low-affinity [³H]ifenprodil site does not strictly correspond to that of calmodulin, and its identity remains to be further characterized. The restricted localization of high-affinity [³H]ifenprodil binding sites to regions rich in NMDAR2B subunit mRNA may explain the atypical nature of this NMDA antagonist.