The selective degradation of many short-lived proteins in eukaryotic cells is carried out by the ubiquitin system. In this pathway, proteins are targeted for degradation by covalent ligation to ubiquitin, a highly conserved small protein. Ubiquitin-mediated degradation of regulatory proteins plays important roles in the control of numerous processes, including cell-cycle progression, signal transduction, transcriptional regulation, receptor down-regulation, and endocytosis. The ubiquitin system has been implicated in the immune response, development, and programmed cell death. Abnormalities in ubiquitin-mediated processes have been shown to cause pathological conditions, including malignant transformation. In this review we discuss recent information on functions and mechanisms of the ubiquitin system. Since the selectivity of protein degradation is determined mainly at the stage of ligation to ubiquitin, special attention is focused on what we know, and would like to know, about the mode of action of ubiquitin-protein ligation systems and about signals in proteins recognized by these systems.

The Ubiquitin System

more acidic solutions, with pH < 7 0, a few seconds elapsed before equilibrium was attained. Taking into account the ionization of the haem-linked group on MetMb and the higher oxidation state, the variation of Kb,. with pH is shown to confirm the conclusion that 2 moles ofH+ are liberated/mole of acidic MetMb. Using 6-1 for the pK of the group in MetMb as established in other studies, the results give apK of75 for the group in the higher oxidation state at 200 and I= 0 04. 3. The variation of KRb, with temperature gives AHO = 10-0 ± 2*0 kcal./g.mol.: if the ionization of the haem-linked group is allowed for, the value 9*0 ± 1.0 kcal./g.mol. is obtained. 4. The dependence of Kob. on ionic strength is in accord with a change in charge from + 1 on MetMb to zero on the higher oxidation state. 5. The results are shown to favour the ferryl ion structure, or an isomer of this structure, for the higher oxidation state. The isomeric structures would, in general, require the presence of another ionizing group in myoglobin, but no evidence for such an ionization could be found. With other direct evidence favouring the ferryl ion structure this is to be preferred, and the higher oxidation state may provisionally be named ferrylmyoglobin.

Tissue fractionation studies. 6. Intracellular distribution patterns of enzymes in rat-liver tissue

We report that the dye nile red, 9-diethylamino-5H-benzo[alpha]phenoxazine-5-one, is an excellent vital stain for the detection of intracellular lipid droplets by fluorescence microscopy and flow cytofluorometry. The specificity of the dye for lipid droplets was assessed on cultured aortic smooth muscle cells and on cultured peritoneal macrophages that were incubated with acetylated low density lipoprotein to induce cytoplasmic lipid overloading. Better selectivity for cytoplasmic lipid droplets was obtained when the cells were viewed for yellow-gold fluorescence (excitation, 450-500 nm; emission, greater than 528 nm) rather than red fluorescence (excitation, 515-560 nm; emission, greater than 590 nm). Nile red-stained, lipid droplet-filled macrophages exhibited greater fluorescence intensity than did nile red-stained control macrophages, and the two cell populations could be differentiated and analyzed by flow cytofluorometry. Such analyses could be performed with either yellow-gold or red fluorescence, but when few lipid droplets per cell were present, the yellow-gold fluorescence was more discriminating. Nile red exhibits properties of a near-ideal lysochrome. It is strongly fluorescent, but only in the presence of a hydrophobic environment. The dye is very soluble in the lipids it is intended to show, and it does not interact with any tissue constituent except by solution. Nile red can be applied to cells in an aqueous medium, and it does not dissolve the lipids it is supposed to reveal.

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Nile red: a selective fluorescent stain for intracellular lipid droplets.

Preparations of rat-liver mitochondria catalyze the oxidation of exogenous NADH by added cytochrome c or ferricyanide by a reaction that is insensitive to the respiratory chain inhibitors, antimycin A, amytal, and rotenone, and is not coupled to phosphorylation. Experiments with tritiated NADH are described which demonstrate that this "external" pathway of NADH oxidation resembles stereochemically the NADH-cytochrome c reductase system of liver microsomes, and differs from the respiratory chain-linked NADH dehydrogenase. Enzyme distributation data are presented which substantiate the conclusion that microsomal contamination cannot account for the rotenone-insensitive NADH-cytochrome c reductase activity observed with the mitochondria. A procedure is developed, based on swelling and shrinking of the mitochondria followed by sonication and density gradient centrifugation, which permits the separation of two particulate subfractions, one containing the bulk of the respiratory chain components, and the other the bulk of the rotenone-insensitive NADH-cytochrome c reductase system. Morphological evidence supports the conclusion that the former subfraction consists of mitochondria devoid of outer membrane, and that the latter represents derivatives of the outer membrane. The data indicate that the electron-transport system associated with the mitochondrial outer membrane involves catalytic components similar to, or identical with, the microsomal NADH-cytochrome b5 reductase and cytochrome b5.

/pdf/an-electron-transport-system-associated-with-the-outer-3t7n0ebk2y.pdf

An electron-transport system associated with the outer membrane of liver mitochondria. A biochemical and morphological study.

In 2000, it was suggested to me that "Autophagy will be the wave of the future; it will become the new apoptosis." Few people would have agreed at the time, but this statement turned out to be prophetic, and this process of 'self-eating' rapidly exploded as a research field, as scientists discovered connections to cancer, neurodegeneration and even lifespan extension. Amazingly, the molecular breakthroughs in autophagy have taken place during only the past decade.

Autophagy: from phenomenology to molecular understanding in less than a decade

/pdf/tissue-fractionation-studies-5-the-association-of-acid-4cjg8m3xwb.pdf

Tissue fractionation studies. 5. The association of acid phosphatase with a special class of cytoplasmic granules in rat liver.

Tissue fractionation studies. 2. The nature of the linkage between acid phosphatase and mitochondria in rat-liver tissue

/pdf/tissue-fractionation-studies-3-further-observations-on-the-18ug5vp293.pdf

Tissue fractionation studies. 3. Further observations on the binding of acid phosphatase by rat-liver particles.

A LARGE number of enzymes have been located in the mitochondria fraction isolated by means of differential centrifugation; this fact is generally assumed to indicate that they are structurally associated within the living cell. Recent studies, part of which were presented at the second International Congress of Biochemistry1, have shown that this conclusion is not necessarily warranted. It has been found that the acid phosphatase of rat liver, which comes down predominantly with the large granules in a form which, in the native particles, is practically devoid of activity towards added glycerophosphate at pH 5 2–4, does not belong to the same type of granules as cytochrome oxidase.

F. Appelmans

Papers

Tissue fractionation studies. 6. Intracellular distribution patterns of enzymes in rat-liver tissue

Tissue fractionation studies. 5. The association of acid phosphatase with a special class of cytoplasmic granules in rat liver.

Tissue fractionation studies. 2. The nature of the linkage between acid phosphatase and mitochondria in rat-liver tissue

Tissue fractionation studies. 3. Further observations on the binding of acid phosphatase by rat-liver particles.

Enzymic Content of the Mitochondria Fraction