Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals

Changes in the abundance of individual proteins in the proteome can be elicited by modulation of protein synthesis (the rate of input of newly synthesized proteins into the protein pool) or degradation (the rate of removal of protein molecules from the pool). A full understanding of proteome changes therefore requires a definition of the roles of these two processes in proteostasis, collectively known as protein turnover. Because protein turnover occurs even in the absence of overt changes in pool abundance, turnover measurements necessitate monitoring the flux of stable isotope–labeled precursors through the protein pool such as labeled amino acids or metabolic precursors such as ammonium chloride or heavy water. In cells in culture, the ability to manipulate precursor pools by rapid medium changes is simple, but for more complex systems such as intact animals, the approach becomes more convoluted. Individual methods bring specific complications, and the suitability of different methods has not been comprehensively explored. In this study, we compare the turnover rates of proteins across four mouse tissues, obtained from the same inbred mouse strain maintained under identical husbandry conditions, measured using either [¹³C₆]lysine or [²H₂]O as the labeling precursor. We show that for long-lived proteins, the two approaches yield essentially identical measures of the first-order rate constant for degradation. For short-lived proteins, there is a need to compensate for the slower equilibration of lysine through the precursor pools. We evaluate different approaches to provide that compensation. We conclude that both labels are suitable, but careful determination of precursor enrichment kinetics in amino acid labeling is critical and has a considerable influence on the numerical values of the derived protein turnover rates.     

Proteome-wide mapping of short-lived proteins in human cells

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An application case of ecological indicator values (Zeigerwerte) calculated with a simple algorithmic approach

Abstract

The vegetation of the study site near Rome (Castelporziano Estate), where different woodland types occur, was analysed on the basis of ecological indicator values (Zeigerwerte) for light, temperature, continentality of climate, soil moisture, soil pH and nitrogen. Indicator values were estimated with Hill's reprediction algorithm for the flora of Central-Southern Italy relying on a database of 4,207 original relevés representing a balanced survey of the vegetation of this and surrounding areas. It was possible to obtain indicator values for an important fraction of the Italian Mediterranean flora. Results are ecologically reasonable, and it was possible to find strong correlation between the recalculated values and a few environmental variables. These correlations were not significant in an analogous test with subjectively derived scores of Ellenberg indicator values.     

Terminal modification,sequence, length,and PIWI-protein identity determine piRNA stability

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Studies of Specificity and Inhibition of Human Cerebrospinal Fluid Dynorphin Converting Enzyme

Abstract

Dynorphin-converting activity was recently discovered in human cerebrospinal fluid.¹ This enzyme (hCSF-DCE) cleaves dynorphin A, dynorphin B and alpha-neoendorphin to release Leu-enkephalin-Arg⁶. To characterize the enzyme further we used several protease inhibitors, including N-peptidyl-O-acyl hydroxylamines which are known to act as potent irreversible inhibitors of serine and cysteine proteinases.^2-4

No irreversible inactivation occurred but strong, reversible effects on the dynorphin-converting activity by some of the inhibitors tested could be observed. Although, hCSF-DCE binds its substrates (dynorphin A and B) in the μM-mM concentration range, it exhibits high specificity in recognizing and cleaving the linkage between the two basic amino acids in the substrate sequence.     

Binding and degredation of insulin by plasma membranes from bovine liver isolated by a large scale preparation

With the large-scale preparation described, as much as 1 kg of bovine liver can be processed, giving a yield of more than 1 g plasma membrane protein. From analytical and morphological criteria the plasma membrane fraction isolated mainly derives from bile-canalicular and contiguous areas of the hepatocytes.The insulin binding activity is quite similar to insulin receptors in otherr cell systems and membrane preparations. Insulin-degrading activity is very low in the isolated plasma fraction. Most of degrading activity is located in a microsomal membrane fraction. Neverthless the K_m and the pH dependence of the insulin-degrading activity in both fractions are nearly identical.From these studies we conclude that binding and degradation of insulin are two independent processes located on different cell organelles.