New insights into the mechanisms of protein palmitoylation

Since its discovery more than 30 years ago, protein palmitoylation has been shown to have a role in protein-membrane interactions, protein trafficking, and enzyme activity. Until recently, however, the molecular machinery that carries out reversible palmitoylation of proteins has been elusive. In fact, both enzymatic and nonenzymatic S-acylation reaction mechanisms have been proposed. Recent reports of protein palmitoyltransferases in Saccharomyces cerevisiae and Drosophila provide the first glimpse of enzymes that carry out protein palmitoylation. Equally important is the mechanism of depalmitoylation. Two major classes of protein palmitoylthioesterases have been described. One family is lysosomal and is involved in protein degradation. The second is cytosolic and removes palmitoyl moieties preferentially from proteins associated with membranes. This review discusses recent advances in the understanding of mechanisms of addition of palmitate to proteins and removal of palmitate from proteins.     

Palmitoylation and plasma membrane localization of Ras2p by a nonclassical trafficking pathway in Saccharomyces cerevisiae

Subcellular localization of Ras proteins to the plasma membrane is accomplished in part by covalent attachment of a farnesyl moiety to the conserved CaaX box cysteine. Farnesylation targets Ras to the endoplasmic reticulum (ER), where additional processing steps occur, resulting in translocation of Ras to the plasma membrane. The mechanism(s) by which this occurs is not well understood. In this report, we show that plasma membrane localization of Ras2p in Saccharomyces cerevisiae does not require the classical secretory pathway or a functional Golgi apparatus. However, when the classical secretory pathway is disrupted, plasma membrane localization requires Erf2p, a protein that resides in the ER membrane and is required for efficient palmitoylation of Ras2p. Deletion of ERF2 results in a Ras2p steady-state localization defect that is more severe when combined with sec-ts mutants or brefeldin A treatment. The Erf2p-dependent localization of Ras2p correlates with the palmitoylation of Cys-318. An Erf2p-Erf4p complex has recently been shown to be an ER-associated palmitoyltransferase that can palmitoylate Cys-318 of Ras2p (S. Lobo, W. K. Greentree, M. E. Linder, and R. J. Deschenes, J. Biol. Chem. 277:41268-41273, 2002). Erf2-dependent palmitoylation as well as localization of Ras2p requires a region of the hypervariable domain adjacent to the CaaX box. These results provide evidence for the existence of a palmitoylation-dependent, nonclassical endomembrane trafficking system for the plasma membrane localization of Ras proteins.     

Parental care trade‐offs in the inter‐brood phase in Barn Swallows Hirundo rustica

In seasonal environments with limited time and energy resources, double‐brooded birds face trade‐offs in the timing of their two reproductive attempts and in the effort allocated to the first and the second broods. In the Barn Swallow Hirundo rustica a long care period for the first brood enhances the survival of first‐brood chicks, but also delays the start of the second brood, which in turn reduces the survival prospects of second‐brood chicks. Probably as a response to this trade‐off, double‐brooded Barn Swallows reduce the period of post‐fledging care for first‐brood fledglings. By radiotracking whole families, we investigated the determinants of this behaviour and its consequences for the survival of the first‐brood fledglings. The end of the females’ investment in post‐fledging care of the first brood was related to the beginning of egg synthesis for the second clutch. With the start of egg synthesis, females significantly reduced provisioning rates to the first‐brood fledglings to less than one‐fifth of the previous rates, while the proportion of time they spent foraging remained high. Assuming that the females’ foraging success was constant, we conclude that their energy income was allocated to egg production rather than fledgling provision. Males did not compensate for the females’ reduced feeding rates. Thus the start of egg production for the second clutch had a marked effect on the quantity of food received by first‐brood fledglings. In parallel with the changes in parental behaviour and provisioning rates, we observed a marked drop in the daily survival rate of first‐brood chicks. These results support the hypothesis that females face a strong trade‐off in the allocation of energy to subsequent broods. Energy allocation to a second clutch involves a cost in terms of reduced provisioning, and as a result the survival of first‐brood chicks is compromised. This is probably outweighed by the improved success of an early second brood.     

Identification of a potent and selective non-basic cathepsin K inhibitor

Based on our previous study with trifluoroethylamine as a P2-P3 amide isostere of cathepsin K inhibitor, further optimization led to identification of compound 22 (L-873724) as a potent and selective non-basic cathepsin K inhibitor. This compound showed excellent pharmacokinetics and efficacy in an ovariectomized (OVX) rhesus monkey model. The volumes of distribution close to unity were consistent with this compound not being lysosomotropic, which is a characteristic of basic cathepsin K inhibitors.     

Protein palmitoylation by a family of DHHC protein S-acyltransferases

Protein palmitoylation refers to the posttranslational addition of a 16 carbon fatty acid to the side chain of cysteine, forming a thioester linkage. This acyl modification is readily reversible, providing a potential regulatory mechanism to mediate protein-membrane interactions and subcellular trafficking of proteins. The mechanism that underlies the transfer of palmitate or other long-chain fatty acids to protein was uncovered through genetic screens in yeast. Two related S-palmitoyltransferases were discovered. Erf2 palmitoylates yeast Ras proteins, whereas Akr1 modifies the yeast casein kinase, Yck2. Erf2 and Akr1 share a common sequence referred to as a DHHC (aspartate-histidine-histidine-cysteine) domain. Numerous genes encoding DHHC domain proteins are found in all eukaryotic genome databases. Mounting evidence is consistent with this signature motif playing a direct role in protein acyltransferase (PAT) reactions, although many questions remain. This review presents the genetic and biochemical evidence for the PAT activity of DHHC proteins and discusses the mechanism of protein-mediated palmitoylation.     

Atmospheric water vapor as driver of litter decomposition in Mediterranean shrubland and grassland during rainless seasons

Litter production in many drought‐affected ecosystems coincides with the beginning of an extended season of no or limited rainfall. Because of lack of moisture litter decomposition during such periods has been largely ignored so far, despite potential importance for the overall decay process in such ecosystems. To determine drivers and extent of litter decay in rainless periods, a litterbag study was conducted in Mediterranean shrublands, dwarf shrublands and grasslands. Heterogeneous local and common straw litter was left to decompose in open and shaded patches of various field sites in two study regions. Fresh local litter lost 4–18% of its initial mass over about 4 months without rainfall, which amounted to 15–50% of total annual decomposition. Lab incubations and changes in chemical composition suggested that litter was degraded by microbial activity, enabled by absorption of water vapor from the atmosphere. High mean relative humidity of 85% was measured during 8–9 h of most nights, but the possibility of fog deposition or dew formation at the soil surface was excluded. Over 95% of the variation in mass loss and changes in litter nitrogen were explained by characteristics of water‐vapor uptake by litter. Photodegradation induced by the intense solar radiation was an additional mechanism of litter decomposition as indicated by lignin dynamics. Lignin loss from litter increased with exposure to ultraviolet radiation and with initial lignin concentration, together explaining 90%–97% of the variation in lignin mass change. Our results indicate that water vapor, solar radiation and litter quality controlled decomposition and changes in litter chemistry during rainless seasons. Many regions worldwide experience transient periods without rainfall, and more land area is expected to undergo reductions in rainfall as a consequence of climate change. Therefore, absorption of water vapor might play a role in decomposition and nutrient cycling in an increasing number of ecosystems.     

RnaPredict--an evolutionary algorithm for RNA secondary structure prediction

This paper presents two in-depth studies on RnaPredict, an evolutionary algorithm for RNA secondary structure prediction. The first study is an analysis of the performance of two thermodynamic models, Individual Nearest Neighbor (INN) and Individual Nearest Neighbor Hydrogen Bond (INN-HB). The correlation between the free energy of predicted structures and the sensitivity is analyzed for 19 RNA sequences. Although some variance is shown, there is a clear trend between a lower free energy and an increase in true positive base pairs. With increasing sequence length, this correlation generally decreases. In the second experiment, the accuracy of the predicted structures for these 19 sequences are compared against the accuracy of the structures generated by the mfold dynamic programming algorithm (DPA) and also to known structures. RnaPredict is shown to outperform the minimum free energy structures produced by mfold and has comparable performance when compared to sub-optimal structures produced by mfold.     

Modulation of yeast Sln1 kinase activity by the CCW12 cell wall protein

The yeast Sln1p sensor kinase is best known as an osmosensor involved in the regulation of the hyperosmolarity glycerol mitogen-activated protein kinase cascade. Down-regulation of Sln1 kinase activity occurs under hypertonic conditions and leads to phosphorylation of the Hog1p mitogen-activated protein kinase and increased osmotic stress-response gene expression. Conditions leading to kinase up-regulation include osmotic imbalance caused by glycerol retention in the glycerol channel mutant, fps1 (Tao, W., Deschenes, R. J., and Fassler, J. S. (1999) J. Biol. Chem. 274, 360-367). The hypothesis that Sln1p kinase activity is responsive to turgor was first suggested by the increased Sln1p kinase activity in mutants lacking Fps1p in which glycerol accumulation leads to water uptake. Also consistent with the turgor hypothesis is the observation that reduced turgor caused by treatment of cells with nystatin, a drug that increases membrane permeability and causes cell shrinkage, reduced Sln1p kinase activity (Tao, W., Deschenes, R. J., and Fassler, J. S. (1999) J. Biol. Chem. 274, 360-367; Reiser, V., Raitt, D. C., and Saito, H. (2003) J. Cell Biol. 161, 1035-1040). The turgor hypothesis is revisited here in the context of the identification and characterization of the cell wall gene, CCW12, as a determinant of Sln1p activity. Results of this analysis suggest that the activity of the plasma membrane localized Sln1p is affected by the presence or absence of specific outer cell wall proteins and that this effect is independent of turgor.     

Akr1p-dependent palmitoylation of Yck2p yeast casein kinase 1 is necessary and sufficient for plasma membrane targeting

The Yck2 protein is a plasma membrane-associated casein kinase 1 isoform that attaches to membranes via palmitoylation of its C terminus. We have demonstrated that Yck2p traffics to the plasma membrane on secretory vesicles. Because Akr1p, the palmitoyl transferase for Yck2p, is located on Golgi membranes, it is likely that Yck2p first associates with Golgi membranes, and then is somehow recruited to budding plasma membrane-destined vesicles. We show here that residues 499-546 are sufficient for minimal Yck2p palmitoylation and plasma membrane localization. We previously described normal plasma membrane targeting of a Yck2p construct with the final five amino acids of Ras2p substituting for the final two Cys residues of Yck2p. This Yck2p variant no longer requires Akr1p for membrane association, but targets normally. We have generated the C-terminal deletions previously shown to affect Yck2p membrane association in this variant to determine which residues are important for targeting and/or modification. We find that all of the sequences previously identified as important for plasma membrane association are required only for Akr1p-dependent modification. Furthermore, palmitoylation is sufficient for specific association of Yck2p with secretory vesicles destined for the plasma membrane. Finally, both C-terminal Cys residues are palmitoylated, and dual acylation is required for efficient membrane association.