Phospho-Proteomic Analysis of Cardiac Dyssynchrony and Resynchronization Therapy.

Cardiac dyssynchrony arises from conduction abnormalities during heart failure and worsens morbidity and mortality. Cardiac resynchronization therapy (CRT) re-coordinates contraction using bi-ventricular pacing, but the cellular and molecular mechanisms involved remain largely unknown. The aim is to determine how dyssynchronous heart failure (HFdys ) alters the phospho-proteome and how CRT interacts with this unique phospho-proteome by analyzing Ser/Thr and Tyr phosphorylation. Phospho-enriched myocardium from dog models of Control, HFdys , and CRT is analyzed via MS. There were 209 regulated phospho-sites among 1761 identified sites. Compared to Con and CRT, HFdys is hyper-phosphorylated and tyrosine phosphorylation is more likely to be involved in signaling that increased with HFdys and was exacerbated by CRT. For each regulated site, the most-likely targeting-kinase is predicted, and CK2 is highly specific for sites that are "fixed" by CRT, suggesting activation of CK2 signaling occurs in HFdys that is reversed by CRT, which is supported by western blot analysis. These data elucidate signaling networks and kinases that may be involved and deserve further study. Importantly, a possible role for CK2 modulation in CRT has been identified. This may be harnessed in the future therapeutically to compliment CRT, improving its clinical effects.

An Empirical Approach to Signature Peptide Choice for Selected Reaction Monitoring: Quantification of Uromodulin in Urine.

BACKGROUND: Many avenues have been proposed for a seamless transition between biomarker discovery data and selected reaction monitoring (SRM) assays for biomarker validation. Unfortunately, studies with the abundant urinary protein uromodulin have shown that these methods do not converge on a consistent set of surrogate peptides for targeted mass spectrometry. As an alternative, we present an empirical peptide selection work flow for robust protein quantification. METHODS: We compared the relative SRM signal intensity of 12 uromodulin-derived peptides between tryptic digests of 9 urine samples. Pairwise CVs between the 12 peptides were 0.19-0.99. We used a correlation matrix to identify peptides that reproducibly tracked the amount of uromodulin protein and selected 4 peptides with robust and highly correlated SRM signals. Absolute quantification was performed with stable isotope-labeled versions of these peptides as internal standards and a standard curve prepared from a tryptic digest of purified uromodulin. RESULTS: Absolute quantification of uromodulin in 40 clinical urine samples yielded interpeptide correlations of ≥0.984 and correlations of ≥0.912 with ELISA data. The SRM assays were linear over >3 orders of magnitude and had typical interdigest CVs of <10%, interinjection CVs of <7%, and intertransition CVs of <7%. CONCLUSIONS: Comparing the apparent abundance of a plurality of peptides derived from the same target protein makes it possible to select signature peptides that are unaffected by the unpredictable confounding factors inevitably present in biological samples.

Constrained selected reaction monitoring: quantification of selected post-translational modifications and protein isoforms.

Selected reaction monitoring (SRM) is a mass spectrometry method that can target signature peptides to provide for the detection and quantitation of specific proteins in complex biological samples. When quantifying a protein, multiple peptides are generated using a specific protease such as trypsin, thereby allowing a choice of signature peptides with robust signals. In contrast, signature peptide selection can be constrained when the goal is to monitor a specific post-translational modification (PTM) or protein isoform, as the signature peptide must include the amino acid residue(s) of PTM attachment or sequence variation. This can force the selection of a signature peptide with a weak SRM response or one that is confounded by high background. In this article, we discuss steps that can be optimized to maximize peptide selection and assay performance of constrained SRM assays, including tuning instrument parameters, fragmenting product ions, using a different protease, and enriching the sample. Examples are provided for phosphorylated or citrullinated peptides and protein isoforms.

Secretion is required for late events in the cell-fusion pathway of mating yeast.

Secretory vesicles accumulate adjacent to the contact site between the two cells of a yeast mating pair before they fuse, but there is no direct evidence that secretion is required to complete fusion. In this study, temperature-sensitive secretion (sec(ts)) mutants were used to investigate the role of secretion in yeast cell fusion. Cell fusion arrested less than 5 minutes after inhibiting secretion. This rapid fusion arrest was not an indirect consequence of reduced mating pheromone signaling, mating-pair assembly or actin polarity. Furthermore, secretion was required to complete cell fusion when it was transiently inhibited by addition and removal of the lipophilic styryl dye, FM4-64. These results indicate that ongoing secretion is required for late events in the cell-fusion pathway, which include plasma-membrane fusion and the completion of cell-wall remodeling, and they demonstrate a just-in-time delivery mechanism for the cell-fusion machinery.

Prm1 functions as a disulfide-linked complex in yeast mating.

Prm1 is a pheromone-induced membrane glycoprotein that promotes plasma membrane fusion in yeast mating pairs. HA-Prm1 migrates at twice its expected molecular weight on non-reducing SDS-PAGE gels and coprecipitates with Prm1-TAP, indicating that Prm1 is a disulfide-linked homodimer. The N terminus of a plasma membrane-localized GFP-Prm1 endocytic mutant projects into the cytoplasm, where it is protected from low pH quenching in live cells and from external protease in spheroplasts. In a revised topological map, Prm1 has four transmembrane domains and two large extracellular loops. Mutation of all four cysteines in the extracellular loops blocked disulfide bond formation and destabilized the Prm1 homodimer without preventing Prm1 transport to contact sites in mating pairs. Cys(120) in loop 1 and Cys(545) in loop 2 form disulfide cross-links in the Prm1 homodimer and are required for fusion activity. Cys(120) lies between a hydrophobic segment formerly thought to be a transmembrane domain and an amphipathic helix. An interaction between either of these regions and the opposing membrane could promote fusion.

Prm1 targeting to contact sites enhances fusion during mating in Saccharomyces cerevisiae.

Prm1 is a pheromone-regulated membrane glycoprotein involved in the plasma membrane fusion event of Saccharomyces cerevisiae mating. Although this function suggests that Prm1 should act at contact sites in pairs of mating yeast cells where plasma membrane fusion occurs, only a small percentage of the total Prm1 was actually detected on the plasma membrane. We therefore investigated the intracellular transport of Prm1 and how this transport contributes to cell fusion. Two Prm1 chimeras that were sorted away from the contact site had reduced fusion activity, indicating that Prm1 indeed functions at contact sites. However, most Prm1 is located in endosomes and other cytoplasmic organelles and is targeted to vacuoles for degradation. Mutations in a putative endocytosis signal in a cytoplasmic loop partially stabilized the Prm1 protein and caused it to accumulate on the plasma membrane, but this endocytosis mutant actually had reduced mating activity. When Prm1 was expressed from a galactose-regulated promoter and its synthesis was repressed at the start of mating, vanishingly small amounts of Prm1 protein remained at the time when the plasma membranes came into contact. Nevertheless, this stable pool of Prm1 was retained at polarized sites on the plasma membrane and was sufficient to promote plasma membrane fusion. Thus, the amount of Prm1 expressed in mating yeast is far in excess of the amount required to facilitate fusion.

N-terminal residues of the yeast pheromone receptor, Ste2p, mediate mating events independently of G1-arrest signaling.

In Saccharomyces cerevisiae, mechanisms modulating the mating steps following cell cycle arrest are not well characterized. However, the N-terminal domain of Ste2p, a G protein-coupled pheromone receptor, was recently proposed to mediate events at this level. Toward deciphering receptor mechanisms associated with this mating functionality, scanning mutagenesis of targeted regions of the N-terminal domain has been completed. Characterization of ste2 yeast overexpressing Ste2p variants indicated that residues Ile 24 and Ile 29 as well as Pro 15 are critical in mediating mating efficiency. This activity was shown to be independent of Ste2p mediated G1 arrest signaling. Further analysis of Ile 24 and Ile 29 highlight the residues' solvent accessibility, as well as the importance of the hydrophobic nature of the sites, and in the case of Ile 24 the specific size and shape of the side chain. Mutation of these Ile's led to arrest of mating after cell contact, but before completion of cell wall degradation. We speculate that these extracellular residues mediate novel receptor interactions with ligand or proteins, leading to stimulation of alternate signaling effector pathways.

FUS1 regulates the opening and expansion of fusion pores between mating yeast.

Mating yeast cells provide a genetically accessible system for the study of cell fusion. The dynamics of fusion pores between yeast cells were analyzed by following the exchange of fluorescent markers between fusion partners. Upon plasma membrane fusion, cytoplasmic GFP and DsRed diffuse between cells at rates proportional to the size of the fusion pore. GFP permeance measurements reveal that a typical fusion pore opens with a burst and then gradually expands. In some mating pairs, a sudden increase in GFP permeance was found, consistent with the opening of a second pore. In contrast, other fusion pores closed after permitting a limited amount of cytoplasmic exchange. Deletion of FUS1 from both mating partners caused a >10-fold reduction in the initial permeance and expansion rate of the fusion pore. Although fus1 mating pairs also have a defect in degrading the cell wall that separates mating partners before plasma membrane fusion, other cell fusion mutants with cell wall remodeling defects had more modest effects on fusion pore permeance. Karyogamy is delayed by >1 h in fus1 mating pairs, possibly as a consequence of retarded fusion pore expansion.

Multiple signaling pathways regulate yeast cell death during the response to mating pheromones.

Mating pheromones promote cellular differentiation and fusion of yeast cells with those of the opposite mating type. In the absence of a suitable partner, high concentrations of mating pheromones induced rapid cell death in approximately 25% of the population of clonal cultures independent of cell age. Rapid cell death required Fig1, a transmembrane protein homologous to PMP-22/EMP/MP20/Claudin proteins, but did not require its Ca2+ influx activity. Rapid cell death also required cell wall degradation, which was inhibited in some surviving cells by the activation of a negative feedback loop involving the MAP kinase Slt2/Mpk1. Mutants lacking Slt2/Mpk1 or its upstream regulators also underwent a second slower wave of cell death that was independent of Fig1 and dependent on much lower concentrations of pheromones. A third wave of cell death that was independent of Fig1 and Slt2/Mpk1 was observed in mutants and conditions that eliminate calcineurin signaling. All three waves of cell death appeared independent of the caspase-like protein Mca1 and lacked certain "hallmarks" of apoptosis. Though all three waves of cell death were preceded by accumulation of reactive oxygen species, mitochondrial respiration was only required for the slowest wave in calcineurin-deficient cells. These findings suggest that yeast cells can die by necrosis-like mechanisms during the response to mating pheromones if essential response pathways are lacking or if mating is attempted in the absence of a partner.

Cell fusion assays for yeast mating pairs.

Yeast mating provides an accessible genetic system for the discovery of fundamental mechanisms in eukaryotic cell fusion. Although aspects of yeast mating related to pheromone signaling and polarized growth have been intensively investigated, fusion itself is poorly understood. This chapter describes methods for measuring the overall efficiency of yeast cell fusion and for monitoring various stages of the fusion process including cell wall remodeling, plasma membrane fusion, and nuclear fusion.

Cell-cell fusion.

Cell-cell fusion is a highly regulated and dramatic cellular event that is required for development and homeostasis. Fusion may also play a role in the development of cancer and in tissue repair by stem cells. While virus-cell fusion and the fusion of intracellular membranes have been the subject of intense investigation during the past decade, cell-cell fusion remains poorly understood. Given the importance of this cell-biological phenomenon, a number of investigators have begun analyses of the molecular mechanisms that mediate the specialized fusion events of a variety of cell types and species. We discuss recent genetic and biochemical studies that are beginning to yield exciting insights into the fusion mechanisms of Saccharomyces cerevisiae mating pairs, Caenorhabditis elegans epithelial cells and gametes, Drosophila melanogaster and mammalian myoblasts, and mammalian macrophages.

Using pure protein to build a multiple reaction monitoring mass spectrometry assay for targeted detection and quantitation.

Multiple reaction monitoring (MRM) is an increasingly popular mass spectrometry-based method to simultaneously detect and quantify multiple proteins. MRM is particularly useful for validating biomarkers discovered with a mass spectrometer and any analite discovered by MS can be monitored by MR because an MRM assay can be developed without the need to generate specific antibodies. In this chapter, we present a robust and systematic procedure to rapidly build a high-sensitivity MRM assay using purified protein as the starting material. Theoretical digestion of the protein with trypsin is used to identify mass spectrometry--compatible peptides and to generate preliminary MRM transitions to detect these peptides. Peptides generated by trypsin cleavage of the actual protein are then run on a liquid chromatography column coupled to a triple quadrupole mass spectrometer, which is programmed with the preliminary transitions. Whenever a transition is detected, it triggers dissociation of the corresponding peptide and collection of a full mass range scan of the resulting fragment ions. From this scan, fragment ions yielding the strongest and most reproducible signals are utilized to design empirical MRM transitions. The assay is further refined by optimizing the collision energy and creating a standard curve to measure sensitivity. Once MRM transitions have been established for a particular protein, they can be combined with transitions for other target proteins to create multiplex assays and used to quantify proteins in samples arising from serum, urine, subcellular fractions, or any other specemen of interest.

Ergosterol promotes pheromone signaling and plasma membrane fusion in mating yeast.

Ergosterol depletion independently inhibits two aspects of yeast mating: pheromone signaling and plasma membrane fusion. In signaling, ergosterol participates in the recruitment of Ste5 to a polarized site on the plasma membrane. Ergosterol is thought to form microdomains within the membrane by interacting with the long acyl chains of sphingolipids. We find that although sphingolipid-free ergosterol is concentrated at sites of cell-cell contact, transmission of the pheromone signal at contact sites depends on a balanced ratio of ergosterol to sphingolipids. If a mating pair forms between ergosterol-depleted cells despite the attenuated pheromone response, the subsequent process of membrane fusion is retarded. Prm1 also participates in membrane fusion. However, ergosterol and Prm1 have independent functions and only prm1 mutant mating pairs are susceptible to contact-dependent lysis. In contrast to signaling, plasma membrane fusion is relatively insensitive to sphingolipid depletion. Thus, the sphingolipid-free pool of ergosterol promotes plasma membrane fusion.

Prm1 prevents contact-dependent lysis of yeast mating pairs.

Membrane fusion requires localized destabilization of two phospholipid bilayers, but unrestrained membrane destabilization could result in lysis. prm1 mutant yeast cells have a defect at the plasma membrane fusion stage of mating that typically results in the accumulation of prezygotes that have fingers of membrane-bound cytoplasm projecting from one cell of each pair into its mating partner in the direction of the osmotic gradient between the cells. However, some prm1 mating pairs fuse successfully whereas the two cells in other prm1 mating pairs simultaneously lyse. Lysis only occurs if both mating partners are prm1 mutants. Osmotic stabilization does not protect prm1 mating pairs from lysis, indicating that lysis is not caused by a cell wall defect. prm1 mating pairs without functional mitochondria still lyse, ruling out programmed cell death. No excess lysis was found after pheromone treatment of haploid prm1 cells, and lysis did not occur in mating pairs when prm1 was combined with the fus1 and fus2 mutations to block cell wall remodeling. Furthermore, short (<1 microm) cytoplasmic microfingers indicating the completion of cell wall remodeling appeared immediately before lysis. In combination, these results demonstrate that plasma membrane contact is a prerequisite for lysis. Cytoplasmic microfingers are unlikely to cause lysis since most prm1 mating pairs with microfingers do not lyse, and microfingers were also detected before fusion in some wild-type mating pairs. The lysis of prm1 mutant mating pairs suggests that the Prm1 protein stabilizes the membrane fusion event of yeast mating.