Combining MALDI-FTMS and bioinformatics for rapid peptidomic comparisons

Increasing research efforts in large-scale mass spectral analyses of peptides and proteins have led to many advances in technology and method development for collecting data and improving the quality of data. However, the resultant large data sets often pose significant challenges in extracting useful information in a high-throughput manner. Here, we describe one such method where we analyzed a large mass spectral data set collected using decapod crustacean nervous tissue extracts separated via high-performance liquid chromatography (HPLC) coupled to high-resolution matrix-assisted laser desorption/ionization Fourier transform mass spectrometry (MALDI-FTMS). Following their acquisition, the data collected from discrete LC fractions was compiled and analyzed using an in-house developed software package that deisotoped, compressed, calibrated, and matched peaks to a list of known crustacean neuropeptides. By processing these data via bioinformatics tools such as hierarchical clustering, more than 110 neuropeptides that belong to 14 peptide families were mapped in five crustacean species. Overall, we demonstrate the utility of MALDI-FTMS in combination with a bioinformatics software package for the elucidation and comparison of peptidomes of varying crustacean species. This study established an effective methodology and will provide the basis for future investigations into more comprehensive comparative peptidomics with larger collection of species and phyla in order to gain a deeper understanding of the evolution and diversification of peptide families.     

Role of PUG1 in inducible porphyrin and heme transport in Saccharomyces cerevisiae

Unlike pathogenic fungi, the budding yeast Saccharomyces cerevisiae is not efficient at using heme as a nutritional source of iron. Here we report that for this yeast, heme uptake is induced under conditions of heme starvation. Heme synthesis requires oxygen, and yeast grown anaerobically exhibited an increased uptake of hemin. Similarly, a strain lacking aminolevulinate synthase exhibited a sixfold increase in hemin uptake when grown without 2-aminolevulinic acid. We used microarray analysis of cells grown under reduced oxygen tension or reduced intracellular heme conditions to identify candidate genes involved in heme uptake. Surprisingly, overexpression of PUG1 (protoporphyrin uptake gene 1) resulted in reduced utilization of exogenous heme by a heme-deficient strain and, conversely, increased the utilization of protoporphyrin IX. Pug1p was localized to the plasma membrane by indirect immunofluorescence and subcellular fractionation. Strains overexpressing PUG1 exhibited decreased accumulation of [(55)Fe]hemin but increased accumulation of protoporphyrin IX compared to the wild-type strain. To measure the effect of PUG1 overexpression on intracellular heme pools, we used a CYC1-lacZ reporter, which is activated in the presence of heme, and we monitored the activity of a heme-containing metalloreductase, Fre1p, expressed from a constitutive promoter. The data from these experiments were consistent with a role for Pug1p in inducible protoporphyrin IX influx and heme efflux.     

Decision tree-driven tandem mass spectrometry for shotgun proteomics

Mass spectrometry has become a key technology for modern large-scale protein sequencing. Tandem mass spectrometry, the process of peptide ion dissociation followed by mass-to-charge ratio (m/z) analysis, is the critical component for peptide identification. Recent advances in mass spectrometry now permit two discrete, and complementary, types of peptide ion fragmentation: collision-activated dissociation (CAD) and electron transfer dissociation (ETD) on a single instrument. To exploit this complementarity and increase sequencing success rates, we designed and embedded a data-dependent decision tree algorithm (DT) to make unsupervised, real-time decisions of which fragmentation method to use based on precursor charge and m/z. Applying the DT to large-scale proteome analyses of Saccharomyces cerevisiae and human embryonic stem cells, we identified 53,055 peptides in total, which was greater than by using CAD (38,293) or ETD (39,507) alone. In addition, the DT method also identified 7,422 phosphopeptides, compared to either 2,801 (CAD) or 5,874 (ETD) phosphopeptides.     

Profiling Synaptic Proteins Identifies Regulators of Insulin Secretion and Lifespan

Cells are organized into distinct compartments to perform specific tasks with spatial precision. In neurons, presynaptic specializations are biochemically complex subcellular structures dedicated to neurotransmitter secretion. Activity-dependent changes in the abundance of presynaptic proteins are thought to endow synapses with different functional states; however, relatively little is known about the rules that govern changes in the composition of presynaptic terminals. We describe a genetic strategy to systematically analyze protein localization at Caenorhabditis elegans presynaptic specializations. Nine presynaptic proteins were GFP-tagged, allowing visualization of multiple presynaptic structures. Changes in the distribution and abundance of these proteins were quantified in 25 mutants that alter different aspects of neurotransmission. Global analysis of these data identified novel relationships between particular presynaptic components and provides a new method to compare gene functions by identifying shared protein localization phenotypes. Using this strategy, we identified several genes that regulate secretion of insulin-like growth factors (IGFs) and influence lifespan in a manner dependent on insulin/IGF signaling.     

Eicosapentaenoic-acid-derived isoprostanes: synthesis and discovery of two major isoprostanes

The stereospecific synthesis of two all-syn-EPA-derived isoprostanes (iPs), 5-epi-8,12-iso-iPF(3alpha)-VI 17 and 8,12-iso-iPF(3alpha)-VI 18, has been accomplished. These two synthetic probes have been used to discover and identify their presence in human urine. The eventual quantitative measurement of these two iPs may be a valuable index of oxidative stress in people with eicosapentaenoic acid- (EPA) and docosahexaenoic acid- (DHA) enriched phospholipids.     

Mechanisms and innovations: Traumatic brain injury: Can the consequences be stopped?

Traumatic brain injury is a leading cause of morbidity and death in both industrialized and developing countries. To date, there is no targeted pharmacological treatment that effectively limits the progression of secondary injury. The delayed progression of deterioration of grey and white matter gives hope that a meaningful intervention can be applied in a realistic timeframe following initial trauma. In this review we discuss new insights into the subcellular mechanisms of secondary injury that have highlighted numerous potential targets for intervention.We provide an overview of traumatic brain injury and, in particular, the mechanisms of secondary injury and emerging novel concepts for future intervention strategies. Understanding these processes in greater detail can identify feasible time frame for treatment and targets for meaningful interventions.Severe traumatic brain injury continues to be a leading cause of death and morbidity in North America.^1–8 The incidence of mild traumatic brain injury is high, and it is a major management problem for clinicians and a considerable source of frustration for patients. The economic and social burden of traumatic brain injury has implications on a global scale, with incidences in developing countries rising as the rate of vehicle use outpaces the development of safety infrastructure.^9,10 In addition, traumatic brain injury is now a major focus of casualty care in combat areas, as it is the principal cause of mortality and morbidity especially because of the recent surge in the use of low-cost, yet powerful, explosive devices directed at civilian and military personnel.¹¹Extensive literature aimed at understanding the tissue, cellular, inflammatory and subcellular processes following traumatic brain injury have proven unequivocally that these pathophysiological events are delayed and progressive in nature. Although the greatest impact on survival and outcome to date may be attributed to systemic and intracranial physiologic management (e.g., fluid resuscitation, intracranial pressure monitoring), future mitigation of the progression of secondary injury will likely be through molecular, gene and pharmacologic interventions. The prospect of gene therapy and pharmacologic treatments require physicians to be familiar with the subcellular mechanisms of brain injury.     

Oxidative stress in diseases of the human cornea

Intense exposure to light, robust metabolic activity, and high oxygen tension render the human eye particularly vulnerable to oxidative damage and the list of ophthalmological disorders implicating reactive oxygen and nitrogen species is rapidly expanding. Here, we review the roles of oxidative stress in the etiopathogeneses and pathophysiology of diseases of the human cornea including pterygium, keratoconus, trauma and chemical injury, and a host of inflammatory, metabolic, degenerative, and iatrogenic conditions. Data from animal and tissue culture experimentation germane to these conditions are also adduced.     

Behavioral and electrophysiological indices of negative affect predict cocaine self-administration

The motivation to seek cocaine comes in part from a dysregulation of reward processing manifested in dysphoria, or affective withdrawal. Learning is a critical aspect of drug abuse; however, it remains unclear whether drug-associated cues can elicit the emotional withdrawal symptoms that promote cocaine use. Here we report that a cocaine-associated taste cue elicited a conditioned aversive state that was behaviorally and neurophysiologically quantifiable and predicted subsequent cocaine self-administration behavior. Specifically, brief intraoral infusions of a cocaine-predictive flavored saccharin solution elicited aversive orofacial responses that predicted early-session cocaine taking in rats. The expression of aversive taste reactivity also was associated with a shift in the predominant pattern of electrophysiological activity of nucleus accumbens (NAc) neurons from inhibitory to excitatory. The dynamic nature of this conditioned switch in affect and the neural code reveals a mechanism by which cues may exert control over drug self-administration.