Pentapeptide sharing between Corynebacterium diphtheria toxin and the human neural protein network

We describe the pentapeptides shared between the Corynebacterium diphtheria toxin and the human proteins associated with fundamental neural functions. We report that diphtheria toxin pentapeptides are spread among human antigens such as tuberous sclerosis proteins 1 and 2, reelin, contactin-4, neuroligins, semaphorin-5A, sodium channel protein type 1 subunit α, Williams–Beuren syndrome chromosomal region 1 protein, Williams–Beuren syndrome chromosomal region 20A protein. Williams–Beuren syndrome chromosomal region 8 protein, Bardet–Biedl syndrome 9 protein, Bardet–Biedl syndrome 10 protein, oligodendrocyte-myelin glycoprotein, neurofibromin-2, and periaxin. The data are discussed in relation to the bacterial immune escape phenomenon, and in the context of potential cross-reactions in diagnostic tests and immune therapies.     

Collagen derived species-specific peptides for distinguishing donkey-hide gelatin (Asini Corii Colla)

Objective: As an important food therapy product with traditional Chinese medicine (TCM) applications, donkey-hide gelatin (Asini Corii Colla, ACC) has been used for thousands of years. However, till now no effective strategy had been proposed to distinguish ACC from other animal hide gelatins, especially closely related horse- and mule-hide gelatins, which was an embarrassment of ACC quality control. Methods: Combined mass spectrometry and bioinformatic methods have been applied to identify and verify two ACC-specific peptides (Pep-1 and Pep-2) capable of distinguishing ACC from other closely related animal gelatins with high selectivity. Results: It confirmed that these two peptides could be not only used for distinguishing ACC from highly homologous horse-hide and mule-hide gelatins as well as other animal hide gelatins. Conclusion: The present study provides a simple method for species-specific peptides discovery, which can be used for assessing the quality of animal gelatin products, and ensure they are authenticable and traceable.     

Urinary peptidomics in kidney disease and drug research

Introduction: Due to its close connection with the renal system, urine is considered a valuable source of information in kidney disease research. Peptidomics methods focus on the discovery of endogenous peptides, given their wide range of biological functions and diagnostic and therapeutic potential. Representing a non-invasive and sensitive method, technological prospects of urinary peptidomics should be evaluated in the context of drug discovery and research.

Areas covered: This review describes urinary peptidomics with focus on its application in drug research in the field of kidney diseases. The authors provide an overview of current achievements and potential future applications.

Expert opinion: The urinary peptidome is a dynamically changing source of information, able to reflect sudden and long-term changes affecting the renal system. Studies utilizing urinary peptidomics techniques have demonstrated their value in patient stratification and detection of early pathological changes in kidney disease. Serving as a liquid biopsy, urinary peptides are an invaluable tool for drug response monitoring. Nevertheless, peptidomics is largely underexplored in drug research in general, as evidenced by the scarce number of scientific publications on this topic. Further progress will be driven by the successful validation of current discoveries and continued efforts to improve the translation of results into therapeutic applications.     

Mass spectrometry-based discovery of circadian peptides

A significant challenge to understanding dynamic and heterogeneous brain systems lies in the chemical complexity of secreted intercellular messengers that change rapidly with space and time. Two solid-phase extraction collection strategies are presented that relate time and location of peptide release with mass spectrometric characterization. Here, complex suites of peptide-based cell-to-cell signaling molecules are characterized from the mammalian suprachiasmatic nucleus (SCN), site of the master circadian clock. Observed SCN releasates are peptide rich and demonstrate the co-release of established circadian neuropeptides and peptides with unknown roles in circadian rhythms. Additionally, the content of SCN releasate is stimulation specific. Stimulation paradigms reported to alter clock timing, including electrical stimulation of the retinohypothalamic tract, produce releasate mass spectra that are notably different from the spectra of compounds secreted endogenously over the course of the 24-h cycle. In addition to established SCN peptides, we report the presence of proSAAS peptides in releasates. One of these peptides, little SAAS, exhibits robust retinohypothalamic tract–stimulated release from the SCN, and exogenous application of little SAAS induces a phase delay consistent with light-mediated cues regulating circadian timing. These mass spectrometry-based analyses provide a new perspective on peptidergic signaling within the SCN and demonstrate that the integration of secreted compounds with information relating time and location of release generates new insights into intercellular signaling in the brain.     

基于转录组学-蛋白质组学-多肽组学整合关联分析策略的动物药蛋白多肽类成分研究思路及方法

动物药是传统中药的重要组成部分,其特有功效在中药临床应用中具有不可替代性。鉴于目前动物药研究主要存在化学成分、药效物质基础、毒性物质基础不明确,动物药质量控制体系不健全等关键问题,通过构建基于转录组学-蛋白质组学-多肽组学整合关联分析策略的动物药蛋白多肽类成分研究思路及方法,主要包括基于转录组学的动物药蛋白数据库的构建、动物药蛋白多肽类成分的高分辨质谱分析、蛋白多肽类成分的匹配分析与鉴定以及关联功效的蛋白多肽类成分活性评价等研究内容,试图为动物药蛋白多肽类成分的分析鉴定提供一种切实可行的研究思路及方法,为进一步解决动物药研究存在的关键问题提供技术支持。     

Drosophila carboxypeptidase D (SILVER) is a key enzyme in neuropeptide processing required to maintain locomotor activity levels and survival rate

Neuropeptides are processed from larger preproproteins by a dedicated set of enzymes. The molecular and biochemical mechanisms underlying preproprotein processing and the functional importance of processing enzymes are well‐characterised in mammals, but little studied outside this group. In contrast to mammals, Drosophila melanogaster lacks a gene for carboxypeptidase E (CPE), a key enzyme for mammalian peptide processing. By combining peptidomics and neurogenetics, we addressed the role of carboxypeptidase D (dCPD) in global neuropeptide processing and selected peptide‐regulated behaviours in Drosophila. We found that a deficiency in dCPD results in C‐terminally extended peptides across the peptidome, suggesting that dCPD took over CPE function in the fruit fly. dCPD is widely expressed throughout the nervous system, including peptidergic neurons in the mushroom body and neuroendocrine cells expressing adipokinetic hormone. Conditional hypomorphic mutation in the dCPD‐encoding gene silver in the larva causes lethality, and leads to deficits in starvation‐induced hyperactivity and appetitive gustatory preference, as well as to reduced viability and activity levels in adults. A phylogenomic analysis suggests that loss of CPE is not common to insects, but only occurred in Hymenoptera and Diptera. Our results show that dCPD is a key enzyme for neuropeptide processing and peptide‐regulated behaviour in Drosophila. dCPD thus appears as a suitable target to genetically shut down total neuropeptide production in peptidergic neurons. The persistent occurrence of CPD in insect genomes may point to important further CPD functions beyond neuropeptide processing which cannot be fulfilled by CPE.     

Identification of ageing-associated naturally occurring peptides in human urine

To assess normal and pathological peptidomic changes that may lead to an improved understanding of molecular mechanisms underlying ageing, urinary peptidomes of 1227 healthy and 10333 diseased individuals between 20 and 86 years of age were investigated. The diseases thereby comprised diabetes mellitus, renal and cardiovascular diseases. Using age as a continuous variable, 116 peptides were identified that significantly (p < 0.05; |ρ|≥0.2) correlated with age in the healthy cohort. The same approach was applied to the diseased cohort. Upon comparison of the peptide patterns of the two cohorts 112 common age-correlated peptides were identified. These 112 peptides predominantly originated from collagen, uromodulin and fibrinogen. While most fibrillar and basement membrane collagen fragments showed a decreased age-related excretion, uromodulin, beta-2-microglobulin and fibrinogen fragments showed an increase. Peptide-based in silico protease analysis was performed and 32 proteases, including matrix metalloproteinases and cathepsins, were predicted to be involved in ageing. Identified peptides, predicted proteases and patient information were combined in a systems biology pathway analysis to identify molecular pathways associated with normal and/or pathological ageing. While perturbations in collagen homeostasis, trafficking of toll-like receptors and endosomal pathways were commonly identified, degradation of insulin-like growth factor-binding proteins was uniquely identified in pathological ageing.     

Mass Spectrometry-Based Proteomics and Peptidomics for Biomarker Discovery in Neurodegenerative Diseases

There is an urgent need to search for biomarkers that are indicative of neurodegenerative diseases, as the clinical diagnosis of which remains unsatisfactory. Mass spectrometry (MS) has been playing an important role in studying peptide and protein identities, structures, modifications and interactions that collectively drive their biological functions. MS-based proteomics technology is thus well suited for the biomarker discovery. This article reviews the overall strategies and workflows employed for biomarker discovery and recent applications of MS-based proteomics in neurodegenerative diseases. Special emphasis is placed on the studies of protein post-translational modification pattern changes and differential peptidomics under these pathological conditions.