DINeR: Database for Insect Neuropeptide Research

Neuropeptides are responsible for regulating a variety of functions, including development, metabolism, water and ion homeostasis, and as neuromodulators in circuits of the central nervous system. Numerous neuropeptides have been identified and characterized. However, both discovery and functional characterization of neuropeptides across the massive Class Insecta has been sporadic. To leverage advances in post-genomic technologies for this rapidly growing field, insect neuroendocrinology requires a consolidated, comprehensive and standardised resource for managing neuropeptide information. The Database for Insect Neuropeptide Research (DINeR) is a web-based database-application used for search and retrieval of neuropeptide information of various insect species detailing their isoform sequences, physiological functionality and images of their receptor-binding sites, in an intuitive, accessible and user-friendly format. The curated data includes representatives of 50 well described neuropeptide families from over 400 different insect species. Approximately 4700 FASTA formatted, neuropeptide isoform amino acid sequences and over 200 records of physiological functionality have been recorded based on published literature. Also available are images of neuropeptide receptor locations. In addition, the data include comprehensive summaries for each neuropeptide family, including their function, location, known functionality, as well as cladograms, sequence alignments and logos covering most insect orders. Moreover, we have adopted a standardized nomenclature to address inconsistent classification of neuropeptides

The neuropeptide transcriptome of a model echinoderm, the sea urchin Strongylocentrotus purpuratus

The work reported here was supported by a grant from the University of London Central Research Fun

A Pattern Search Method for Discovering Conserved Motifs in Bioactive Peptide Families

status: publishe

The angiotensin-converting enzyme (ACE) gene family of Anopheles gambiae

Background Members of the M2 family of peptidases, related to mammalian angiotensin converting enzyme (ACE), play important roles in regulating a number of physiological processes. As more invertebrate genomes are sequenced, there is increasing evidence of a variety of M2 peptidase genes, even within a single species. The function of these ACE-like proteins is largely unknown. Sequencing of the A. gambiae genome has revealed a number of ACE-like genes but probable errors in the Ensembl annotation have left the number of ACE-like genes, and their structure, unclear. Results TBLASTN and sequence analysis of cDNAs revealed that the A. gambiae genome contains nine genes (AnoACE genes) which code for proteins with similarity to mammalian ACE. Eight of these genes code for putative single domain enzymes similar to other insect ACEs described so far. AnoACE9, however, has several features in common with mammalian somatic ACE such as a two domain structure and a hydrophobic C terminus. Four of the AnoACE genes (2, 3, 7 and 9) were shown to be expressed at a variety of developmental stages. Expression of AnoACE3, AnoACE7 and AnoACE9 is induced by a blood meal, with AnoACE7 showing the largest (approximately 10-fold) induction. Conclusion Genes coding for two-domain ACEs have arisen several times during the course of evolution suggesting a common selective advantage to having an ACE with two active-sites in tandem in a single protein. AnoACE7 belongs to a sub-group of insect ACEs which are likely to be membrane-bound and which have an unusual, conserved gene structure

Coordinated RNA-Seq and peptidomics identify neuropeptides and G-protein coupled receptors (GPCRs) in the large pine weevil Hylobius abietis, a major forestry pest

Hylobius abietis (Linnaeus), or large pine weevil (Coleoptera, Curculionidae), is a pest of European coniferous forests. In order to gain understanding of the functional physiology of this species, we have assembled a de novo transcriptome of H. abietis, from sequence data obtained by Next Generation Sequencing. In particular, we have identified genes encoding neuropeptides, peptide hormones and their putative G-protein coupled receptors (GPCRs) to gain insights into neuropeptide-modulated processes. The transcriptome was assembled de novo from pooled paired-end, sequence reads obtained from RNA from whole adults, gut and central nervous system tissue samples. Data analysis was performed on the transcripts obtained from the assembly including, annotation, gene ontology and functional assignment as well as transcriptome completeness assessment and KEGG pathway analysis. Pipelines were created using Bioinformatics tools and techniques for prediction and identification of neuropeptides and neuropeptide receptors. Peptidomic analysis was also carried out using a combination of MALDI-TOF as well as Q-Exactive Orbitrap mass spectrometry to confirm the identified neuropeptide. 41 putative neuropeptide families were identified in H. abietis, including Adipokinetic hormone (AKH), CAPA and DH31. Neuropeptide F, which has not been yet identified in the model beetle T. castaneum, was identified. Additionally, 24 putative neuropeptide and 9 leucine-rich repeat containing G protein coupled receptor-encoding transcripts were determined using both alignment as well as non-alignment methods. This information, submitted to the NCBI sequence read archive repository (SRA accession: SRP133355), can now be used to inform understanding of neuropeptide-modulated physiology and behaviour in H. abietis; and to develop specific neuropeptide-based tools for H. abietis control

A peptidomic investigation into enteroendocrine cells and islets of humans and mice

Enteroendocrine cells (EECs) of the gastrointestinal (GI) tract and islets of Langerhans (islets) of the pancreas are endocrine cells capable of sensing nutrient intake or the nutrient content of the blood and responding by secreting peptide hormones to control various physiological functions. This thesis focuses on characterising the peptidome of EECs and islets by utilising liquid-chromatography coupled to mass spectrometry (LC-MS). Due to their ability to control food intake and glucose tolerance, hormones from EECs and islets are of great therapeutic interest for the treatment of type 2 diabetes (T2D) and obesity. I hypothesised that there may be undiscovered peptide hormones derived from EECs or islets that could also be of therapeutic interest for the treatment of T2D. In order to identify potentially novel hormone candidates, peptidomic analyses of mouse EECs, mouse islets and human GI tissue were carried out utilising LC-MS. 13 interesting peptide candidates identified in the peptidomic analyses were picked out to be synthesised for in vivo and/or in vitro characterisation. All 13 peptides were screened for activity at Gs or Gi signalling pathways in various cell lines although unfortunately no peptide seemed to exhibit activity through these signalling mechanisms in the cell lines tested. Despite this, studies were carried out to assess the ability of the 2 top peptide candidates to control food intake and glucose tolerance in vivo. 1 of these peptides, a peptide derived from progastrin, seemed to mildly improve glucose tolerance in lean mice, an effect that was seen in across several studies. I hypothesised that this progastrin derived peptide may be altering peptide secretions from islets to modulate glucose tolerance but no effect of this novel peptide was seen on insulin, somatostatin-14 or glucagon secretion from islets. The progastrin derived peptide was then administered to diet-induced obese mice to assess its therapeutic potential but unfortunately no effect was seen on glucose tolerance. More work needs to be performed to verifying my findings and investigating a possible mechanism of action before this novel progastrin derived peptide may be considered a gut hormone. In regard to the peptidome of islets, there are some gaps in the literature that our initial peptidomic analysis did not answer. Questions such as do islets produce GLP1 (glucagon-like peptide 1) receptor agonists and how is the islet peptidome altered in response to metabolic stress. I therefore carried out an investigation to address these questions. Targeted LC-MS methodology was used to search for intra-islet GLP1 receptor agonists. No peptides derived from glucose-dependent insulinotropic polypeptide (GIP) were found in mouse islets but active GLP-1 was found in both human and mouse islets. Comparisons were made between the abundance of active GLP-1 and glucagon to assess which of these peptides might be responsible for the intra-islet “incretin” effect. My peptidomic analysis of islets from T2D humans and obese mice may not have revealed new major findings but it has provided some clarity over how metabolic stress alters the peptidome of islets in T2D an obesity. In summary; a comprehensive analysis of the peptidome of EECs and islets was carried out, a number of novel peptide hormone candidates were synthesised and one of which exhibited a mild improvement in the glucose tolerance of lean mice, and clarity was provided on how metabolic stress alters the islet peptidome in mice and humans. I hope that the data produced in this thesis can contribute to a better understanding of the peptidome of the EECs and islets and may contribute to advances in therapeutic options for patients suffering from obesity or T2D

The New Pharmacological Approaches for the Regulation of Functional Activity of G Protein-Coupled Receptors

The G protein-coupled receptors (GPCRs), a large family of the receptors that specifically interact with a number of signal molecules, play a key role in the regulation of fundamental cell processes, and the pharmacological action of over 40% of drugs is carried out through GPCRs. In the last years, a significant progress was made in the creation of selective regulators of GPCRs interacting with their allosteric sites, such as the synthetic peptides corresponding to intracellular regions of receptors (GPCR-peptides) and the low-molecular weight agonists and antagonists of GPCRs. This review describes the recent results obtained by us and other authors in the development of GPCR-peptides and low-molecular weight agonists and the prospects of their use in clinics

The sequence flanking the N-terminus of the CLV3 peptide is critical for its cleavage and activity in stem cell regulation in Arabidopsis

The "Shakespeare Authorship Question"—regarding the identity of the poet-playwright—has been debated for over 150 years. Now, with the growing list of signatories to the "Declaration of Reasonable Doubt," the creation of a Master's Degree program in Authorship Studies at Brunel University in London, the opening of the Shakespeare Authorship Research Studies Center at the Library of Concordia University in Portland, and the release of two competing high-profile books both entitled Shakespeare Beyond Doubt, academic libraries are being presented with a unique and timely opportunity to participate in and encourage this debate, which has long been considered a taboo subject in the academy.https://journal.lib.uoguelph.ca/index.php/perj/article/view/280

QUANTITATIVE CHARACTERIZATION OF PROTEINS AND POST-TRANSLATIONAL MODIFICATIONS IN COMPLEX PROTEOMES USING HIGH-RESOLUTION MASS SPECTROMETRY-BASED PROTEOMICS

Mass spectrometry-based proteomics is focused on identifying the entire suite of proteins and their post-translational modifications (PTMs) in a cell, organism, or community. In particular, quantitative proteomics measures abundance changes of thousands of proteins among multiple samples and provides network-level insight into how biological systems respond to environmental perturbations. Various quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling. This dissertation starts with systematic comparison of these three methods, and shows that isobaric chemical labeling provides accurate, precise, and reproducible quantification for thousands of proteins. Based on these results, we applied this approach to characterizing the proteome of Arabidopsis seedlings treated with Strigolactones (SLs), a new class of plant hormones that modulate various developmental processes. Our study reveals that SLs regulate the expression of a range of proteins that have not been assigned to SL pathways, which provides novel targets for follow-up genetic and biochemical characterization of SL signaling. The same approach was also used to measure how elevated temperature impacts the physiology of individual microbial groups in an acid mine drainage (AMD) microbial community, and shows that related organisms differed in their abundance and functional responses to temperature. Elevated temperature repressed carbon fixation by two Leptospirillum genotypes, whereas carbon fixation was significantly up-regulated at higher temperature by a third member of this genus. Further, we developed a new proteomic approach that harnessed high-resolution mass spectrometry and supercomputing for direct identification and quantification of a broad range of PTMs from an AMD microbial community. We find that PTMs are extraordinarily diverse between different growth stages and highly divergent between closely related bacteria. The findings of this study motivate further investigation of the role of PTMs in the ecology and evolution of microbial communities. Finally, a computational approach has been developed to improve the sensitivity of phosphopeptide identification. Overall, the research presented in the dissertation not only reveals biological insights with existing quantitative proteomics methods, but also develops novel methodologies that open up new avenues in studying PTMs of proteins (e.g. PTM cross-talk)

Hmrbase: a database of hormones and their receptors

<p>Abstract</p> <p>Background</p> <p>Hormones are signaling molecules that play vital roles in various life processes, like growth and differentiation, physiology, and reproduction. These molecules are mostly secreted by endocrine glands, and transported to target organs through the bloodstream. Deficient, or excessive, levels of hormones are associated with several diseases such as cancer, osteoporosis, diabetes etc. Thus, it is important to collect and compile information about hormones and their receptors.</p> <p>Description</p> <p>This manuscript describes a database called Hmrbase which has been developed for managing information about hormones and their receptors. It is a highly curated database for which information has been collected from the literature and the public databases. The current version of Hmrbase contains comprehensive information about ~2000 hormones, e.g., about their function, source organism, receptors, mature sequences, structures etc. Hmrbase also contains information about ~3000 hormone receptors, in terms of amino acid sequences, subcellular localizations, ligands, and post-translational modifications etc. One of the major features of this database is that it provides data about ~4100 hormone-receptor pairs. A number of online tools have been integrated into the database, to provide the facilities like keyword search, structure-based search, mapping of a given peptide(s) on the hormone/receptor sequence, sequence similarity search. This database also provides a number of external links to other resources/databases in order to help in the retrieving of further related information.</p> <p>Conclusion</p> <p>Owing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission, DrugPedia linkage etc. Hmrbase is available online for public from <url>http://crdd.osdd.net/raghava/hmrbase/</url>.</p