Global substrate specificity profiling of post‐translational modifying enzymes

Enzymes that modify the proteome, referred to as post‐translational modifying (PTM) enzymes, are central regulators of cellular signaling. Determining the substrate specificity of PTM enzymes is a critical step in unraveling their biological functions both in normal physiological processes and in disease states. Advances in peptide chemistry over the last century have enabled the rapid generation of peptide libraries for querying substrate recognition by PTM enzymes. In this article, we highlight various peptide‐based approaches for analysis of PTM enzyme substrate specificity. We focus on the application of these technologies to proteases and also discuss specific examples in which they have been used to uncover the substrate specificity of other types of PTM enzymes, such as kinases. In particular, we highlight our multiplex substrate profiling by mass spectrometry (MSP‐MS) assay, which uses a rationally designed, physicochemically diverse library of tetradecapeptides. We show how this method has been applied to PTM enzymes to uncover biological function, and guide substrate and inhibitor design. We also briefly discuss how this technique can be combined with other methods to gain a systems‐level understanding of PTM enzyme regulation and function.     

Proteomics for Biological Discovery. * Edited by Timothy D. Veenstra and John R. Yates III

‘Proteomics for Biological Discovery’ edited byTimothy D. Veenstra and John R. Yates III (342 pages, John-Wiley& Sons, publishers), defines the modern analytical challengesof proteomics in terms of quantification, detection and accuracyfor biomedical research. The logic and possibly the eleganceof this text comes from the way that the reader is able to conversewith more than two dozen experts on a nearly complete collectionof separation, automation and bioinformatics techniques requiredfor quantitative and functional proteomic analysis. The bookis divided into three parts: Part I is on the fundamentals ofprotein separations and mass spectrometry, Part II is on functionalproteomic analysis and Part III discusses new methods that areat the frontier of the proteomics field. All of     

Association of NMT2 with the acyl-CoA carrier ACBD6 protects the N-myristoyltransferase reaction from palmitoyl-CoA

The covalent attachment of a 14-carbon aliphatic tail on a glycine residue of nascent translated peptide chains is catalyzed in human cells by two N-myristoyltransferase (NMT) enzymes using the rare myristoyl-CoA (C₁₄-CoA) molecule as fatty acid donor. Although, NMT enzymes can only transfer a myristate group, they lack specificity for C₁₄-CoA and can also bind the far more abundant palmitoyl-CoA (C₁₆-CoA) molecule. We determined that the acyl-CoA binding protein, acyl-CoA binding domain (ACBD)6, stimulated the NMT reaction of NMT2. This stimulatory effect required interaction between ACBD6 and NMT2, and was enhanced by binding of ACBD6 to its ligand, C_18:2-CoA. ACBD6 also interacted with the second human NMT enzyme, NMT1. The presence of ACBD6 prevented competition of the NMT reaction by C₁₆-CoA. Mutants of ACBD6 that were either deficient in ligand binding to the N-terminal ACBD or unable to interact with NMT2 did not stimulate activity of NMT2, nor could they protect the enzyme from utilizing the competitor C₁₆-CoA. These results indicate that ACBD6 can locally sequester C₁₆-CoA and prevent its access to the enzyme binding site via interaction with NMT2. Thus, the ligand binding properties of the NMT/ACBD6 complex can explain how the NMT reaction can proceed in the presence of the very abundant competitive substrate, C₁₆-CoA.     

Next‐Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water

Tailings ponds in the Athabasca oil sands (Canada) contain fluid wastes, generated by the extraction of bitumen from oil sands ores. Although the autochthonous prokaryotic communities have been relatively well characterized, almost nothing is known about microbial eukaryotes living in the anoxic soft sediments of tailings ponds or in the thin oxic layer of water that covers them. We carried out the first next‐generation sequencing study of microbial eukaryotic diversity in oil sands tailings ponds. In metagenomes prepared from tailings sediment and surface water, we detected very low numbers of sequences encoding eukaryotic small subunit ribosomal RNA representing seven major taxonomic groups of protists. We also produced and analysed three amplicon‐based 18S rRNA libraries prepared from sediment samples. These revealed a more diverse set of taxa, 169 different OTUs encompassing up to eleven higher order groups of eukaryotes, according to detailed classification using homology searching and phylogenetic methods. The 10 most abundant OTUs accounted for > 90% of the total of reads, vs. large numbers of rare OTUs (< 1% abundance). Despite the anoxic and hydrocarbon‐enriched nature of the environment, the tailings ponds harbour complex communities of microbial eukaryotes indicating that these organisms should be taken into account when studying the microbiology of the oil sands.     

Characterization of a Gene Coding for the Complement System Component FB from Loxosceles laeta Spider Venom Glands

The human complement system is composed of more than 30 proteins and many of these have conserved domains that allow tracing the phylogenetic evolution. The complement system seems to be initiated with the appearance of C3 and factor B (FB), the only components found in some protostomes and cnidarians, suggesting that the alternative pathway is the most ancient. Here, we present the characterization of an arachnid homologue of the human complement component FB from the spider Loxosceles laeta. This homologue, named Lox-FB, was identified from a total RNA L. laeta spider venom gland library and was amplified using RACE-PCR techniques and specific primers. Analysis of the deduced amino acid sequence and the domain structure showed significant similarity to the vertebrate and invertebrate FB/C2 family proteins. Lox-FB has a classical domain organization composed of a control complement protein domain (CCP), a von Willebrand Factor domain (vWFA), and a serine protease domain (SP). The amino acids involved in Mg²⁺ metal ion dependent adhesion site (MIDAS) found in the vWFA domain in the vertebrate C2/FB proteins are well conserved; however, the classic catalytic triad present in the serine protease domain is not conserved in Lox-FB. Similarity and phylogenetic analyses indicated that Lox-FB shares a major identity (43%) and has a close evolutionary relationship with the third isoform of FB-like protein (FB-3) from the jumping spider Hasarius adansoni belonging to the Family Salcitidae.     

Investigating Sources of Heterogeneity in Randomized Controlled Trials of the Effects of Pharmacist Interventions on Glycemic Control in Type 2 Diabetic Patients: A Systematic Review and Meta-Analysis

Objective

To assess the effect of pharmacist interventions on glycemic control in type 2 diabetic patients and to examine factors that could explain the variation across studies.

Methods

A comprehensive literature search was performed in PubMed, Scopus, and LILACS databases for randomized controlled trials (RCTs) published up to July 2015. The search strategy included the use of MeSH terms or text words related to pharmacist interventions, type 2 diabetes, and randomized controlled trials. RCTs published in English, Portuguese, or Spanish that evaluated the effect of pharmacist intervention on glycemic control in type 2 diabetic outpatients were included. Two independent authors executed study selection, data extraction, and risk of bias assessment. Mean differences in glycosylated hemoglobin (HbA1c) were estimated using random-effect models, and heterogeneity was evaluated by subgroup and meta-regression analyses.

Results

The literature search yielded 963 records of potential interest, of which 30 were included in the systematic review and 22 in the meta-analysis. Most of these RCTs were conducted in the United States in patients in outpatient clinics using face-to-face contact only. All RCTs performed patient education, and most executed the medication review. The appraised sample showed uncertain or high risk of bias in most of the items evaluated, resulting in low-quality studies. In comparison with usual care, pharmacist interventions were associated with significant reductions in HbA1c levels (-8.5% [95% CI: -1.06, -0.65]; P < 0.0001; I² = 67.3%). Subgroup analysis indicated differences of heterogeneity by country, baseline HbA1c levels, setting, intervention frequency, and random allocation. Age and HbA1c levels partly explained the variability across studies by meta-regression.

Conclusions

Our findings confirmed that pharmacist interventions improve glycemic control in patients with type 2 diabetes compared with usual care and suggest that younger patients or with higher baseline HbA1c levels may be the main beneficiaries of pharmacist care.

Protocol PROSPERO Registration Number

CRD42014007457     

Mesoamerican Origin and Pre- and Post-Columbian Expansions of the Ranges of Acanthoscelides obtectus Say,a Cosmopolitan Insect Pest of the Common Bean

An unprecedented global transfer of agricultural resources followed the discovery of the New World; one consequence of this process was that staple food plants of Neotropical origin, such as the common bean (Phaseolus vulgaris), soon expanded their ranges overseas. Yet many pests and diseases were also transported. Acanthoscelides obtectus is a cosmopolitan seed predator associated with P. vulgaris. Codispersal within the host seed seems to be an important determinant of the ability of A. obtectus to expand its range over long distances. We examined the phylogeographic structure of A. obtectus by (a) sampling three mitochondrial gene sequences (12s rRNA, 16s rRNA, and the gene that encodes cytochrome c oxidase subunit I (COI)) throughout most of the species’ range and (b) exploring its late evolutionary history. Our findings indicate a Mesoamerican origin for the current genealogical lineages of A. obtectus. Each of the two major centers of genetic diversity of P. vulgaris (the Andes and Mesoamerica) contains a highly differentiated lineage of the bean beetle. Brazil has two additional, closely related lineages, both of which predate the Andean lineage and have the Mesoamerican lineage as their ancestor. The cosmopolitan distribution of A. obtectus has resulted from recent expansions of the two Brazilian lineages. We present additional evidence for both pre-Columbian and post-Columbian range expansions as likely events that shaped the current distribution of A. obtectus worldwide.