CONAN: a web application to detect specificity determinants and functional sites by amino acids co-variation network analysis

2020 ◽  
Author(s):  
N J Fonseca ◽  
M Q L Afonso ◽  
L Carrijo ◽  
L Bleicher
Keyword(s):  
Amino Acids ◽  
Network Analysis ◽  
Web Application ◽  
Source Code ◽  
Functional Sites ◽  
Networks Analysis ◽  
And Function ◽  
Go Terms ◽  
Specificity Determinants

Abstract Summary CONAN is a web application developed to detect specificity determinants and function-related sites by amino acids co-variation networks analysis, emphasizing local coevolutionary constraints. The software allows the characterization of structurally and functionally relevant groups of residues and their relationship with subsets of sequences by automatic cross-referencing with GO terms, UniprotKb annotations and INTERPRO. Availability and implementation CONAN is free and open-source, being distributed in the terms of the GPLV3 license. The software is available as a web application and python script versions and can be accessed at http://bioinfo.icb.ufmg.br/conan. We also provide running instructions, the source code and a user guide.

scholarly journals ISOLATION AND CHARACTERIZATION OF AMBER SUPPRESSORS IN YEAST

Genetics ◽  
1976 ◽  
Vol 82 (2) ◽  
pp. 251-272
Author(s):  
Susan W Liebman ◽  
Fred Sherman ◽  
John W Stewart
Keyword(s):  
Amino Acids ◽  
Cytochrome C ◽  
Yeast Strain ◽  
Normal Amount ◽  
Amber Mutation ◽  
Genetic Analyses ◽  
Isolation And Characterization ◽  
And Function ◽  
Nonsense Suppressors

ABSTRACT Nonsense suppressors were obtained in a haploid yeast strain containing eight nutritional mutations, that are assumed to be amber or ochre, and the cyc1-179 amber mutation that has a UAG codon corresponding to position 9 in iso-1-cytochrome c. Previous studies established that the biosynthesis and function of iso-1-cytochrome c is compatible with replacements at position 9 of amino acids having widely different structures (Stewart and Sherman 1972). UV-induced revertants, selected on media requiring the reversion of one or two of the amber nutritional markers, were presumed to contain a suppressor if there was the unselected reversion of at least one other marker. The 1088 suppressors that were isolated could be divided into 78 phenotypic classes. Only 43 suppressors of three classes caused the production of more than 50% of the normal amount of iso-1-cytochrome c in the cyc1-179 strain. Genetic analyses indicated that all of these highly efficient amber suppressors are allelic to one or another of the eight suppressors which cause the insertion of tyrosine at ochre (UAA) codons (Gilmore, Stewart and Sherman 1971). Furthermore, only tyrosine has been identified at position 9 in iso-1-cytochrome cin cyc1-179 strains suppressed with these efficient amber suppressors.

scholarly journals Prioritization of antimicrobial targets by CRISPR-based oligo recombineering

2021 ◽  
Author(s):  
HJ. Benns ◽  
M. Storch ◽  
J. Falco ◽  
FR. Fisher ◽  
E. Alves ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Function ◽  
Proof Of Concept ◽  
Fitness Effect ◽  
Diverse Range ◽  
Functional Sites ◽  
Wide Range ◽  
And Function ◽  
Intrinsic Reactivity ◽  
Subsequent Target

SummaryNucleophilic amino acids are important in covalent drug development yet underutilized as antimicrobial targets. Over recent years, several chemoproteomic technologies have been developed to mine chemically-accessible residues via their intrinsic reactivity toward electrophilic probes. However, these approaches cannot discern which reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based Oligo Recombineering (CORe) platform to systematically prioritize reactive amino acids according to their contribution to protein function. Our approach directly couples protein sequence and function with biological fitness. Here, we profile the reactivity of >1,000 cysteines on ~700 proteins in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. We competitively compared the fitness effect of 370 codon switches at 74 cysteines and identify functional sites in a diverse range of proteins. In our proof of concept, CORe performed >800 times faster than a standard genetic workflow. Reactive cysteines decorating the ribosome were found to be critical for parasite growth, with subsequent target-based screening validating the apicomplexan translation machinery as a target for covalent ligand development. CORe is system-agnostic, and supports expedient identification, functional prioritization, and rational targeting of reactive sites in a wide range of organisms and diseases.

scholarly journals Characterization of the role of glycine lipids inBacteroides thetaiotaomicron

2018 ◽  
Author(s):  
Alli Lynch ◽  
Seshu R. Tammireddy ◽  
Mary K. Doherty ◽  
Phillip D. Whitfield ◽  
David J. Clarke
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Deletion Mutant ◽  
Cellular Membrane ◽  
Liquid Chromatography Mass Spectrometry ◽  
Human Gut ◽  
Acyltransferase Activity ◽  
And Function

AbstractAcylated amino acids function as important components of the cellular membrane in some bacteria. Biosynthesis is initiated by the N-acylation of the amino acid and this is followed by subsequent O-acylation of the acylated molecule resulting in the production of the mature diacylated amino acid lipid. In this study we use both genetics and liquid chromatography-mass spectrometry (LC-MS) to characterize the biosynthesis and function of novel diacylated glycine lipid (GL) species inBacteroides thetaiotaomicron. We, and others, have previously reported the identification of a gene, namedglsBin this study, that encodes a N-acyltransferase activity responsible for the production of a monoacylated glycine called N-acyl-3-hydroxy-palmitoyl glycine (or commendamide). In all of theBacteroidalesgenomes so far sequenced theglsBgene is located immediately downstream from a gene, namedglsA, also predicted to encode a protein with acyltransferase activity. We use LC-MS to show that co-expression ofglsBandglsAresults in the production of GL inEscherichia coli. We constructed a deletion mutant of theglsBgene inB. thetaiotaomicronand we confirm thatglsBis required for the production of GL inB. thetaiotaomicron. Moreover, we show thatglsBis important for the ability ofB. thetaiotaomicronto adapt to stress and colonize the mammalian gut. Therefore, this report is the first to describe the genetic requirements for the biosynthesis of GL, a novel diacylated amino acids species that contributes to fitness in the human gut bacterium,B. thetaiotaomicron.

scholarly journals Discovery of lysine post-translational modifications through mass spectrometric detection

2012 ◽  
Vol 52 ◽  
pp. 147-163 ◽  
Author(s):  
Barry M. Zee ◽  
Benjamin A. Garcia
Keyword(s):  
Mass Spectrometry ◽  
Amino Acids ◽  
Mass Spectrometric ◽  
Mass Spectrometric Detection ◽  
Post Translational Modifications ◽  
Target Set ◽  
Modified Proteins ◽  
And Function

The complexity of an organism's proteome is in part due to the diversity of post-translational modifications present that can direct the location and function of a protein. To address the growing interest in characterizing these modifications, mass spectrometric-based proteomics has emerged as one of the most essential experimental platforms for their discovery. In searching for post-translational modifications within a target set of proteins to global surveys of particularly modified proteins within a given proteome, various experimental MS (mass spectrometry) and allied techniques have been developed. Out of 20 naturally encoded amino acids, lysine is essentially the most highly post-translationally modified residue. This chapter provides a succinct overview of such methods for the characterization of protein lysine modifications as broadly classified, such as methylation and ubiquitination.

Functional characterization of human brown adipose tissue metabolism

2020 ◽  
Vol 477 (7) ◽  
pp. 1261-1286 ◽  
Author(s):  
Marie Anne Richard ◽  
Hannah Pallubinsky ◽  
Denis P. Blondin
Keyword(s):  
Adipose Tissue ◽  
Brown Adipose Tissue ◽  
Functional Characterization ◽  
Human Infants ◽  
Positron Emission ◽  
Brown Adipose ◽  
Treatment Of Obesity ◽  
And Function

Brown adipose tissue (BAT) has long been described according to its histological features as a multilocular, lipid-containing tissue, light brown in color, that is also responsive to the cold and found especially in hibernating mammals and human infants. Its presence in both hibernators and human infants, combined with its function as a heat-generating organ, raised many questions about its role in humans. Early characterizations of the tissue in humans focused on its progressive atrophy with age and its apparent importance for cold-exposed workers. However, the use of positron emission tomography (PET) with the glucose tracer [18F]fluorodeoxyglucose ([18F]FDG) made it possible to begin characterizing the possible function of BAT in adult humans, and whether it could play a role in the prevention or treatment of obesity and type 2 diabetes (T2D). This review focuses on the in vivo functional characterization of human BAT, the methodological approaches applied to examine these features and addresses critical gaps that remain in moving the field forward. Specifically, we describe the anatomical and biomolecular features of human BAT, the modalities and applications of non-invasive tools such as PET and magnetic resonance imaging coupled with spectroscopy (MRI/MRS) to study BAT morphology and function in vivo, and finally describe the functional characteristics of human BAT that have only been possible through the development and application of such tools.

Parasite defense mechanisms in bees: behavior, immunity, antimicrobials, and symbionts

2019 ◽  
Vol 4 (1) ◽  
pp. 59-76 ◽  
Author(s):  
Alison E. Fowler ◽  
Rebecca E. Irwin ◽  
Lynn S. Adler
Keyword(s):  
Defense Mechanisms ◽  
Poor Quality ◽  
Future Research ◽  
Immune Priming ◽  
Social Bees ◽  
Bee Health ◽  
Landscape Scales ◽  
And Function ◽  
Solitary Species

Parasites are linked to the decline of some bee populations; thus, understanding defense mechanisms has important implications for bee health. Recent advances have improved our understanding of factors mediating bee health ranging from molecular to landscape scales, but often as disparate literatures. Here, we bring together these fields and summarize our current understanding of bee defense mechanisms including immunity, immunization, and transgenerational immune priming in social and solitary species. Additionally, the characterization of microbial diversity and function in some bee taxa has shed light on the importance of microbes for bee health, but we lack information that links microbial communities to parasite infection in most bee species. Studies are beginning to identify how bee defense mechanisms are affected by stressors such as poor-quality diets and pesticides, but further research on this topic is needed. We discuss how integrating research on host traits, microbial partners, and nutrition, as well as improving our knowledge base on wild and semi-social bees, will help inform future research, conservation efforts, and management.

Gaunilo Parodies Anselm

2014 ◽  
Vol 17 (1) ◽  
pp. 45-71
Author(s):  
Geo Siegwart
Keyword(s):  
Detailed Comparison ◽  
The Third ◽  
Common Structure ◽  
Logical Reconstruction ◽  
Points Of View ◽  
And Function

The main objective is an interpretation of the island parody, in particular a logical reconstruction of the parodying argument that stays close to the text. The parodied reasoning is identified as the proof in the second chapter of the Proslogion, more specifically, this proof as it is represented by Gaunilo in the first chapter of his Liber pro insipiente. The second task is a detailed comparison between parodied and parodying argument as well as an account of their common structure. The third objective is a tentative characterization of the nature and function of parodies of arguments. It seems that parodying does not add new pertinent points of view to the usual criticism of an argument.

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