Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation

Gammaproteobacteria from the family Endozoicomonadaceae have emerged as widespread associates of dense marine animal communities. Their abundance in coral reefs involves symbiotic relationships and possibly host nutrition. We explored functions encoded in the genome of an uncultured Endozoicomonadaceae ‘Candidatus Acestibacter aggregatus’ that lives inside gill cells of large Acesta excavata clams in deep-water coral reefs off mid-Norway. The dominance and deep branching lineage of this symbiont was confirmed using 16S rRNA gene sequencing and phylogenomic analysis from shotgun sequencing data. The 4.5 Mb genome binned in this study has a low GC content of 35% and is enriched in transposon and chaperone gene annotations indicating ongoing adaptation. Genes encoding functions potentially involved with the symbiosis include ankyrins, repeat in toxins, secretion and nutritional systems. Complete pathways were identified for the synthesis of eleven amino acids and six B-vitamins. A minimal chitinolytic machinery was indicated from a glycosyl hydrolase GH18 and a lytic polysaccharide monooxygenase LPMO10. Expression of the latter was confirmed using proteomics. Signal peptides for secretion were identified for six polysaccharide degrading enzymes, ten proteases and three lipases. Our results suggest a nutritional symbiosis fuelled by enzymatic products from extracellular degradation processes.publishedVersio

Effects of Yeast Species and Processing on Intestinal Health and Transcriptomic Profiles of Atlantic Salmon (Salmo salar) Fed Soybean Meal-Based Diets in Seawater

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The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes

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New tools to enhance the detection of post-translational modifications: Development and application of a mass spectrometry-based proteomic software and of specific antibodies detecting propionylated lysines

Mass spectrometry based proteomics has evolved into a powerful tool in characterising proteins and their respective function in the cell. A proteins cellular localisation, concentration and activity is regulated by several cellular processes including the regulation by protein post-translational modifications (PTMs). PTMs can be viewed as cellular switches that enable or disable specific functions for a protein and they represent a huge potential in understanding protein pathways in the context of protein and protein complex regulation. To date there are over 300 known PTMs which regulate protein structure and function, and their characterisation, as well as the discovery of new PTMs, have immense implications for cell biological and clinical research. However, the detection of PTMs using mass spectrometry is not straightforward. An automatic setup of a mass spectrometer traditionally selects the 2-5 most intense peptides for fragmentation and identification, leaving the rest, less abundant peptides, to pass. Since the majority of post-translationally modified peptides are low abundant and therefore probably not selected for fragmentation and identification, this is a sub-optimal procedure for detecting PTMs. Based on this we wanted to develop bioinformatics software able to increase fragmentation events and identifications of post-translationally modified peptides, using a targeted mass spectrometry approach. This resulted in the development of POSTMan (POST-translational Modification analysis). The underlying principle of this software is to compare two LC-MS runs and search for post-translationally modified peptides as pairs with their unmodified counterparts, either between the two individual LC-MS runs or within one run. POSTMan was designed to be as generic as possible, meaning that in principle any PTM irrespective of mass could be identified with this software. We applied the software to an acetylated model protein of Cytochrome c to verify its capability in identifying the acetylated peptides, as well as the tumour suppressor protein p53 to assess the PTM patterns of acetylation and propionylation. Propionylation was recently discovered as a novel in vivo PTM both on histones and non-histone proteins. The biological role of propionylation however, is currently unknown. Propionylation as an in vivo PTM, as well as its possible involvement in p53 regulation, was addressed using POSTMan and immunoblotting. Novel pan-specific anti-propionyllysine antibodies were raised, characterised and utilized in the study of p53 propionylation. These antibodies showed specificity for propionyllysine with no cross reaction to acetyllysine, and will be important reagents that can be used for global proteomic investigation of propionylation as a regulatory PTM

Outer membrane vesicles from Fibrobacter succinogenes S85 contain an array of Carbohydrate-Active Enzymes with versatile polysaccharide-degrading capacity

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Quantitative comparison of the biomass-degrading enzyme repertoires of five filamentous fungi

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Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits

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Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes

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Gluten-specific antibodies of celiac disease gut plasma cells recognize long proteolytic fragments that typically harbor T-cell epitopes

This study aimed to identify proteolytic fragments of gluten proteins recognized by recombinant IgG1 monoclonal antibodies generated from single IgA plasma cells of celiac disease lesions. Peptides bound by monoclonal antibodies in complex gut-enzyme digests of gluten treated with the deamidating enzyme transglutaminase 2, were identified by mass spectrometry after antibody pull-down with protein G beads. The antibody bound peptides were long deamidated peptide fragments that contained the substrate recognition sequence of transglutaminase 2. Characteristically, the fragments contained epitopes with the sequence QPEQPFP and variants thereof in multiple copies, and they typically also harbored many different gluten T-cell epitopes. In the pull-down setting where antibodies were immobilized on a solid phase, peptide fragments with multivalent display of epitopes were targeted. This scenario resembles the situation of the B-cell receptor on the surface of B cells. Conceivably, B cells of celiac disease patients select gluten epitopes that are repeated multiple times in long peptide fragments generated by gut digestive enzymes. As the fragments also contain many different T-cell epitopes, this will lead to generation of strong antibody responses by effective presentation of several distinct T-cell epitopes and establishment of T-cell help to B cells

Quantitative comparison of the biomass-degrading enzyme repertoires of five filamentous fungi

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