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      An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion

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          Abstract

          Thermobia domestica belongs to an ancient group of insects and has a remarkable ability to digest crystalline cellulose without microbial assistance. By investigating the digestive proteome of Thermobia, we have identified over 20 members of an uncharacterized family of lytic polysaccharide monooxygenases (LPMOs). We show that this LPMO family spans across several clades of the Tree of Life, is of ancient origin, and was recruited by early arthropods with possible roles in remodeling endogenous chitin scaffolds during development and metamorphosis. Based on our in-depth characterization of Thermobia’s LPMOs, we propose that diversification of these enzymes toward cellulose digestion might have endowed ancestral insects with an effective biochemical apparatus for biomass degradation, allowing the early colonization of land during the Paleozoic Era. The vital role of LPMOs in modern agricultural pests and disease vectors offers new opportunities to help tackle global challenges in food security and the control of infectious diseases.

          Abstract

          LPMOs catalyze the oxidative breakdown of polysaccharides, thereby facilitating biomass degradation. By analyzing the digestive proteome of firebrats, the authors here identify a yet uncharacterized LPMO family and provide phylogenetic, structural and biochemical insights into its origin and functions.

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          Amino acid substitution matrices from protein blocks.

          Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.
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            EasySpin, a comprehensive software package for spectral simulation and analysis in EPR.

            EasySpin, a computational package for spectral simulation and analysis in EPR, is described. It is based on Matlab, a commercial technical computation software. EasySpin provides extensive EPR-related functionality, ranging from elementary spin physics to data analysis. In addition, it provides routines for the simulation of liquid- and solid-state EPR and ENDOR spectra. These simulation functions are built on a series of novel algorithms that enhance scope, speed and accuracy of spectral simulations. Spin systems with an arbitrary number of electron and nuclear spins are supported. The structure of the toolbox as well as the theoretical background underlying its simulation functionality are presented, and some illustrative examples are given.
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              Using FlyAtlas to identify better Drosophila melanogaster models of human disease.

              FlyAtlas, a new online resource, provides the most comprehensive view yet of expression in multiple tissues of Drosophila melanogaster. Meta-analysis of the data shows that a significant fraction of the genome is expressed with great tissue specificity in the adult, demonstrating the need for the functional genomic community to embrace a wide range of functional phenotypes. Well-known developmental genes are often reused in surprising tissues in the adult, suggesting new functions. The homologs of many human genetic disease loci show selective expression in the Drosophila tissues analogous to the affected human tissues, providing a useful filter for potential candidate genes. Additionally, the contributions of each tissue to the whole-fly array signal can be calculated, demonstrating the limitations of whole-organism approaches to functional genomics and allowing modeling of a simple tissue fractionation procedure that should improve detection of weak or tissue-specific signals.
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                Author and article information

                Contributors
                simon.mcqueenmason@york.ac.uk
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                22 February 2018
                22 February 2018
                2018
                : 9
                : 756
                Affiliations
                [1 ]ISNI 0000 0004 1936 9668, GRID grid.5685.e, Centre for Novel Agricultural Products, Department of Biology, , University of York, ; York, YO10 5DD UK
                [2 ]ISNI 0000 0004 1936 8403, GRID grid.9909.9, School of Molecular and Cellular Biology, Faculty of Biological Sciences, , University of Leeds, ; Leeds, LS2 9JT UK
                [3 ]ISNI 0000 0004 1936 8403, GRID grid.9909.9, Astbury Centre for Structural Molecular Biology, , University of Leeds, ; Leeds, LS2 9JT UK
                [4 ]ISNI 0000 0004 1936 9668, GRID grid.5685.e, Department of Chemistry, , University of York, ; York, YO10 5DD UK
                [5 ]ISNI 0000 0001 2176 4817, GRID grid.5399.6, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, , Université Aix-Marseille, ; 163 Avenue de Luminy, 13288 Marseille, France
                [6 ]INRA, USC 1408 AFMB, 13288 Marseille, France
                [7 ]ISNI 0000 0001 0619 1117, GRID grid.412125.1, Department of Biological Sciences, , King Abdulaziz University, ; Jeddah, 21589 Saudi Arabia
                [8 ]ISNI 0000000121885934, GRID grid.5335.0, Department of Biochemistry, , University of Cambridge, ; Cambridge, CB2 1QW UK
                [9 ]ISNI 0000 0004 1936 9668, GRID grid.5685.e, Department of Biology, , University of York, ; York, YO10 5DD UK
                [10 ]ISNI 0000 0004 1936 9668, GRID grid.5685.e, Bioscience Technology Facility, Department of Biology, , University of York, ; York, YO10 5DD UK
                Author information
                http://orcid.org/0000-0002-8226-1380
                http://orcid.org/0000-0002-1667-0856
                http://orcid.org/0000-0001-9270-6286
                http://orcid.org/0000-0003-2673-9578
                http://orcid.org/0000-0002-7343-776X
                http://orcid.org/0000-0002-1152-1480
                Article
                3142
                10.1038/s41467-018-03142-x
                5823890
                29472725
                1fd57283-e728-4af2-9d13-4d497459b684
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 11 July 2017
                : 22 January 2018
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