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      Identification and characterization of andalusicin: N-terminally dimethylated class III lantibiotic from Bacillus thuringiensis sv. andalousiensis

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          Summary

          Lanthipeptides, ribosomally synthesized and post-translationally modified peptides (RiPPs), can be divided into five classes based on their structures and biosynthetic pathways. Class I and II lanthipeptides have been well characterized, whereas less is known about members of the other three classes. Here, we describe a new family of class III lanthipeptides from Firmicutes. Members of the family are distinguished by the presence of a single carboxy-terminal labionin. We identified and characterized andalusicin, a representative of this family. Andalusicin bears two methyl groups at the α-amino terminus, a post-translational modification that has not previously been identified in class III lanthipeptides. Mature andalusicin A shows bioactivity against various Gram-positive bacteria, an activity that is highly dependent on the α-N dimethylation.

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          Highlights

          • Type III lanthipeptide andalusicin A inhibits the growth of Gram-positive bacteria

          • Andalusicin A has an unusual pastor's crook structure

          • Genes encoding methyltransferases are frequently found in andalusicin-like BGCs

          • N-terminal methylation is necessary for andalusicin A biological activity

          Abstract

          Chemistry; Biosynthesis; Biochemistry; Medical biochemistry

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          Most cited references55

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          Cytoscape: a software environment for integrated models of biomolecular interaction networks.

          Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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            NIH Image to ImageJ: 25 years of image analysis

            For the past twenty five years the NIH family of imaging software, NIH Image and ImageJ have been pioneers as open tools for scientific image analysis. We discuss the origins, challenges and solutions of these two programs, and how their history can serve to advise and inform other software projects.
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              RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

              Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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                Author and article information

                Contributors
                Journal
                iScience
                iScience
                iScience
                Elsevier
                2589-0042
                29 April 2021
                21 May 2021
                29 April 2021
                : 24
                : 5
                : 102480
                Affiliations
                [1 ]Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
                [2 ]Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
                [3 ]Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
                [4 ]Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
                [5 ]A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia
                [6 ]Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL 61801 USA
                [7 ]Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse 31077, France
                [8 ]Waksman Institute for Microbiology, Piscataway, NJ 08854-8020, USA
                Author notes
                []Corresponding author severik@ 123456waksman.rutgers.edu
                [∗∗ ]Corresponding author svetlana.dubiley@ 123456gmail.com
                [9]

                Lead contact

                Article
                S2589-0042(21)00448-X 102480
                10.1016/j.isci.2021.102480
                8169954
                34113822
                44055811-ede1-4a29-a87c-55fb57182aaa
                © 2021 The Author(s)

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

                History
                : 24 December 2020
                : 21 March 2021
                : 23 April 2021
                Categories
                Article

                chemistry,biosynthesis,biochemistry,medical biochemistry

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