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      Evolution of cnidariantrans‐defensins: Sequence, structure and exploration of chemical space

      1 , 2 , 3 , 4 , 5 , 6 , 2 , 7 , 8 , 9 , 10 , 1
      Proteins: Structure, Function, and Bioinformatics
      Wiley

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          Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals

          Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts. Our data represent the most comprehensive dinoflagellate EST data set to date. This study provides a comprehensive resource to further analyze the genetic makeup, metabolic capacities, and gene repertoire of Symbiodinium and dinoflagellates. Overall, our findings indicate that Symbiodinium possesses some unique characteristics, in particular the transcriptional regulation in Symbiodinium may differ from the currently known mechanisms of eukaryotic gene regulation.
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            TOP-IDP-Scale: A New Amino Acid Scale Measuring Propensity for Intrinsic Disorder

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              Convergent evolution of defensin sequence, structure and function.

              Defensins are a well-characterised group of small, disulphide-rich, cationic peptides that are produced by essentially all eukaryotes and are highly diverse in their sequences and structures. Most display broad range antimicrobial activity at low micromolar concentrations, whereas others have other diverse roles, including cell signalling (e.g. immune cell recruitment, self/non-self-recognition), ion channel perturbation, toxic functions, and enzyme inhibition. The defensins consist of two superfamilies, each derived from an independent evolutionary origin, which have subsequently undergone extensive divergent evolution in their sequence, structure and function. Referred to as the cis- and trans-defensin superfamilies, they are classified based on their secondary structure orientation, cysteine motifs and disulphide bond connectivities, tertiary structure similarities and precursor gene sequence. The utility of displaying loops on a stable, compact, disulphide-rich core has been exploited by evolution on multiple occasions. The defensin superfamilies represent a case where the ensuing convergent evolution of sequence, structure and function has been particularly extreme. Here, we discuss the extent, causes and significance of these convergent features, drawing examples from across the eukaryotes.
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                Author and article information

                Journal
                Proteins: Structure, Function, and Bioinformatics
                Proteins
                Wiley
                0887-3585
                1097-0134
                June 2019
                July 2019
                March 18 2019
                July 2019
                : 87
                : 7
                : 551-560
                Affiliations
                [1 ]Medicinal ChemistryMonash Institute of Pharmaceutical Sciences, Monash University Melbourne Victoria Australia
                [2 ]Bioinformatics DivisionWalter & Eliza Hall Institute of Medical Research Parkville Victoria Australia
                [3 ]Marine Invertebrates, Museum Victoria Melbourne Victoria Australia
                [4 ]Biodiversity and Geosciences, Queensland Museum South Brisbane Queensland Australia
                [5 ]Department of Biochemistry and GeneticsLa Trobe Institute for Molecular Science, La Trobe University Melbourne Victoria Australia
                [6 ]Department of AnimalPlant, and Soil Sciences, AgriBio, La Trobe University Melbourne Victoria Australia
                [7 ]Peter MacCallum Cancer Centre Melbourne Victoria Australia
                [8 ]Department of Medical BiologyUniversity of Melbourne Melbourne Victoria Australia
                [9 ]Sir Peter MacCallum Department of OncologyUniversity of Melbourne Melbourne Victoria Australia
                [10 ]Department of Mathematics and StatisticsUniversity of Melbourne Melbourne Victoria Australia
                Article
                10.1002/prot.25679
                30811678
                94543624-37d2-4fae-b215-1fad3f8be541
                © 2019

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                http://doi.wiley.com/10.1002/tdm_license_1.1

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