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      Ancestral function of the phytochelatin synthase C-terminal domain in inhibition of heavy metal-mediated enzyme overactivation

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          Abstract

          The characterization of Marchantia polymorpha phytochelatin synthase provides novel insights into the evolutionary function of the enzyme’s elusive C-terminus as a regulatory domain inhibiting enzyme overactivation by metal ions.

          Abstract

          Phytochelatin synthases (PCSs) play essential roles in detoxification of a broad range of heavy metals in plants and other organisms. Until now, however, no PCS gene from liverworts, the earliest branch of land plants and possibly the first one to acquire a PCS with a C-terminal domain, has been characterized. In this study, we isolated and functionally characterized the first PCS gene from a liverwort, Marchantia polymorpha ( MpPCS). MpPCS is constitutively expressed in all organs examined, with stronger expression in thallus midrib. The gene expression is repressed by Cd 2+ and Zn 2+. The ability of MpPCS to increase heavy metal resistance in yeast and to complement cad1-3 (the null mutant of the Arabidopsis ortholog AtPCS1) proves its function as the only PCS from M. polymorpha. Site-directed mutagenesis of the most conserved cysteines of the C-terminus of the enzyme further uncovered that two twin-cysteine motifs repress, to different extents, enzyme activation by heavy metal exposure. These results highlight an ancestral function of the PCS elusive C-terminus as a regulatory domain inhibiting enzyme overactivation by essential and non-essential heavy metals. The latter finding may be relevant for obtaining crops with decreased root to shoot mobility of cadmium, thus preventing its accumulation in the food chain.

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          New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

          PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the original publication (Guindon S., Gascuel O. 2003. A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704), PhyML has been widely used (>2500 citations in ISI Web of Science) because of its simplicity and a fair compromise between accuracy and speed. In the meantime, research around PhyML has continued, and this article describes the new algorithms and methods implemented in the program. First, we introduce a new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves. The parsimony criterion is used here to filter out the least promising topology modifications with respect to the likelihood function. The analysis of a large collection of real nucleotide and amino acid data sets of various sizes demonstrates the good performance of this method. Second, we describe a new test to assess the support of the data for internal branches of a phylogeny. This approach extends the recently proposed approximate likelihood-ratio test and relies on a nonparametric, Shimodaira-Hasegawa-like procedure. A detailed analysis of real alignments sheds light on the links between this new approach and the more classical nonparametric bootstrap method. Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from http://www.atgc-montpellier.fr/phyml/.
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            MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

            Abstract This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.
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              Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.

              Alignment quality may have as much impact on phylogenetic reconstruction as the phylogenetic methods used. Not only the alignment algorithm, but also the method used to deal with the most problematic alignment regions, may have a critical effect on the final tree. Although some authors remove such problematic regions, either manually or using automatic methods, in order to improve phylogenetic performance, others prefer to keep such regions to avoid losing any information. Our aim in the present work was to examine whether phylogenetic reconstruction improves after alignment cleaning or not. Using simulated protein alignments with gaps, we tested the relative performance in diverse phylogenetic analyses of the whole alignments versus the alignments with problematic regions removed with our previously developed Gblocks program. We also tested the performance of more or less stringent conditions in the selection of blocks. Alignments constructed with different alignment methods (ClustalW, Mafft, and Probcons) were used to estimate phylogenetic trees by maximum likelihood, neighbor joining, and parsimony. We show that, in most alignment conditions, and for alignments that are not too short, removal of blocks leads to better trees. That is, despite losing some information, there is an increase in the actual phylogenetic signal. Overall, the best trees are obtained by maximum-likelihood reconstruction of alignments cleaned by Gblocks. In general, a relaxed selection of blocks is better for short alignment, whereas a stringent selection is more adequate for longer ones. Finally, we show that cleaned alignments produce better topologies although, paradoxically, with lower bootstrap. This indicates that divergent and problematic alignment regions may lead, when present, to apparently better supported although, in fact, more biased topologies.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                J Exp Bot
                J Exp Bot
                exbotj
                Journal of Experimental Botany
                Oxford University Press (UK )
                0022-0957
                1460-2431
                22 October 2020
                16 September 2020
                16 September 2020
                : 71
                : 20
                : 6655-6669
                Affiliations
                [1 ] Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach , San Michele all’Adige, Trento, Italy
                [2 ] Dipartimento di Biologia, Università di Pisa , Pisa, Italy
                [3 ] Dipartimento di Patologia Chirurgica, Medica, Molecolare e dell’Area Critica, Università di Pisa , Pisa, Italy
                [4 ] Hasselt University , Belgium
                Author notes
                Author information
                http://orcid.org/0000-0003-2074-1546
                http://orcid.org/0000-0003-1809-4394
                http://orcid.org/0000-0001-6542-3897
                http://orcid.org/0000-0003-0611-5549
                http://orcid.org/0000-0001-5018-087X
                Article
                eraa386
                10.1093/jxb/eraa386
                7586750
                32936292
                d5f748f3-adb8-4cfe-ac46-911c75b3667e
                © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Experimental Biology.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/),which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 10 April 2020
                : 11 August 2020
                : 17 August 2020
                : 16 September 2020
                Page count
                Pages: 15
                Funding
                Funded by: Ministero dell’Istruzione, dell’Università e della Ricerca, DOI 10.13039/501100003407;
                Award ID: 20158HTL58
                Categories
                Research Papers
                Plant—Environment Interactions
                AcademicSubjects/SCI01210

                Plant science & Botany
                cadmium,c-terminal domain,marchantia polymorpha,overactivation,phytochelatin,phytochelatin synthase,site-directed mutagenesis,twin-cysteine motif,zinc

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