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      RNA-dependent synthesis of ergosteryl-3β- O-glycine in Ascomycota expands the diversity of steryl-amino acids

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      1 , § , 1 , , § , 1 , , 2 , , 2 , 2 , 3 , 3 , 4 , 1 , 1 , 1 , 1 , , 1 ,
      The Journal of Biological Chemistry
      American Society for Biochemistry and Molecular Biology
      aminoacyl-tRNA, ergosterol, ergosteryl-3β-O-glycine, ergosteryl-3β-O-L-aspartate, fungi, DUF2156, sterol aminoacylation, aa-tRNA, aminoacyl-transfer RNA, aaGL, aminoacylated glycerolipid, aaGLS, aminoacyl-glycerolipid synthase, aaRS, aminoacyl-tRNA synthetase, Afm, Aspergillus fumigatus, Aor, Aspergillus oryzae, Asp, L-aspartate, AspRS, aspartyl-tRNA synthetase, ATT, aminoacyl-tRNA transferase, Bba, Beauveria bassiana, Cho, cholesterol, DUF2156, Domain of Unknown Function 2156, ErdS, ergosteryl-3β-O-L-aspartate synthase, Erg, ergosterol, Erg-Asp, ergosteryl-3β-O-L-aspartate, Erg-Gly, ergosteryl-3β-O-glycine, ErgS, ergosteryl-3β-O-glycine synthase, FC, flash column chromatography, fDUF, freestanding DUF2156, GL, glycerolipid, Gly∼AMP, glycyl-adenylate, GlyRS, glycyl-tRNA synthetase, GNAT, Gcn5-N-acetyltransferase domain, HPTLC, high-performance TLC, MBP, maltose-binding protein, PE, phosphatidylethanolamine, PG, phosphatidylglycerol, Sce, Saccharomyces cerevisiae, Yli, Yarrowia lipolytica, YPD, yeast extract peptone dextrose

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          Abstract

          A wide range of bacteria possess virulence factors such as aminoacyl-tRNA transferases (ATTs) that are capable of rerouting aminoacyl-transfer RNAs away from protein synthesis to conjugate amino acids onto glycerolipids. We recently showed that, although these pathways were thought to be restricted to bacteria, higher fungi also possess ergosteryl-3β- O-L-aspartate synthases (ErdSs), which transfer the L-Asp moiety of aspartyl-tRNA Asp onto the 3β-OH group of ergosterol (Erg), yielding ergosteryl-3β- O-L-aspartate (Erg-Asp). Here, we report the discovery, in fungi, of a second type of fungal sterol-specific ATTs, namely, ergosteryl-3β- O-glycine (Erg-Gly) synthase (ErgS). ErgS consists of a freestanding DUF2156 domain encoded by a gene distinct from and paralogous to that of ErdS. We show that the enzyme only uses Gly-tRNA Gly produced by an independent glycyl-tRNA synthetase (GlyRS) to transfer glycine onto the 3β-OH of Erg, producing Erg-Gly. Phylogenomics analysis also show that the Erg-Gly synthesis pathway exists only in Ascomycota, including species of biotechnological interest, and more importantly, in human pathogens, such as Aspergillus fumigatus. The discovery of a second type of Erg-aa not only expands the repertoire of this particular class of fungal lipids but suggests that Erg-aa synthases might constitute a genuine subfamily of lipid-modifying ATTs.

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          IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

          Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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            Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

            S Altschul (1997)
            The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.
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              The Phyre2 web portal for protein modeling, prediction and analysis.

              Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission.
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                Author and article information

                Contributors
                Journal
                J Biol Chem
                J Biol Chem
                The Journal of Biological Chemistry
                American Society for Biochemistry and Molecular Biology
                0021-9258
                1083-351X
                04 February 2022
                March 2022
                04 February 2022
                : 298
                : 3
                : 101657
                Affiliations
                [1 ]CNRS, Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, Université de Strasbourg, Strasbourg Cedex, France
                [2 ]School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
                [3 ]Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
                [4 ]Plant Isoprenoid Biology (PIB) Team, Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
                Author notes
                []For correspondence: Frédéric Fischer; Nassira Mahmoudi; Hubert D. Becker nmahmoudikaidi@ 123456unistra.fr h.becker@ 123456unistra.fr frfischer@ 123456unistra.fr
                [§]

                Share first co-authorship.

                [‡]

                These authors contributed equally to this work.

                Article
                S0021-9258(22)00097-7 101657
                10.1016/j.jbc.2022.101657
                8913301
                35131263
                dddf398c-a043-4e69-80a2-2bf18b2aef2f

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

                History
                : 27 July 2021
                : 13 January 2022
                Categories
                Research Article
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                Biochemistry
                aminoacyl-trna,ergosterol,ergosteryl-3β-o-glycine,ergosteryl-3β-o-l-aspartate,fungi,duf2156,sterol aminoacylation,aa-trna, aminoacyl-transfer rna,aagl, aminoacylated glycerolipid,aagls, aminoacyl-glycerolipid synthase,aars, aminoacyl-trna synthetase,afm, aspergillus fumigatus,aor, aspergillus oryzae,asp, l-aspartate,asprs, aspartyl-trna synthetase,att, aminoacyl-trna transferase,bba, beauveria bassiana,cho, cholesterol,duf2156, domain of unknown function 2156,erds, ergosteryl-3β-o-l-aspartate synthase,erg, ergosterol,erg-asp, ergosteryl-3β-o-l-aspartate,erg-gly, ergosteryl-3β-o-glycine,ergs, ergosteryl-3β-o-glycine synthase,fc, flash column chromatography,fduf, freestanding duf2156,gl, glycerolipid,gly∼amp, glycyl-adenylate,glyrs, glycyl-trna synthetase,gnat, gcn5-n-acetyltransferase domain,hptlc, high-performance tlc,mbp, maltose-binding protein,pe, phosphatidylethanolamine,pg, phosphatidylglycerol,sce, saccharomyces cerevisiae,yli, yarrowia lipolytica,ypd, yeast extract peptone dextrose

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