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      Structure of dual BON-domain protein DolP identifies phospholipid binding as a new mechanism for protein localisation

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      eLife
      eLife Sciences Publications, Ltd
      BON domain, Escherichia coli, YraP, phospholipids, cell division, E. coli

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          Abstract

          The Gram-negative outer-membrane envelops the bacterium and functions as a permeability barrier against antibiotics, detergents, and environmental stresses. Some virulence factors serve to maintain the integrity of the outer membrane, including DolP (formerly YraP) a protein of unresolved structure and function. Here, we reveal DolP is a lipoprotein functionally conserved amongst Gram-negative bacteria and that loss of DolP increases membrane fluidity. We present the NMR solution structure for Escherichia coli DolP, which is composed of two BON domains that form an interconnected opposing pair. The C-terminal BON domain binds anionic phospholipids through an extensive membrane:protein interface. This interaction is essential for DolP function and is required for sub-cellular localisation of the protein to the cell division site, providing evidence of subcellular localisation of these phospholipids within the outer membrane. The structure of DolP provides a new target for developing therapies that disrupt the integrity of the bacterial cell envelope.

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          One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.

          We have developed a simple and highly efficient method to disrupt chromosomal genes in Escherichia coli in which PCR primers provide the homology to the targeted gene(s). In this procedure, recombination requires the phage lambda Red recombinase, which is synthesized under the control of an inducible promoter on an easily curable, low copy number plasmid. To demonstrate the utility of this approach, we generated PCR products by using primers with 36- to 50-nt extensions that are homologous to regions adjacent to the gene to be inactivated and template plasmids carrying antibiotic resistance genes that are flanked by FRT (FLP recognition target) sites. By using the respective PCR products, we made 13 different disruptions of chromosomal genes. Mutants of the arcB, cyaA, lacZYA, ompR-envZ, phnR, pstB, pstCA, pstS, pstSCAB-phoU, recA, and torSTRCAD genes or operons were isolated as antibiotic-resistant colonies after the introduction into bacteria carrying a Red expression plasmid of synthetic (PCR-generated) DNA. The resistance genes were then eliminated by using a helper plasmid encoding the FLP recombinase which is also easily curable. This procedure should be widely useful, especially in genome analysis of E. coli and other bacteria because the procedure can be done in wild-type cells.
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            A RAPID METHOD OF TOTAL LIPID EXTRACTION AND PURIFICATION

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              Universal sample preparation method for proteome analysis.

              We describe a method, filter-aided sample preparation (FASP), which combines the advantages of in-gel and in-solution digestion for mass spectrometry-based proteomics. We completely solubilized the proteome in sodium dodecyl sulfate, which we then exchanged by urea on a standard filtration device. Peptides eluted after digestion on the filter were pure, allowing single-run analyses of organelles and an unprecedented depth of proteome coverage.
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                Author and article information

                Contributors
                Role: Reviewing Editor
                Role: Senior Editor
                Journal
                eLife
                Elife
                eLife
                eLife
                eLife Sciences Publications, Ltd
                2050-084X
                14 December 2020
                2020
                : 9
                : e62614
                Affiliations
                [1 ]Institute of Microbiology and Infection, University of Birmingham EdgbastonUnited Kingdom
                [2 ]School of Biosciences, University of Birmingham EdgbastonUnited Kingdom
                [3 ]Institute for Cancer and Genomic Sciences, University of Birmingham EdgbastonUnited Kingdom
                [4 ]Infection & Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University ClaytonAustralia
                [5 ]Department of Chemistry, National University of Singapore SingaporeSingapore
                [6 ]Institute for Molecular Bioscience, University of Queensland St. LuciaAustralia
                [7 ]School of Life Sciences, The University of Warwick CoventryUnited Kingdom
                [8 ]Institute of Inflammation and Immunotherapy, University of Birmingham EdgbastonUnited Kingdom
                [9 ]Department of Biochemistry, University of Alberta EdmontonCanada
                University of Freiburg Germany
                Weill Cornell Medicine United States
                University of Freiburg Germany
                Iowa State University
                Author notes
                [†]

                These authors contributed equally to this work.

                [‡]

                These authors also contributed equally to this work.

                Author information
                https://orcid.org/0000-0002-7912-2144
                https://orcid.org/0000-0002-9021-0452
                https://orcid.org/0000-0003-4413-3756
                https://orcid.org/0000-0003-4846-6566
                https://orcid.org/0000-0002-7815-8591
                https://orcid.org/0000-0001-5466-7183
                https://orcid.org/0000-0002-9954-4977
                Article
                62614
                10.7554/eLife.62614
                7806268
                33315009
                8b18b534-f91f-4506-879e-ff6e9552ef31
                © 2020, Bryant et al

                This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

                History
                : 31 August 2020
                : 11 December 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/M00810X/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/L00335X/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/P009840/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100013054, Campus Alberta Neuroscience;
                Award ID: RCP-12-002C
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000038, Natural Sciences and Engineering Research Council of Canada;
                Award ID: RGPIN-2018–04994
                Award Recipient :
                The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
                Categories
                Research Article
                Biochemistry and Chemical Biology
                Microbiology and Infectious Disease
                Custom metadata
                Analysis of the E. coli protein DolP reveals the first dual BON-domain structure and identifies phospholipid binding as a new mechanism for protein localisation to the outer membrane division site.

                Life sciences
                bon domain,escherichia coli,yrap,phospholipids,cell division,e. coli
                Life sciences
                bon domain, escherichia coli, yrap, phospholipids, cell division, e. coli

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