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      Inter-membrane association of the Sec and BAM translocons for bacterial outer-membrane biogenesis

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          Abstract

          The outer-membrane of Gram-negative bacteria is critical for surface adhesion, pathogenicity, antibiotic resistance and survival. The major constituent – hydrophobic β-barrel Outer- Membrane Proteins (OMPs) – are first secreted across the inner-membrane through the Sec-translocon for delivery to periplasmic chaperones, for example SurA, which prevent aggregation. OMPs are then offloaded to the β- Barrel Assembly Machinery (BAM) in the outer-membrane for insertion and folding. We show the Holo- Trans Locon (HTL) – an assembly of the protein-channel core-complex SecYEG, the ancillary sub-complex SecDF, and the membrane ‘insertase’ YidC – contacts BAM through periplasmic domains of SecDF and YidC, ensuring efficient OMP maturation. Furthermore, the proton-motive force (PMF) across the inner-membrane acts at distinct stages of protein secretion: (1) SecA-driven translocation through SecYEG and (2) communication of conformational changes via SecDF across the periplasm to BAM. The latter presumably drives efficient passage of OMPs. These interactions provide insights of inter-membrane organisation and communication, the importance of which is becoming increasingly apparent.

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          RELION: Implementation of a Bayesian approach to cryo-EM structure determination

          RELION, for REgularized LIkelihood OptimizatioN, is an open-source computer program for the refinement of macromolecular structures by single-particle analysis of electron cryo-microscopy (cryo-EM) data. Whereas alternative approaches often rely on user expertise for the tuning of parameters, RELION uses a Bayesian approach to infer parameters of a statistical model from the data. This paper describes developments that reduce the computational costs of the underlying maximum a posteriori (MAP) algorithm, as well as statistical considerations that yield new insights into the accuracy with which the relative orientations of individual particles may be determined. A so-called gold-standard Fourier shell correlation (FSC) procedure to prevent overfitting is also described. The resulting implementation yields high-quality reconstructions and reliable resolution estimates with minimal user intervention and at acceptable computational costs.
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            Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.

            A computational procedure is described for assigning the absolute hand of the structure of a protein or assembly determined by single-particle electron microscopy. The procedure requires a pair of micrographs of the same particle field recorded at two tilt angles of a single tilt-axis specimen holder together with the three-dimensional map whose hand is being determined. For orientations determined from particles on one micrograph using the map, the agreement (average phase residual) between particle images on the second micrograph and map projections is determined for all possible choices of tilt angle and axis. Whether the agreement is better at the known tilt angle and axis of the microscope or its inverse indicates whether the map is of correct or incorrect hand. An increased discrimination of correct from incorrect hand (free hand difference), as well as accurate identification of the known values for the tilt angle and axis, can be used as targets for rapidly optimizing the search or refinement procedures used to determine particle orientations. Optimized refinement reduces the tendency for the model to match noise in a single image, thus improving the accuracy of the orientation determination and therefore the quality of the resulting map. The hand determination and refinement optimization procedure is applied to image pairs of the dihydrolipoyl acetyltransferase (E2) catalytic core of the pyruvate dehydrogenase complex from Bacillus stearothermophilus taken by low-dose electron cryomicroscopy. Structure factor amplitudes of a three-dimensional map of the E2 catalytic core obtained by averaging untilted images of 3667 icosahedral particles are compared to a scattering reference using a Guinier plot. A noise-dependent structure factor weight is derived and used in conjunction with a temperature factor (B=-1000A(2)) to restore high-resolution contrast without amplifying noise and to visualize molecular features to 8.7A resolution, according to a new objective criterion for resolution assessment proposed here.
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              EMAN2: an extensible image processing suite for electron microscopy.

              EMAN is a scientific image processing package with a particular focus on single particle reconstruction from transmission electron microscopy (TEM) images. It was first released in 1999, and new versions have been released typically 2-3 times each year since that time. EMAN2 has been under development for the last two years, with a completely refactored image processing library, and a wide range of features to make it much more flexible and extensible than EMAN1. The user-level programs are better documented, more straightforward to use, and written in the Python scripting language, so advanced users can modify the programs' behavior without any recompilation. A completely rewritten 3D transformation class simplifies translation between Euler angle standards and symmetry conventions. The core C++ library has over 500 functions for image processing and associated tasks, and it is modular with introspection capabilities, so programmers can add new algorithms with minimal effort and programs can incorporate new capabilities automatically. Finally, a flexible new parallelism system has been designed to address the shortcomings in the rigid system in EMAN1.
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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
                04 November 2020
                2020
                : 9
                : e60669
                Affiliations
                [1 ]School of Biochemistry, University of Bristol BristolUnited Kingdom
                [2 ]Biological Mass Spectrometry and Proteomics, MRC Laboratory of Molecular Biology CambridgeUnited Kingdom
                [3 ]Department of Life Sciences, Imperial College London LondonUnited Kingdom
                [4 ]Living Systems Institute, University of Exeter ExeterUnited Kingdom
                [5 ]College of Life and Environmental Sciences, University of Exeter ExeterUnited Kingdom
                Goethe University Germany
                University of California, Berkeley United States
                Goethe University Germany
                Goethe University Germany
                Author notes
                [†]

                These authors contributed equally to this work.

                Author information
                https://orcid.org/0000-0003-3825-5036
                http://orcid.org/0000-0002-9513-4786
                https://orcid.org/0000-0002-1755-0805
                http://orcid.org/0000-0001-6413-9835
                https://orcid.org/0000-0002-3767-264X
                https://orcid.org/0000-0002-6908-0745
                https://orcid.org/0000-0002-3931-0503
                Article
                60669
                10.7554/eLife.60669
                7695460
                33146611
                a70e1997-8eb1-4510-a404-693dbf876abb
                © 2020, Alvira 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
                : 02 July 2020
                : 03 November 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/S008349/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/N015126/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/M003604/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100003043, EMBO;
                Award ID: ALTF 710-2015
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100003043, EMBO;
                Award ID: LTFCOFUND2013
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100003043, EMBO;
                Award ID: GA-2013-609409
                Award Recipient :
                Funded by: Elizabeth Blackwell Institute for Health Research;
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/M009122/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/J014400/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004440, Wellcome;
                Award ID: 202904/Z/16/Z
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100000268, Biotechnology and Biological Sciences Research Council;
                Award ID: BB/R000484/1
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/100004440, Wellcome;
                Award ID: 206181/Z/17/Z
                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
                Custom metadata
                The protein translocation apparatus of the inner- (Sec) and outer-membrane (BAM) interact to form a trans-periplasmic super-complex capable of long-range, PMF-dependent conformational changes to facilitate efficient outer-membrane protein maturation.

                Life sciences
                bam complex,sec complex,holotranslocon,outer membrane protein,htl-bam,secyeg,e. coli
                Life sciences
                bam complex, sec complex, holotranslocon, outer membrane protein, htl-bam, secyeg, e. coli

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