Shotgun EM of mycobacterial protein complexes during stationary phase stress

Bairoch, 2000, The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000, Nucleic Acids Res, 28, 45, 10.1093/nar/28.1.45 Berman, 2000, The protein data bank, Nucleic Acids Res, 28, 235, 10.1093/nar/28.1.235 Contreras, 2014, Characterization of a Mycobacterium tuberculosis nanocompartment and its potential cargo proteins, J Biol Chem, 289, 18279, 10.1074/jbc.M114.570119 Cottrell, 2011, Protein identification using MS/MS data, J. Proteomics, 74, 1842, 10.1016/j.jprot.2011.05.014 de Souza, 2011, Bacterial proteins with cleaved or uncleaved signal peptides of the general secretory pathway, J. Proteom, 75, 502, 10.1016/j.jprot.2011.08.016 Edwards, 2002, Bridging structural biology and genomics: assessing protein interaction data with known complexes, Trends Genet, 18, 529, 10.1016/S0168-9525(02)02763-4 Erickson, 2009, Size and shape of protein molecules at the nanometer level determined by sedimentation, gel filtration, and electron microscopy, Biol Proced Online, 11, 32, 10.1007/s12575-009-9008-x Frank, 1996, A Leith, SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields, J Struct Biol, 116, 190, 10.1006/jsbi.1996.0030 Gill, 2001, TB Structural Genomics Consortium (TBSGC), Crystallographic structure of a relaxed glutamine synthetase from Mycobacterium tuberculosis, Protein Data Bank Han, 2009, Survey of large protein complexes in D. vulgaris reveals great structural diversity, Proc Natl Acad Sci Unit States Am, 106, 16580, 10.1073/pnas.0813068106 Henderson, 2013, Avoiding the pitfalls of single particle cryo-electron microscopy: einstein from noise, Proc Natl Acad Sci Unit States Am, 110, 18037, 10.1073/pnas.1314449110 Hirosawa, 1993, MASCOT: multiple alignment system for protein sequences based on three-way dynamic programming, Bioinformatics, 9, 161, 10.1093/bioinformatics/9.2.161 Ho, 2020, Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu, Nat Methods, 17, 79, 10.1038/s41592-019-0637-y Huo, 2015, Prediction of host-pathogen protein interactions between Mycobacterium tuberculosis and Homo sapiens using sequence motifs, BMC Bioinf, 16, 100, 10.1186/s12859-015-0535-y Hu, 2015, A consensus subunit-specific model for annotation of substrate specificity for ABC transporters, RSC Adv, 5, 42009, 10.1039/C5RA05304H Kastritis, 2017, Capturing protein communities by structural proteomics in a thermophilic eukaryote, Mol Syst Biol, 13, 936, 10.15252/msb.20167412 Kapopoulou, 2011, The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes, Tuberculosis, 91, 8, 10.1016/j.tube.2010.09.006 Kühner, 2009, Proteome organization in a genome-reduced bacterium, Science, 326, 1235, 10.1126/science.1176343 Khare, 2011, Ferritin structure from Mycobacterium tuberculosis: comparative study with homologues identifies extended C-terminus involved in ferroxidase activity, PloS One, 6, 10.1371/journal.pone.0018570 Kyrilis, 2019, Integrative biology of native cell extracts: a new era for structural characterization of life processes, Biol Chem, 400, 831, 10.1515/hsz-2018-0445 LaFrance, 2020, CryoEM structure of the holo-SrpI encapsulin complex from Synechococcus elongatus PCC 7942, Protein Data Bank Mackay, 2007, Protein interactions: is seeing believing?, Trends Biochem Sci, 32, 530, 10.1016/j.tibs.2007.09.006 Maco, 2011, Proteomic and electron microscopy survey of large assemblies in macrophage cytoplasm, Mol Cell Proteomics, 10, 10.1074/mcp.M111.008763 Cuff McMath, 2011, Mycobacterium tuberculosis ferritin homolog, BfrB, Protein Data Bank Nguyen, 2014, Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeriginosa, Protein Data Bank, 10.2210/pdb4njq/pdb Nichols, 2017, Encapsulins: molecular biology of the shell, Crit Rev Biochem Mol Biol, 52, 583, 10.1080/10409238.2017.1337709 Noens, 2011, Improved mycobacterial protein production using a Mycobacterium smegmatis groEL1ΔCexpression strain, BMC Biotechnol, 11, 27, 10.1186/1472-6750-11-27 Ó’Fágáin, 2011, Gel-filtration chromatography, 25 Peyret, 2015, A protocol for the gentle purification of virus-like particles produced in plants,, J Virol Methods, 225, 59, 10.1016/j.jviromet.2015.09.005 Pettersen, 2004, UCSF Chimera-a visualization system for exploratory research and analysis, J Comput Chem, 25, 1605, 10.1002/jcc.20084 Putri, 2017, Structural characterization of native and modified encapsulins as nanoplatforms for in vitro catalysis and cellular uptake, ACS Nano, 11, 12796, 10.1021/acsnano.7b07669 Rosenkrands, 1998, Identification and characterization of a 29-kilodalton protein from Mycobacterium tuberculosis culture filtrate recognized by mouse memory effector cells, Infect Immun, 66, 2728, 10.1128/IAI.66.6.2728-2735.1998 Rosenthal, 2015, Validating maps from single particle electron cryomicroscopy, Curr Opin Struct Biol, 34, 135, 10.1016/j.sbi.2015.07.002 Scheres, 2012, RELION: implementation of a Bayesian approach to cryo-EM structure determination, J Struct Biol, 180, 519, 10.1016/j.jsb.2012.09.006 Smeulders, 1999, Adaptation of Mycobacterium smegmatis to stationary phase, J Bacteriol, 181, 270, 10.1128/JB.181.1.270-283.1999 Sutter, 2008, Crystal structure of Thermotoga maritima encapsulin, Protein Data Bank, 10.2210/pdb3dkt/pdb Sutter, 2008, Structural basis of enzyme encapsulation into a bacterial nanocompartment, Nat Struct Mol Biol, 15, 939, 10.1038/nsmb.1473 Sun, 2018, Integrating multifaceted information to predict Mycobacterium tuberculosis-human protein-protein interactions, J. Proteome Res, 17, 3810, 10.1021/acs.jproteome.8b00497 Tagari, 2002, New electron microscopy database and deposition system, Trends Biochem Sci, 27, 589, 10.1016/S0968-0004(02)02176-X Tullius, 2003, Glutamine synthetase GlnA1 is essential for growth of Mycobacterium tuberculosis in human THP-1 macrophages and Guinea pigs, infect, Immunology, 71, 3927 Tullius, 2001, High extracellular levels of Mycobacterium tuberculosis glutamine synthetase and superoxide dismutase in actively growing cultures are due to high expression and extracellular stability rather than to a protein-specific export mechanism, Infect Immun, 69, 6348, 10.1128/IAI.69.10.6348-6363.2001 Van Heel, 1987, Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction, Ultramicroscopy, 21, 111, 10.1016/0304-3991(87)90078-7 Verbeke, 2020, Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections, J Struct Biol, 209, 107416, 10.1016/j.jsb.2019.107416 Verbeke, 2018, Classification of single particles from human cell extract reveals distinct structures, Cell Rep, 24, 259, 10.1016/j.celrep.2018.06.022 Wang, 2010, Global protein− protein interaction network in the human pathogen Mycobacterium tuberculosis H37Rv, J. Proteome Res, 9, 6665 Wittig, 2006, Blue native PAGE, Nat Protoc, 1, 418, 10.1038/nprot.2006.62 Yi, 2019, Electron microscopy snapshots of single particles from single cells, J Biol Chem, 294, 1602, 10.1074/jbc.RA118.006686 Zhai, 2019, The immune escape mechanisms of Mycobacterium tuberculosis, Int, J Mol Sci, 20, 340 Zheng, 2011, Combining blue native polyacrylamide gel electrophoresis with liquid chromatography tandem mass spectrometry as an effective strategy for analyzing potential membrane protein complexes of Mycobacterium bovis bacillus Calmette-Guerin, BMC Genom, 12, 40, 10.1186/1471-2164-12-40 Zivanov, 2018, New tools for automated high-resolution cryo-EM structure determination in RELION-3, Elife, 7, 10.7554/eLife.42166 Zubieta, 2007, Crystal structures of two novel dye-decolorizing peroxidases reveal a β-barrel fold with a conserved heme-binding motif, Proteins Struct. Funct. Bioinforma, 69, 223, 10.1002/prot.21550