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Loos MS, Ramakrishnan R, Vranken W, Tsirigotaki A, Tsare EP, Zorzini V, Geyter JD, Yuan B, Tsamardinos I, Klappa M, Schymkowitz J, Rousseau F, Karamanou S, Economou A. Structural Basis of the Subcellular Topology Landscape of Escherichia coli. Front Microbiol 2019; 10:1670. [PMID: 31404336 PMCID: PMC6677119 DOI: 10.3389/fmicb.2019.01670] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/08/2019] [Indexed: 11/21/2022] Open
Abstract
Cellular proteomes are distributed in multiple compartments: on DNA, ribosomes, on and inside membranes, or they become secreted. Structural properties that allow polypeptides to occupy subcellular niches, particularly to after crossing membranes, remain unclear. We compared intrinsic and extrinsic features in cytoplasmic and secreted polypeptides of the Escherichia coli K-12 proteome. Structural features between the cytoplasmome and secretome are sharply distinct, such that a signal peptide-agnostic machine learning tool distinguishes cytoplasmic from secreted proteins with 95.5% success. Cytoplasmic polypeptides are enriched in aliphatic, aromatic, charged and hydrophobic residues, unique folds and higher early folding propensities. Secretory polypeptides are enriched in polar/small amino acids, β folds, have higher backbone dynamics, higher disorder and contact order and are more often intrinsically disordered. These non-random distributions and experimental evidence imply that evolutionary pressure selected enhanced secretome flexibility, slow folding and looser structures, placing the secretome in a distinct protein class. These adaptations protect the secretome from premature folding during its cytoplasmic transit, optimize its lipid bilayer crossing and allowed it to acquire cell envelope specific chemistries. The latter may favor promiscuous multi-ligand binding, sensing of stress and cell envelope structure changes. In conclusion, enhanced flexibility, slow folding, looser structures and unique folds differentiate the secretome from the cytoplasmome. These findings have wide implications on the structural diversity and evolution of modern proteomes and the protein folding problem.
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Affiliation(s)
- Maria S Loos
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Reshmi Ramakrishnan
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.,VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Wim Vranken
- Interuniversity Institute of Bioinformatics in Brussels, Free University of Brussels, Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel and Center for Structural Biology, Brussels, Belgium
| | - Alexandra Tsirigotaki
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Evrydiki-Pandora Tsare
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas, Patras, Greece
| | - Valentina Zorzini
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Jozefien De Geyter
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Biao Yuan
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Ioannis Tsamardinos
- Gnosis Data Analysis PC, Heraklion, Greece.,Department of Computer Science, University of Crete, Heraklion, Greece
| | - Maria Klappa
- Metabolic Engineering & Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas, Patras, Greece
| | - Joost Schymkowitz
- VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- VIB Switch Laboratory, Department for Cellular and Molecular Medicine, VIB-KU Leuven Center for Brain & Disease Research, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute, KU Leuven, Leuven, Belgium.,Gnosis Data Analysis PC, Heraklion, Greece
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