Structural Basis of the Subcellular Topology Landscape of Escherichia coli.

Maria S Loos,Jozefien De Geyter,Wim Vranken,Valentina Zorzini,Spyridoula Karamanou,Alexandra Tsirigotaki,Frederic Rousseau,Evrydiki-Pandora Tsare,Reshmi Ramakrishnan,Anastassios Economou,Biao Yuan,Joost Schymkowitz,Maria Klappa,Ioannis Tsamardinos

doi:10.3389/fmicb.2019.01670

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.

Highlights

All cells have specialized, membrane-bound subcellular compartments
ML and AE wrote the manuscript with contributions from RR, AT, WV, IT, JS, VZ, SK, and JDG
All authors reviewed the final version of the manuscript

Summary

Introduction

More than a third of their proteome exits the cytoplasm after synthesis. How proteins find these extracytoplasmic locations, enter them after crossing membranes and acquire folded states, is a central biological problem. Gram− bacterial cells, like the Escherichia coli K-12 model, have a cytoplasm bound by a multi-layered cell envelope consisting of: the IM phospholipid bilayer; the periplasm (containing proteins, small molecules and the peptidoglycan mesh); an additional external lipid bilayer and the OM, which contains anchored lipopolysaccharide molecules (Figure 1A; Silhavy et al, 2010). Polypeptides that exit the cytoplasm of E. coli, i.e., the “exportome,” are either embedded in the IM (IM proteins or “membranome”) or comprise the “secretome.” Secreted proteins reside in the cell envelope or become fully released in the surrounding milieu (Figure 1A). Understanding protein subcellular locations, interactions and dynamics is important for the physicochemical understanding and the in silico modeling of cells, their evolutionary connections, environmental responses, pathologies, chemotherapeutic interventions and biotechnological re-engineering

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Discussion

Conclusion