Dataset Information

Signature of Pareto optimization in the Escherichia coli proteome.

ABSTRACT: Proteins have coevolved with cellular environments to improve or preserve their functions, maintaining at the same time the degree of hydrophobicity necessary to fold correctly and enough solubility to perform their biological roles. Here, we study the Escherichia coli proteome using a Pareto front analysis in the solubility-hydrophobicity space. The results indicate the existence of a Pareto optimal front, a triangle whose vertices correspond to archetypal proteins specialized in distinct tasks, such as regulatory processes, membrane transport, outer-membrane pore formation, catalysis, and binding. The vertices are further enriched with proteins that occupy different subcellular compartments, namely, cytoplasmic, inner membrane, outer membrane, and outer membrane bounded periplasmic space. The combination of various enriching features offers an interpretation of how bacteria use the physico-chemical properties of proteins, both to drive them into their final destination in the cell and to have their tasks accomplished.

SUBMITTER: Kocillari L

PROVIDER: S-EPMC6002381 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Signature of Pareto optimization in the Escherichia coli proteome.

Koçillari Loren L Fariselli Piero P Trovato Antonio A Seno Flavio F Maritan Amos A

Scientific reports 20180614 1

Proteins have coevolved with cellular environments to improve or preserve their functions, maintaining at the same time the degree of hydrophobicity necessary to fold correctly and enough solubility to perform their biological roles. Here, we study the Escherichia coli proteome using a Pareto front analysis in the solubility-hydrophobicity space. The results indicate the existence of a Pareto optimal front, a triangle whose vertices correspond to archetypal proteins specialized in distinct tasks ...[more]

PMID: 29904084

Similar Datasets

Project description:Biological membranes are essential for cell viability. Their functional characteristics strongly depend on their protein content, which consists of transmembrane (integral) and peripherally associated membrane proteins. Both integral and peripheral inner membrane proteins mediate a plethora of biological processes. Whereas transmembrane proteins have characteristic hydrophobic stretches and can be predicted using bioinformatics approaches, peripheral inner membrane proteins are hydrophilic, exist in equilibria with soluble pools, and carry no discernible membrane targeting signals. We experimentally determined the cytoplasmic peripheral inner membrane proteome of the model organism Escherichia coli using a multidisciplinary approach. Initially, we extensively re-annotated the theoretical proteome regarding subcellular localization using literature searches, manual curation, and multi-combinatorial bioinformatics searches of the available databases. Next we used sequential biochemical fractionations coupled to direct identification of individual proteins and protein complexes using high resolution mass spectrometry. We determined that the proposed cytoplasmic peripheral inner membrane proteome occupies a previously unsuspected ?19% of the basic E. coli BL21(DE3) proteome, and the detected peripheral inner membrane proteome occupies ?25% of the estimated expressed proteome of this cell grown in LB medium to mid-log phase. This value might increase when fleeting interactions, not studied here, are taken into account. Several proteins previously regarded as exclusively cytoplasmic bind membranes avidly. Many of these proteins are organized in functional or/and structural oligomeric complexes that bind to the membrane with multiple interactions. Identified proteins cover the full spectrum of biological activities, and more than half of them are essential. Our data suggest that the cytoplasmic proteome displays remarkably dynamic and extensive communication with biological membrane surfaces that we are only beginning to decipher.

Dataset Information

Signature of Pareto optimization in the Escherichia coli proteome.

Publications

Signature of Pareto optimization in the Escherichia coli proteome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets