EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations

Horler, Richard S. P.; Butcher, Andrew; Papangelopoulos, Nikitas; Ashton, Peter D.; Thomas, Gavin H.

doi:10.1093/bioinformatics/btn596

Cited by 28 publications

(25 citation statements)

References 29 publications

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“…Another example was FtsZ, which was gradually removed during the various treatments as indicated by its abundance values (ϳ90-fold decrease) and detection rate (found in all repeats in the untreated IMVs and in only 1 out of the 13 repeats in the DDM-treated IMVs). Remarkably, several proteins classified previously as cytoplasmic, suchas HemG/HemH/ YbbO (involved in heme biosynthesis), DeoB/DeoC/DeoD (involved in the synthesis of nucleoside catabolic enzymes), and (81) and EchoLOCATION (23). A set of bioinformatics tools was used to predict topologies and features of the unassigned and differently assigned proteins and to further validate existing protein annotations (see supplemental text).…”

Section: Curation Of the Theoretical Inner Membrane Peripherome Of Ementioning

confidence: 99%

The Escherichia coli Peripheral Inner Membrane Proteome

Papanastasiou

Orfanoudaki

Koukaki

et al. 2013

Molecular & Cellular Proteomics

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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 ϳ19% of the basic E. coli BL21(DE3) proteome, and the detected peripheral inner membrane proteome occupies ϳ25% 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. Molecular & Cellular Proteomics

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Section: Curation Of the Theoretical Inner Membrane Peripherome Of Ementioning

confidence: 99%

The Escherichia coli Peripheral Inner Membrane Proteome

Papanastasiou

Orfanoudaki

Koukaki

et al. 2013

Molecular & Cellular Proteomics

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“…The subcellular location of E. coli proteins was obtained from the EchoLOCATION database (24). We included lipoproteins in periplasmic proteins but excluded those expected to be exported by the twin-arginine translocation (Tat) pathway because they are exported in folded states (25).…”

Section: Resultsmentioning

confidence: 99%

“…The lists of proteins in various compartments in E. coli were obtained from the EchoLOCATION database (https://www.york.ac.uk/res/thomas/echolocadv.cfm) (24). Cytoplasmic proteins also include membrane-associated proteins on the cytoplasmic side of the inner membrane.…”

Section: Methodsmentioning

confidence: 99%

A Small Periplasmic Protein with a Hydrophobic C-Terminal Residue Enhances DegP Proteolysis as a Suicide Activator

et al. 2018

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DegP is a highly conserved protease that performs regulated proteolysis to selectively remove misfolded proteins in the periplasm of Escherichia coli. Binding of misfolded proteins is known to be the main mechanism of DegP activation, but it is unknown whether any native proteins can alter DegP activity. Here, we show that a small periplasmic protein, YjfN, which is highly upregulated by the Cpx envelope stress response, functions as a "suicide activator" for DegP and promotes efficient degradation of misfolded proteins. YjfN readily binds to and is degraded by DegP, for which a hydrophobic C-terminal residue and transient unfolding of YjfN are critical. YjfN also activates DegP in trans while it is being degraded and accelerates degradation of a denatured outer membrane protein, OmpA, that is not easily recognized by DegP. Although YjfN also prevents OmpA aggregation, the trans-activation effect is mainly responsible for efficient OmpA degradation. Overexpression of YjfN enhances the viability of cells in misfolded protein stress that is induced by the presence of a less-active variant of DegP at high temperature. Collectively, we suggest that YjfN can enhance DegP proteolysis for relieving envelope stresses that may generate toxic misfolded proteins.IMPORTANCE Proper degradation of toxic misfolded proteins is essential for bacterial survival. This function is mainly performed by a highly conserved protease, DegP, in the periplasm of Escherichia coli. It is known that binding of misfolded proteins is the main mechanism for activating the DegP protease. Here, we find that a small periplasmic protein, YjfN, can be a substrate and an activator of DegP. It is the first example of a native protein showing an ability to directly alter DegP activity. The YjfN-mediated trans activation of DegP promotes efficient degradation of misfolded proteins. Our results suggest that YjfN is a novel "suicide activator" for DegP that enhances DegP proteolysis under misfolded protein stress.

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“…Subcellular annotation of STEPdb was based on bioinformatic prediction tools that were combined with the updated annotations of databases (29,32) that were further corroborated by biochemical and proteomic data and a manual curation process. Manual curation contributed 1547 proteins of experimentally verified subcellular location that was based on 397 literature studies.…”

Section: Discussionmentioning

confidence: 99%

“…Uniprot (29)) and others dedicated to E. coli (e.g. EcoWiki (30) and EcoCyc (31)), incorporate partial or mostly predicted cellular compartment annotation (EchoLOCATION (32)) for the E. coli K-12 proteome. Here we present STEPdb, a database that brings together, corrects, resolves conflicts, and re-annotates available subcellular annotation for E. coli K-12, contributes additional validated topological annotation, amalgamates this with proteome-wide biophysical information and provides visualization of proteins in a cell-context through a "cell atlas."…”

mentioning

confidence: 99%

Proteome-wide Subcellular Topologies of E. coli Polypeptides Database (STEPdb)

Orfanoudaki

Economou

2014

Molecular & Cellular Proteomics

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Cell compartmentalization serves both the isolation and the specialization of cell functions. After synthesis in the cytoplasm, over a third of all proteins are targeted to other subcellular compartments. Knowing how proteins are distributed within the cell and how they interact is a prerequisite for understanding it as a whole. Surface and secreted proteins are important pathogenicity determinants. Here we present the STEP database (STEPdb) that contains a comprehensive characterization of subcellular localization and topology of the complete proteome of Escherichia coli. Two widely used E. coli proteomes (K-12 and BL21) are presented organized into thirteen subcellular classes. STEPdb exploits the wealth of genetic, proteomic, biochemical, and functional information on protein localization, secretion, and targeting in E. coli, one of the best understood model organisms. Subcellular annotations were derived from a combination of bioinformatics prediction, proteomic, biochemical, functional, topological data and extensive literature re-examination that were refined through manual curation. Strong experimental support for the location of 1553 out of 4303 proteins was based on 426 articles and some experimental indications for another 526. Annotations were provided for another 320 proteins based on firm bioinformatic predictions. STEPdb is the first database that contains an extensive set of peripheral IM proteins (PIM proteins) and includes their graphical visualization into complexes, cellular functions, and interactions. It also summarizes all currently known protein export machineries of E. coli K-12 and pairs them, where available, with the secretory proteins that use them. It catalogs the Sec-and TAT-utilizing secretomes and summarizes their topological features such as signal peptides and transmembrane regions, transmembrane topologies and orientations. It also catalogs physicochemical and structural features that influence topology such as abundance, solubility, disorder, heat resistance, and structural domain families. Finally, STEPdb incorporates prediction tools for topology (TMHMM, SignalP, and Phobius) and disorder (IUPred) and implements the BLAST2STEP that performs protein homology searches against the STEPdb. Molecular &

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EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations

Cited by 28 publications

References 29 publications

The Escherichia coli Peripheral Inner Membrane Proteome

The Escherichia coli Peripheral Inner Membrane Proteome

A Small Periplasmic Protein with a Hydrophobic C-Terminal Residue Enhances DegP Proteolysis as a Suicide Activator

Proteome-wide Subcellular Topologies of E. coli Polypeptides Database (STEPdb)

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