Preprotein mature domains contain translocase targeting signals that are essential for secretion

Secretory proteins are only temporary cytoplasmic residents. They are typically synthesized as preproteins, carrying signal peptides N-terminally fused to their mature domains. In bacteria secretion largely occurs posttranslationally through the membrane-embedded SecA-SecYEG translocase. Upon crossing the plasma membrane, signal peptides are cleaved off and mature domains reach their destinations and fold. Targeting to the translocase is mediated by signal peptides. The role of mature domains in targeting and secretion is unclear. We now reveal that mature domains harbor their own independent targeting signals (mature domain targeting signals [MTSs]). These are multiple, degenerate, interchangeable, linear or 3D hydrophobic stretches that become available because of the unstructured states of targeting-competent preproteins. Their receptor site on the cytoplasmic face of the SecYEG-bound SecA is also of hydrophobic nature and is located adjacent to the signal peptide cleft. Both the preprotein MTSs and their receptor site on SecA are essential for protein secretion. Evidently, mature domains have their own previously unsuspected distinct roles in preprotein targeting and secretion

The Escherichia coli Peripheral Inner Membrane Proteome

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.status: publishe

Rapid label-free quantitative analysis of the E. coli BL21(DE3) inner membrane proteome

Biological membranes define cells and cellular compartments and are essential in regulating bidirectional flow of chemicals and signals. Characterizing their protein content therefore is required to determine their function, nevertheless, the comprehensive determination of membrane-embedded sub-proteomes remains challenging. Here, we experimentally characterized the inner membrane proteome (IMP) of the model organism E. coli BL21(DE3). We took advantage of the recent extensive re-annotation of the theoretical E. coli IMP regarding the sub-cellular localization of all its proteins. Using surface proteolysis of IMVs with variable chemical treatments followed by nanoLC-MS/MS analysis, we experimentally identified ∼45% of the expressed IMP in wild type E. coli BL21(DE3) with 242 proteins reported here for the first time. Using modified label-free approaches we quantified 220 IM proteins. Finally, we compared protein levels between wild type cells and those over-synthesizing the membrane-embedded translocation channel SecYEG proteins. We propose that this proteomics pipeline will be generally applicable to the determination of IMP from other bacteria. This article is protected by copyright. All rights reserved.status: publishe

A polysulfobetaine hydrogel for immobilization of a glucose-binding protein

A hydrogel based on sulfobetaine methacrylate monomer N-(methacryloyloxyethyl)-N,N-dimethyl-N-(3-sulfopropyl)ammonium betaine and N,N-bis(methacryloyloxyethyl)-N-methyl-N-(3-sulfopropyl)ammonium betaine used as a crosslinker was investigated as a potential material for biosensor applications. The glucose diffusion coefficient of 1.2 × 10−10 m2 s−1 was determined from the glucose release experiment. Inverse size-exclusion chromatography was performed to determine the molecular weight cut-off of the hydrogel to be 8 kDa with respect to pullulans that corresponds to a viscosity radius of 2.1 nm. The narrow pore-size distribution suggests that using the sulfobetaine crosslinker suppresses the composition drift and results in a homogeneous hydrogel network. Furthermore, a glucose biosensor construct comprising the periplasmic glucose-binding protein of Escherichia coli fused to cyan and yellow fluorescent proteins was effectively entrapped in the hydrogel exhibiting no leakage for at least 7 days. The glucose-binding protein showed stability of its secondary structure and sensitivity to glucose as assessed by circular dichroism and Förster (fluorescence) resonance energy transfer measurements under physiological conditions and a physiological range of glucose concentration, respectively.Scopu

A polysulfobetaine hydrogel for immobilization of a glucose-binding protein

© The Royal Society of Chemistry 2016. A hydrogel based on sulfobetaine methacrylate monomer N-(methacryloyloxyethyl)-N,N-dimethyl-N-(3-sulfopropyl)ammonium betaine and N,N-bis(methacryloyloxyethyl)-N-methyl-N-(3-sulfopropyl)ammonium betaine used as a crosslinker was investigated as a potential material for biosensor applications. The glucose diffusion coefficient of 1.2 × 10 -10 m 2 s -1 was determined from the glucose release experiment. Inverse size-exclusion chromatography was performed to determine the molecular weight cut-off of the hydrogel to be 8 kDa with respect to pullulans that corresponds to a viscosity radius of 2.1 nm. The narrow pore-size distribution suggests that using the sulfobetaine crosslinker suppresses the composition drift and results in a homogeneous hydrogel network. Furthermore, a glucose biosensor construct comprising the periplasmic glucose-binding protein of Escherichia coli fused to cyan and yellow fluorescent proteins was effectively entrapped in the hydrogel exhibiting no leakage for at least 7 days. The glucose-binding protein showed stability of its secondary structure and sensitivity to glucose as assessed by circular dichroism and Förster (fluorescence) resonance energy transfer measurements under physiological conditions and a physiological range of glucose concentration, respectively.crosscheck: This document is CrossCheck deposited copyright_licence: The Royal Society of Chemistry has an exclusive publication licence for this journal history: Received 3 June 2016; Accepted 31 August 2016; Accepted Manuscript published 31 August 2016; Version of Record published 5 September 2016status: publishe

Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR

Recognition of signal sequences by cognate receptors controls the entry of virtually all proteins to export pathways. Despite its importance, this process remains poorly understood. Here, we present the solution structure of a signal peptide bound to SecA, the 204 kDa ATPase motor of the Sec translocase. Upon encounter, the signal peptide forms an α-helix that inserts into a flexible and elongated groove in SecA. The mode of binding is bimodal, with both hydrophobic and electrostatic interactions mediating recognition. The same groove is used by SecA to recognize a diverse set of signal sequences. Impairment of the signal-peptide binding to SecA results in significant translocation defects. The C-terminal tail of SecA occludes the groove and inhibits signal-peptide binding, but autoinhibition is relieved by the SecB chaperone. Finally, it is shown that SecA interconverts between two conformations in solution, suggesting a simple mechanism for polypeptide translocation. © 2007 Elsevier Inc. All rights reserved

Long-Lived Folding Intermediates Predominate the Targeting-Competent Secretome

Secretory preproteins carry signal peptides fused amino-terminally to mature domains. They are post-translationally targeted to cross the plasma membrane in non-folded states with the help of translocases, and fold only at their final destinations. The mechanism of this process of postponed folding is unknown, but is generally attributed to signal peptides and chaperones. We herein demonstrate that, during targeting, most mature domains maintain loosely packed folding intermediates. These largely soluble states are signal peptide independent and essential for translocase recognition. These intermediates are promoted by mature domain features: residue composition, elevated disorder, and reduced hydrophobicity. Consequently, a mature domain folds slower than its cytoplasmic structural homolog. Some mature domains could not evolve stable, loose intermediates, and hence depend on signal peptides for slow folding to the detriment of solubility. These unique features of secretory proteins impact our understanding of protein trafficking, folding, and aggregation, and thus place them in a distinct class.status: publishe