Assembly and misassembly of cystic fibrosis transmembrane conductance regulator: folding defects caused by deletion of F508 occur before and after the calnexin-dependent association of membrane spanning domain (MSD) 1 and MSD2

Cystic fibrosis transmembrane conductance regulator (CFTR) is a polytopic membrane protein that functions as a Cl⁻ channel and consists of two membrane spanning domains (MSDs), two cytosolic nucleotide binding domains (NBDs), and a cytosolic regulatory domain. Cytosolic 70-kDa heat shock protein (Hsp70), and endoplasmic reticulum-localized calnexin are chaperones that facilitate CFTR biogenesis. Hsp70 functions in both the cotranslational folding and posttranslational degradation of CFTR. Yet, the mechanism for calnexin action in folding and quality control of CFTR is not clear. Investigation of this question revealed that calnexin is not essential for CFTR or CFTRΔF508 degradation. We identified a dependence on calnexin for proper assembly of CFTR's membrane spanning domains. Interestingly, efficient folding of NBD2 was also found to be dependent upon calnexin binding to CFTR. Furthermore, we identified folding defects caused by deletion of F508 that occurred before and after the calnexin-dependent association of MSD1 and MSD2. Early folding defects are evident upon translation of the NBD1 and R-domain and are sensed by the RMA-1 ubiquitin ligase complex.     

Oligomers of Heat-Shock Proteins: Structures That Don’t Imply Function

Most proteins must remain soluble in the cytosol in order to perform their biological functions. To protect against undesired protein aggregation, living cells maintain a population of molecular chaperones that ensure the solubility of the proteome. Here we report simulations of a lattice model of interacting proteins to understand how low concentrations of passive molecular chaperones, such as small heat-shock proteins, suppress thermodynamic instabilities in protein solutions. Given fixed concentrations of chaperones and client proteins, the solubility of the proteome can be increased by tuning the chaperone–client binding strength. Surprisingly, we find that the binding strength that optimizes solubility while preventing irreversible chaperone binding also promotes the formation of weakly bound chaperone oligomers, although the presence of these oligomers does not significantly affect the thermodynamic stability of the solution. Such oligomers are commonly observed in experiments on small heat-shock proteins, but their connection to the biological function of these chaperones has remained unclear. Our simulations suggest that this clustering may not have any essential biological function, but rather emerges as a natural side-effect of optimizing the thermodynamic stability of the proteome.     

Protein quality control and regulated proteolysis in the genome‐reduced organism Mycoplasma pneumoniae

Protein degradation is a crucial cellular process in all‐living systems. Here, using Mycoplasma pneumoniae as a model organism, we defined the minimal protein degradation machinery required to maintain proteome homeostasis. Then, we conditionally depleted the two essential ATP‐dependent proteases. Whereas depletion of Lon results in increased protein aggregation and decreased heat tolerance, FtsH depletion induces cell membrane damage, suggesting a role in quality control of membrane proteins. An integrative comparative study combining shotgun proteomics and RNA‐seq revealed 62 and 34 candidate substrates, respectively. Cellular localization of substrates and epistasis studies supports separate functions for Lon and FtsH. Protein half‐life measurements also suggest a role for Lon‐modulated protein decay. Lon plays a key role in protein quality control, degrading misfolded proteins and those not assembled into functional complexes. We propose that regulating complex assembly and degradation of isolated proteins is a mechanism that coordinates important cellular processes like cell division. Finally, by considering the entire set of proteases and chaperones, we provide a fully integrated view of how a minimal cell regulates protein folding and degradation.     

Structural Basis of Cyclophilin B Binding by the Calnexin/Calreticulin P-domain

Little is known about how chaperones in the endoplasmic reticulum are organized into complexes to assist in the proper folding of secreted proteins. One notable exception is the complex of ERp57 and calnexin that functions as part the calnexin cycle to direct disulfide bond formation in N-glycoproteins. Here, we report three new complexes composed of the peptidyl prolyl cis-trans-isomerase cyclophilin B and any of the lectin chaperones: calnexin, calreticulin, or calmegin. The 1.7 Å crystal structure of cyclophilin with the proline-rich P-domain of calmegin reveals that binding is mediated by the same surface that binds ERp57. We used NMR titrations and mutagenesis to measure low micromolar binding of cyclophilin to all three lectin chaperones and identify essential interfacial residues. The immunosuppressant cyclosporin A did not affect complex formation, confirming the functional independence of the P-domain binding and proline isomerization sites of cyclophilin. Our results reveal the P-domain functions as a unique protein-protein interaction domain and implicate a peptidyl prolyl isomerase as a new element in the calnexin cycle.     

Localization of the lectin,ERp57 binding,and polypeptide binding sites of calnexin and calreticulin

Calnexin and calreticulin are membrane-bound and soluble chaperones, respectively, of the endoplasmic reticulum (ER) which interact transiently with a broad spectrum of newly synthesized glycoproteins. In addition to sharing substantial sequence identity, both calnexin and calreticulin bind to monoglucosylated oligosaccharides of the form Glc(1)Man(5-9)GlcNAc(2), interact with the thiol oxidoreductase, ERp57, and are capable of acting as chaperones in vitro to suppress the aggregation of non-native proteins. To understand how these diverse functions are coordinated, we have localized the lectin, ERp57 binding, and polypeptide binding sites of calnexin and calreticulin. Recent structural studies suggest that both proteins consist of a globular domain and an extended arm domain comprised of two sequence motifs repeated in tandem. Our results indicate that the primary lectin site of calnexin and calreticulin resides within the globular domain, but the results also point to a much weaker secondary site within the arm domain which lacks specificity for monoglucosylated oligosaccharides. For both proteins, a site of interaction with ERp57 is centered on the arm domain, which retains approximately 50% of binding compared with full-length controls. This site is in addition to a Zn(2+)-dependent site located within the globular domain of both proteins. Finally, calnexin and calreticulin suppress the aggregation of unfolded proteins via a polypeptide binding site located within their globular domains but require the arm domain for full chaperone function. These findings are integrated into a model that describes the interaction of glycoprotein folding intermediates with calnexin and calreticulin.     

The Number and Location of Glycans on Influenza Hemagglutinin Determine Folding and Association with Calnexin and Calreticulin

Calnexin and calreticulin are homologous molecular chaperones that promote proper folding, oligomeric assembly, and quality control of newly synthesized glycoproteins in the endoplasmic reticulum (ER). Both are lectins that bind to substrate glycoproteins that have monoglucosylated N-linked oligosaccharides. Their binding to newly translated influenza virus hemagglutinin (HA), and various mutants thereof, was analyzed in microsomes after in vitro translation and expression in live CHO cells. A large fraction of the HA molecules was found to occur in ternary HA– calnexin–calreticulin complexes. In contrast to calnexin, calreticulin was found to bind primarily to early folding intermediates. Analysis of HA mutants with different numbers and locations of N-linked glycans showed that although the two chaperones share the same carbohydrate specificity, they display distinct binding properties; calreticulin binding depends on the oligosaccharides in the more rapidly folding top/hinge domain of HA whereas calnexin is less discriminating. Calnexin's binding was reduced if the HA was expressed as a soluble anchor-free protein rather than membrane bound. When the co- and posttranslational folding and trimerization of glycosylation mutants was analyzed, it was observed that removal of stem domain glycans caused accelerated folding whereas removal of the top domain glycans (especially the oligosaccharide attached to Asn81) inhibited folding. In summary, the data established that individual N-linked glycans in HA have distinct roles in calnexin/calreticulin binding and in co- and posttranslational folding.     

The mouse nicotinamide mononucleotide adenylyltransferase chaperones diverse pathological amyloid client proteins

Molecular chaperones safeguard cellular protein homeostasis and obviate proteotoxicity. In the process of aging, as chaperone networks decline, aberrant protein amyloid aggregation accumulates in a mechanism that underpins neurodegeneration, leading to pathologies such as Alzheimer’s disease and Parkinson’s disease. Thus, it is important to identify and characterize chaperones for preventing such protein aggregation. In this work, we identified that the NAD⁺ synthase–nicotinamide mononucleotide adenylyltransferase (NMNAT) 3 from mouse (mN3) exhibits potent chaperone activity to antagonize aggregation of a wide spectrum of pathological amyloid client proteins including α-synuclein, Tau (K19), amyloid β, and islet amyloid polypeptide. By combining NMR spectroscopy, cross-linking mass spectrometry, and computational modeling, we further reveal that mN3 uses different region of its amphiphilic surface near the active site to directly bind different amyloid client proteins. Our work demonstrates a client recognition mechanism of NMNAT via which it chaperones different amyloid client proteins against pathological aggregation and implies a potential protective role for NMNAT in different amyloid-associated diseases.     

Multiple C2 domain–containing transmembrane proteins promote lipid droplet biogenesis and growth at specialized endoplasmic reticulum subdomains

Lipid droplets (LDs) are neutral lipid-containing organelles enclosed in a single monolayer of phospholipids. LD formation begins with the accumulation of neutral lipids within the bilayer of the endoplasmic reticulum (ER) membrane. It is not known how the sites of formation of nascent LDs in the ER membrane are determined. Here we show that multiple C2 domain–containing transmembrane proteins, MCTP1 and MCTP2, are at sites of LD formation in specialized ER subdomains. We show that the transmembrane domain (TMD) of these proteins is similar to a reticulon homology domain. Like reticulons, these proteins tubulate the ER membrane and favor highly curved regions of the ER. Our data indicate that the MCTP TMDs promote LD biogenesis, increasing LD number. MCTPs colocalize with seipin, a protein involved in LD biogenesis, but form more stable microdomains in the ER. The MCTP C2 domains bind charged lipids and regulate LD size, likely by mediating ER–LD contact sites. Together, our data indicate that MCTPs form microdomains within ER tubules that regulate LD biogenesis, size, and ER–LD contacts. Interestingly, MCTP punctae colocalized with other organelles as well, suggesting that these proteins may play a general role in linking tubular ER to organelle contact sites.     

SRP,FtsY, DnaK and YidC Are Required for the Biogenesis of the E. coli Tail-Anchored Membrane Proteins DjlC and Flk

Tail-anchored membrane proteins (TAMPs) are relatively simple membrane proteins characterized by a single transmembrane domain (TMD) at their C-terminus. Consequently, the hydrophobic TMD, which acts as a subcellular targeting signal, emerges from the ribosome only after termination of translation precluding canonical co-translational targeting and membrane insertion. In contrast to the well-studied eukaryotic TAMPs, surprisingly little is known about the cellular components that facilitate the biogenesis of bacterial TAMPs. In this study, we identify DjlC and Flk as bona fide Escherichia coli TAMPs and show that their TMDs are necessary and sufficient for authentic membrane targeting of the fluorescent reporter mNeonGreen. Using strains conditional for the expression of known E. coli membrane targeting and insertion factors, we demonstrate that the signal recognition particle (SRP), its receptor FtsY, the chaperone DnaK and insertase YidC are each required for efficient membrane localization of both TAMPs. A close association between the TMD of DjlC and Flk with both the Ffh subunit of SRP and YidC was confirmed by site-directed in vivo photo-crosslinking. In addition, our data suggest that the hydrophobicity of the TMD correlates with the dependency on SRP for efficient targeting.     

ATP regulates RNA‐driven cold inducible RNA binding protein phase separation

Intrinsically disordered proteins and proteins containing intrinsically disordered regions are highly abundant in the proteome of eukaryotes and are extensively involved in essential biological functions. More recently, their role in the organization of biomolecular condensates has become evident and along with their misregulation in several neurologic disorders. Currently, most studies involving these proteins are carried out in vitro and using purified proteins. Given that in cells, condensate‐forming proteins are exposed to high, millimolar concentrations of cellular metabolites, we aimed to reveal the interactions of cellular metabolites and a representative condensate‐forming protein. Here, using the arginine–glycine/arginine–glycine–glycine (RG/RGG)‐rich cold inducible RNA binding protein (CIRBP) as paradigm, we studied binding of the cellular metabolome to CIRBP. We found that most of the highly abundant cellular metabolites, except nucleotides, do not directly bind to CIRBP. ATP, ADP, and AMP as well as NAD⁺, NADH, NADP⁺, and NADPH directly interact with CIRBP, involving both the folded RNA‐recognition motif and the disordered RG/RGG region. ATP binding inhibited RNA‐driven phase separation of CIRBP. Thus, it might be beneficial to include cellular metabolites in in vitro liquid–liquid phase separation studies of RG/RGG and other condensate‐forming proteins in order to better mimic the cellular environment in the future.     

Functional Analysis of the Transmembrane Domains of Presenilin 1: PARTICIPATION OF TRANSMEMBRANE DOMAINS 2 AND 6 IN THE FORMATION OF INITIAL SUBSTRATE-BINDING SITE OF γ-SECRETASE*

γ-Secretase is a multimeric membrane protein complex composed of presenilin (PS), nicastrin, Aph-1, and Pen-2, which mediates intramembrane proteolysis of a range of type I transmembrane proteins. We previously analyzed the functional roles of the N-terminal transmembrane domains (TMDs) 1–6 of PS1 in the assembly and proteolytic activity of the γ-secretase using a series of TMD-swap PS1 mutants. Here we applied the TMD-swap method to all the TMDs of PS1 for the structure-function analysis of the proteolytic mechanism of γ-secretase. We found that TMD2- or -6-swapped mutant PS1 failed to bind the helical peptide-based, substrate-mimic γ-secretase inhibitor. Cross-linking experiments revealed that both TMD2 and TMD6 of PS1 locate in proximity to the TMD9, the latter being implicated in the initial substrate binding. Taken together, our data suggest that TMD2 and the luminal side of TMD6 are involved in the formation of the initial substrate-binding site of the γ-secretase complex.     

Bro1 stimulates Vps4 to promote intralumenal vesicle formation during multivesicular body biogenesis

Endosomal sorting complexes required for transport (ESCRT-0, -I, -II, -III) execute cargo sorting and intralumenal vesicle (ILV) formation during conversion of endosomes to multivesicular bodies (MVBs). The AAA-ATPase Vps4 regulates the ESCRT-III polymer to facilitate membrane remodeling and ILV scission during MVB biogenesis. Here, we show that the conserved V domain of ESCRT-associated protein Bro1 (the yeast homologue of mammalian proteins ALIX and HD-PTP) directly stimulates Vps4. This activity is required for MVB cargo sorting. Furthermore, the Bro1 V domain alone supports Vps4/ESCRT–driven ILV formation in vivo without efficient MVB cargo sorting. These results reveal a novel activity of the V domains of Bro1 homologues in licensing ESCRT-III–dependent ILV formation and suggest a role in coordinating cargo sorting with membrane remodeling during MVB sorting. Moreover, ubiquitin binding enhances V domain stimulation of Vps4 to promote ILV formation via the Bro1–Vps4–ESCRT-III axis, uncovering a novel role for ubiquitin during MVB biogenesis in addition to facilitating cargo recognition.     

Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol

The formation of protein aggregates is a hallmark of neurodegenerative diseases. Observations on patient samples and model systems demonstrated links between aggregate formation and declining mitochondrial functionality, but causalities remain unclear. We used Saccharomyces cerevisiae to analyze how mitochondrial processes regulate the behavior of aggregation‐prone polyQ protein derived from human huntingtin. Expression of Q97‐GFP rapidly led to insoluble cytosolic aggregates and cell death. Although aggregation impaired mitochondrial respiration only slightly, it considerably interfered with the import of mitochondrial precursor proteins. Mutants in the import component Mia40 were hypersensitive to Q97‐GFP, whereas Mia40 overexpression strongly suppressed the formation of toxic Q97‐GFP aggregates both in yeast and in human cells. Based on these observations, we propose that the post‐translational import of mitochondrial precursor proteins into mitochondria competes with aggregation‐prone cytosolic proteins for chaperones and proteasome capacity. Mia40 regulates this competition as it has a rate‐limiting role in mitochondrial protein import. Therefore, Mia40 is a dynamic regulator in mitochondrial biogenesis that can be exploited to stabilize cytosolic proteostasis.     

Neurexin‐2 is a potential regulator of inflammatory pain in the spinal dorsal horn of rats

Chronic pain is one of the serious conditions that affect human health and remains cure still remains a serious challenge as the molecular mechanism remains largely unclear. Here, we used label‐free proteomics to identify potential target proteins that regulate peripheral inflammatory pain and reveal its mechanism of action. Inflammation in peripheral tissue was induced by injecting complete Freund''s adjuvant (CFA) into rat hind paw. A proteomic method was adopted to compare the spinal dorsal horn (SDH) in peripheral inflammatory pain (PIP) model rats with controls. Differential proteins were identified in SDH proteome by label‐free quantification. The role of screened target proteins in the PIP was verified by small interfering RNA (siRNA). A total of 3072 and 3049 proteins were identified in CFA and normal saline (NS) groups, respectively, and 13 proteins were identified as differentially expressed in the CFA group. One of them, neurexin‐2, was validated for its role in the inflammatory pain. Neurexin‐2 was up‐regulated in the CFA group, which was confirmed by quantitative PCR. Besides, intrathecal siRNA‐mediated knock‐down of neurexin‐2 attenuated CFA‐induced mechanical and thermal hyperalgesia and reduced the expression of SDH membrane glutamate receptors (eg mGlu receptor 1, AMPA receptor) and postsynaptic density (eg PSD‐95, DLG2). These findings increased the understanding of the role of neurexin‐2 in the inflammatory pain, implicating that neurexin‐2 acts as a potential regulatory protein of inflammatory pain through affecting synaptic plasticity in the SDH of rats.     

Chaperoning transmembrane helices in the lipid bilayer

Elimination of membrane proteins often requires recognition of their transmembrane domains (TMDs) in the lipid bilayer. In this issue, Arines et al. (2020. J. Cell Biol. https://doi.org/10.1083/jcb.202001116) show that in Saccharomyces cerevisiae, the vacuole-associated Rsp5 ubiquitin ligase uses a TMD in substrate adaptor Ssh4 to recognize membrane helices in Ypq1, which targets this lysine transporter for lysosomal degradation during lysine starvation.

In eukaryotic cells, protein quality control (PQC) mediates the degradation of not only aberrant but also unwanted polypeptides, safeguarding both the quality and quantity of the cellular proteome (1). A central goal in PQC research is to delineate the mechanism of substrate selection, which, if inappropriately executed, could lead to undesired destruction of functional proteins and thus the collapse of the proteostasis network. For soluble proteins that succumb to PQC, it is usually the surface exposure of hydrophobic elements that alerts cellular chaperones to potential folding catastrophe (2). Chaperones often serve a dual triaging role: while giving their clients additional time to fold, they can also interface with degradation machineries such as the ubiquitin proteasome system or lysosomes, causing the elimination of terminally misfolded or unwanted polypeptides.Unlike PQC of soluble proteins, substrate recognition for membrane proteins bearing abnormal transmembrane domain (TMD) is largely unknown, even for the best characterized PQC process, ER-associated degradation (ERAD; 3). Early studies on PQC of unassembled T cell receptor α chain (TCRα) showed that the single TMD of TCRα contains two charged residues, which are thermodynamically unfavored in the lipid environment and thus must be shielded when TCRα assembles with CD3σ. Accordingly, unassembled TCRα is eliminated by ERAD via a mechanism dependent on these charged residues (4), but TMD-specific chaperones responsible for recognizing charged residues in the lipid bilayer have not been identified. Likewise, recent investigations into the function of the Hrd1 ubiquitin ligase suggested a role for the TMDs of Hrd1 in recognition of specific aberrant membrane proteins in ERAD (5). Cryo-EM studies further showed two juxtaposed central cavities with a lateral gate poised to receive TMDs in the yeast Hrd1 complex (6), but how aberrant TMDs in ERAD substrates are recognized and retrotranslocated by Hrd1 remains an open question.The issue of substrate recognition becomes even more complex for feedback-regulated degradation of unwanted membrane proteins. In this case, substrates are initially stable and functionally essential, but a change in environmental cues renders them dispensable and results in a short-lived fate. One such example is the sterol-regulated degradation of a sterol-synthesizing enzyme called HMG-CoA reductase (HMGR). HMGR is a stable ER protein when the sterol level is low, but an increase in membrane sterol abundance alters the conformation of a sterol-sensing domain in HMGR, exposing an element functionally equivalent to a degron in short-lived proteasomal substrates (7). Despite extensive studies, the molecular signature of the degron in HMGR is still undefined, let alone the molecular basis of its recognition. In this issue, Arines and colleagues investigate how Ypq1, a multi-spanning lysine transporter of the yeast vacuole, is regulated by lysine availability, a regulated membrane protein turnover event analogous to HMGR degradation. Their study identifies critical residues in Ypq1 TMDs for its turnover and establishes the Rsp5 ubiquitin ligase adaptor Ssh4 as a TMD-specific chaperone that recognizes these elements (8).Ypq1 is a seven-transmembrane, PQ loop–containing lysine transporter localized to the yeast vacuole membrane. Under lysine-replete conditions, Ypq1 is stable as it uses a PQ loop–dependent conformational cycle to import excess lysine into the vacuole. When lysine is depleted, Ypq1 is sorted into the multivesicular body (MVB) for degradation (Fig. 1). This process is initiated once Ypq1 is ubiquitinated by the ubiquitin ligase complex Rsp5–Ssh4, but how Ypq1 is targeted by Rsp5–Ssh4 has been unclear (9).Open in a separate windowFigure 1.Regulated recognition of Ypq1 by Ssh4. When lysine in the cytosol is abundant, Ypq1 undergoes a rapid conformational cycle to transport lysine from the cytosol into the vacuole lumen. Under lysine-depleted conditions, the transporter is trapped in a conformation recognizable by Ssh4, which recruits Rsp5 to catalyze Ypq1 ubiquitination and internalization into the MVB. Ub, ubiquitin.To understand the mechanism of Ypq1 recognition, Arines et al. first engineered a Ypq1 mutant that uncouples ligase-mediated degradation from lysine availability. This Ypq1 mutant is constitutively degraded in an Ssh4-dependent manner even under lysine-replete conditions. With this tool in hand, they performed a random mutagenesis-based suppressor screen, which identified many suppressor mutants. Mapping these mutations revealed several elements in Ypq1 that are critical for ligase recognition, which include two TMDs (TM5 and TM7) and a cytosolic loop. Importantly, when these mutations were introduced back into wild-type Ypq1, they also block Ssh4-dependent, lysine-regulated Ypq1 degradation. As expected, coimmunoprecipitation showed that Ypq1 suppressor mutants have reduced affinity to Ssh4. Since the cytosolic loop contains a previously known Rsp5 recognition motif, they further characterized the role of Ypq1 TMDs in ligase recruitment.Structural modeling suggests that TM5 and TM7 are juxtaposed to each other. Systematic mutagenesis targeting each residue of these two TMDs further consolidated the residues essential for Ssh4-mediated degradation. A similar mutagenesis study on Ssh4 revealed an important role for the Ssh4 TMD in Ypq1 degradation. Interestingly, for both Ssh4 and Ypq1, many identified residues are clustered on one side of the membrane helices. Arines et al. propose that Ssh4 uses its TMD to recognize TM5 and TM7 in Ypq1 based on a charge complementation experiment: a charged residue introduced into TM5 of Ypq1 abolished Ssh4-mediated degradation, but introducing an opposite charge into the TMD of Ssh4 restored lysine-regulated Ypq1 degradation.The recognition of Ypq1 by Ssh4 appears to occur when Ypq1 adopts a specific conformation during lysine transport because charge complementarity–based degradation of Ypq1 depends on the PQ loop, which is required for lysine transport. Additionally, structural modeling of Ypq1 suggested that in the inward-open and occluded conformations, TM5 is packed against TM7, but the two TMDs become distant from each other in the outward-open conformation, which exposes residues critical for Ssh4 recognition. These findings suggest that the rapid conformational cycling during lysine transport may prevent Ssh4 recognition, but lysine depletion stalls Ypq1 in a conformation recognizable by Ssh4 (Fig. 1).The study, together with the recent discovery of the ER membrane protein complex (EMC) in the biogenesis of multi-spanning membrane proteins at the ER, suggests a new class of chaperones that recognize specific features in TMDs. While emerging evidence suggests that the EMC recognizes exposed charged or polar residues in TMDs (10), the molecular basis of Ssh4 substrate interaction remains unclear. Like cytosolic chaperones, the EMC at the ER appears to play a dual role: while initially shielding charged/polar residues to facilitate TMD assembly, it may eventually target misassembled membrane proteins for degradation. By contrast, TMD-specific chaperones in other organelles like Ssh4 may have a more dedicated function in PQC. Clearly, more TMD-specific chaperones await to be discovered. Additionally, future studies will surely reveal not only the range of substrates and functions for each TMD-specific chaperone but also the structural basis of TMD recognition.     

Novel proteomic tools reveal essential roles of SRP and importance of proper membrane protein biogenesis

The signal recognition particle (SRP), which mediates cotranslational protein targeting to cellular membranes, is universally conserved and essential for bacterial and mammalian cells. However, the current understanding of the role of SRP in cell physiology and pathology is still poor, and the reasons behind its essential role in cell survival remain unclear. Here, we systematically analyzed the consequences of SRP loss in E. coli using time-resolved quantitative proteomic analyses. A series of snapshots of the steady-state and newly synthesized proteome unveiled three stages of cellular responses to SRP depletion, and demonstrated essential roles of SRP in metabolism, membrane potential, and protein and energy homeostasis in both the membrane and cytoplasm. We also identified a group of periplasmic proteins, including key molecular chaperones, whose localization was impaired by the loss of SRP; this and additional results showed that SRP is crucial for protein homeostasis in the bacterial envelope. These results reveal the extensive roles that SRP plays in bacterial physiology, emphasize the importance of proper membrane protein biogenesis, and demonstrate the ability of time-resolved quantitative proteomic analysis to provide new biological insights.     

Tail-anchored membrane protein insertion into the endoplasmic reticulum

Membrane proteins are inserted into the endoplasmic reticulum (ER) by two highly conserved parallel pathways. The well-studied co-translational pathway uses signal recognition particle (SRP) and its receptor for targeting and the SEC61 translocon for membrane integration. A recently discovered post-translational pathway uses an entirely different set of factors involving transmembrane domain (TMD)-selective cytosolic chaperones and an accompanying receptor at the ER. Elucidation of the structural and mechanistic basis of this post-translational membrane protein insertion pathway highlights general principles shared between the two pathways and key distinctions unique to each.