Characterization of the rough endoplasmic reticulum ribosome-binding activity

Bio-Coreactant-Enhanced Electrochemiluminescence Microscopy of Intracellular Structure and Transport

A bio-coreactant-enhanced electrochemiluminescence (ECL) microscopy realizes the ECL imaging of intracellular structure and dynamic transport. This microscopy uses Ru(bpy)₃ ²⁺ as the electrochemical molecular antenna connecting extracellular and intracellular environments, and uses intracellular biomolecules as the coreactants of ECL reactions via a "catalytic route". Accordingly, intracellular structures are identified without using multiple labels, and autophagy involving DNA oxidative damage is detected using nuclear ECL signals. A time-resolved image sequence discloses the universal edge effect of cellular electroporation due to the influence of the geometric properties of cell membranes on the induced transmembrane voltage. The dynamic transport of Ru(bpy)₃ ³⁺ in the different cellular compartments unveils the heterogeneous intracellular diffusivity correlating with the actin cytoskeleton. In addition to single-cell studies, the bio-coreactant-enhanced ECL microscopy is used to image a slice of a mouse liver and a colony of Shewanella oneidensis MR-1.

Diversity and selectivity in mRNA translation on the endoplasmic reticulum

Pioneering electron microscopy studies defined two primary populations of ribosomes in eukaryotic cells: one freely dispersed through the cytoplasm and the other bound to the surface of the endoplasmic reticulum (ER). Subsequent investigations revealed a specialized function for each population, with secretory and integral membrane protein-encoding mRNAs translated on ER-bound ribosomes, and cytosolic protein synthesis was widely attributed to free ribosomes. Recent findings have challenged this view, and transcriptome-scale studies of mRNA distribution and translation have now demonstrated that ER-bound ribosomes also function in the translation of a large fraction of mRNAs that encode cytosolic proteins. These studies suggest a far more expansive role for the ER in transcriptome expression, where membrane and secretory protein synthesis represents one element of a multifaceted and dynamic contribution to post-transcriptional gene expression.

Localization of mRNAs to the endoplasmic reticulum

Almost all cells use mRNA localization to establish spatial control of protein synthesis. One of the best-studied examples is the targeting and anchoring of mRNAs encoding secreted, organellar, and membrane-bound proteins to the surface of the endoplasmic reticulum (ER). In this review, we provide a historical perspective on the research that elucidated the canonical protein-mediated targeting of nascent-chain ribosome mRNA complexes to the surface of the ER. We then discuss subsequent studies which provided concrete evidence that a subpopulation of mRNAs utilize a translation-independent mechanism to localize to the surface of this organelle. This alternative mechanism operates alongside the signal recognition particle (SRP) mediated co-translational targeting pathway to promote proper mRNA localization to the ER. Recent work has uncovered trans-acting factors, such as the mRNA receptor p180, and cis-acting elements, such as transmembrane domain coding regions, that are responsible for this alternative mRNA localization process. Furthermore, some unanticipated observations have raised the possibility that this alternative pathway may be conserved from bacteria to mammalian cells.

p180 promotes the ribosome-independent localization of a subset of mRNA to the endoplasmic reticulum

The localization of many secretory mRNAs to the endoplasmic reticulum does not require ribosomes or translation, but is instead promoted by p180, an abundant, membrane-bound protein that likely binds directly to mRNA.

In metazoans, the majority of mRNAs coding for secreted and membrane-bound proteins are translated on the surface of the endoplasmic reticulum (ER). Although the targeting of these transcripts to the surface of the ER can be mediated by the translation of a signal sequence and their maintenance is mediated by interactions between the ribosome and the translocon, it is becoming increasingly clear that additional ER-localization pathways exist. Here we demonstrate that many of these mRNAs can be targeted to, and remain associated with, the ER independently of ribosomes and translation. Using a mass spectrometry analysis of proteins that associate with ER-bound polysomes, we identified putative mRNA receptors that may mediate this alternative mechanism, including p180, an abundant, positively charged membrane-bound protein. We demonstrate that p180 over-expression can enhance the association of generic mRNAs with the ER. We then show that p180 contains a lysine-rich region that can directly interact with RNA in vitro. Finally, we demonstrate that p180 is required for the efficient ER-anchoring of bulk poly(A) and of certain transcripts, such as placental alkaline phosphatase and calreticulin, to the ER. In summary, we provide, to our knowledge, the first mechanistic details for an alternative pathway to target and maintain mRNA at the ER. It is likely that this alternative pathway not only enhances the fidelity of protein sorting, but also localizes mRNAs to various subdomains of the ER and thus contributes to cellular organization.

Messenger RNAs (mRNAs) that encode secreted or membrane-bound proteins must be delivered to, and then maintained on, the surface of the endoplasmic reticulum (ER). These mRNAs encode a short polypeptide that targets the mRNA/ribosome/nascent protein complexes to the ER surface during translation; however, recent studies support the existence of additional ER-localization signals that might be present within the mRNA molecules themselves. Here, we demonstrate that a fraction of these mRNAs, whose encoded proteins are destined for secretion, contain information that targets and anchors them to the ER independently of their encoded polypeptide or their association to ribosomes. We identify proteins on the ER that may serve as receptors for these mRNAs. We then show that one of these candidate membrane-bound receptors, p180, is required for the maintenance of certain mRNAs on the surface of the ER even after their translation into protein is disrupted. We also demonstrate that p180 contains a region that binds directly to RNA and likely mediates the anchoring of mRNA to the ER. Our study thus provides the first mechanistic details of an alternative pathway used to ensure that secretory mRNAs, and their encoded proteins, reach their proper destination in the ER.

Protein translocation into the endoplasmic reticulum: a light at the end of the tunnel

Intracellular transport of secretory of proteins and many membrane proteins in eukaryotic cells commences with their translocation into or across the membrane of the rough endoplasmic reticulum. Several components of the cellular machinery that mediates this process have been elucidated using in vitro assays or by genetic means. An analysis of how they function will depend on the ability to reassemble them into translocation-competent lipid vesicles.

The case for extending storage and secretion functions of human mast cell granules to include synthesis

Ultrastructural studies using standard procedures have for years indicated close associations of ribosomes and secretory granules in human mast cells. These descriptive studies have informed new studies, using established and new ultrastructural methods based on different principles, designed to investigate the possible role of RNA metabolism in secretory granules of human mast cells. In aggregate, these studies indicate human mast cell secretory granule associations with ribosomes, the protein synthetic machine of cells, with ribosomal proteins, with RNA, with poly(A)-positive mRNA and with various long-lived, or short-lived, uridine-rich, and poly(A)-poor RNA species with key roles in RNA processing and splicing. These studies indicate that secretory-storage granules in human mast cells may also be synthetic granules.

Ribosome-independent regulation of translocon composition and Sec61alpha conformation

In this study, the contributions of membrane-bound ribosomes to the regulation of endoplasmic reticulum translocon composition and Sec61alpha conformation were examined. Following solubilization of rough microsomes (RM) with digitonin, ribosomes co-sedimented in complexes containing the translocon proteins Sec61alpha, ribophorin I, and TRAPalpha, and endoplasmic reticulum phospholipids. Complexes of similar composition were identified in digitonin extracts of ribosome-free membranes, indicating that the ribosome does not define the composition of the digitonin-soluble translocon. Whereas in digitonin solution a highly electrostatic ribosome-translocon junction is observed, no stable interactions between ribosomes and Sec61alpha, ribophorin I, or TRAPalpha were observed following solubilization of RM with lipid-derived detergents at physiological salt concentrations. Sec61alpha was found to exist in at least two conformational states, as defined by mild proteolysis. A protease-resistant form was observed in RM and detergent-solubilized RM. Removal of peripheral proteins and ribosomes markedly enhanced the sensitivity of Sec61alpha to proteolysis, yet the readdition of inactive ribosomes to salt-washed membranes yielded only modest reductions in protease sensitivity. Addition of sublytic concentrations of detergents to salt-washed RM markedly decreased the protease sensitivity of Sec61alpha, indicating that a protease-resistant conformation of Sec61alpha can be conferred in a ribosome-independent manner.

Translocation of proteins across the endoplasmic reticulum membrane

Secretory protein biogenesis begins with the insertion of a preprotein into the lumen of the endoplasmic reticulum (ER). This insertion event, known as ER protein translocation, can occur either posttranslationally, in which the preprotein is completely synthesized on cytosolic ribosomes before being translocated, or cotranslationally, in which membrane-associated ribosomes direct the nascent polypeptide chain into the ER concomitant with polypeptide elongation. In either case, preproteins are targeted to the ER membrane through specific interactions with cytosolic and/or ER membrane factors. The preprotein is then transferred to a multiprotein translocation machine in the ER membrane that includes a pore through which the preprotein passes into the ER lumen. The energy required to drive protein translocation may derive either from the coupling of translation to translocation (during cotranslational translocation) or from ER lumenal molecular chaperones that may harness the preprotein or regulate the translocation machinery (during posttranslational translocation).

Receptor-mediated ribosome binding to liposomes depends on lipid composition

Ribosome binding to the endoplasmic reticulum has been traditionally studied using an in vitro assay in which potential ribosome receptors have been purified, incorporated into synthetic liposomes, and tested for activity. One such receptor (180 kDa; "p180") has been shown to bind ribosomes with high affinity in such a system when purified to homogeneity. This result has been challenged by data generated in other laboratories, and as a result, doubt has lingered as to the authenticity of p180 as a ribosome receptor. The contribution of the major difference between these studies, the lipid composition of the liposomes used in the in vitro assays, was assessed when identical fractions of rough endoplasmic reticulum-specific membrane proteins were incorporated into liposomes composed of only phosphatidylcholine (as used in other laboratories), a 50:50 mix of phosphatidylcholine and phosphatidylserine (as used in our original studies), or lipids derived from canine pancreatic microsomes (as a physiologically relevant control). The presence of PS was found to be crucial for the incorporation into and ribosome binding activity of p180 in liposomes. These observations are compatible with published studies on the importance of acidic phospholipids in ribosome binding to intact microsomes and reconcile the apparently conflicting in vitro results surrounding the assignment of p180 as a ribosome receptor.

Identification of a novel stage of ribosome/nascent chain association with the endoplasmic reticulum membrane

Protein translocation in the mammalian endoplasmic reticulum (ER) occurs cotranslationally and requires the binding of translationally active ribosomes to components of the ER membrane. Three candidate ribosome receptors, p180, p34, and Sec61p, have been identified in binding studies with inactive ribosomes, suggesting that ribosome binding is mediated through a receptor-ligand interaction. To determine if the binding of nascent chain-bearing ribosomes is regulated in a manner similar to inactive ribosomes, we have investigated the ribosome/nascent chain binding event that accompanies targeting. In agreement with previous reports, indicating that Sec61p displays the majority of the ER ribosome binding activity, we observed that Sec61p is shielded from proteolytic digestion by native, bound ribosomes. The binding of active, nascent chain bearing ribosomes to the ER membrane is, however, insensitive to the ribosome occupancy state of Sec61p. To determine if additional, Sec61p independent, stages of the ribosome binding reaction could be identified, ribosome/nascent chain binding was assayed as a function of RM concentration. At limiting RM concentrations, a protease resistant ribosome-membrane junction was formed, yet the nascent chain was salt extractable and cross-linked to Sec61p with low efficiency. At nonlimiting RM concentrations, bound nascent chains were protease and salt resistant and cross-linked to Sec61p with higher efficiency. On the basis of these and other data, we propose that ribosome binding to the ER membrane is a multi-stage process comprised of an initial, Sec61p independent binding event, which precedes association of the ribosome/nascent chain complex with Sec61p.

The intrinsic ability of ribosomes to bind to endoplasmic reticulum membranes is regulated by signal recognition particle and nascent-polypeptide-associated complex

Signal peptides direct the cotranslational targeting of nascent polypeptides to the endoplasmic reticulum (ER). It is currently believed that the signal recognition particle (SRP) mediates this targeting by first binding to signal peptides and then by directing the ribosome/nascent chain/SRP complex to the SRP receptor at the ER. We show that ribosomes can mediate targeting by directly binding to translocation sites. When purified away from cytosolic factors, including SRP and nascent-polypeptide-associated complex (NAC), in vitro assembled translation intermediates representing ribosome/nascent-chain complexes efficiently bound to microsomal membranes, and their nascent polypeptides could subsequently be efficiently translocated. Because removal of cytosolic factors from the ribosome/nascent-chain complexes also resulted in mistargeting of signalless nascent polypeptides, we previously investigated whether readdition of cytosolic factors, such as NAC and SRP, could restore fidelity to targeting. Without SRP, NAC prevented all nascent-chain-containing ribosomes from binding to the ER membrane. Furthermore, SRP prevented NAC from blocking ribosome-membrane association only when the nascent polypeptide contained a signal. Thus, NAC is a global ribosome-binding prevention factor regulated in activity by signal-peptide-directed SRP binding. A model presents ribosomes as the targeting vectors for delivering nascent polypeptides to translocation sites. In conjunction with signal peptides, SRP and NAC contribute to this specificity of ribosomal function by regulating exposure of a ribosomal membrane attachment site that binds to receptors in the ER membrane.

Binding of ribosomes to the rough endoplasmic reticulum mediated by the Sec61p-complex

The cotranslational translocation of proteins across the ER membrane involves the tight binding of translating ribosomes to the membrane, presumably to ribosome receptors. The identity of the latter has been controversial. One putative receptor candidate is Sec61 alpha, a multi-spanning membrane protein that is associated with two additional membrane proteins (Sec61 beta and gamma) to form the Sec61p-complex. Other receptors of 34 and 180 kD have also been proposed on the basis of their ability to bind at low salt concentration ribosomes lacking nascent chains. We now show that the Sec61p-complex has also binding activity but that, at low salt conditions, it accounts for only one third of the total binding sites in proteoliposomes reconstituted from a detergent extract of ER membranes. Under these conditions, the assay has also limited specificity with respect to ribosomes. However, if the ribosome-binding assay is performed at physiological salt concentration, most of the unspecific binding is lost; the Sec61p-complex then accounts for the majority of specific ribosome-binding sites in reconstituted ER membranes. To study the membrane interaction of ribosomes participating in protein translocation, native rough microsomes were treated with proteases. The amount of membrane-bound ribosomes is only slightly reduced by protease treatment, consistent with the protease-resistance of Sec61 alpha which is shielded by these ribosomes. In contrast, p34 and p180 can be readily degraded, indicating that they are not essential for the membrane anchoring of ribosomes in protease-treated microsomes. These data provide further evidence that the Sec61p-complex is responsible for the membrane-anchoring of ribosomes during translocation and make it unlikely that p34 or p180 are essential for this process.

Translocation of proteins across the endoplasmic reticulum

The past year has seen significant advances in the field of protein translocation: the roles of the signal recognition particle and its receptor have been understood in greater detail; many membrane components responsible for translocation have been identified; and insight has been gained into how proteins cross membranes.

Protein secretion in Bacillus species

Bacilli secrete numerous proteins into the environment. Many of the secretory proteins, their export signals, and their processing steps during secretion have been characterized in detail. In contrast, the molecular mechanisms of protein secretion have been relatively poorly characterized. However, several components of the protein secretion machinery have been identified and cloned recently, which is likely to lead to rapid expansion of the knowledge of the protein secretion mechanism in Bacillus species. Comparison of the presently known export components of Bacillus species with those of Escherichia coli suggests that the mechanism of protein translocation across the cytoplasmic membrane is conserved among gram-negative and gram-positive bacteria differences are found in steps preceding and following the translocation process. Many of the secretory proteins of bacilli are produced industrially, but several problems have been encountered in the production of Bacillus heterologous secretory proteins. In the final section we discuss these problems and point out some possibilities to overcome them.

180-kD ribosome receptor is essential for both ribosome binding and protein translocation

We have previously isolated a 180-kD ribosome receptor (p180) from mammalian rough ER that, when incorporated into liposomes, bound ribosomes with an affinity similar to intact membranes. To directly assess the contribution of p180 to ribosome binding as well as protein translocation, monoclonal antibodies were used to selectively deplete p180 from the detergent extracts of rough ER membranes used in the preparation of translocation-competent proteoliposomes. Proteoliposomes prepared from p180-depleted extracts showed a reduction in ribosome binding to the level of trypsin-inactivated controls as well as a loss in their ability to cotranslationally translocate two different secretory protein precursors. When purified p180 was added back to depleted extracts before proteoliposome formation, both ribosome binding and translocation activity were restored. In addition, the monoclonal antibodies, as well as their Fab' fragments, were able to inhibit ribosome binding and protein translocation when bound to intact rough microsomes. These data provide direct evidence that the 180-kD ribosome receptor is essential for ribosome binding and for the translocation of nascent proteins across the membrane of the rough ER.

Transport of proteins across the endoplasmic reticulum membrane

The biosynthesis of many eukaryotic proteins requires their transport across the endoplasmic reticulum (ER) membrane. The process can be divided into two phases: (i) a targeting cycle, during which, by virtue of their signal sequences, nascent polypeptides are directed to translocation sites in the ER and (ii) the actual transfer of proteins across the membrane. The first phase has been well characterized, whereas the latter until recently was completely unresolved. Key components of the translocation apparatus have now been identified and it seems likely that they form a protein-conducting channel in the ER membrane. The transport process is similar to the process of protein export in bacteria.

A mammalian homolog of SEC61p and SECYp is associated with ribosomes and nascent polypeptides during translocation

SEC61p is essential for protein translocation across the endoplasmic reticulum membrane of S. cerevisiae. We have found a mammalian homolog that shows more than 50% sequence identity with the yeast protein. Moreover, several regions of SEC61p have significant similarities with corresponding ones of SecYp of bacteria, indicating a strong evolutionary conservation of the mechanism of protein translocation. Mammalian Sec61p, like the yeast protein, is located in the immediate vicinity of nascent polypeptides during their membrane passage. It is tightly associated with membrane-bound ribosomes, suggesting that the nascent chain passes directly from the ribosome into a protein-conducting channel. These results define Sec61p as a ubiquitous key component of the protein translocation apparatus.

Protein targeting to and translocation across the membrane of the endoplasmic reticulum

Several approaches are currently being taken to elucidate the mechanisms and the molecular components responsible for protein targeting to and translocation across the membrane of the endoplasmic reticulum. Two experimental systems dominate the field: a biochemical system derived from mammalian exocrine pancreas, and a combined genetic and biochemical system employing the yeast, Saccharomyces cerevisiae. Results obtained in each of these systems have contributed novel, mostly non-overlapping information. Recently, much effort in the field has been dedicated to identifying membrane proteins that comprise the translocon. Membrane proteins involved in translocation have been identified both in the mammalian system, using a combination of crosslinking and reconstitution approaches, and in S. cerevisiae, by selecting for mutants in the translocation pathway. None of the membrane proteins isolated, however, appears to be homologous between the two experimental systems. In the case of the signal recognition particle, the two systems have converged, which has led to a better understanding of how proteins are targeted to the endoplasmic reticulum membrane.

The signal sequence receptor, unlike the signal recognition particle receptor, is not essential for protein translocation

Detergent extracts of canine pancreas rough microsomal membranes were depleted of either the signal recognition particle receptor (SR), which mediates the signal recognition particle (SRP)-dependent targeting of the ribosome/nascent chain complex to the membrane, or the signal sequence receptor (SSR), which has been proposed to function as a membrane bound receptor for the newly targeted nascent chain and/or as a component of a multi-protein translocation complex responsible for transfer of the nascent chain across the membrane. Depletion of the two components was performed by chromatography of detergent extracts on immunoaffinity supports. Detergent extracts lacking either SR or SSR were reconstituted and assayed for activity with respect to SR dependent elongation arrest release, nascent chain targeting, ribosome binding, secretory precursor translocation, and membrane protein integration. Depletion of SR resulted in the loss of elongation arrest release activity, nascent chain targeting, secretory protein translocation, and membrane protein integration, although ribosome binding was unaffected. Full activity was restored by addition of immunoaffinity purified SR before reconstitution of the detergent extract. Surprisingly, depletion of SSR was without effect on any of the assayed activities, indicating that SSR is either not required for translocation or is one of a family of functionally redundant components.

Isolation and some properties of a 34-kDa-membrane protein that may be responsible for ribosome binding in rat liver rough microsomes

We have isolated, by hydroxyapatite chromatography with a non ionic detergent and a high salt concentration, a non-glycosylated, membrane protein with a relative molecular weight of 34 kDa that had previously been found to be a major constituent of the membrane protein fraction showing ribosome-binding activity derived from rat liver rough microsomes (RM). The isolated 34 kDa protein (p34), when incorporated into a liposome model membrane, exhibited significant binding activity toward ribosomes, its binding properties being similar to those observed with intact RM. Immunochemical analyses using antibodies directed against p34 suggested that it is a membrane-embedded RM surface protein, which is specifically localized in ribosome-attached organelles and widely distributed among mammalian tissues. These results would constitute evidence that p34 is a likely candidate for an RM ribosome-binding protein.

An ATP-binding membrane protein is required for protein translocation across the endoplasmic reticulum membrane

The role of nucleotides in providing energy for polypeptide transfer across the endoplasmic reticulum (ER) membrane is still unknown. To address this question, we treated ER-derived mammalian microsomal vesicles with a photoactivatable analogue of ATP, 8-N3ATP. This treatment resulted in a progressive inhibition of translocation activity. Approximately 20 microsomal membrane proteins were labeled by [alpha 32P]8-N3ATP. Two of these were identified as proteins with putative roles in translocation, alpha signal sequence receptor (SSR), the 35-kDa subunit of the signal sequence receptor complex, and ER-p180, a putative ribosome receptor. We found that there was a positive correlation between inactivation of translocation activity and photolabeling of alpha SSR. In contrast, our data demonstrate that the ATP-binding domain of ER-p180 is dispensable for translocation activity and does not contribute to the observed 8-N3ATP sensitivity of the microsomal vesicles.