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Results for “Signal Recognition Particle”

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PubMed1992

Role of pilA, an essential regulatory gene of Neisseria gonorrhoeae, in the stress response.

Sequence analysis has shown that PilA, a transcriptional regulator of pilin gene expression in Neisseria gonorrhoeae, has extensive homology with the 54-kDa protein of the signal recognition particle of eukaryotes and its receptor, as well as with two proteins of Escherichia coli, FtsY and Ffh, which have been proposed to be a part of a signal recognition particle-like apparatus. We tested the putative role of PilA in protein export in N. gonorrhoeae and did not find any effect. However, we did observe induction of a heat shock response and a previously described slow-growth phenotype when PilA function was impaired. We also examined the interference of pilA expression in E. coli with the function of the products of ftsY and ffh and observed an accumulation of pre-beta-lactamase. We argue against a direct role for PilA in protein export in gonococci and propose instead that PilA is involved in the modulation of cell growth rate in response to different environmental conditions.

Bacterial Outer Membrane Proteins↗

PubMed1999

Signal sequence recognition and protein targeting.

Intracellular traffic is often controlled not by highways, but by handshakes and partner introductions within a cellular network. Recently determined structures suggest how signal sequences are recognized and how the GTP affinities of the signal recognition particle and its receptor are coupled to the targeting of ribosomes to translocational membrane pores. The structure of signal peptidase suggests how it releases functional proteins.

Base Sequence↗

PubMed1994

Identification of an internal topogenic signal sequence in human Band 3, the erythrocyte anion exchanger.

The insertion of Band 3, the human erythrocyte anion exchanger, into microsomal membranes was studied in an in vitro reticulocyte lysate translation system. Band 3 consists of a 43-kDa amino-terminal cytosolic domain and a carboxyl-terminal 52-kDa membrane domain containing up to 14 transmembrane segments with a single N-glycosylation site at Asn-642. Insertion of truncated Band 3 molecules into microsomal membranes was assayed by glycosylation, resistance to alkaline extraction, and tryptic removal of the cytosolic domain. Truncations containing either the first four or the last eight putative transmembrane segments were stably integrated into microsomes showing that an intact membrane domain was not required for membrane integration. Furthermore, the extracytosolic domain following the seventh transmembrane segment was properly translocated across the microsomal membrane and glycosylated whether the seventh transmembrane segment was the first, last, or the only transmembrane segment in the construct. The ability of the entire membrane domain, the truncated domain beginning with the seventh transmembrane segment, or the seventh transmembrane segment to insert into microsomes was dependent on the presence of the signal recognition particle receptor. The seventh transmembrane segment in Band 3 therefore has the topogenic properties of an internal signal sequence.

Amino Acid Sequence↗

PubMed1997

Empty site forms of the SRP54 and SR alpha GTPases mediate targeting of ribosome-nascent chain complexes to the endoplasmic reticulum.

The SRP54 and SR alpha subunits of the signal recognition particle (SRP) and the SRP receptor (SR) undergo a tightly coupled GTPase cycle that mediates the signal sequence-dependent attachment of ribosomes to the Sec61 complex. Here, we show that SRP54 and SR alpha are in the empty site conformation prior to contact between the SRP-ribosome complex and the membrane-bound SR. Cooperative binding of GTP to SRP54 and SR alpha stabilizes the SRP-SR complex and initiates signal sequence transfer from SRP54 to Sec61 alpha. The GTP-bound conformations of SR alpha and SRP54 perform distinct roles, with SR alpha performing a predominant role in complex stabilization. Hydrolysis by both SRP54 and SR alpha is a prerequisite for dissociation of the SRP-SR complex.

Animals↗

PubMed1996

A two-step recognition of signal sequences determines the translocation efficiency of proteins.

The cytosolic and secreted, N-glycosylated, forms of plasminogen activator inhibitor-2 (PAI-2) are generated by facultative translocation. To study the molecular events that result in the bi-topological distribution of proteins, we determined in vitro the capacities of several signal sequences to bind the signal recognition particle (SRP) during targeting, and to promote vectorial transport of murine PAI-2 (mPAI-2). Interestingly, the six signal sequences we compared (mPAI-2 and three mutated derivatives thereof, ovalbumin and preprolactin) were found to have the differential activities in the two events. For example, the mPAI-2 signal sequence first binds SRP with moderate efficiency and secondly promotes the vectorial transport of only a fraction of the SRP-bound nascent chains. Our results provide evidence that the translocation efficiency of proteins can be controlled by the recognition of their signal sequences at two steps: during SRP-mediated targeting and during formation of a committed translocation complex. This second recognition may occur at several time points during the insertion/translocation step. In conclusion, signal sequences have a more complex structure than previously anticipated, allowing for multiple and independent interactions with the translocation machinery.

Amino Acid Sequence↗

PubMed2004

Protein traffic for secretion and related machinery of Bacillus subtilis.

Gram-positive sporulating Bacillus subtilis secretes high levels of protein. Its complete genome sequence, published in 1997, encodes 4,106 proteins. Bioinformatic searches have predicted that about half of all B. subtilis proteins are related to the cell membrane through export to the extracellular medium, insertion, and attachment. Key features of the B. subtilis protein secretion machinery are the absence of an Escherichia coli SecB homolog and the presence of an SRP (signal recognition particle) that is structurally rather similar to human SRP. In addition, B. subtilis contains five type I signal peptidases (SipS, T, U, V, and W). Our in vitro assay system indicated that co-operation between the SRP-protein targeting system to the cell membrane and the Sec protein translocation machinery across the cytoplasmic membrane constitutes the major protein secretion pathway in B. subtilis. Furthermore, the function of the SRP-Sec pathway in protein localization to the cell membrane and spore was analyzed.

Bacillus subtilis↗

PubMed1998

Ribonucleoprotein particles of quiescent maize embryonic axes.

Certain RNA molecules are known to be sequestered and stored as ribonucleoprotein particles (RNPs) in many different tissues, particularly at some stages of metabolic quiescence. In this research RNPs from embryonic axes of mature maize seeds were isolated by sucrose and CsCl gradient centrifugation and characterized based on their RNA and protein contents. Two types of RNP particles of non-ribosomal nature were identified by northern blot analysis with specific probes: the 7S RNP and the signal recognition particle (SRP) particles which contain 5S rRNA and 7S RNA respectively. The proteins associated to these RNA molecules were the transcription factor TFIIIA-homologous protein associated to 7S RNP, and the p72, p68 and p54-GTPase proteins associated to SRP.

Base Sequence↗

PubMed2000

Crystal structure of the ffh and EF-G binding sites in the conserved domain IV of Escherichia coli 4.5S RNA.

BACKGROUND: Bacterial signal recognition particle (SRP), consisting of 4.5S RNA and Ffh protein, plays an essential role in targeting signal-peptide-containing proteins to the secretory apparatus in the cell membrane. The 4.5S RNA increases the affinity of Ffh for signal peptides and is essential for the interaction between SRP and its receptor, protein FtsY. The 4.5S RNA also interacts with elongation factor G (EF-G) in the ribosome and this interaction is required for efficient translation. RESULTS: We have determined by multiple anomalous dispersion (MAD) with Lu(3+) the 2.7 A crystal structure of a 4.5S RNA fragment containing binding sites for both Ffh and EF-G. This fragment consists of three helices connected by a symmetric and an asymmetric internal loop. In contrast to NMR-derived structures reported previously, the symmetric loop is entirely constituted by non-canonical base pairs. These pairs continuously stack and project unusual sets of hydrogen-bond donors and acceptors into the shallow minor groove. The structure can therefore be regarded as two double helical rods hinged by the asymmetric loop that protrudes from one strand. CONCLUSIONS: Based on our crystal structure and results of chemical protection experiments reported previously, we predicted that Ffh binds to the minor groove of the symmetric loop. An identical decanucleotide sequence is found in the EF-G binding sites of both 4.5S RNA and 23S rRNA. The decanucleotide structure in the 4.5S RNA and the ribosomal protein L11-RNA complex crystals suggests how 4.5S RNA and 23S rRNA might interact with EF-G and function in translating ribosomes.

Bacterial Proteins↗

PubMed1998

Membrane topology of NADPH-cytochrome P450 reductase on the endoplasmic reticulum.

Topology of the membrane-anchoring segment of mouse NADPH-cytochrome P450 reductase in the endoplasmic reticulum membrane was elucidated. An N-glycosylation site was generated in the amino-terminal hydrophilic sequence of the reductase, and the mutated protein was expressed in a cell-free system in the presence of microsomal vesicles. The in vitro synthesized reductase protein was integrated into the microsomal membrane and N-glycosylated depending on the presence of signal recognition particles. We conclude that the amino-terminal membrane-anchoring segment of the reductase is a type I signal-anchor sequence which shows amino-terminus-lumen and carboxy-terminus-cytoplasm topology.

Amino Acid Sequence↗

PubMed1989

Association of 7 SL RNA and an SRP-like particle with polysomes and endoplasmic reticulum in the developing sea urchin embryo.

We have identified the sea urchin cognate of the mammalian signal recognition particle (SRP). This particle contains the diagnostic 7 SL small RNA, sediments at a similar velocity to that reported for the mammalian particle, and is found associated with the ER and polysomes. We have examined its subcellular localization during embryogenesis in order to determine whether it could serve in a translational regulatory capacity for a subset of the stored maternal mRNAs. In these studies the 7 SL RNA was used as a marker for the particle, since we determined that the 7 SL RNA exists exclusively within the SRP-like particle at all developmental stages. The relative distribution of the SRP among cytoplasmic structures changes dramatically during development. This represents an actual change in subcellular localization because the 7 SL RNA level remains nearly constant per embryo until the pluteus stage, when it increases slightly. In eggs, the SRP exists almost entirely free in the cytoplasm as an 11 S particle. Very soon after fertilization and throughout development there is an increase in the association of the particle with rapidly sedimenting structures, until by the pluteus stage greater than 90% of the SRP exists in a bound state. The nature of the associations is complex, and the bound structures include, at least in part, ribosomes, polysomes, and microsomes. The SRP is associated with microsomal membranes in gastrula (36 hr) but not in blastula (12 hr) or earlier embryos. Using the criteria of sensitivity to Triton X-100, we determined that 16% of the SRP in a 10,000g cytoplasmic fraction was bound to membranes in a microsomal (endoplasmic reticulum)-containing fraction in the gastrula. In contrast, less than 1% was membrane associated in the blastula. The SRP was also found in a ribosome-polysome fraction in 12-, 36-, and 48-hr embryos, but not in eggs. Finally, a small but significant portion of the SRP was found associated with monosomes in cleavage stage embryos. The possible role the SRP could play in the elongation arrest of stored maternal messages for secreted proteins is discussed.

Animals↗

PubMed1989

SRP-dependent membrane integration of the beta-subunit of Na+,K+-ATPase.

cDNA clones coding for either full-length or truncated forms of the beta-subunit of the Na+,K+-ATPase from pig kidney were engineered into a transcription vector based on a T7 promotor. In vitro transcription and subsequent translation of the mRNA in the presence of rough microsomes (RM) yielded beta-subunit molecules that were N-glycosylated and correctly inserted into the membrane. The signal peptide was not cleaved off. This membrane integration was found to be dependent on the function of the signal recognition particle (SRP). Several lines of evidence suggest that the hydrophilic aminoterminal domain of 34 amino acid residues preceding the postulated signal sequence is located on the cytoplasmic side whereas the carboxyterminal glycosylated domain is located on the exoplasmic side of the ER (endoplasmic reticulum)-membrane (type II membrane protein).

Animals↗

PubMed1994

Formation of SRP-like particle induces a conformational change in E. coli 4.5S RNA.

E. coli P48 protein is homologous to the SRP54 component of the eukaryotic signal recognition particle. In vivo, P48 is associated with 4.5S RNA which shares a homology with eukaryotic SRP RNA. To study the interaction between P48 and 4.5S RNA in vitro, we used 4.5S RNA with fluorescein coupled to the 3'-terminal ribose. Upon binding of P48, the fluorescent 4.5S RNA shows a substantial decrease in fluorescence. Fluorescence quenching as well as anisotropy measurements reveal that the effect is not due to a direct interaction of P48 with the dye. This suggests that the binding of P48 induces a conformational change in 4.5S RNA which affects the structure at the 3' end of the RNA. From equilibrium titrations with fluorescent 4.5S RNA, a dissociation constant of 0.15 microns is obtained for the RNA.protein complex. The formation of the complex is not affected by GTP binding to or hydrolysis by P48.

Bacterial Proteins↗

PubMed1991

Biochemical fractionation and assembly of the membrane components that mediate nascent chain targeting and translocation.

Fractionation of a microsomal detergent extract with ammonium sulfate allows separation of the signal recognition particle receptor (SR alpha), which is required for targeting of the nascent chain, from other microsomal proteins, such as signal peptidase, whose activity is displayed during subsequent translocation. The reconstituted SR alpha-enriched fraction is functional in assays of precursor targeting and elongation arrest release but lacks translocation activity. This defect can be complemented by addition, prior to reconstitution, of a separate protein subfraction. In addition, protein components necessary for translocation can be reversibly depleted from the complementary fraction, under conditions where precursor targeting is retained, by sulfhydryl-directed chromatography. Thus, precursor binding and translocation can be biochemically uncoupled, indicating that they are sequential reactions mediated by distinct components.

Animals↗

PubMed1987

Nascent secretory polypeptides synthesized on Escherichia coli ribosomes are not translocated across mammalian endoplasmic reticulum.

Cell-free protein-synthesizing systems from Escherichia coli and wheat germ were compared for their capacity to support the translocation of secretory proteins across microsomal membranes derived from mammalian endoplasmic reticulum. Three different secretory proteins, two of bacterial and one of eucaryotic origin, were tested in this respect. In all three cases a contrast between the results in the eucaryotic and procaryotic protein-synthesizing systems was revealed. Whereas the eucaryotic system, as expected, supported the translocation of nascent secretory proteins across the microsomal membranes, the procaryotic system failed to do so. This failure was not due to the absence of a translocation-promoting activity or the presence of a translocation-blocking activity in the procaryotic system. These results demonstrate a specificity in the requirement of components of the protein-synthesizing machinery for protein translocation. These components might participate in forming a functional ribosome-membrane junction during protein translocation. The nascent secretory chain alone is not sufficient for making this junction, which might involve the postulated binding of the ribosome to the signal recognition particle or another component of the membrane.

Bacterial Proteins↗

PubMed2004

Membrane targeting of a bacterial virulence factor harbouring an extended signal peptide.

Filamentous haemagglutinin (FHA) is the major adhesin of Bordetella pertussis, the whooping cough agent. FHA is synthesized as a 367-kDa precursor harbouring a remarkably long signal peptide with an N-terminal extension that is conserved among related virulence proteins. FHA is secreted via the two-partner secretion pathway that involves transport across the outer membrane by a cognate transporter protein. Here we have analyzed the mechanism by which FHA is targeted to, and translocated across, the inner membrane. Studies were performed both in vitro using Escherichia coli inside-out inner membrane vesicles and in vivo by pulse-chase labelling of Bordetella pertussis cells. The data collectively indicate that like classical periplasmic and outer membrane proteins, FHA requires SecA and SecB for its export through the SecYEG translocon in the inner membrane. Although short nascent chains of FHA were found to cross-link to signal recognition particle (SRP), we did not obtain indication for an SRP-dependent, co-translational membrane targeting provoked by the FHA signal sequence. Our results rule out that the extended signal peptide of FHA determines a specific mode of membrane targeting but rather suggest that it might influence the export rate at the inner membrane.

Adenosine Triphosphatases↗

PubMed2001

Evidence for a novel GTPase priming step in the SRP protein targeting pathway.

Protein targeting by the signal recognition particle (SRP) pathway requires the interaction of two homologous GTPases that reciprocally regulate each other's GTPase activity, the SRP signal peptide- binding subunit (SRP54) and the SRP receptor alpha-subunit (SRalpha). The GTPase domain of both proteins abuts a unique 'N domain' that appears to facilitate external ligand binding. To examine the relationship between the unusual regulation and unique architecture of the SRP pathway GTPases, we mutated an invariant glycine in Escherichia coli SRP54 and SRalpha orthologs ('Ffh' and 'FtsY', respectively) that resides at the N-GTPase domain interface. A G257A mutation in Ffh produced a lethal phenotype. The mutation did not significantly affect Ffh function, but severely reduced interaction with FtsY. Likewise, mutation of FtsY Gly455 produced growth defects and inhibited interaction with Ffh. The data suggest that Ffh and FtsY interact only in a 'primed' conformation which requires interdomain communication. Based on these results, we propose that the distinctive features of the SRP pathway GTPases evolved to ensure that SRP and the SR engage external ligands before interacting with each other.

Alleles↗

PubMed2001

The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase.

BACKGROUND: The signal recognition particle (SRP) is a phylogenetically conserved ribonucleoprotein that mediates cotranslational targeting of secreted and membrane proteins to the membrane. Targeting is regulated by GTP binding and hydrolysis events that require direct interaction between structurally homologous "NG" GTPase domains of the SRP signal recognition subunit and its membrane-associated receptor, SR alpha. Structures of both the apo and GDP bound NG domains of the prokaryotic SRP54 homolog, Ffh, and the prokaryotic receptor homolog, FtsY, have been determined. The structural basis for the GTP-dependent interaction between the two proteins, however, remains unknown. RESULTS: We report here two structures of the NG GTPase of Ffh from Thermus aquaticus bound to the nonhydrolyzable GTP analog GMPPNP. Both structures reveal an unexpected binding mode in which the beta-phosphate is kinked away from the binding site and magnesium is not bound. Binding of the GTP analog in the canonical conformation found in other GTPase structures is precluded by constriction of the phosphate binding P loop. The structural difference between the Ffh complex and other GTPases suggests a specific conformational change that must accompany movement of the nucleotide from an "inactive" to an "active" binding mode. CONCLUSIONS: Conserved side chains of the GTPase sequence motifs unique to the SRP subfamily may function to gate formation of the active GTP bound conformation. Exposed hydrophobic residues provide an interaction surface that may allow regulation of the GTP binding conformation, and thus activation of the GTPase, during the association of SRP with its receptor.

Amino Acid Motifs↗

PubMed2004

Saccharomyces SRP RNA secondary structures: a conserved S-domain and extended Alu-domain.

The contribution made by the RNA component of signal recognition particle (SRP) to its function in protein targeting is poorly understood. We have generated a complete secondary structure for Saccharomyces cerevisiae SRP RNA, scR1. The structure conforms to that of other eukaryotic SRP RNAs. It is rod-shaped with, at opposite ends, binding sites for proteins required for the SRP functions of signal sequence recognition (S-domain) and translational elongation arrest (Alu-domain). Micrococcal nuclease digestion of purified S. cerevisiae SRP separated the S-domain of the RNA from the Alu-domain as a discrete fragment. The Alu-domain resolved into several stable fragments indicating a compact structure. Comparison of scR1 with SRP RNAs of five yeast species related to S. cerevisiae revealed the S-domain to be the most conserved region of the RNA. Extending data from nuclease digestion with phylogenetic comparison, we built the secondary structure model for scR1. The Alu-domain contains large extensions, including a sequence with hallmarks of an expansion segment. Evolutionarily conserved bases are placed in the Alu- and S-domains as in other SRP RNAs, the exception being an unusual GU(4)A loop closing the helix onto which the signal sequence binding Srp54p assembles (domain IV). Surprisingly, several mutations within the predicted Srp54p binding site failed to disrupt SRP function in vivo. However, the strength of the Srp54p-scR1 and, to a lesser extent, Sec65p-scR1 interaction was decreased in these mutant particles. The availability of a secondary structure for scR1 will facilitate interpretation of data from genetic analysis of the RNA.

Alu Elements↗