Translocation Reaction Research Articles

Endogenous SecA Catalyzes Preprotein Translocation at SecYEG

SecA is found in the cytosol and bound to the plasma membrane of Escherichia coli. Binding occurs either with high affinity at SecYEG or with low affinity to lipid. Domains of 65 and 30 kDa of SecYEG-bound SecA insert into the membrane upon interaction with preprotein and ATP. Azide blocks preprotein translocation, in vivo and in vitro, through interacting with SecA and preventing SecA deinsertion. This provides a measure of the translocation relevance of each form of SecA membrane association. We now report that azide acts exclusively on SecA that is cycling at SecYEG and has no effect on SecA lipid associations. SecA molecules recovered with sucrose gradient-purified inner membrane vesicles ("endogenous" SecA) support translocation at the same rate as "added" SecA molecules bound at SecYEG. Both endogenous and added SecA yield the same proteolytic fragments, which are distinct from those obtained from SecA once it has inserted into membranes at SecYEG or from SecA at lipidic sites. Endogenous and added SecA differ, however, in their resistance to urea extraction. The translocation supported by either endogenous or added SecA is blocked by azide or by antibody to SecY. We conclude that SecA functions in preprotein translocation only through cycling at SecYEG.

Functional Significance of the “Signature Cysteine” in Helix 8 of the Escherichia coli 4-Aminobutyrate Transporter from the Amine-Polyamine-Choline Superfamily: RESTORATION OF CYS-300 TO THE CYS-LESS GabP

gab permease (GabP) is the exclusive mediator of 4-aminobutyrate (GABA) transport across the Escherichia coli plasma membrane. Helix 8 and a portion of the adjoining cytoplasmic region (loop 8-9) constitute the GabP "consensus amphipathic region" (CAR), a potential channel-forming domain that is found to be evolutionarily conserved within the APC (amine-polyamine-choline) transporter superfamily. Upon the polar surface of the CAR, all known gab permeases display a "signature cysteine" not found in other members of the APC superfamily, suggesting that discrete features within the CAR might play a role in imparting specificity (kcat/Km) to the translocation reaction. Here we show that among the five cysteine residues in the E. coli GabP, only Cys-300, the signature cysteine, can restore wild type properties to the Cys-less GabP mutant. We conclude (i) from partial reaction studies (equilibrium exchange, counterflow) that rapid translocation of the GABA binding site from one side of the membrane to the other is greatly facilitated by Cys-300 and (ii) from pharmacological studies that loss of Cys-300 has little effect on the affinity that GabP exhibits for a structurally diverse array (kojic amine, 5-aminovaleric acid, GABA, nipecotic acid, and cis-4-aminocrotonic acid) of competitive ligands. These results raise the possibility that other GABA transporters might rely analogously upon conserved cysteine residues positioned within the amphipathic helix 8 and loop 8-9 regions.

Form follows function: structure of an elongation factor G-ribosome complex.

Not so long ago, the idea of deriving functional models from just looking at large subcellular structures in different functional states seemed unrealistic. In the meantime, the visualization of such structures by three-dimensional reconstructions from cryoelectron microscopic images has made enormous progress. Studies on ribosomes, from both prokaryotes and eukaryotes, have been particularly rewarding. The structure of the Escherichia coli ribosome was determined at ≈25-A resolution in 1995 by the groups of Frank (1) and van Heel (2) and was improved to 18 A recently (3). Likewise, reconstructions of eukaryotic ribosomes have been obtained recently (4–6). Regarding functional complexes, it was possible to localize tRNA molecules in three binding sites (A, P, and E) on the E. coli ribosome (7) and to determine their respective pre- and post-translocation positions (8). The complex of elongation factor (EF) Tu with Phe-tRNA was visualized in the ribosomal A site at 18-A resolution (3), and, by fitting the crystal structure of the complex (9), the structure could be interpreted in terms of specific interactions with the ribosome. Another recent reconstruction visualized at the protein exit site of the eukaryotic ribosome a protein complex, Sec 61, that is involved in cotranslational protein translocation through the membrane of the endoplasmic reticulum (4). The paper by Agrawal et al. (10) in a recent issue of the Proceedings reports the structure of another important functional ribosomal complex that is a complex of EF-G with E. coli ribosomes. The structure represents a late state of the translocation reaction in the ribosomal elongation cycle. Translocation is catalyzed by EF-G at the expense of GTP and consists of the coordinated movement of two mRNA-bound tRNAs from their pretranslocational positions to their post-translocation positions. The present reconstruction has a resolution of 20 A and clearly shows the factor, a …

Cis and trans Sites of the TOM Complex of Mitochondria in Unfolding and Initial Translocation of Preproteins

Translocation of preproteins across the mitochondrial outer membrane is mediated by the TOM complex. Our previous studies led to the concept of two preprotein binding sites acting in series, the surface-exposed cis site and the trans site exposed to the intermembrane space. We report here that preproteins are bound to the cis site in a labile fashion even at low ionic strength, whereas intermediates arrested at the trans site remained firmly bound at higher salt concentration. The stability of the trans site intermediate results from interactions of both the presequence and unfolded parts of the mature part of the preprotein with the TOM complex. Binding to the trans site proceeded at rates comparable with those of unfolding of the mature domain and appeared to be kinetically limited by the unfolding reaction. Efficient binding to the trans site and unfolding were observed with both outer membrane vesicles and intact mitochondria whose membrane potential, DeltaPsi, was dissipated. Upon re-establishing DeltaPsi, trans site-bound preprotein resumed translocation into the matrix. The rates of unfolding and binding to the trans site were the same as those for translocation into intact energized mitochondria. We conclude that preprotein unfolding in intact mitochondria can take place without the involvement of the translocation machinery of the inner membrane and, in particular, the matrix Hsp70 chaperone. Further, preprotein unfolding at the outer membrane can be a rate-limiting step for formation of the trans site intermediate and for the entire translocation reaction.

The Sec system

Proteins designated to be secreted by Escherichia coli are synthesized with an amino-terminal signal peptide and associate as nascent chains with the export-specific chaperone SecB. Translocation occurs at a multisubunit membrane-bound enzyme termed translocase, which consists of a peripheral preprotein-binding site and an ATPase domain termed SecA, a core heterotrimeric integral membrane protein comlex with SecY, SecE and SecG as subunits, and an accesory integral membrane protein complex containing SecD and SecF. Major new insights have been gained into the cascade of preprotein targeting events and the enzymatic mechanism of preprotein translocation. It has become clear that preproteins are translocated in a stepwise fashion involving large nucleotide-induced conformational changes of the molecular motor SecA that propels the translocation reaction.

Intramolecular Homolytic Translocation Chemistry: An ab Initio Study of 1,n-Halogen Atom Transfer Reactions in Some omega-Haloalkyl Radicals.

Ab initio calculations using all-electron (3-21G(()()), 6-311G) and pseudopotential (DZP) basis sets, with (MP2, QCISD) and without (UHF) the inclusion of electron correlation, predict that 1,n-halogen transfer reactions in the 5-halo-1-pentyl (6), 6-halo-1-hexyl (7), and 7-halo-1-heptyl radicals (8) proceed via C(s)- and/or C(2)-symmetric transition states (9-11), except for the 5-bromo-1-pentyl (6, X = Br) radical for which a C(s)-symmetric transition state (9) was located only at the UHF/3-21G(()()) level of theory and the 5-iodo-1-pentyl radical (6, X = I) for which no transition state (9) could be located at any level of theory used in this study. Energy barriers for these translocation reactions of between 120.0 (1,7-iodine transfer) and 191.0 kJ mol(-)(1) (1,5-chlorine transfer) are predicted at the MP2/DZP level of theory; QCISD/DZP (single-point) calculations predict similar energy barriers. These high energy barriers are a consequence of unfavorable factors associated with ring size and long carbon-halogen separations in transition states (9-11) which lead to significant deviations from the collinear arrangement of attacking and leaving radicals preferred in transition states involved in homolytic substitution reactions at halogen. The dependence of transition state energy on attack angle at halogen has been explored for the attack of methyl radical at chloromethane. At the MP2/DZP level of theory, attack angles of between 80 and 90 degrees are calculated to lead to increases in energy barrier of about 100 kJ mol(-)(1) when compared with the collinear (180 degrees ) arrangement of attacking and leaving groups. The mechanistic implications of these predictions are discussed.

A novel cell-free system for peptide synthesis driven by pyridine.

Previously we demonstrated that ribosomes can synthesize polypeptides in the presence of high concentrations (40-60%) of pyridine without any protein factors. Here we analyze additional ribosomal parameters in 60% pyridine using Escherichia coli ribosomes. Ribosomal subunits once exposed to pyridine failed to re-associate to 70S ribosomes in aqueous buffer systems even in the presence of 20 mM Mg2+, whereas they formed 70S complexes in the presence of 60% pyridine. Two-dimensional gel electrophoresis of ribosomal proteins revealed that some proteins located at the protuberances of the large subunit, e. g. L7/L12 and L11 forming the elongation factor-binding domain, were released in the pyridine system. The aminoglycoside neomycin, a strong inhibitor of the ribosomal (factor-independent) translocation reaction, completely blocked poly(Phe) synthesis and translocation activities in the pyridine system, whereas these activities were not affected at all by gypsophilin, a ribotoxin that inhibits factor-dependent translocation. Another inhibitor of the ribosomal translocation, thiostrepton, had no effect concerning the two activities, which is consistent with the fact that this antibiotic requires L11 for its binding to the ribosome. These results suggest that the ribosomes can perform a translocation reaction in the pyridine system, but in a factor-independent (spontaneous) manner.

Small angle scattering in ribosomal structure research: localization of the messenger RNA within ribosomal elongation states.

Besides EM and biochemical studies small angle scattering (SAS) examinations have contributed significantly to our current knowledge about the ribosomal structure. SAS does not only allow the validation of competing models but permits independent model building. However, the major contribution of SAS to ribosomal structure research derived from its ability to reveal the spatial distribution of the individual ribosomal components (57 in the E. coli ribosome) within the ribosomal structure. More recently, an improved scattering method (proton-spin contrast variation) made it possible also to address the question of mapping functional ligands in defined ribosomal elongation states. Here, we review the contributions of SAS to the current understanding of the ribosome. Furthermore we present the direct localization of a small mRNA fragment within 70S elongation complexes and describe its movement upon the translocation reaction. The successful mapping of this fragment comprising only about 0.6% of the total mass of the complex proves that proton-spin contrast-variation is a powerful tool in modern ribosome research.

Ran-unassisted nuclear migration of a 97-kD component of nuclear pore-targeting complex.

A 97-kD component of nuclear pore-targeting complex (the beta-subunit of nuclear pore-targeting complex [PTAC]/importin/karyopherin) mediates the import of nuclear localization signal (NLS)-containing proteins by anchoring the NLS receptor protein (the alpha-subunit of PTAC/importin/karyopherin) to the nuclear pore complex (NPC). The import requires a small GTPase Ran, which interacts directly with the beta-subunit. The present study describes an examination of the behavior of the beta-subunit in living cells and in digitonin-permeabilized cells. In living cells, cytoplasmically injected beta-subunit rapidly migrates into the nucleus. The use of deletion mutants reveals that nuclear migration of the beta-subunit requires neither Ran- nor alpha-subunit-binding but only the NPC-binding domain of this molecule, which is also involved in NLS-mediated import. Furthermore, unlike NLS-mediated import, a dominant-negative Ran, defective in GTP-hydrolysis, did not inhibit nuclear migration of the beta-subunit. In the digitonin-permeabilized cell-free import assay, the beta-subunit transits rapidly through the NPC into the nucleus in a saturating manner in the absence of exogenous addition of soluble factors. These results show that the beta-subunit undergoes translocation at the NPC in a Ran-unassisted manner when it does not carry alpha-subunit/NLS substrate. Therefore, a requirement for Ran arises only when the beta-subunit undergoes a translocation reaction together with the alpha-subunit/NLS substrate. The results provide an insight to the yet unsolved question regarding the mechanism by which proteins are directionally transported through the NPC, and the role of Ran in this process.

The SecDFyajC domain of preprotein translocase controls preprotein movement by regulating SecA membrane cycling.

Escherichia coli preprotein translocase comprises a membrane-embedded hexameric complex of SecY, SecE, SecG, SecD, SecF and YajC (SecYEGDFyajC) and the peripheral ATPase SecA. The energy of ATP binding and hydrolysis promotes cycles of membrane insertion and deinsertion of SecA and catalyzes the movement of the preprotein across the membrane. The proton motive force (PMF), though not essential, greatly accelerates late stages of translocation. We now report that the SecDFyajC domain of translocase slows the movement of preprotein in transit against both reverse and forward translocation and exerts this control through stabilization of the inserted form of SecA. This mechanism allows the accumulation of specific translocation intermediates which can then complete translocation under the driving force of the PMF. These findings establish a functional relationship between SecA membrane insertion and preprotein translocation and show that SecDFyajC controls SecA membrane cycling to regulate the movement of the translocating preprotein.

Co-translational protein targeting catalyzed by the Escherichia coli signal recognition particle and its receptor.

The Ffh-4.5S ribonucleoprotein particle (RNP) and FtsY from Escherichia coli are homologous to essential components of the mammalian signal recognition particle (SRP) and SRP receptor, respectively. The ability of these E. coli components to function in a bona fide co-translational targeting pathway remains unclear. Here we demonstrate that the Ffh-4.5S RNP and FtsY can efficiently replace their mammalian counterparts in targeting nascent secretory proteins to microsomal membranes in vitro. Targeting in the heterologous system requires a hydrophobic signal sequence, utilizes GTP and, moreover, occurs co-translationally. Unlike mammalian SRP, however, the Ffh-4.5S RNP is unable to arrest translational elongation, which results in a narrow time window for the ribosome nascent chain to interact productively with the membrane-bound translocation machinery. The highly negatively charged N-terminal domain of FtsY, which is a conserved feature among prokaryotic SRP receptor homologs, is important for translocation and acts to localize the protein to the membrane. Our data illustrate the extreme functional conservation between prokaryotic and eukaryotic SRP and SRP receptors and suggest that the basic mechanism of co-translational protein targeting is conserved between bacteria and mammals.

Structure and folding of nascent polypeptide chains during protein translocation in the endoplasmic reticulum.

To investigate the role of protein folding and chaperone-nascent chain interactions in translocation across the endoplasmic reticulum membrane, the translocation of wild type and mutant forms of preprolactin were studied in vivo and in vitro. The preprolactin mutant studied contains an 18-amino acid substitution at the amino terminus of the mature protein, eliminating a disulfide-bonded loop domain. In COS-7 cells, mutant prolactin accumulated in the endoplasmic reticulum as stable protein-protein and disulfide-bonded aggregates, whereas wild type prolactin was efficiently secreted. In vitro, wild type and mutant preprolactin translocated with equal efficiency although both translation products were recovered as heterogeneous aggregates. Studies with translocation intermediates indicated that aggregation occurred co-translationally. To evaluate the contribution of lumenal chaperones to translocation and folding, in vitro studies were performed with native and reconstituted, chaperone-deficient membranes. The absence of lumenal chaperones was associated with a decrease in translocation efficiency and pronounced aggregation of the translation products. These studies suggest that chaperone-nascent chain interactions significantly enhance translocation and indicate that in the absence of such interactions, aggregation can serve as the predominant in vitro protein folding end point. The ramifications of these observations on investigations into the mechanism of translocation are discussed.

Distinct catalytic roles of the SecYE, SecG and SecDFyajC subunits of preprotein translocase holoenzyme.

Escherichia coli preprotein translocase contains a membrane-embedded trimeric complex of SecY, SecE and SecG (SecYEG) and the peripheral SecA protein. SecYE is the conserved functional 'core' of the SecYEG complex. Although sufficient to provide sites for high-affinity binding and membrane insertion of SecA, and for its activation as a preprotein-dependent ATPase, SecYE has only very low capacity to support translocation. The proteins encoded by the secD operon--SecD, SecF and YajC--also form an integral membrane heterotrimeric complex (SecDFyajC). Physical and functional studies show that these two trimeric complexes are associated to form SecYEGDFyajC, the hexameric integral membrane domain of the preprotein translocase 'holoenzyme'. Either SecG or SecDFyajC can support the translocation activity of SecYE by facilitating the ATP-driven cycle of SecA membrane insertion and de-insertion at different stages of the translocation reaction. Our findings show that each of the prokaryote-specific subunits (SecA, SecG and SecDFyajC) function together to promote preprotein movement at the SecYE core of the translocase.

ChemInform Abstract: Radical Sequential Processes Promoted by 1,5‐Radical Translocation Reaction: Formation and (3 + 2) Annulation of Alkenesulfanyl Radicals.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

On the radical Brook and related reactions: an ab initio study of some (1,2)-silyl, germyl and stannyl translocations

Ab initio molecular orbital calculations using a (valence) double-ζ pseudopotential basis set (DZP) with (MP2, QCISD) and without (SCF) the inclusion of electron correlation predict that the transition states (12–14) involved in homolytic (1,2)-translocation reactions of silyl (SiH3), germyl (GeH3) and stannyl (SnH3) groups between carbon centres, between carbon and nitrogen, and between carbon and oxygen proceed via homolytic substitution mechanisms involving front-side attack at the group (IV) heteroatom. While migrations between carbons are predicted to be unlikely, with calculated activation barriers of 71–137 kJ mol–1, depending on the level of theory, migrations from carbon to nitrogen and from carbon to oxygen are predicted to be facile. For example, rearrangement of the (silylmethyl)aminyl radical (H3SiCH2NH˙) to the silylaminomethyl species (H3SiNHCH2˙) is predicted to proceed with a barrier of 50.8–63.2 kJ mol–1 when electron correlation is included, in excellent agreement with experimental data. In addition, the analogous translocation to oxygen in the silylmethoxyl radical (H3SiCH2O˙), the prototypical radical Brook rearrangement, is calculated to require only 19.9 kJ mol–1 at the MP2/DZP + ZPVE level. Somewhat unexpectedly, MP2/DZP calculations predict that the stannylmethoxyl radical (H3SnCH2O˙) rearranges to the stannyloxymethyl radical (H3SnOCH2˙) without barrier.

ChemInform Abstract: 1,3‐Asymmetric Induction via 1,5‐Hydrogen Atom Translocation Reactions. Highly Enantioselective Synthesis of β‐Substituted β‐Amino Acids.

AbstractChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Characterization of the nuclear protein import mechanism using Ran mutants with altered nucleotide binding specificities.

The small nuclear GTP binding protein Ran is required for transport of nuclear proteins through the nuclear pore complex (NPC). Although it is known that GTP hydrolysis by Ran is essential for this reaction, it has been unclear whether additional energy-consuming steps are also required. To uncouple the energy requirements for Ran from other nucleoside triphosphatases, we constructed a mutant derivative of Ran that has an altered nucleotide specificity from GTP to xanthosine 5' triphosphate. Using this Ran mutant, we demonstrate that nucleotide hydrolysis by Ran is sufficient to promote efficient nuclear protein import in vitro. Under these conditions, protein import could no longer be inhibited with non-hydrolysable nucleotide analogues, indicating that no Ran-independent energy-requiring steps are essential for the protein translocation reaction through the NPC. We further provide evidence that nuclear protein import requires Ran in the GDP form in the cytoplasm. This suggests that a coordinated exchange reaction from Ran-GDP to Ran-GTP at the pore is necessary for translocation into the nucleus.

Characterization of a Potential Catalytic Residue, Asp-133, in the High Affinity ATP-binding Site of Escherichia coli SecA, Translocation ATPase

The high affinity ATP-binding site of SecA is located in its amino-terminal domain possessing amino acid sequences, the Walker A (GXXXXGKT) and B (ZZZZD) motifs, that are characteristic of a major class of nucleotide-binding sites (Walker, J. E., Saraste, M., Runswick, M. J., and Gay, N. J. (1982) EMBO J. 1, 945-951). Recently, we proposed that proteins possessing a typical set of Walker A and B motifs contain a conserved Glu or Asp between the two motifs. This Glu or Asp acts as a "catalytic residue" that activates a water molecule for an in-line attack on the gamma-phosphate of ATP (Amano, T., Yoshida, M., Matsuo, Y., and Nishikawa, K.(1995) FEBS Lett. 359, 1-5). In the present study, the aspartate residue at position 133 in Escherichia coli SecA, which could be the "catalytic residue," was mutated to an asparagine. The mutant SecA (SecA D133N) protein was expressed in E. coli CK4706, encoding a duplication of the secA gene, and purified to homogeneity. The in vitro protein translocation activity and membrane vesicle stimulated ATPase activity of SecA D133N were drastically reduced. Proteolytic studies indicated that the conformational changes of the mutant SecA occurring on interaction with ATP, presecretory proteins, phospholipids, and membrane vesicles, were similar to those of wild-type SecA. The mutant SecA allowed the signal peptide cleavage of proOmpA during translocation, indicating that the mutant retains the ability to bind ATP to perform the initial step of the translocation reaction. These data indicate that the carboxyl group of Asp-133 plays a role as a catalytic carboxylate, which activates a water molecule to attack gamma-phosphate of ATP, and the mutant lacking this residue cannot perform the total translocation but can still perform the initial step of the protein translocation.

The major pathways of protein translocation across membranes

The initial events in the localization of cell surface proteins include targeting of precursor molecules to the membrane and subsequent translocation across the membrane. The translocation reaction is mediated through a series of molecular interactions involving a number of protein factors. The trimeric SecY/Sec61 core complex, which is conserved throughout evolution, provides a proteinaceous pathway for translocation. The driving force for translocation is provided by the dynamic motion of the SecA ATPase in prokaryotes and by polypeptide elongation through the ribosome-Sec61 junction in eukaryotes.

Radical Sequential Processes Promoted by 1,5-Radical Translocation Reaction: Formation and [3 + 2] Anulation of Alkenesulfanyl Radicals.

Radical addition of 2-substituted ethanethiols 1-5 to alkyl-, dialkyl-, and phenylacetylenes affords the corresponding beta-sulfanylalkenyl radicals, which can undergo 1,5-radical translocation (RT reaction) in competition with intermolecular hydrogen abstraction (HA reaction). The RT reaction is the first step of a sequential radical process leading to alkenesulfanyl radicals through an "intermolecular sulfanyl radical transaddition" from an alkene to an alkyne molecule. Alkenesulfanyl radicals can undergo a regioselective [3 + 2] anulation reaction with a CC triple bond, eventually leading to thiophene products through 5-endo cyclization of vinyl radicals onto CC double bond. The effect of the nature of ethanethiol and alkyne substituents on the RT/HA ratio has been investigated, and results will be discussed.