Topology Inversion Research Articles

TM4SF19 controls GABP-dependent YAP transcription in head and neck cancer under oxidative stress conditions

Tobacco and alcohol are risk factors for human papillomavirus-negative head and neck squamous cell carcinoma (HPV- HNSCC), which arises from the mucosal epithelium of the upper aerodigestive tract. Notably, despite the mutagenic potential of smoking, HPV- HNSCC exhibits a low mutational load directly attributed to smoking, which implies an undefined role of smoking in HPV- HNSCC. Elevated YAP (Yes-associated protein) mRNA is prevalent in HPV- HNSCC, irrespective of the YAP gene amplification status, and the mechanism behind this upregulation remains elusive. Here, we report that oxidative stress, induced by major risk factors for HPV- HNSCC such as tobacco and alcohol, promotes YAP transcription via TM4SF19 (transmembrane 4 L six family member 19). TM4SF19 modulates YAP transcription by interacting with the GABP (Guanine and adenine-binding protein) transcription factor complex. Mechanistically, oxidative stress induces TM4SF19 dimerization and topology inversion in the endoplasmic reticulum membrane, which in turn protects the GABPβ1 subunit from proteasomal degradation. Conversely, depletion of TM4SF19 impairs the survival, proliferation, and migration of HPV- HNSCC cells, highlighting the potential therapeutic relevance of targeting TM4SF19. Our findings reveal the roles of the key risk factors of HPV- HNSCC in tumor development via oxidative stress, offering implications for upcoming therapeutic approaches in HPV- HNSCC.

Identification of residues critical for topology inversion of the transmembrane protein TM4SF20 through regulated alternative translocation

Adopting a proper topology is crucial for transmembrane proteins to perform their functions. We previously reported that ceramide regulates a transmembrane protein called TM4SF20 (transmembrane 4 L six family member 20) through topological inversion by altering the direction through which the protein is translocated across membranes during translation. This regulatory mechanism, denoted regulated alternative translocation (RAT), depends on a GXXXN motif present in the first transmembrane helix of TM4SF20. Here, using site-directed mutagenesis, we show that Asn-26 in the motif is crucial for RAT of TM4SF20, as it cannot be replaced even by Gln. In contrast, Gly-22 in the motif could be substituted by other small residues such as Ala and Ser without affecting RAT of TM4SF20. We further demonstrate that the GXXXN motif alone is insufficient to induce RAT of a transmembrane protein because TM4SF4, a relative of TM4SF20 that also contains the motif in the first transmembrane helix, did not undergo RAT. Using TM4SF40-TM4SF20 chimeras, we identified Pro-29 of TM4SF20 as another important element required for RAT of the protein. Substituting Pro-29 alone did not affect RAT of TM4SF20, whereas replacing Pro-29 together with either Leu-25 or Val-17 of TM4SF20 with the corresponding residues of TM4SF4 abolished RAT of TM4SF20. Because Val-17, Gly-22, Leu-25, Asn-26, and Pro-29 are predicted to reside along the same surface of the transmembrane helix, our results suggest that interactions with other proteins mediated by this surface during translocation may be critical for RAT of TM4SF20.

Regulating a G Protein‐Coupled Receptor by Topological Inversion through Regulated Alternative Translocation

BackgroundWe have recently reported the first example that ceramide stimulates the topology inversion of a newly synthesized transmembrane protein. This novel regulation, which is designated as Regulated Alternative Translocation (RAT), requires a GXXXN motif in the first transmembrane domain. Utilizing a bioinformatics approach, we have discovered over 100 proteins that contain a GXXXN motif in the first transmembrane domain and therefore can potentially undergo RAT. Greater than 90% of these proteins are G Protein‐Coupled Receptors, including nearly all of the C‐C and C‐X‐C Chemokine Receptors. In the current study, we determine whether C‐C Chemokine Receptor 5 (CCR5) can be regulated through RAT.Study SummaryWe demonstrate though multiple approaches that CCR5 undergoes topological inversion via RAT in response to exogenously added ceramide in transfected cells. In primary macrophages, we demonstrate Lipopolysaccharide (LPS) treatment induces dihydroceramide to catalyze the RAT of CCR5. LPS‐induced RAT of CCR5 is the mechanism by which LPS inhibits chemotaxis of macrophages towards C‐C Motif Chemokine Ligand (CCL5).ConclusionsThis study demonstrates that LPS‐induced dihydroceramide causes the topology inversion of CCR5 through RAT in primary macrophages. The resulting topology inversion of CCR5 prevents macrophage migration towards CCL5. This finding provides a novel regulation of macrophage chemotaxis and suggests that topological inversion through RAT is a general mechanism to regulate G Protein‐Coupled Receptors.Support or Funding InformationNIH GM‐116106 and HL‐20948This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Complete topology inversion can be part of normal membrane protein biogenesis.

The topology of helical membrane proteins is generally defined during insertion of the transmembrane helices, yet it is now clear that it is possible for topology to change under unusual circumstances. It remains unclear, however, if topology reorientation is part of normal biogenesis. For dual topology dimer proteins such as the multidrug transporter EmrE, there may be evolutionary pressure to allow topology flipping so that the populations of both orientations can be equalized. We previously demonstrated that when EmrE is forced to insert in a distorted topology, topology flipping of the first transmembrane helix can occur during translation. Here, we show that topological malleability also extends to the C-terminal helix and that even complete topology inversion of the entire EmrE protein can occur after the full protein is translated and inserted. Thus, topology rearrangements are possible during normal biogenesis. Wholesale topology flipping is remarkable given the physical constraints of the membrane and expands the range of possible membrane protein folding pathways, both productive and detrimental.

Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State

The bacterial SecYEG translocon functions as a conserved protein-conducting channel. Conformational transitions of SecYEG allow protein translocation across the membrane without perturbation of membrane permeability. Here, we report the crystal structures of intact SecYEG at 2.7-Å resolution and of peptide-bound SecYEG at 3.6-Å resolution. The higher-resolution structure revealed that the cytoplasmic loop of SecG covers the hourglass-shaped channel, which was confirmed to also occur in the membrane by disulfide bond formation analysis and molecular dynamics simulation. The cytoplasmic loop may be involved in protein translocation. In addition, the previously unknown peptide-bound crystal structure of SecYEG implies that interactions between the cytoplasmic side of SecY and signal peptides are related to lateral gate opening at the first step of protein translocation. These SecYEG structures therefore provide a number of structural insights into the Sec machinery for further study.

Configuration Analysis of RV Transmission Based on Topology Graph Theory

This paper puts forward the method of obtaining new types of RV transmission. Research shows that the topological graph can effectively express the topology unit and topological structure of RV transmission; the process that through topology degradation and evolutionary method to Obtain the RV transmission of topology map and through the topology inversion to get the new organization is practical and feasible. The topological evolution methods have tie bar evolution, tree, increasing gear tooth ring and mixing superimposed evolution. The RV transmission topology inversion is implemented by the way of gear ring, Gear meshing, the gear, the shaft, tie rod and the frame. Method was developed to get the evolutions of a variety of RV transmission, and the evolution of a graph of the inverse mapping was enumerated. The topology graph theory methods used in the RV transmission for the structure of RV transmission innovation provides an important theoretical method.

Topological Plasticity of Enzymes Involved in Disulfide Bond Formation Allows Catalysis in Either the Periplasm Or the Cytoplasm

The transmembrane enzymes disulfide bond forming enzyme B (DsbB) and vitamin K epoxide reductase (VKOR) are central to oxidative protein folding in the periplasm of prokaryotes. Catalyzed formation of structural disulfide bonds in proteins also occurs in the cytoplasm of some hyperthermophilic prokaryotes through currently, poorly defined mechanisms. We aimed to determine whether DsbB and VKOR can be inverted in the membrane with retention of activity. By rational design of inversion of membrane topology, we engineered DsbB mutants that catalyze disulfide bond formation in the cytoplasm of Escherichia coli. This represents the first engineered inversion of a transmembrane protein with demonstrated conservation of activity and substrate specificity. This successful designed engineering led us to identify two naturally occurring and oppositely oriented VKOR homologues from the hyperthermophile Aeropyrum pernix that promote oxidative protein folding in the periplasm or cytoplasm, respectively, and hence defines the probable route for disulfide bond formation in the cytoplasm of hyperthermophiles. Our findings demonstrate how knowledge on the determinants of membrane protein topology can be used to de novo engineer a metabolic pathway and to unravel an intriguingly simple evolutionary scenario where a new “adaptive” cellular process is constructed by means of membrane protein topology inversion.

Glycolipozyme MPIase is essential for topology inversion of SecG during preprotein translocation

Presecretory proteins are translocated across biological membranes through protein-conducting channels such as Sec61 (eukaryotes) and SecYEG (bacteria). SecA, a translocation ATPase, pushes preproteins out with dynamic structural changes through SecYEG. SecG, a subunit of the SecYEG channel possessing two transmembrane stretches (TMs), undergoes topology inversion coupled with SecA-dependent translocation. Recently, we characterized membrane protein integrase (MPIase), a glycolipozyme involved in not only protein integration into membranes but also preprotein translocation. We report here that SecG inversion occurs only when MPIase associates with SecYEG. We also found that MPIase modulates the dimer orientation of SecYEG. Cysteine-scanning mutagenesis mapped SecG TM 2 to a relatively hydrophilic environment. The dimer formation of SecG, crosslinked at TM 2, was not observed on SecG inversion, indicating that SecYEG undergoes a dynamic structural change during preprotein translocation.

Multiple SecA Molecules Drive Protein Translocation across a Single Translocon with SecG Inversion

SecA is a translocation ATPase that drives protein translocation. D209N SecA, a dominant-negative mutant, binds ATP but is unable to hydrolyze it. This mutant was inactive to proOmpA translocation. However, it generated a translocation intermediate of 18 kDa. Further addition of wild-type SecA caused its translocation into either mature OmpA or another intermediate of 28 kDa that can be translocated into mature by a proton motive force. The addition of excess D209N SecA during translocation caused a topology inversion of SecG. Moreover, an intermediate of SecG inversion was identified when wild-type and D209N SecA were used in the same amounts. These results indicate that multiple SecA molecules drive translocation across a single translocon with SecG inversion. Here, we propose a revised model of proOmpA translocation in which a single catalytic cycle of SecA causes translocation of 10-13 kDa with ATP binding and hydrolysis, and SecG inversion is required when the next SecA cycle begins with additional ATP hydrolysis.

Preparation of a highly translocation‐competent proOmpA/SecB complex

Methods for reproducibly preparing highly translocation-competent proOmpA were developed. Only a competent form of proOmpA was sorted out from incompetent one using SecB, a translocation-dedicated chaperone, as a probe. Trypsin digestion revealed that the incompetent form of proOmpA was partially folded at its N-terminus, consistent with the jamming of proOmpA within translocon. Although the incompetent form of proOmpA was not active as to topology inversion of SecG, the isolated proOmpA/SecB complex had recovered the ability of SecG inversion. These results let us prepare a proOmpA/SecB complex both in vivo and in vitro that is highly translocation-competent. E. coli cells harboring a plasmid, in which ompA and secB were encoded as a synthetic operon, accumulated the proOmpA/SecB complex in the cytosol. The complex, purified by means of a His tag attached to SecB, was found to be translocation-competent as revealed by the occurrence of SecG inversion, although the signal peptide of proOmpA was sensitive to proteolytic digestion. ProOmpA, in vitro synthesized by means of a continuous exchange cell free system in the presence of SecB-His, was purified as a complex with SecB, which was active as to SecG inversion as well.

Topology Inversion of SecG Is Essential for Cytosolic SecA-dependent Stimulation of Protein Translocation

SecG, a subunit of the protein translocon, undergoes a cycle of topology inversion. To further examine the role of this topology inversion, we analyzed the activity of membrane vesicles carrying a SecG-PhoA fusion protein (SecG-PhoA inverted membrane vesicles (IMVs)). In the absence of externally added SecA, SecG-PhoA IMVs were as active in protein translocation as SecG(+) IMVs per SecA. Consistent with this observation, insertion of membrane-bound SecA into SecG-PhoA IMVs was normally observed. On the other hand, externally added SecA did not affect the activity of SecG-PhoA IMVs, but it caused >10-fold stimulation of the translocation activity of SecG(+) IMVs, indicating that the topology inversion of SecG, which cannot occur in SecG-PhoA IMVs, is essential for cytosolic SecA-dependent stimulation of protein translocation. SecG-PhoA IMVs generated a 46-kDa fragment of SecA upon trypsin treatment. The accumulation of this membrane-inserted SecA in the SecG-PhoA IMVs was responsible for the loss of the soluble SecA-dependent stimulation. Moreover, fixation of the inverted SecG topology was found to be dependent on soluble SecA. The dual functions of SecG in protein translocation will be discussed.

Topologically Fixed SecG Is Fully Functional

It has been proposed that the bitopic membrane protein SecG undergoes topology inversion during translocation of (pre)proteins via SecYEG. Here we show that SecG covalently cross-linked to SecY cannot invert its topology while remaining fully functional in protein translocation. Our results strongly disfavor topology inversion of SecG during protein translocation.

Membrane topology inversion of SecG detected by labeling with a membrane-impermeable sulfhydryl reagent that causes a close association of SecG with SecA.

SecG stimulates protein translocation in Escherichia coli by facilitating the membrane insertion-deinsertion cycle of SecA. SecG was previously shown to undergo membrane topology inversion, since SecA-dependent protein translocation renders the membrane-protected region of SecG sensitive to external proteases. To examine this topology inversion in more detail without protease-treatment, SecG derivatives with a single cysteine residue at various positions were labeled in the presence and absence of protein translocation with a membrane impermeable SH reagent, 4-acetamido-4'-maleimidylstilbene-2-2'-disulfonic acid (AMS). Treatment of spheroplasts with AMS revealed that a cysteine residue in the cytoplasmic region of SecG could be labeled from the periplasm side only in the presence of protein translocation, whereas a cytoplasmic protein, elongation factor, Tu, remained unlabeled. Treatment of inverted membrane vesicles with AMS also revealed that cysteine residues in the periplasmic region were labeled from the cytoplasmic side of membranes only when protein translocation was in progress. This labeling required ATP, SecA and a precursor protein, and became more efficient as the position of the cysteine residue became closer to the C-terminus. Crosslinking analyses revealed that the interaction between SecG and SecA in membranes markedly increases when SecA and SecG undergo membrane-insertion and topology inversion, respectively. Thus, the two most dynamic components of the translocation machinery were found for the first time to interact with each other when both undergo conformational changes.

Two SecG molecules present in a single protein translocation machinery are functional even after crosslinking.

SecG, a membrane component of the protein translocation apparatus of Escherichia coli, undergoes membrane topology inversion, which is coupled to the membrane insertion and deinsertion cycle of SecA. Eighteen SecG derivatives possessing a single cysteine residue at various positions were constructed and expressed in a secG null mutant. All the SecG-Cys derivatives retained the SecG function, and stimulated protein translocation both in vivo and in vitro. Inverted membrane vesicles containing a SecG-Cys derivative were labeled with a membrane-permeable or -impermeable sulfhydryl reagent before or after solubilization with a detergent. The accessibility of these reagents to the cysteine residue of each derivative determined the topological arrangement of SecG in the membrane. Derivatives having the cysteine residue in the periplasmic region each existed as a homodimer crosslinked through disulfide bonds, indicating that two SecG molecules closely co-exist in a single translocation machinery. The crosslinking did not abolish the SecG function and the crosslinked SecG dimer underwent topology inversion upon protein translocation.

Ultra‐high‐temperature metamorphism in Central Brazil: the Barro Alto complex

The Barro Alto complex, central Brazil, is a layered mafic–ultramafic intrusion, which was subjected to granulite facies metamorphism during the Neoproterozoic. Ultra‐high‐temperature conditions are recorded by parageneses that occur in some lenses of quartz‐bearing rock (metagranite, metapelite and impure quartzite). The peak paragenesis consists of spinel+quartz±cordierite±leucosome (recording the former presence of melt with quartz in excess), which is replaced by either orthopyroxene+sillimanite or garnet+sillimanite. Quartz+biotite±sillimanite±garnet symplectites are ubiquitous and indicate reactions between Fe–Mg phases and melt. Late kyanite porphyroblasts have overgrown these symplectites. The direct replacement of spinel+quartz±cordierite by orthopyroxene+sillimanite or garnet+sillimanite occurred around the [Sa] invariant point, which appears only in a petrogenetic grid with inverted topology. The topology inversion occurs at conditions of high oxygen fugacity or due to the presence of ZnO‐bearing spinel. Minimum peak conditions of ultra‐high‐temperature metamorphism were calculated as c. 980 °C and c. 7.9 kbar. The succession of observed mineral textures can be explained by a near‐isobaric cooling P–T path, with a cooling stage occurring between c. 980 and 750 °C.

Coupled structure changes of SecA and SecG revealed by the synthetic lethality of the secAcsR11 and delta secG::kan double mutant.

An Escherichia coli strain carrying either the secAcsR11 or delta secG::kan mutation is unable to grow at low temperature owing to cold-sensitive protein translocation but grows normally at 37 degree C. However, introduction of the two mutations into the same cells caused a severe defect in protein translocation and the cells were unable to grow at any temperature examined, indicating that secG is essential for the secAcsR11 mutant. The mutant SecA (csSecA) was found to possess a single amino acid substitution in the precursor-binding region and was defective in the interaction with the precursor protein. Furthermore, the membrane insertion of SecA and the membrane topology inversion of SecG, both of which took place upon the initiation of protein translocation, were significantly retarded even at 37 degree C, when csSecA was used instead of the wild-type SecA. The insertion of the wild-type SecA was also significantly defective when SecG-depleted membrane vesicles were used in place of SecG-containing ones. No insertion of csSecA occurred into SecG-depleted membrane vesicles. Examination of in vitro protein translocation at 37 degree C revealed that SecG is essential for csSecA-dependent protein translocation. We conclude that SecG and SecA undergo a coupled structure change, that is critical for efficient protein translocation.

Amino-terminal region of SecA is involved in the function of SecG for protein translocation into Escherichia coli membrane vesicles.

Protein translocation across the cytoplasmic membrane of Escherichia coli is accomplished by concerted actions of the translocation ATPase SecA and the membrane-embedded SecE/Y/G complex. SecA interacts with preproteins and undergoes ATP-driven cycles of membrane insertion-deinsertion. To address how SecA interacts functionally with other components in the translocation machinery, we characterized a SecA mutant lacking amino-terminal 8 amino acid residues (SecA N-8). Although the absence of the 8 residues did not grossly affect the interaction of SecA with a preprotein, ATP, or phospholipids, nor did it affect the intrinsic ATPase activity, it gave differential effects on the translocation of different preproteins. It also affected the translocation ATPase activity, the ability of membrane insertion, and the topology inversion of SecG coupled with the membrane insertion-deinsertion of SecA. Most noteworthy, SecA N-8 was pronouncedly defective in the translocation of proton motive force-dependent preproteins, in which SecG might have a role. We propose that the amino-terminal region of SecA is important for the functional interaction with SecG.

Topology inversion of CYP2D6 in the endoplasmic reticulum is not required for plasma membrane transport.

The presence of CYP2D6 at the surface of isolated rat and human hepatocytes and its recognition by autoantibodies were reported recently. We wondered whether the unexpected outside orientation at the plasma membrane could be related to topological inversion (luminal-oriented form) of cytochrome P450 in the endoplasmic reticulum. To examine the potential role of cDNA polymorphism, a CYP2D6 variant carrying three positive charges at the amino terminus (2D6ext) was constructed and expressed in yeast. Immunoblotting, flow cytometry, and electron microscopy showed that wild-type CYP2D6 expressed in yeast was present on the outer face of the cell plasma membrane in addition to the regular microsomal location. This location reproduces the hepatocyte situation. 2D6ext expressed in yeast and COS7 cells seemed to be partially N-glycosylated and was located at the plasma membrane surface. Nevertheless, the glycosylated form was not enriched in the plasma membranes compared with microsomes. The relationship between CYP2D6 and 2D6ext topologies and catalytic competence was tested. Cumene hydroperoxide-dependent dextromethorphan demethylation was performed on microsomal vesicles after combined proteolysis and immunoinhibition experiments. CYP2D6 activity was completely abolished, whereas the glycosylated and luminal-oriented fraction of 2D6ext remained active. This suggests that a luminal-oriented glycosylated form is not involved in cytochrome P450 transport to the plasma membrane. Yeast thus reproduces the unusual CYP2D6 plasma membrane location and orientation, which do not require sequence alteration, glycosylation, or even an inverted endoluminal orientation.

Structure changes of SecA and SecG coupled with protein translocation.

Both SecA and SecG, components of the protein translocation machinery of E. coli, were found to undergo significant structure changes during protein translocation. SecA repeats the cycle of membrane-insertion and deinsertion while SecG repeats the cycle of membrane topology inversion. Molecular mechanisms whereby the structure changes of SecA and SecG drive protein translocation are discussed.

Expression of gpsA encoding biosynthetic sn-glycerol 3-phosphate dehydrogenase suppresses both the LB- phenotype of a secB null mutant and the cold-sensitive phenotype of a secG null mutant.

SecB maintains the structures of a subset of precursor proteins competent for translocation across the Escherichia coli cytoplasmic membrane. SecG, a membrane component of the translocation machinery, stimulates protein translocation by undergoing the cycle of membrane topology inversion. Null mutants of secB and secG are unable to form isolated colonies on rich medium and at low temperature respectively. A 3.2 kb DNA fragment carrying the secB-gpsA region on a multicopy plasmid was found to suppress the null mutation of either gene. However, subcloning of the DNA fragment revealed that secB is not involved in the suppression of either mutation. Instead, gpsA located downstream from the secB gene was found to be responsible for the suppression of both mutations. The activity of the gpsA-encoded sn-glycerol-3-phosphate dehydrogenase, which is involved in phospholipid synthesis, was significantly lower in the secB null mutant than in the wild type, presumably because of a polar effect. Suppression of the secB null mutation required the wild-type level of GpsA activity. In contrast, overexpression of the enzyme was essential for suppression of the secG null mutation. Moreover, the gpsA-dependent suppression of the secG null mutation occurred only on rich medium, i.e. not on minimal medium. These results indicate that the SecB function is dispensable even in rich medium, and further demonstrate that overexpression of enzymes involved in phospholipid synthesis partly compensates for the SecG function.