Browsing by Subject "Membraninsertion"

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Functional and structural studies of a C-terminally extended YidC
(2015) Seitl, Ines; Kuhn, Andreas
Members of the YidC/Oxa1/Alb3 protein family catalyze the insertion of integral membrane proteins into the lipid bilayer of the bacterial plasma membrane (YidC), the inner mitochondrial membrane (Oxa1), and the chloroplast thylakoid membrane (Alb3) (Saller et al., 2012; Dalbey et al., 2014). The insertase homologs are comprised of a conserved core region of 5 transmembrane domains, but are provided with additionally flanking N- and C-terminal regions of variable lengths and functions. The Gram-negative YidC is characterized by an additional N-terminal domain, while Gram-positive bacteria, mitochondria and plastids developed C-terminally extended insertase-domains. These domains are involved e.g. in direct interaction with ribosomes and facilitate a functional overlap with the co-translational SRP-targeting pathway. An extended C-terminal highly positively charged tail region was also found in the YidC homologs of the Gram-negative marine bacteria Rhodopirellula baltica and Oceanicaulis alexandrii, but not in Escherichia coli. The primary subject of this work was to characterize and analyze in detail the C-terminally extended YidC chimera, composed of the E. coli YidC and the C-terminally extended domains of the marine YidC homologs. Biochemical binding assays with the purified YidC proteins and isolated, vacant E. coli 70S ribosomes showed that the C-tails mediate specific binding to ribosomes independently of the translational state of the ribosome. Furthermore, a ribosome-bound insertase complex was visualized by cryo-electron microscopy. The enhanced affinity of the C-terminally extended YidC was used to isolate stable complexes with stalled ribosomes, carrying a nascent polypeptide chain of a YidC substrate protein (MscL). The cryo-EM structure of a YidC-ribosome nascent chain complex (RNC) was solved to a 8,6 Å resolution and allowed the visualization of the nascent chain from the peptidyl transferase center through the ribosomal exit tunnel into the YidC density. The structure revealed the helix H59 of the 23S rRNA and the two ribosomal proteins L24 and L29 as the major contacts sites of YidC at the ribosomal tunnel exit. Pull down assays confirmed a significantly interaction of the C-terminal ribosome binding domain and the ribosomal protein L29, while L24 seems to be a universal contact site for the YidC-insertase core domain. Strikingly, the cryo-EM structure clearly showed a single monomer of YidC bound to the translating ribosome. This suggests that monomeric YidC might be the minimal functional unit for YidC-dependent, co-translational insertion of inner membrane proteins. In addition to the in vitro tests, a possible role of the C-terminal YidC extensions in co-translational protein targeting was tested in vivo in E. coli. For that purpose the targeting and localization of the SRP-dependent YidC-substrate protein MscL (Facey et al., 2007) was investigated as a GFP fusion protein via fluorescence microscopy. In addition, the proper membrane insertion of MscL was analyzed in radioactive pulse chase experiments via AMS gel shift assays, either in the absence of a functional SRP or SRP receptor (FtsY). Both in vivo assays clearly showed that the C-terminal ribosome binding domain of the R. baltica YidC homolog can partially substitute for the SRP receptor function in E. coli, while the cytosolic signal recognition particle is still required for correct insertion of the MscL protein. Therefore, a new co-translational targeting and insertion model of YidC-only substrates was proposed. This works also highlights evolutionary aspects of the accessory YidC domains and indicates that the C-terminal extended tail of YidC in the planctomycete group may be an ancestral remnant of a primordial translocation system operating without a typical SRP receptor. The second part focuses on the interaction of the signal recognition particle with SRP signal sequences. Isolated mutant signal sequence peptides were used to determine the specificity of SRP recognition in proteins. The interaction studies were established in an in vitro system and binding affinities of purified SRP to the isolated signal sequence peptides were determined via microscale thermophoresis (MST). A short sequence of 27 amino acid residues at the very N-terminal tail of the large cytoplasmic domain of KdpD was identified as a SRP signal sequence. Furthermore, a direct influence of the amino acid composition in the signal peptide on its SRP binding affinity in vitro was demonstrated. This confirms a low influence of an altered charge in the N-terminal region while mutations in the hydrophobic core region causes significantly reduced binding affinities to SRP. Taken together, this study contributes to the understanding of the molecular mechanisms of co-translational membrane protein biogenesis in bacteria.
Funktion und Dynamik eines gemeinsamen Insertionskomplexes der Sec-Translokase und YidC-Insertase in der bakteriellen Membran
(2020) Steudle, Anja; Kuhn, Andreas
YidC/Oxa1/Alb3-insertases and the Sec-translocase are conserved across all three kingdoms of life and constitute the most important pathway for integral proteins into cell membranes and membranes of eukaryotic organelles. The insertion of membrane proteins into the inner membrane of Gram-negative bacteria occurs mainly via the SecYEG-translocase and the YidC-insertase acting independently or in cooperation. For the cooperative insertion a close contact between SecY and YidC is assumed. Previous interaction-studies and a recently solved low-resolution structure of the so-called holo-translocon (14 Å) indicate a contact between the lateral gate of SecY and the hydrophobic substrate slide of YidC. Which specific domains of YidC and SecY thereby interact directly with each other was unknown so far. The aim of this study was to describe the contact between SecY and YidC in more detail. A high affinity for the interaction of the two proteins in detergent and in DOPC-proteoliposomes was determined via FRET measurements with fluorescently labeled SecY and YidC. For the stoichiometric ratio of the SecY/YidC-interaction a factor of one was calculated. To identify the specific contacts between SecY and YidC in vivo disulphide cross-linking experiments were performed. Direct interactions between the transmembrane domain (TM) 3 and TM8 of the SecY lateral gate and TM3 and TM5 of the hydrophobic slide of YidC were found, respectively. Furthermore, a YidC mutant with five serine substitutions, which was unable to rescue a YidC depletion strain, was investigated. Even though the serine positions are located in the middle and the periplasmic half of the hydrophobic slide of YidC and four of the positions are identical with substrate contact sites, no inhibition of insertion for the YidC-dependent substrates M13 procoat and Pf3 coat by the 5S mutant compared to the wildtype YidC was observed. For the YidC-only pathway a minimum of hydrophobicity seems to be required sufficient to allow the insertion of these substrates. In vitro FRET measurements showed an impaired interaction between SecY and the YidC 5S mutant and confirmed once again an involvement of the hydrophobic slide in the SecY/YidC-contact. Based on the cross-linking contacts and the results of the FRET measurements a possible model of the SecY/YidC-contact was established, which shows the SecY lateral gate vis-à-vis of the hydrophobic slide and the hydrophilic groove between TM3 and TM5 of YidC generating a combined SecY/YidC-cavity. Taken together, the present study provides further evidence that the lateral gate of the Sec-translocase directly interacts with the hydrophobic slide of YidC. In a further project, a SecY-YidC fusion protein was cloned to ensure the two proteins are in close proximity, the correct orientation and proper stoichiometry after reconstitution into proteoliposomes. For a collaboration with the ETH Zürich, proteoliposomes hosting the fusion protein, SecYEG, YidC or SecYEG and YidC together were prepared by myself in Hohenheim. The stepwise insertion of the Sec/YidC-dependent substrate LacY into these proteoliposomes was observed by a collaborating group of the ETH Zürich using AFM–based single-molecule force spectroscopy. The insertion of LacY was observed for the different cases but for the fusion protein and SecYEG combined with YidC the insertion process is dominated by the Sec-translocase, whereas YidC probably only has a supporting function in the folding of the protein.
Die Insertion des „minor coat“ Proteins G3P des Bakteriophagen M13 in die innere E. coli Membran benötigt die Insertase YidC und die Translokase SecYEG.
(2021) Kleinbeck, Farina; Kuhn, Andreas
The membrane of every cell forms a spacial limitation for this smallest unit of a life form. Such a very simple unicellular life form is also the Gram-negative bacterium Escherichia coli (E. coli) and is therefore a valid model organism for a living cell. Due to the inner membrane the cellular components are held together in close proximity and are separated from the extracellular environment. Most substrates cannot pass the lipid bilayer, which forms the membrane, so an import and export system had to be developed to accomplish this. For these import and export systems, very complex, polytopic transmembrane protein complexes are needed. Examples are ion channels, ion pumps or large complexes through which energy production, secretion of toxins and the transfer of nutrients are catalysed. Moreover, proteins with functions in the periplasm or outer membrane must also travel from their site of synthesis in the cytoplasm to their destination. For these different processes proteins must be inserted into or translocated across the inner membrane. Of the total proteome in prokaryotes approximately 25 to 30% is either inserted into or secreted across the inner membrane. This work identified several components required for the insertion of the "minor coat" protein G3P of M13 bacteriophage. This protein is important for the assembly of the phage particle that occurs in the inner membrane. The outermost C-terminus of G3P is anchored in the inner membrane via a single transmembrane domain, while the bulk of the approximately 42 kDa protein is located in the periplasm. Using an N-terminal cleavable signal peptide, the major portion of G3P is translocated into the periplasm via SecYEG with the help of SecA and the membrane potential. Targeting, on the other hand, could not be clearly assigned to one of the known post- or co-translational pathways. Although contact via disulfide crosslink studies to Ffh, the protein component of the ribonucleoprotein SRP, was observed via stalled ribosome nascent chains (RNCs), insertion into the membrane in vivo was independent of Ffh. Even when the interaction between SecY and FtsY, the receptor for SRP at the membrane, was impaired, G3P was inserted via SecYEG. Although the chaperone SecB was able to bind to G3P in vitro, G3P inserted independently of SecB in vivo. For membrane incorporation of G3P, it was shown that YidC is required in vivo in addition to SecYEG. Disulphide crosslink studies demonstrated that G3P first contacts the plug domain TM2b and lateral gate (TM2a and TM7) via the signal peptide of G3P, and finally the C-terminal transmembrane domain of G3P contacts YidC via TM3 and TM5 of the hydrophilic slide. Based on these contact sites, a possible insertion model was confirmed, with SecY and YidC mediating defined steps in the insertion process, providing new insights into this largely unknown process.
Membraneinbau von MscL und MscL-Mutanten aus Escherichia coli
(2012) Neugebauer, Stella; Kuhn, Andreas
About one third of all synthesized proteins in a cell are membrane proteins. To accomplish their function, it is important to ensure, that they safely reach their destination, insert efficiently into the membrane, where they fold into their correct tertiary structure. Previous studies have shown that various molecules are responsible for the targeting and insertion of membrane proteins in Escherichia coli that operate as individual modules. The mechanosensitive channel MscL is a pentameric complex in the cytoplasmic membrane of E. coli. By its action as a safety valve, MscL allows the adaption to hypoosmotic conditions of bacteria living under varying circumstances. The two transmembrane segments of the MscL monomer are connected by a periplasmic loop of 29 amino acid residues. In previous studies, the membrane insertion of MscL was analyzed in vivo in depletion strains and was monitored by modification of a single cysteine residue in the periplasmic domain of the MscL protein (Facey et al., 2007). The targeting of MscL to the inner membrane occurs in a cotranslational manner via the signal recognition particle (SRP). At the membrane, the MscL protein inserts independently of the membrane potential and the Sec-components SecAYEG, but requires YidC for the insertion process. The present thesis is about the molecular mechanisms regarding the decision whether the nascent polypeptide chain of MscL is recognized and bound by YidC or by the Sec-translocase. The periplasmic localized loop of MscL was altered by introducing negatively or positively charged residues as well as uncharged side chains and the effects on the translocation were investigated. Translocation of the periplasmic domain of MscL was detected using AMS-derivatization (4-acetamido-4´-maleimidylstilbene-2, 2´-disulfonic acid) of a single cysteine residue. The extension of the loop region by one, two or three negatively charged residues (aspartic acid residues) made the insertion of MscL dependent on the membrane potential and the Sec translocon. The requirement of SecYE was gradually affected by increasing the number of charged residues. Efficient translocation of the periplasmic loop with three additional uncharged (asparagines) residues also required the Sec-complex. The insertion of these MscL mutants was independent on the SecA component, but all the investigated mutants still showed a strict dependence on YidC. The ability of the altered MscL proteins to form functional pentameric channels was verified by growth tests and native gel electrophoresis. The presence of three additional positively charged arginine residues in the periplasmic domain inhibited MscL insertion into the lipid bilayer as well as the mutant with five additional negatively charged aspartic acid residues. As a logical consequence, the expression of these two MscL proteins could not protect the cells from osmolysis within growth tests. The direct involvement of the membrane insertase YidC with MscL and the MscL mutants was corroborated with in vivo crosslinking. YidC interacts with both transmembrane regions of MscL. Earlier studies have shown that YidC makes contact with the Pf3 coat protein in the center of the membrane. Here, the same interaction sites of YidC were identified contacting MscL during its insertion. Besides considering the significance of YidC for efficient membrane insertion, the present work has demonstrated that YidC is also essential for oligomerization of MscL into a functional channel.
Membraninsertion des Phagenproteins M13 procoat in Lipidvesikel mit rekonstituiertem Escherichia coli YidC
(2011) Stiegler, Natalie; Kuhn, Andreas
Translocation of proteins across or into the cytoplasmic membrane of Escherichia coli is accomplished by several mechanisms. The cellular secretion machinery, the translocase SecYEG, mediates the transport of unfolded proteins into the periplasm with the help of the ATPase SecA or passes the membrane proteins for bilayer integration to the insertase YidC. Membrane insertion is catalysed by YidC, whereby the native conformation of the proteins in the lipid bilayer is achieved. The translocation of a few membrane proteins occurs Sec-independently solely with the help of the insertase YidC. One of these Sec-independent proteins is the major capsid protein of the bacteriophage M13. This protein is inserted as preprotein, termed M13 procoat, with the orientation Nin-Cin into the inner membrane and a central loop domain located in the periplasm. This process is catalysed by the electrochemical membrane potential and YidC. M13 procoat is then processed by the leader peptidase to its mature form, M13 coat (orientation Nout-Cin). In the present thesis an analysis of the different transport systems of the inner membrane is performed using the example of the M13 procoat protein and its mutants. One mutant is the procoat H5EE which has 2 additional acidic residues introduced between residues +2 and +3. The insertion of this mutant requires the Sec translocase and strictly depends on the electrochemical potential. Membrane insertion of M13 procoat and derived proteins into the cytoplasmic membrane was followed in an in vitro reconstitution and translocation system. Therefore, all components of the Sec translocase (SecYEG and SecA), the insertase YidC and the different procoat proteins were purified and tested with the in vitro translocation system. Reconstitution of YidC into phospholipid vesicles depended on the lipid composition for its orientation. The cytoplasmic-out orientation corresponds to the active topology in E. coli where both termini are located in the cytoplasm. Certain lipid compositions caused the inversed orientation, which affected the catalytic activity of the reconstituted insertase. The procoat mutants H5 und H5EE were membrane inserted only in the presence of reconstituted YidC. Both proteins inserted efficiently into the vesicles with the periplasmic loop in the interior of the vesicles like the mutant PClep of procoat H5 with the C-terminal extension of the leader peptidase. Spontaneous insertion of H5 und H5EE into liposomes occurred only into leaky vesicles of the E. coli lipids. The membrane integrity was improved by the addition of an adequate amount of diacylglycerol (DAG) to the phospholipids. The leaky phospholipids were sealed by the addition of 3-4% DAG. The proteins H5 und H5EE showed a dependency of the membrane potential. Insertion occured more efficiently into YidC proteoliposomes when a stable membrane potential was generated. Proteoliposomes with reconstituted SecYEG translocase were also tested for protein insertion. Remarkedly, the protein M13 procoat H5EE efficiently inserted into SecYEG proteoliposomes, where the wildtype-like protein H5 did not.
Untersuchungen zur autonomen und YidC-vermittelten Membraninsertion von Pf3 coat-Protein mit Hilfe Fluoreszenz-spektroskopischer Einzelmolekülmessungen
(2011) Schönbauer, Anne-Kathrin; Kuhn, Andreas
Pf3 coat is the capsid protein of the bacteriophage Pf3. The phage leaves the host cell by continuous extrusion without damaging the cell. The protein itself consists of 44 amino acid residues and has a rod-like shape. Because of its simple structure, the protein needs only the help of the insertase YidC to insert into the bacterial inner membrane. 3L-Pf3 coat, a protein mutant with three additional leucine residues in the center of the transmembrane region (TMD), has an increased hydrophobicity. It is independent of YidC and inserts into the membrane autonomously (Serek et al., 2004). In this work, a newly developed physical method was used to find out whether the elongation or the increased hydrophobicity accounts for the autonomous insertion of the protein. For this reason, two new protein mutants were constructed. Each mutant has only one of the changed properties of the 3L-Pf3 coat protein: GAT-Pf3 coat has an elongated TMD with three additional residues (glycine, alanin and threonine). The second mutant, 2M-Pf3 coat, shows an increased hydrophobicity due to the substitution of two alanine residues by two methionine residues at the positions 30 and 31. So it had an increased hydrophobicity like 3L-Pf3 coat. The above mentioned proteins, wt-Pf3 coat and its mutants, were modified with a fluorescent label to follow the proteins with optical methods. The Proteins were first modified with a single cysteine and then labeled by a fluorescent marker, Atto520 maleimid. Proteins with a labeled N-terminal tail were called NC-Pf3 coat, whereas CC-Pf3 coat had a labeled C-terminal tail. In addition, the orientation of the protein in the membrane was identified by quenching the fluorescence of the NC- and CC- labeled proteins. A new method employing single molecules was developed using fluorescence correlation spectroscopy. This method allows real time observations of binding and insertion of the protein into semisynthetical liposomes. By using fluorescent quenching the membrane insertion and binding were distinguished. It became clear that both the elongation of the TMD as well as an increased hydrophobicity play a crucial role in the autonomous insertion of the protein into the membrane. Therefore, the interaction between the hydrophobic region of the protein and the hydrophobic core region of the membrane is important for the binding of the protein and its insertion into the membrane.