Decoding the molecular mechanisms of membrane protein targeting and insertion

• Applicant: Professor Dr. Hans-Georg Koch
• Subject Area: Biochemistry
• Term: from 2014 to 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 263098192

• Final Report Year: 2024

Final Report Abstract

The spatial and temporal coordination of protein trafficking is essential in all cells and in particular important for aggregation-prone membrane proteins. Coupling protein synthesis with protein trafficking is an elegant solution to this conundrum and such a cotranslational transport is executed in both prokaryotic and eukaryotic cells by the signal recognition particle (SRP). However, our data demonstrate that the ability of SRP to cotranslationally interact with its substrates is restricted to (1) proteins of at least 50 amino acids in length, (2) proteins with an N-terminal signal anchor sequence and (3) only possible during exponential phase, when the concentration of the alarmones (p)ppGpp are low. Thus, alternative strategies for membrane targeting of proteins are required and we show that co-translational targeting can also be executed by the ATPase SecA. We also show that SRP is able to post-translationally target small membrane proteins and finally, our data demonstrate that mRNA-targeting provides an SRP-independent strategy for membrane protein insertion. Either the SecYEG-translocon or the YidC-insertase are required for SRP-dependent and -independent protein insertion and we have further characterized their interactomes and explored the mechanisms of protein insertion. In a collaborative project these studies were further extended to protein transport in mitochondria. In conclusion, during both funding periods, we have revealed and explored the enormous plasticity of protein targeting strategies in bacteria.

Publications

• Dynamic Interaction of the Sec Translocon with the Chaperone PpiD. Journal of Biological Chemistry, 289(31), 21706-21715.
  Sachelaru, Ilie; Petriman, Narcis-Adrian; Kudva, Renuka & Koch, Hans-Georg
  
• Einblicke in die Funktionsweise komplexer Transportmaschinerien. BIOspektrum, 21(7), 696-698.
  Petriman, Narcis-Adrian; Jauß, Benjamin & Koch, Hans-Georg
  
• Ribosome binding induces repositioning of the signal recognition particle receptor on the translocon. Journal of Cell Biology, 211(1), 91-104.
  Kuhn, Patrick; Draycheva, Albena; Vogt, Andreas; Petriman, Narcis-Adrian; Sturm, Lukas; Drepper, Friedel; Warscheid, Bettina; Wintermeyer, Wolfgang & Koch, Hans-Georg
  
• Targeting and Insertion of Membrane Proteins. EcoSal Plus, 7(2).
  Kuhn, Andreas; Koch, Hans-Georg & Dalbey, Ross E.
  
• The Sec61/SecY complex is inherently deficient in translocating intrinsically disordered proteins. Journal of Biological Chemistry, 292(52), 21383-21396.
  Gonsberg, Anika; Jung, Sebastian; Ulbrich, Sarah; Origi, Andrea; Ziska, Anke; Baier, Michael; Koch, Hans-Georg; Zimmermann, Richard; Winklhofer, Konstanze F. & Tatzelt, Jörg
  
• The signal recognition particle contacts uL23 and scans substrate translation inside the ribosomal tunnel. Nature Microbiology, 2(4).
  Denks, Kärt; Sliwinski, Nadine; Erichsen, Veronika; Borodkina, Bogdana; Origi, Andrea & Koch, Hans-Georg
  
• YidC and SecYEG form a heterotetrameric protein translocation channel. Scientific Reports, 7(1).
  Sachelaru, Ilie; Winter, Lukas; Knyazev, Denis G.; Zimmermann, Mirjam; Vogt, Andreas; Kuttner, Roland; Ollinger, Nicole; Siligan, Christine; Pohl, Peter & Koch, Hans-Georg
  
• Co-translational protein targeting in bacteria. FEMS Microbiology Letters, 365(11).
  Steinberg, Ruth; Knüpffer, Lara; Origi, Andrea; Asti, Rossella & Koch, Hans-Georg
  
• The interaction network of the YidC insertase with the SecYEG translocon, SRP and the SRP receptor FtsY. Scientific Reports, 8(1).
  Petriman, Narcis-Adrian; Jauß, Benjamin; Hufnagel, Antonia; Franz, Lisa; Sachelaru, Ilie; Drepper, Friedel; Warscheid, Bettina & Koch, Hans-Georg
  
• Molecular Mimicry of SecA and Signal Recognition Particle Binding to the Bacterial Ribosome. mBio, 10(4).
  Knüpffer, Lara; Fehrenbach, Clara; Denks, Kärt; Erichsen, Veronika; Petriman, Narcis-Adrian & Koch, Hans-Georg
  
• Noncompetitive binding of PpiD and YidC to the SecYEG translocon expands the global view on the SecYEG interactome in Escherichia coli. Journal of Biological Chemistry, 294(50), 19167-19183.
  Jauss, Benjamin; Petriman, Narcis-Adrian; Drepper, Friedel; Franz, Lisa; Sachelaru, Ilie; Welte, Thomas; Steinberg, Ruth; Warscheid, Bettina & Koch, Hans-Georg
  
• Yet another job for the bacterial ribosome. Microbial Cell, 6(11), 524-526.
  Origi, Andrea; Natriashivili, Ana; Knüpffer, Lara; Fehrenbach, Clara; Denks, Kärt; Asti, Rosella & Koch, Hans-Georg
  
• Eeyarestatin 24 impairs SecYEG‐dependent protein trafficking and inhibits growth of clinically relevant pathogens. Molecular Microbiology, 115(1), 28-40.
  Steenhuis, Maurice; Koningstein, Gregory M.; Oswald, Julia; Pick, Tillman; O’Keefe, Sarah; Koch, Hans‐Georg; Cavalié, Adolfo; Whitehead, Roger C.; Swanton, Eileithyia; High, Stephen & Luirink, Joen
  
• Posttranslational insertion of small membrane proteins by the bacterial signal recognition particle. PLOS Biology, 18(9), e3000874.
  Steinberg, Ruth; Origi, Andrea; Natriashvili, Ana; Sarmah, Pinku; Licheva, Mariya; Walker, Princess M.; Kraft, Claudine; High, Stephen; Luirink, Joen; Shi, Wei. Q.; Helmstädter, Martin; Ulbrich, Maximilian H. & Koch, Hans-Georg
  
• SecY-mediated quality control prevents the translocation of non-gated porins. Scientific Reports, 10(1).
  Jung, Sebastian; Bader, Verian; Natriashvili, Ana; Koch, Hans-Georg; Winklhofer, Konstanze F. & Tatzelt, Jörg
  
• The Dynamic SecYEG Translocon. Frontiers in Molecular Biosciences, 8.
  Oswald, Julia; Njenga, Robert; Natriashvili, Ana; Sarmah, Pinku & Koch, Hans-Georg
  
• The largely unexplored biology of small proteins in pro‐ and eukaryotes. The FEBS Journal, 288(24), 7002-7024.
  Steinberg, Ruth & Koch, Hans‐Georg
  
• A common evolutionary origin reveals fundamental principles of protein insertases. PLOS Biology, 20(3), e3001558.
  Vögtle, F.-Nora; Koch, Hans-Georg & Meisinger, Chris
  
• Inhibition of SRP-dependent protein secretion by the bacterial alarmone (p)ppGpp. Nature Communications, 13(1).
  Czech, Laura; Mais, Christopher-Nils; Kratzat, Hanna; Sarmah, Pinku; Giammarinaro, Pietro; Freibert, Sven-Andreas; Esser, Hanna Folke; Musial, Joanna; Berninghausen, Otto; Steinchen, Wieland; Beckmann, Roland; Koch, Hans-Georg & Bange, Gert
  
• Central role of Tim17 in mitochondrial presequence protein translocation. Nature, 621(7979), 627-634.
  Fielden, Laura F.; Busch, Jakob D.; Merkt, Sandra G.; Ganesan, Iniyan; Steiert, Conny; Hasselblatt, Hanna B.; Busto, Jon V.; Wirth, Christophe; Zufall, Nicole; Jungbluth, Sibylle; Noll, Katja; Dung, Julia M.; Butenko, Ludmila; von der Malsburg, Karina; Koch, Hans-Georg; Hunte, Carola; van der Laan, Martin & Wiedemann, Nils
  
• Coping with stress: How bacteria fine-tune protein synthesis and protein transport. Journal of Biological Chemistry, 299(9), 105163.
  Njenga, Robert; Boele, Julian; Öztürk, Yavuz & Koch, Hans-Georg
  
• mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria. Cell Reports, 42(3), 112140.
  Sarmah, Pinku; Shang, Wenkang; Origi, Andrea; Licheva, Mariya; Kraft, Claudine; Ulbrich, Maximilian; Lichtenberg, Elisabeth; Wilde, Annegret & Koch, Hans-Georg
  
• YidC from Escherichia coli Forms an Ion-Conducting Pore upon Activation by Ribosomes. Biomolecules, 13(12), 1774.
  Knyazev, Denis G.; Winter, Lukas; Vogt, Andreas; Posch, Sandra; Öztürk, Yavuz; Siligan, Christine; Goessweiner-Mohr, Nikolaus; Hagleitner-Ertugrul, Nora; Koch, Hans-Georg & Pohl, Peter
  
• Control of a Chemical Chaperone by a Universally Conserved Atpase.
  Jiang, Hong; Milanov, Martin; Jüngert, Gabriela; Angebauer, Larissa; Flender, Clara; Smudde, Eva; Gather, Fabian; Vogel, Tanja; jessen, henning & Koch, Hans-Georg
  
• The contribution of mRNA targeting to spatial protein localization in bacteria. The FEBS Journal, 291(21), 4639-4659.
  Shang, Wenkang; Lichtenberg, Elisabeth; Mlesnita, Andreea Mihaela; Wilde, Annegret & Koch, Hans‐Georg