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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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Knyazev DG, Winter L, Vogt A, Posch S, Öztürk Y, Siligan C, Goessweiner-Mohr N, Hagleitner-Ertugrul N, Koch HG, Pohl P. YidC from Escherichia coli Forms an Ion-Conducting Pore upon Activation by Ribosomes. Biomolecules 2023; 13:1774. [PMID: 38136645 PMCID: PMC10741985 DOI: 10.3390/biom13121774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The universally conserved protein YidC aids in the insertion and folding of transmembrane polypeptides. Supposedly, a charged arginine faces its hydrophobic lipid core, facilitating polypeptide sliding along YidC's surface. How the membrane barrier to other molecules may be maintained is unclear. Here, we show that the purified and reconstituted E. coli YidC forms an ion-conducting transmembrane pore upon ribosome or ribosome-nascent chain complex (RNC) binding. In contrast to monomeric YidC structures, an AlphaFold parallel YidC dimer model harbors a pore. Experimental evidence for a dimeric assembly comes from our BN-PAGE analysis of native vesicles, fluorescence correlation spectroscopy studies, single-molecule fluorescence photobleaching observations, and crosslinking experiments. In the dimeric model, the conserved arginine and other residues interacting with nascent chains point into the putative pore. This result suggests the possibility of a YidC-assisted insertion mode alternative to the insertase mechanism.
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Affiliation(s)
- Denis G. Knyazev
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Lukas Winter
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Andreas Vogt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
- Spemann-Graduate School of Biology and Medicine (SGBM), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - Sandra Posch
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Yavuz Öztürk
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Nikolaus Goessweiner-Mohr
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Nora Hagleitner-Ertugrul
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert Ludwig University of Freiburg, 79104 Freiburg, Germany (Y.Ö.); (H.-G.K.)
- Spemann-Graduate School of Biology and Medicine (SGBM), Albert Ludwig University of Freiburg, 79104 Freiburg, Germany
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, A-4020 Linz, Austria; (D.G.K.); (L.W.); (S.P.); (C.S.); (N.G.-M.); (N.H.-E.)
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Njenga R, Boele J, Öztürk Y, Koch HG. Coping with stress: How bacteria fine-tune protein synthesis and protein transport. J Biol Chem 2023; 299:105163. [PMID: 37586589 PMCID: PMC10502375 DOI: 10.1016/j.jbc.2023.105163] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/08/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Maintaining a functional proteome under different environmental conditions is challenging for every organism, in particular for unicellular organisms, such as bacteria. In order to cope with changing environments and stress conditions, bacteria depend on strictly coordinated proteostasis networks that control protein production, folding, trafficking, and degradation. Regulation of ribosome biogenesis and protein synthesis are cornerstones of this cellular adaptation in all domains of life, which is rationalized by the high energy demand of both processes and the increased resistance of translationally silent cells against internal or external poisons. Reduced protein synthesis ultimately also reduces the substrate load for protein transport systems, which are required for maintaining the periplasmic, inner, and outer membrane subproteomes. Consequences of impaired protein transport have been analyzed in several studies and generally induce a multifaceted response that includes the upregulation of chaperones and proteases and the simultaneous downregulation of protein synthesis. In contrast, generally less is known on how bacteria adjust the protein targeting and transport machineries to reduced protein synthesis, e.g., when cells encounter stress conditions or face nutrient deprivation. In the current review, which is mainly focused on studies using Escherichia coli as a model organism, we summarize basic concepts on how ribosome biogenesis and activity are regulated under stress conditions. In addition, we highlight some recent developments on how stress conditions directly impair protein targeting to the bacterial membrane. Finally, we describe mechanisms that allow bacteria to maintain the transport of stress-responsive proteins under conditions when the canonical protein targeting pathways are impaired.
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Affiliation(s)
- Robert Njenga
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany; Faculty of Biology, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Julian Boele
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Faculty of Medicine, Institute for Biochemistry and Molecular Biology, ZBMZ, Albert-Ludwigs University Freiburg, Freiburg, Germany.
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Sarmah P, Shang W, Origi A, Licheva M, Kraft C, Ulbrich M, Lichtenberg E, Wilde A, Koch HG. mRNA targeting eliminates the need for the signal recognition particle during membrane protein insertion in bacteria. Cell Rep 2023; 42:112140. [PMID: 36842086 PMCID: PMC10066597 DOI: 10.1016/j.celrep.2023.112140] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 01/10/2023] [Accepted: 02/02/2023] [Indexed: 02/26/2023] Open
Abstract
Signal-sequence-dependent protein targeting is essential for the spatiotemporal organization of eukaryotic and prokaryotic cells and is facilitated by dedicated protein targeting factors such as the signal recognition particle (SRP). However, targeting signals are not exclusively contained within proteins but can also be present within mRNAs. By in vivo and in vitro assays, we show that mRNA targeting is controlled by the nucleotide content and by secondary structures within mRNAs. mRNA binding to bacterial membranes occurs independently of soluble targeting factors but is dependent on the SecYEG translocon and YidC. Importantly, membrane insertion of proteins translated from membrane-bound mRNAs occurs independently of the SRP pathway, while the latter is strictly required for proteins translated from cytosolic mRNAs. In summary, our data indicate that mRNA targeting acts in parallel to the canonical SRP-dependent protein targeting and serves as an alternative strategy for safeguarding membrane protein insertion when the SRP pathway is compromised.
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Affiliation(s)
- Pinku Sarmah
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Mariya Licheva
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Claudine Kraft
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University Freiburg, 79104 Freiburg, Germany
| | - Maximilian Ulbrich
- Internal Medicine IV, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signaling Studies, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | | | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.
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