1
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Nair AM, Jiang T, Mu B, Zhao R. Plastid Molecular Chaperone HSP90C Interacts with the SecA1 Subunit of Sec Translocase for Thylakoid Protein Transport. PLANTS (BASEL, SWITZERLAND) 2024; 13:1265. [PMID: 38732479 PMCID: PMC11085213 DOI: 10.3390/plants13091265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
The plastid stroma-localized chaperone HSP90C plays a crucial role in maintaining optimal proteostasis within chloroplasts and participates in protein translocation processes. While existing studies have revealed HSP90C's direct interaction with the Sec translocase-dependent client pre-protein PsbO1 and the SecY1 subunit of the thylakoid membrane-bound Sec1 translocase channel system, its direct involvement with the extrinsic homodimeric Sec translocase subunit, SecA1, remains elusive. Employing bimolecular fluorescence complementation (BiFC) assay and other in vitro analyses, we unraveled potential interactions between HSP90C and SecA1. Our investigation revealed dynamic interactions between HSP90C and SecA1 at the thylakoid membrane and stroma. The thylakoid membrane localization of this interaction was contingent upon active HSP90C ATPase activity, whereas their stromal interaction was associated with active SecA1 ATPase activity. Furthermore, we observed a direct interaction between these two proteins by analyzing their ATP hydrolysis activities, and their interaction likely impacts their respective functional cycles. Additionally, using PsbO1, a model Sec translocase client pre-protein, we studied the intricacies of HSP90C's possible involvement in pre-protein translocation via the Sec1 system in chloroplasts. The results suggest a complex nature of the HSP90C-SecA1 interaction, possibly mediated by the Sec client protein. Our studies shed light on the nuanced aspects of HSP90C's engagement in orchestrating pre-protein translocation, and we propose a potential collaborative role of HSP90C with SecA1 in actively facilitating pre-protein transport across the thylakoid membrane.
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Affiliation(s)
| | | | | | - Rongmin Zhao
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON M1C 1A4, Canada; Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; (A.M.N.); (T.J.); (B.M.)
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2
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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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3
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Addabbo RM, Hutchinson RB, Allaman HJ, Dalphin MD, Mecha MF, Liu Y, Staikos A, Cavagnero S. Critical Beginnings: Selective Tuning of Solubility and Structural Accuracy of Newly Synthesized Proteins by the Hsp70 Chaperone System. J Phys Chem B 2023; 127:3990-4014. [PMID: 37130318 PMCID: PMC10829761 DOI: 10.1021/acs.jpcb.2c08485] [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] [Indexed: 05/04/2023]
Abstract
Proteins are particularly prone to aggregation immediately after release from the ribosome, and it is therefore important to elucidate the role of chaperones during these key steps of protein life. The Hsp70 and trigger factor (TF) chaperone systems interact with nascent proteins during biogenesis and immediately post-translationally. It is unclear, however, whether these chaperones can prevent formation of soluble and insoluble aggregates. Here, we address this question by monitoring the solubility and structural accuracy of globin proteins biosynthesized in an Escherichia coli cell-free system containing different concentrations of the bacterial Hsp70 and TF chaperones. We find that Hsp70 concentrations required to grant solubility to newly synthesized proteins are extremely sensitive to client-protein sequence. Importantly, Hsp70 concentrations yielding soluble client proteins are insufficient to prevent formation of soluble aggregates. In fact, for some aggregation-prone protein variants, avoidance of soluble-aggregate formation demands Hsp70 concentrations that exceed cellular levels in E. coli. In all, our data highlight the prominent role of soluble aggregates upon nascent-protein release from the ribosome and show the limitations of the Hsp70 chaperone system in the case of highly aggregation-prone proteins. These results demonstrate the need to devise better strategies to prevent soluble-aggregate formation upon release from the ribosome.
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Affiliation(s)
- Rayna M. Addabbo
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Rachel B. Hutchinson
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Heather J. Allaman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Matthew D. Dalphin
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Miranda F. Mecha
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
| | - Yue Liu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Alexios Staikos
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
| | - Silvia Cavagnero
- Biophysics Graduate Degree Program, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, U.S.A
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4
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Eismann L, Fijalkowski I, Galmozzi CV, Koubek J, Tippmann F, Van Damme P, Kramer G. Selective ribosome profiling reveals a role for SecB in the co-translational inner membrane protein biogenesis. Cell Rep 2022; 41:111776. [PMID: 36476862 DOI: 10.1016/j.celrep.2022.111776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 10/04/2022] [Accepted: 11/11/2022] [Indexed: 12/12/2022] Open
Abstract
The chaperone SecB has been implicated in de novo protein folding and translocation across the membrane, but it remains unclear which nascent polypeptides SecB binds, when during translation SecB acts, how SecB function is coordinated with other chaperones and targeting factors, and how polypeptide engagement contributes to protein biogenesis. Using selective ribosome profiling, we show that SecB binds many nascent cytoplasmic and translocated proteins generally late during translation and controlled by the chaperone trigger factor. Revealing an uncharted role in co-translational translocation, inner membrane proteins (IMPs) are the most prominent nascent SecB interactors. Unlike other substrates, IMPs are bound early during translation, following the membrane targeting by the signal recognition particle. SecB remains bound until translation is terminated, and contributes to membrane insertion. Our study establishes a role of SecB in the co-translational maturation of proteins from all cellular compartments and functionally implicates cytosolic chaperones in membrane protein biogenesis.
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Affiliation(s)
- Lena Eismann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Igor Fijalkowski
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Carla Verónica Galmozzi
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain; Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/ Universidad de Sevilla, 41013 Seville, Spain
| | - Jiří Koubek
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Frank Tippmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
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5
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Smets D, Tsirigotaki A, Smit JH, Krishnamurthy S, Portaliou AG, Vorobieva A, Vranken W, Karamanou S, Economou A. Evolutionary adaptation of the protein folding pathway for secretability. EMBO J 2022; 41:e111344. [PMID: 36031863 PMCID: PMC9713715 DOI: 10.15252/embj.2022111344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/14/2022] [Accepted: 08/02/2022] [Indexed: 01/15/2023] Open
Abstract
Secretory preproteins of the Sec pathway are targeted post-translationally and cross cellular membranes through translocases. During cytoplasmic transit, mature domains remain non-folded for translocase recognition/translocation. After translocation and signal peptide cleavage, mature domains fold to native states in the bacterial periplasm or traffic further. We sought the structural basis for delayed mature domain folding and how signal peptides regulate it. We compared how evolution diversified a periplasmic peptidyl-prolyl isomerase PpiA mature domain from its structural cytoplasmic PpiB twin. Global and local hydrogen-deuterium exchange mass spectrometry showed that PpiA is a slower folder. We defined at near-residue resolution hierarchical folding initiated by similar foldons in the twins, at different order and rates. PpiA folding is delayed by less hydrophobic native contacts, frustrated residues and a β-turn in the earliest foldon and by signal peptide-mediated disruption of foldon hierarchy. When selected PpiA residues and/or its signal peptide were grafted onto PpiB, they converted it into a slow folder with enhanced in vivo secretion. These structural adaptations in a secretory protein facilitate trafficking.
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Affiliation(s)
- Dries Smets
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Alexandra Tsirigotaki
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Jochem H Smit
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Srinath Krishnamurthy
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Athina G Portaliou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Anastassia Vorobieva
- Structural Biology BrusselsVrije Universiteit Brussel and Center for Structural BiologyBrusselsBelgium
- VIB‐VUB Center for Structural Biology, VIBBrusselsBelgium
| | - Wim Vranken
- Structural Biology BrusselsVrije Universiteit Brussel and Center for Structural BiologyBrusselsBelgium
- VIB‐VUB Center for Structural Biology, VIBBrusselsBelgium
- Interuniversity Institute of Bioinformatics in BrusselsFree University of BrusselsBrusselsBelgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular BacteriologyKU LeuvenLeuvenBelgium
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6
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Musik JE, Zalucki YM, Beacham IR, Jennings MP. The role of signal sequence proximal residues in the mature region of bacterial secreted proteins in E. coli. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184000. [PMID: 35798072 DOI: 10.1016/j.bbamem.2022.184000] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 06/18/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Secreted proteins contain an N-terminal signal peptide to guide them through the secretion pathway. Once the protein is translocated, the signal peptide is removed by a signal peptidase, such as signal peptidase I. The signal peptide has been extensively studied and reviewed; however, the mature region has not been the focus of review. Here we cover the experimental evidence that highlights the important role of the mature region amino acid residues in both the efficiency and the ability of secreted proteins to be successfully exported via secretion pathways and cleaved by signal peptidase I.
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Affiliation(s)
- Joanna E Musik
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, 4222, Australia
| | - Yaramah M Zalucki
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, 4222, Australia.
| | - Ifor R Beacham
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, 4222, Australia
| | - Michael P Jennings
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, QLD, 4222, Australia.
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7
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Smets D, Smit J, Xu Y, Karamanou S, Economou A. Signal Peptide-rheostat Dynamics Delay Secretory Preprotein Folding. J Mol Biol 2022; 434:167790. [PMID: 35970402 DOI: 10.1016/j.jmb.2022.167790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 10/15/2022]
Abstract
Sec secretory proteins are distinguished from cytoplasmic ones by N-terminal signal peptides with multiple roles during post-translational translocation. They contribute to preprotein targeting to the translocase by slowing down folding, binding receptors and triggering secretion. While signal peptides get cleaved after translocation, mature domains traffic further and/or fold into functional states. How signal peptides delay folding temporarily, to keep mature domains translocation-competent, remains unclear. We previously reported that the foldon landscape of the periplasmic prolyl-peptidyl isomerase is altered by its signal peptide and mature domain features. Here, we reveal that the dynamics of signal peptides and mature domains crosstalk. This involves the signal peptide's hydrophobic helical core, the short unstructured connector to the mature domain and the flexible rheostat at the mature domain N-terminus. Through this cis mechanism the signal peptide delays the formation of early initial foldons thus altering their hierarchy and delaying mature domain folding. We propose that sequence elements outside a protein's native core exploit their structural dynamics to influence the folding landscape.
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Affiliation(s)
- Dries Smets
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.
| | - Jochem Smit
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.
| | - Ying Xu
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.
| | - Spyridoula Karamanou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.
| | - Anastassios Economou
- KU Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, 3000 Leuven, Belgium.
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8
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Kaushik S, He H, Dalbey RE. Bacterial Signal Peptides- Navigating the Journey of Proteins. Front Physiol 2022; 13:933153. [PMID: 35957980 PMCID: PMC9360617 DOI: 10.3389/fphys.2022.933153] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022] Open
Abstract
In 1971, Blobel proposed the first statement of the Signal Hypothesis which suggested that proteins have amino-terminal sequences that dictate their export and localization in the cell. A cytosolic binding factor was predicted, and later the protein conducting channel was discovered that was proposed in 1975 to align with the large ribosomal tunnel. The 1975 Signal Hypothesis also predicted that proteins targeted to different intracellular membranes would possess distinct signals and integral membrane proteins contained uncleaved signal sequences which initiate translocation of the polypeptide chain. This review summarizes the central role that the signal peptides play as address codes for proteins, their decisive role as targeting factors for delivery to the membrane and their function to activate the translocation machinery for export and membrane protein insertion. After shedding light on the navigation of proteins, the importance of removal of signal peptide and their degradation are addressed. Furthermore, the emerging work on signal peptidases as novel targets for antibiotic development is described.
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9
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Gao J, Ouyang C, Zhao J, Han Y, Guo Q, Liu X, Zhang T, Duan M, Wang X, Xu C. Coexpressing the Signal Peptide of Vip3A and the Trigger Factor of Bacillus thuringiensis Enhances the Production Yield and Solubility of eGFP in Escherichia coli. Front Microbiol 2022; 13:892428. [PMID: 35923407 PMCID: PMC9342664 DOI: 10.3389/fmicb.2022.892428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
Many fusion tags have been developed to improve the expression of recombinant proteins. Besides the translocation of cargo proteins, the signal peptides (SPs) of some secretory proteins, such as the ssTorA and Iasp, have been used as an inclusion body tag (IB-tag) or the recombinant expression enhancer in the cytosol of E. coli. In this study, the approach to utilize the SP of Vip3A (Vasp) from Bacillus thuringiensis (Bt) as a fusion tag was investigated. The results showed that either the Vasp or its predicted N- (VN), H- (VH), and C-regions (VC), as well as their combinations (VNH, VNC, and VHC), were able to significantly enhance the production yield of eGFP. However, the hydrophobic region of the Vasp (VH and/or VC) made more than half of the eGFP molecules aggregated (VeGFP, VHeGFP, VCeGFP, VNHeGFP, VNCeGFP, and VHCeGFP). Interestingly, the addition of the Bt trigger factor (BtTF) led to the neutralization of the negative impact and solubilization of the fusion proteins. Therefore, the coexpression of Vasp or its derivates with the chaperone BtTF could be a novel dual-enhancement system for the production yield and solubility of recombinant proteins. Notably, EcTF was unable to impact the solubility of Vasp or its derivates guided proteins, suggesting its different specificities on the recognition or interaction. Additionally, this study also suggested that the translocation of Vip3 in the host cell would be regulated by the BtTF-involved model.
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Affiliation(s)
- Jianhua Gao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Chunping Ouyang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Juanli Zhao
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Yan Han
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Qinghua Guo
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Xuan Liu
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Tianjiao Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
| | - Ming Duan
- Experimental Teaching Center, Shanxi Agricultural University, Jinzhong, China
| | - Xingchun Wang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
- Xingchun Wang
| | - Chao Xu
- State Key Laboratory of Rice Biology, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- *Correspondence: Chao Xu
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10
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Zhu Z, Wang S, Shan SO. Ribosome profiling reveals multiple roles of SecA in cotranslational protein export. Nat Commun 2022; 13:3393. [PMID: 35697696 PMCID: PMC9192764 DOI: 10.1038/s41467-022-31061-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/26/2022] [Indexed: 11/18/2022] Open
Abstract
SecA, an ATPase known to posttranslationally translocate secretory proteins across the bacterial plasma membrane, also binds ribosomes, but the role of SecA’s ribosome interaction has been unclear. Here, we used a combination of ribosome profiling methods to investigate the cotranslational actions of SecA. Our data reveal the widespread accumulation of large periplasmic loops of inner membrane proteins in the cytoplasm during their cotranslational translocation, which are specifically recognized and resolved by SecA in coordination with the proton motive force (PMF). Furthermore, SecA associates with 25% of secretory proteins with highly hydrophobic signal sequences at an early stage of translation and mediates their cotranslational transport. In contrast, the chaperone trigger factor (TF) delays SecA engagement on secretory proteins with weakly hydrophobic signal sequences, thus enforcing a posttranslational mode of their translocation. Our results elucidate the principles of SecA-driven cotranslational protein translocation and reveal a hierarchical network of protein export pathways in bacteria. Using a combination of ribosome profiling methods, Zhu et al. investigate the principles governing the cotranslational interaction of SecA with nascent proteins and reveal a hierarchical organization of protein export pathways in bacteria.
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Affiliation(s)
- Zikun Zhu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Shuai Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.,Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Shu-Ou Shan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA.
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11
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Chaudhuri D, Banerjee S, Chakraborty S, Chowdhury D, Haldar S. Direct Observation of the Mechanical Role of Bacterial Chaperones in Protein Folding. Biomacromolecules 2022; 23:2951-2967. [PMID: 35678300 DOI: 10.1021/acs.biomac.2c00451] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein folding under force is an integral source of generating mechanical energy in various cellular processes, ranging from protein translation to degradation. Although chaperones are well known to interact with proteins under mechanical force, how they respond to force and control cellular energetics remains unknown. To address this question, we introduce a real-time magnetic tweezer technology herein to mimic the physiological force environment on client proteins, keeping the chaperones unperturbed. We studied two structurally distinct client proteins--protein L and talin with seven different chaperones─independently and in combination and proposed a novel mechanical activity of chaperones. We found that chaperones behave differently, while these client proteins are under force, than their previously known functions. For instance, tunnel-associated chaperones (DsbA and trigger factor), otherwise working as holdase without force, assist folding under force. This process generates an additional mechanical energy up to ∼147 zJ to facilitate translation or translocation. However, well-known cytoplasmic foldase chaperones (PDI, thioredoxin, or DnaKJE) do not possess the mechanical folding ability under force. Notably, the transferring chaperones (DnaK, DnaJ, and SecB) act as holdase and slow down the folding process, both in the presence and absence of force, to prevent misfolding of the client proteins. This provides an emerging insight of mechanical roles of chaperones: they can generate or consume energy by shifting the energy landscape of the client proteins toward a folded or an unfolded state, suggesting an evolutionary mechanism to minimize energy consumption in various biological processes.
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Affiliation(s)
- Deep Chaudhuri
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Souradeep Banerjee
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Soham Chakraborty
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Debojyoti Chowdhury
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
| | - Shubhasis Haldar
- Department of Biological Sciences, Ashoka University, Sonepat, Haryana 131029, India
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12
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Yang CI, Kim J, Shan SO. Ribosome-nascent chain interaction regulates N-terminal protein modification. J Mol Biol 2022; 434:167535. [PMID: 35278477 PMCID: PMC9126151 DOI: 10.1016/j.jmb.2022.167535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/01/2022] [Accepted: 03/04/2022] [Indexed: 01/02/2023]
Abstract
Numerous proteins initiate their folding, localization, and modifications early during translation, and emerging data show that the ribosome actively participates in diverse protein biogenesis pathways. Here we show that the ribosome imposes an additional layer of substrate selection during N-terminal methionine excision (NME), an essential protein modification in bacteria. Biochemical analyses show that cotranslational NME is exquisitely sensitive to a hydrophobic signal sequence or transmembrane domain near the N terminus of the nascent polypeptide. The ability of the nascent chain to access the active site of NME enzymes dictates NME efficiency, which is inhibited by confinement of the nascent chain on the ribosome surface and exacerbated by signal recognition particle. In vivo measurements corroborate the inhibition of NME by an N-terminal hydrophobic sequence, suggesting the retention of formylmethionine on a substantial fraction of the secretory and membrane proteome. Our work demonstrates how molecular features of a protein regulate its cotranslational modification and highlights the active participation of the ribosome in protein biogenesis pathways via interactions of the ribosome surface with the nascent protein.
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13
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Krishnamurthy S, Sardis MF, Eleftheriadis N, Chatzi KE, Smit JH, Karathanou K, Gouridis G, Portaliou AG, Bondar AN, Karamanou S, Economou A. Preproteins couple the intrinsic dynamics of SecA to its ATPase cycle to translocate via a catch and release mechanism. Cell Rep 2022; 38:110346. [PMID: 35139375 DOI: 10.1016/j.celrep.2022.110346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/22/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022] Open
Abstract
Protein machines undergo conformational motions to interact with and manipulate polymeric substrates. The Sec translocase promiscuously recognizes, becomes activated, and secretes >500 non-folded preprotein clients across bacterial cytoplasmic membranes. Here, we reveal that the intrinsic dynamics of the translocase ATPase, SecA, and of preproteins combine to achieve translocation. SecA possesses an intrinsically dynamic preprotein clamp attached to an equally dynamic ATPase motor. Alternating motor conformations are finely controlled by the γ-phosphate of ATP, while ADP causes motor stalling, independently of clamp motions. Functional preproteins physically bridge these independent dynamics. Their signal peptides promote clamp closing; their mature domain overcomes the rate-limiting ADP release. While repeated ATP cycles shift the motor between unique states, multiple conformationally frustrated prongs in the clamp repeatedly "catch and release" trapped preprotein segments until translocation completion. This universal mechanism allows any preprotein to promiscuously recognize the translocase, usurp its intrinsic dynamics, and become secreted.
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Affiliation(s)
- Srinath Krishnamurthy
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Marios-Frantzeskos Sardis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Nikolaos Eleftheriadis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Katerina E Chatzi
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Jochem H Smit
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Konstantina Karathanou
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, 14195 Berlin, Germany
| | - Giorgos Gouridis
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium; Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands; Structural Biology Division, Institute of Molecular Biology and Biotechnology (IMBB-FORTH), Nikolaou Plastira 100, Heraklion, Crete, Greece
| | - Athina G Portaliou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Ana-Nicoleta Bondar
- Freie Universität Berlin, Department of Physics, Theoretical Molecular Biophysics Group, Arnimallee 14, 14195 Berlin, Germany; University of Bucharest, Faculty of Physics, Atomiștilor 405, 077125 Măgurele, Romania; Forschungszentrum Jülich, Institute of Computational Biomedicine, IAS-5/INM-9, Wilhelm-Johnen Straße, 5428 Jülich, Germany
| | - Spyridoula Karamanou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium
| | - Anastassios Economou
- KU Leuven, University of Leuven, Rega Institute, Department of Microbiology and Immunology, 3000 Leuven, Belgium.
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14
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Karyolaimos A, de Gier JW. Strategies to Enhance Periplasmic Recombinant Protein Production Yields in Escherichia coli. Front Bioeng Biotechnol 2021; 9:797334. [PMID: 34970535 PMCID: PMC8712718 DOI: 10.3389/fbioe.2021.797334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022] Open
Abstract
Main reasons to produce recombinant proteins in the periplasm of E. coli rather than in its cytoplasm are to -i- enable disulfide bond formation, -ii- facilitate protein isolation, -iii- control the nature of the N-terminus of the mature protein, and -iv- minimize exposure to cytoplasmic proteases. However, hampered protein targeting, translocation and folding as well as protein instability can all negatively affect periplasmic protein production yields. Strategies to enhance periplasmic protein production yields have focused on harmonizing secretory recombinant protein production rates with the capacity of the secretory apparatus by transcriptional and translational tuning, signal peptide selection and engineering, increasing the targeting, translocation and periplasmic folding capacity of the production host, preventing proteolysis, and, finally, the natural and engineered adaptation of the production host to periplasmic protein production. Here, we discuss these strategies using notable examples as a thread.
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Affiliation(s)
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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15
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Thoma J, Burmann BM. Architects of their own environment: How membrane proteins shape the Gram-negative cell envelope. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 128:1-34. [PMID: 35034716 DOI: 10.1016/bs.apcsb.2021.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gram-negative bacteria are surrounded by a complex multilayered cell envelope, consisting of an inner and an outer membrane, and separated by the aqueous periplasm, which contains a thin peptidoglycan cell wall. These bacteria employ an arsenal of highly specialized membrane protein machineries to ensure the correct assembly and maintenance of the membranes forming the cell envelope. Here, we review the diverse protein systems, which perform these functions in Escherichia coli, such as the folding and insertion of membrane proteins, the transport of lipoproteins and lipopolysaccharide within the cell envelope, the targeting of phospholipids, and the regulation of mistargeted envelope components. Some of these protein machineries have been known for a long time, yet still hold surprises. Others have only recently been described and some are still missing pieces or yet remain to be discovered.
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Affiliation(s)
- Johannes Thoma
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
| | - Björn M Burmann
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
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16
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Zinc-Dependent Oligomerization of Thermus thermophilus Trigger Factor Chaperone. BIOLOGY 2021; 10:biology10111106. [PMID: 34827099 PMCID: PMC8614707 DOI: 10.3390/biology10111106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/20/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Metal ions often play important roles in biological processes. Thermus thermophilus trigger factor (TtTF) is a zinc-dependent molecular chaperone where Zn2+ has been shown to enhance its folding-arrest activity. However, the mechanisms of how Zn2+ binds to TtTF and how Zn2+ affects the activity of TtTF are yet to be elucidated. As a first step in understanding the mechanism, we performed in vitro biophysical experiments on TtTF to investigate the zinc-binding site on TtTF and unveil how Zn2+ alters the physical properties of TtTF, including secondary structure, thermal stability, and oligomeric state. Our results showed that TtTF binds Zn2+ in a 1:1 ratio, and all three domains of TtTF are involved in zinc-binding. We found that Zn2+ does not affect the thermal stability of TtTF, whereas it does induce partial structural change and promote the oligomerization of TtTF. Given that the folding-arrest activity of Escherichia coli TF (EcTF) is regulated by its oligomerization, our results imply that TtTF exploits Zn2+ to modulate its oligomeric state to regulate the activity. Abstract Thermus thermophilus trigger factor (TtTF) is a zinc-dependent molecular chaperone whose folding-arrest activity is regulated by Zn2+. However, little is known about the mechanism of zinc-dependent regulation of the TtTF activity. Here we exploit in vitro biophysical experiments to investigate zinc-binding, the oligomeric state, the secondary structure, and the thermal stability of TtTF in the absence and presence of Zn2+. The data show that full-length TtTF binds Zn2+, but the isolated domains and tandem domains of TtTF do not bind to Zn2+. Furthermore, circular dichroism (CD) and nuclear magnetic resonance (NMR) spectra suggested that Zn2+-binding induces the partial structural changes of TtTF, and size exclusion chromatography-multi-angle light scattering (SEC-MALS) showed that Zn2+ promotes TtTF oligomerization. Given the previous work showing that the activity regulation of E. coli trigger factor is accompanied by oligomerization, the data suggest that TtTF exploits zinc ions to induce the structural change coupled with the oligomerization to assemble the client-binding site, thereby effectively preventing proteins from misfolding in the thermal environment.
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17
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Smit JH, Krishnamurthy S, Srinivasu BY, Parakra R, Karamanou S, Economou A. Probing Universal Protein Dynamics Using Hydrogen-Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy. Anal Chem 2021; 93:12840-12847. [PMID: 34523340 DOI: 10.1021/acs.analchem.1c02155] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful technique to monitor protein intrinsic dynamics. The technique provides high-resolution information on how protein intrinsic dynamics are altered in response to biological signals, such as ligand binding, oligomerization, or allosteric networks. However, identification, interpretation, and visualization of such events from HDX-MS data sets is challenging as these data sets consist of many individual data points collected across peptides, time points, and experimental conditions. Here, we present PyHDX, an open-source Python package and webserver, that allows the user to batch extract the universal quantity Gibbs free energy at residue levels over multiple protein conditions and homologues. The output is directly visualized on a linear map or 3D structures or is exported as .csv files or PyMOL scripts.
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Affiliation(s)
- Jochem H Smit
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Srinath Krishnamurthy
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Bindu Y Srinivasu
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Rinky Parakra
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology, Immunology and Transplantation, Rega Institute of Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, 3000 Leuven, Belgium
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18
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Oswald J, Njenga R, Natriashvili A, Sarmah P, Koch HG. The Dynamic SecYEG Translocon. Front Mol Biosci 2021; 8:664241. [PMID: 33937339 PMCID: PMC8082313 DOI: 10.3389/fmolb.2021.664241] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 12/13/2022] Open
Abstract
The spatial and temporal coordination of protein transport is an essential cornerstone of the bacterial adaptation to different environmental conditions. By adjusting the protein composition of extra-cytosolic compartments, like the inner and outer membranes or the periplasmic space, protein transport mechanisms help shaping protein homeostasis in response to various metabolic cues. The universally conserved SecYEG translocon acts at the center of bacterial protein transport and mediates the translocation of newly synthesized proteins into and across the cytoplasmic membrane. The ability of the SecYEG translocon to transport an enormous variety of different substrates is in part determined by its ability to interact with multiple targeting factors, chaperones and accessory proteins. These interactions are crucial for the assisted passage of newly synthesized proteins from the cytosol into the different bacterial compartments. In this review, we summarize the current knowledge about SecYEG-mediated protein transport, primarily in the model organism Escherichia coli, and describe the dynamic interaction of the SecYEG translocon with its multiple partner proteins. We furthermore highlight how protein transport is regulated and explore recent developments in using the SecYEG translocon as an antimicrobial target.
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Affiliation(s)
- Julia Oswald
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Robert Njenga
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Ana Natriashvili
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Pinku Sarmah
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany.,Faculty of Biology, Albert Ludwigs Universität Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert Ludwigs Universität Freiburg, Freiburg, Germany
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19
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Jiang C, Wynne M, Huber D. How Quality Control Systems AID Sec-Dependent Protein Translocation. Front Mol Biosci 2021; 8:669376. [PMID: 33928127 PMCID: PMC8076867 DOI: 10.3389/fmolb.2021.669376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The evolutionarily conserved Sec machinery is responsible for transporting proteins across the cytoplasmic membrane. Protein substrates of the Sec machinery must be in an unfolded conformation in order to be translocated across (or inserted into) the cytoplasmic membrane. In bacteria, the requirement for unfolded proteins is strict: substrate proteins that fold (or misfold) prematurely in the cytoplasm prior to translocation become irreversibly trapped in the cytoplasm. Partially folded Sec substrate proteins and stalled ribosomes containing nascent Sec substrates can also inhibit translocation by blocking (i.e., “jamming”) the membrane-embedded Sec machinery. To avoid these issues, bacteria have evolved a complex network of quality control systems to ensure that Sec substrate proteins do not fold in the cytoplasm. This quality control network can be broken into three branches, for which we have defined the acronym “AID”: (i) avoidance of cytoplasmic intermediates through cotranslationally channeling newly synthesized Sec substrates to the Sec machinery; (ii) inhibition of folding Sec substrate proteins that transiently reside in the cytoplasm by molecular chaperones and the requirement for posttranslational modifications; (iii) destruction of products that could potentially inhibit translocation. In addition, several stress response pathways help to restore protein-folding homeostasis when environmental conditions that inhibit translocation overcome the AID quality control systems.
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Affiliation(s)
- Chen Jiang
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Max Wynne
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Damon Huber
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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20
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A nexus of intrinsic dynamics underlies translocase priming. Structure 2021; 29:846-858.e7. [PMID: 33852897 DOI: 10.1016/j.str.2021.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/06/2021] [Accepted: 03/25/2021] [Indexed: 11/22/2022]
Abstract
The cytoplasmic ATPase SecA and the membrane-embedded SecYEG channel assemble to form the Sec translocase. How this interaction primes and catalytically activates the translocase remains unclear. We show that priming exploits a nexus of intrinsic dynamics in SecA. Using atomistic simulations, smFRET, and HDX-MS, we reveal multiple dynamic islands that cross-talk with domain and quaternary motions. These dynamic elements are functionally important and conserved. Central to the nexus is a slender stem through which rotation of the preprotein clamp of SecA is biased by ATPase domain motions between open and closed clamping states. An H-bonded framework covering most of SecA enables multi-tier dynamics and conformational alterations with minimal energy input. As a result, cognate ligands select preexisting conformations and alter local dynamics to regulate catalytic activity and clamp motions. These events prime the translocase for high-affinity reception of non-folded preprotein clients. Dynamics nexuses are likely universal and essential in multi-liganded proteins.
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21
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Elfageih R, Karyolaimos A, Kemp G, de Gier J, von Heijne G, Kudva R. Cotranslational folding of alkaline phosphatase in the periplasm of Escherichia coli. Protein Sci 2020; 29:2028-2037. [PMID: 32790204 PMCID: PMC7513700 DOI: 10.1002/pro.3927] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/08/2020] [Accepted: 08/11/2020] [Indexed: 01/10/2023]
Abstract
Cotranslational protein folding studies using Force Profile Analysis, a method where the SecM translational arrest peptide is used to detect folding-induced forces acting on the nascent polypeptide, have so far been limited mainly to small domains of cytosolic proteins that fold in close proximity to the translating ribosome. In this study, we investigate the cotranslational folding of the periplasmic, disulfide bond-containing Escherichia coli protein alkaline phosphatase (PhoA) in a wild-type strain background and a strain background devoid of the periplasmic thiol: disulfide interchange protein DsbA. We find that folding-induced forces can be transmitted via the nascent chain from the periplasm to the polypeptide transferase center in the ribosome, a distance of ~160 Å, and that PhoA appears to fold cotranslationally via at least two disulfide-stabilized folding intermediates. Thus, Force Profile Analysis can be used to study cotranslational folding of proteins in an extra-cytosolic compartment, like the periplasm.
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Affiliation(s)
- Rageia Elfageih
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | | | - Grant Kemp
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Jan‐Willem de Gier
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
| | - Gunnar von Heijne
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Science for Life Laboratory Stockholm UniversitySolnaSweden
| | - Renuka Kudva
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
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22
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De Geyter J, Portaliou AG, Srinivasu B, Krishnamurthy S, Economou A, Karamanou S. Trigger factor is a bona fide secretory pathway chaperone that interacts with SecB and the translocase. EMBO Rep 2020; 21:e49054. [PMID: 32307852 DOI: 10.15252/embr.201949054] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 03/09/2020] [Accepted: 03/19/2020] [Indexed: 11/09/2022] Open
Abstract
Bacterial secretory preproteins are translocated across the inner membrane post-translationally by the SecYEG-SecA translocase. Mature domain features and signal peptides maintain preproteins in kinetically trapped, largely soluble, folding intermediates. Some aggregation-prone preproteins require chaperones, like trigger factor (TF) and SecB, for solubility and/or targeting. TF antagonizes the contribution of SecB to secretion by an unknown molecular mechanism. We reconstituted this interaction in vitro and studied targeting and secretion of the model preprotein pro-OmpA. TF and SecB display distinct, unsuspected roles in secretion. Tightly associating TF:pro-OmpA targets the translocase at SecA, but TF prevents pro-OmpA secretion. In solution, SecB binds TF:pro-OmpA with high affinity. At the membrane, when bound to the SecA C-tail, SecB increases TF and TF:pro-OmpA affinities for the translocase and allows pro-OmpA to resume translocation. Our data reveal that TF, a main cytoplasmic folding pathway chaperone, is also a bona fide post-translational secretory chaperone that directly interacts with both SecB and the translocase to mediate regulated protein secretion. Thus, TF links the cytoplasmic folding and secretion chaperone networks.
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Affiliation(s)
- Jozefien De Geyter
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Athina G Portaliou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Bindu Srinivasu
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Srinath Krishnamurthy
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
| | - Spyridoula Karamanou
- Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Leuven, Belgium
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