Data from: Functional mapping and engineering of the Sec translocon unlocked by a cell-free system
Data files
Jul 27, 2026 version files 4.67 MB
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Fig1D_E-20250212_Translocation.csv
30.69 KB
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Fig1D_E-20250212_Translocation.xlsx
180.82 KB
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Fig1F-250624-translocation-SecA.csv
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Fig1F-250624-translocation-SecA.xlsx
125.23 KB
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Fig2B-241218-RepreppedInserters.csv
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Fig2B-241218-RepreppedInserters.xlsx
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Fig2C-20250211_InsertionDirectionality.csv
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Fig2C-20250211_InsertionDirectionality.xlsx
244.52 KB
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Fig2E_G-AuxSU_data.csv
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Fig2E_G-AuxSU_data.xlsx
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Fig2F-3.04_mNeonGreen_construct_expression.csv
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Fig2F-3.04_mNeonGreen_construct_expression.xlsx
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Fig3B-260420-SecY-mNeonGreen-EG-FluoReads.csv
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Fig3B-260420-SecY-mNeonGreen-EG-FluoReads.xlsx
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Fig3I-241218-RepreppedInserters.csv
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Fig3I-241218-RepreppedInserters.xlsx
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Fig5D-20250219_TranslocationSignalLibraryInitial.csv
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Fig5D-20250219_TranslocationSignalLibraryInitial.xlsx
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Fig5E-250527-Translocation-Nanobody.csv
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Fig5E-250527-Translocation-Nanobody.xlsx
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FigS1A_B-230829-HiBiTalternatives_bulk.csv
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FigS1A_B-230829-HiBiTalternatives_bulk.xlsx
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FigS1C-230720-SUMO-dark_titration-proOmpA-HiBiT.csv
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FigS1C-230720-SUMO-dark_titration-proOmpA-HiBiT.xlsx
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FigS2B_C-240406-TranslocationPure-SignalREduction.csv
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FigS2B_C-240406-TranslocationPure-SignalREduction.xlsx
120.97 KB
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FigS2E-280911-Translocation-PaperTags.csv
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FigS2E-280911-Translocation-PaperTags.xlsx
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FigS3A-231007-translocation-various.csv
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FigS3A-231007-translocation-various.xlsx
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FigS3C_D-240213-Translocation-figure1.csv
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FigS3C_D-240213-Translocation-figure1.xlsx
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FigS4A-20251017-SecA-tritration.csv
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FigS4A-20251017-SecA-tritration.xlsx
96.14 KB
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FigS4B-AuxSU_data.csv
530 B
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FigS4B-AuxSU_data.xlsx
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FigS5A-230907-translocation_PURE_12S.csv
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FigS5A-230907-translocation_PURE_12S.xlsx
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FigS5B_C-Vesicle_nFCM-Pub.xlsx
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FigS5D_E-240527-S12_S30_S50_S80_S105-sfGFP-pepper.csv
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FigS5D_E-240527-S12_S30_S50_S80_S105-sfGFP-pepper.xlsx
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FigS5F-240528-S12_S30_S50_S80_S105-translocation-assay.csv
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FigS5F-240528-S12_S30_S50_S80_S105-translocation-assay.xlsx
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FigS6C_D-231115-secYvariantsPR-MBP.csv
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FigS6C_D-231115-secYvariantsPR-MBP.xlsx
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FigS6E-240229-InsertionDirectionality.csv
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FigS6E-240229-InsertionDirectionality.xlsx
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FigS7B_C_D_E-20250127_Marburg_Samples_DLS___Zeta_potential_analysis.csv
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FigS7B_C_D_E-20250127_Marburg_Samples_DLS___Zeta_potential_analysis.xlsx
39.48 KB
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FigS7B_C_D_E-20250127_Size_Marburg_Samples_t1_t2_Averaged_curves.csv
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FigS7B_C_D_E-20250127_Size_Marburg_Samples_t1_t2_Averaged_curves.xlsx
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FigS7B_C_D_E-20250127_Size_Marburg_Samples_t1_t2.xlsx
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README.md
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Abstract
Dataset DOI: 10.5061/dryad.hmgqnkb0k
Description of the data and file structure
Dear reader, these files contain the raw plate reader, DLS and nanoFCM data for the manuscript "Functional Mapping and Engineering of the Sec Translocon Unlocked by a Cell-Free System". Cured data and annotated graphs are found in the manuscript main text or the supplementary files. For easier identification, each file name starts with the respective Figure number and panel letter, i.e. "Fig1D_E-...." is the raw data for panels D and E in Figure 1 in the main text. The plain unedited data are saved as .csv files and further explanations and annotations are found in the same-named .xlsx files.
Files and variables
Raw data of main text graphs
Description: Raw plate-reader data of main text graphs; conditions and plate positions are always indicated on the right of the general plate-reader settings
- Fig2E_G-AuxSU_data.xlsx
- ProSecCO-based analysis of membrane protein insertion via SecYEG. E) Influence of auxiliary subunits YidC and SRP/SR on PR(-1tm)-pep104 insertion. pYidC was co-expressed with pSecYEG; SRP (Ffh) and SR (FtsY) were pre-expressed separately and added to the pSecYEG CPFS reaction.
- Fig2F-3.04_mNeonGreen_construct_expression.xlsx
- ProSecCO-based analysis of membrane protein insertion via SecYEG. F) Influence of auxiliary components on PR insertion, measured by fluorescence of a PR-mNeonGreen fusion reporter.
- Fig3B-260420-SecY-mNeonGreen-EG-FluoReads.xlsx
- ProSecCO-based screen of translocation and insertion activities of 294 SecY variants. B) Expression and folding analysis of 27 selected SecY variants spanning the full protein length, re-cloned with a C-terminal mNeonGreen reporter; transmembrane helices (green), plug (dark green), and SecA interaction domains C4/C5 are highlighted.
- Fig3I-241218-RepreppedInserters.xlsx
- ProSecCO-based screen of translocation and insertion activities of 294 SecY variants. I) Re-analysis of the seventeen most striking insertion variants; plasmids were re-transformed, purified, and assayed by manually pipetted insertion (20 µl volume, technical triplicates).
- Fig5D-20250219_TranslocationSignalLibraryInitial.xlsx
- ProSecCO-based optimization of signal peptides and SecY pore for enhanced nanobody translocation. D) Translocation activities of the TP1170 nanobody constructs carrying the 11 different signal peptides. SecYEG and SecA were co-expressed from plasmids (two technical replicates).
- Fig5E-250527-Translocation-Nanobody.xlsx
- ProSecCO-based optimization of signal peptides and SecY pore for enhanced nanobody translocation. E) Translocation assays of the TP1170 nanobody carrying the two best signal peptides, YncJ and OmpA(extCore), in combination with SecYEG WT or the super-active SecY variant I408G variant (technical triplicates). As control, the TP1170 nanobody carrying the standard OmpA signal peptide was used.
- Fig1D_E-20250212_Translocation.xlsx
- ProSecCO enables the production and characterization of functional SecYEG translocons on blank-membrane vesicles. D) Real-time translocation data of proOmpA-pep99 reporter in a PURE-based ProSecCO system for SecYEG WT, and SecY variants P276R and C385Y.
- Fig1F-250624-translocation-SecA.xlsx
- ProSecCO enables the production and characterization of functional SecYEG translocons on blank-membrane vesicles. F) Translocation activity of SecYEG in the absence and presence of SecA (pre-expressed separately and added during reporter expression).
- Fig2B-241218-RepreppedInserters.xlsx
- ProSecCO-based analysis of membrane protein insertion via SecYEG. B) PR(-1tm)-pep104 insertion activity (maximum slope) of pre-expressed SecYEG WT, variant P84L, and SecY alone; “spontaneous integration” was measured by replacing pSecYEG with non-tagged PR to compensate resource competition.
- Fig2C-20250211_InsertionDirectionality.xlsx
- ProSecCO-based analysis of membrane protein insertion via SecYEG. C) Directionality of insertion via SecYEG WT, assessed with five PR-based reporters with TMs progressively removed from the C-terminus. The red line shows the fold-change in luminescence signal normalized to the “spontaneous integration” control (non-tagged PR replacing SecYEG), following the expected alternating pattern.
File: RawData-MainTextGraphs-Platereader
Description: Raw plate-reader, nFCM and DLS data of supplementary data graphs; conditions and plate positions are always indicated on the right of the general plate-reader settings
- FigS5B_C-Vesicle_nFCM-Pub.xlsx
- SecYEG dependent protein translocation in PURE and cell-free lysates. B) Particle size distribution of different five cell free lysates produced by homogenization and cleared at varying centrifugal speeds.
- FigS5D_E-240527-S12_S30_S50_S80_S105-sfGFP-pepper.xlsx
- SecYEG dependent protein translocation in PURE and cell-free lysates. D) Transcription and E) translational activity were assessed using a sfGFP-pepper fusion construct and measuring fluorescence.
- FigS5F-240528-S12_S30_S50_S80_S105-translocation-assay.xlsx
- SecYEG dependent protein translocation in PURE and cell-free lysates. F) Translocation assay using the C385Y (superactive) and P276R (inactive) SecY mutants.
- FigS6C_D-231115-secYvariantsPR-MBP.xlsx
- Membrane protein insertion assays. C) Insertion assay in S50 autolysate using the same reporter. The G240D mutant has been reported to be deficient in insertion (20) while Y429D has been reported to have to effect on insertion (20). D) The respective maximum slope values for different SecY variants of pSecYEG.
- FigS6E-240229-InsertionDirectionality.xlsx
- Membrane protein insertion assays. E) Assessment of directionality of insertion via SecYEG in S50 autolysate.
- FigS7B_C_D_E-20250127_Marburg_Samples_DLS___Zeta_potential_analysis.xlsx
- Reporter vesicle analysis during translocation and insertion experiments. B) DLS analysis at t2 after translocation experiments. C) Mean hydrodynamic diameters and polydispersity indices (PDI) at both time points for translocation. D) DLS analysis at t2 after insertion experiments. E) Mean hydrodynamic diameters and PDI at both time points for insertion.
- FigS7B_C_D_E-20250127_Size_Marburg_Samples_t1_t2_Averaged_curves.xlsx
- Reporter vesicle analysis during translocation and insertion experiments. B) DLS analysis at t2 after translocation experiments. C) Mean hydrodynamic diameters and polydispersity indices (PDI) at both time points for translocation. D) DLS analysis at t2 after insertion experiments. E) Mean hydrodynamic diameters and PDI at both time points for insertion.
- FigS7B_C_D_E-20250127_Size_Marburg_Samples_t1_t2.xlsx
- Reporter vesicle analysis during translocation and insertion experiments. B) DLS analysis at t2 after translocation experiments. C) Mean hydrodynamic diameters and polydispersity indices (PDI) at both time points for translocation. D) DLS analysis at t2 after insertion experiments. E) Mean hydrodynamic diameters and PDI at both time points for insertion.
- FigS1A_B-230829-HiBiTalternatives_bulk.xlsx
- Adaption of a split nanoluc system for the use in CFPS. A) Bulk expression kinetic data of proOmpA reporters in S50 autolysate (11S and furimazine present in bulk solution; no vesicles). proOmpA constructs with high/medium/low-affinity complementation tags (pep86/pep99/pep104) with differing binding affinities to 11S were expressed from plasmids. B) Resulting maximum slope data.
- FigS1C-230720-SUMO-dark_titration-proOmpA-HiBiT.xlsx
- Adaption of a split nanoluc system for the use in CFPS. C) Titration of purified SUMO-dark protein in CFPS with proOmpA-pep86 expressed in bulk.
- FigS2B_C-240406-TranslocationPure-SignalREduction.xlsx
- Development of the split nanoluc translocation assay for cell free expressed SecYEG. B) Titration of competitor vesicles (blank membrane; no 11S) in translocation assays using PUREfrex 1.0 and C) their influence on the assay life time.
- FigS2E-280911-Translocation-PaperTags.xlsx
- Development of the split nanoluc translocation assay for cell free expressed SecYEG. E) Translocation assay data comparing the luminescence output for proOmpA fused to the high (pep86) and medium affinity tag (pep99). Different SecY mutants of pSecYEG were used to compare the two tags.
- FigS3A-231007-translocation-various.xlsx
- Validation of the translocation assay in E. coli S50 autolysate. A) Co-expression of pSecYEG together with the motor ATPase SecA and proOmpA-pep99 in S50 autolysate conveys an ATP dependent translocation signal. 20 mM ATP and 1x furimazine were added after 2.5 h of expressing all three plasmids at the same time. Common translocation deficient SecY mutants (G240D (20), Y429D (20, 21) and P276R (19)) do not respond to ATP addition.
- FigS3C_D-240213-Translocation-figure1.xlsx
- Validation of the translocation assay in E. coli S50 autolysate. C) Translocation assay similar to a but testing a super-active SecY variants (C385Y (12, 24)) and the ATP dependence of SecA driven translocation. D) Maximum slope data of C).
- FigS4A-20251017-SecA-tritration.xlsx
- Titrating pre-expressed SecA for translocation experiments. A) Translocation assay in PUREfrex 1.0 adding different amounts of pre-expressed SecA to the reporter CFPS. Final dilutions in the resulting reaction mix are indicated on the x-axis. SecA was pre-expressed in PURE from 0.5 nM pSecA plasmid. SecYEG in the primary CFPS was expressed from 0.5 nM pSecYEG, and the reporter CFPS contained 0.4 nM pTE5636 reporter DNA (nanobody-pep86 with OmpA(extCore) signal peptide). Standard translocation reactions contained 1:40 diluted pre-expressed SecA to ensure saturation.
- FigS4B-AuxSU_data.xlsx
- Titrating pre-expressed SecA for translocation experiments. B) Insertion/translocation assay to test the influence of SecA on LepB-pep86 insertion and translocation. To elucidate the effect of CFPS resource competition, SecA was either co-expressed with pSecYEG or pre-expressed separately and added to the reporter CFPS. GFP and SecA E210Q (‘inactive’) were used as negative controls (62, 63).
- FigS5A-230907-translocation_PURE_12S.xlsx
- SecYEG dependent protein translocation in PURE and cell-free lysates. A) Translocation assays in three different E. coli based CFPS systems using two different variants of pSecYEG with an impaired (P276R (19)) and a super-active SecY mutant (C385Y (12, 24)).
Code/software
Microsoft Excel
