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Engineering of new-generation protein secretion systems

Deliverables

Global models for protein secretion and secretion stress progression

Global models for protein secretion and secretion stress progression.

Supervisory board of the network established

Supervisory board of the network established for all partners

Model for protein trafficking through the secretory pathway

Model for protein trafficking through the secretory pathway.

List of common and critical conditions that are relevant during industrial fermentation processes
New method for predicting membrane protein complexes

New method for predicting membrane protein complexes.

First quantitative data for selected membrane proteins
Membrane proteome data sets for B. subtilis + E. coli under all growth regimes

Membrane proteome data sets for B. subtilis + E. coli under all growth regimes.

Secretion bottlenecks identified
Global quantitative analysis of membrane proteome

Global quantitative analysis of membrane proteome.

Definition of protein production stress responses in E. coli

Definition of protein production stress responses in E. coli.

Refined regulatory model including membrane proteins validated with proteomics data

Refined regulatory model including membrane proteins validated with proteomics data.

New algorithms that predict inter-helix pairings in membrane proteins

New algorithms that predict inter-helix pairings in membrane proteins.

Established model for secretion stress onset

Established model for secretion stress onset.

Validated membrane protein complexes and their dynamics

Validated membrane protein complexes and their dynamics.

Publications

Proteomic Charting of Imipenem Adaptive Responses in a Highly Carbapenem Resistant Clinical Enterobacter roggenkampii Isolate

Author(s): Nepal S, Maaß S, Grasso S, Cavallo FM, Bartel J, Becher D, Bathoorn E, van Dijl JM
Published in: Antibiotics (Basel), Issue 10.5, 2021, Page(s) 501, ISSN 2079-6382
Publisher: MDPI
DOI: 10.3390/antibiotics10050501

Residue-by-residue analysis of cotranslational membrane protein integration in vivo

Author(s): Nicolaus, F., Metola, A., Mermans, D., Liljenström, A., Krč, A., Abdullahi, S. M., Zimmer, M., Miller Iii, T. F., & von Heijne, G
Published in: eLife, Issue 10, 2021, Page(s) 64302, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.64302

Escherichia coli Can Adapt Its Protein Translocation Machinery for Enhanced Periplasmic Recombinant Protein Production

Author(s): Alexandros Karyolaimos1†, Katarzyna Magdalena Dolata2†, Minia Antelo-Varela2†, Anna Mestre Borras1, Rageia Elfageih1, Susanne Sievers2, Dörte Becher2, Katharina Riedel2 and Jan-Willem de Gier
Published in: Front Bioeng Biotech, 2020, Page(s) 465, ISSN 2296-4185
Publisher: Frontiers Media S.A.
DOI: 10.3389/fbioe.2019.00465

Enhancing Recombinant Protein Yields in the E. coli Periplasm by Combining Signal Peptide and Production Rate Screening

Author(s): Alexandros Karyolaimos1†, Henry Ampah-Korsah1†, Tamara Hillenaar1, Anna Mestre Borras1, Katarzyna Magdalena Dolata2, Susanne Sievers2, Katharina Riedel2, Robert Daniels1 and Jan-Willem de Gier1*
Published in: Front Bioeng Biotech, 2019, Page(s) 1511, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2019.01511

Ariadne's Thread in the Analytical Labyrinth of Membrane Proteins: Integration of Targeted and Shotgun Proteomics for Global Absolute Quantification of Membrane Proteins

Author(s): Antelo-Varela M, Bartel J, Quesada-Ganuza A, Appel K, Bernal-Cabas M, Sura T, Otto A, Rasmussen M, van Dijl JM, Nielsen A, Maaß S, Becher D
Published in: Anal Chem, Issue 91(18), 2019, Page(s) 11972-11980, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.9b02869

GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting

Author(s): Gabarrini G, Grasso S, van Winkelhoff AJ, van Dijl JM
Published in: Brief Bioinformation, Issue 22(4), 2021, Page(s) 302, ISSN 1477-4054
Publisher: Oxford Academic
DOI: 10.1093/bib/bbaa302

Redirected Stress Responses in a Genome-Minimized 'midiBacillus' Strain with Enhanced Capacity for Protein Secretion

Author(s): Aguilar Suárez R, Antelo-Varela M, Maaß S, Neef J, Becher D, van Dijl JM
Published in: mSystems, Issue 6(6), 2021, Page(s) e0065521, ISSN 2379-5077
Publisher: ASM Journals
DOI: 10.1128/msystems.00655-21

Signatures of cytoplasmic proteins in the exoproteome distinguish community- and hospital-associated methicillin-resistant Staphylococcus aureus USA300 lineages

Author(s): Mekonnen SA, Palma Medina LM, Glasner C, Tsompanidou E, de Jong A, Grasso S, Schaffer M, Mäder U, Larsen AR, Gumpert H, Westh H, Völker U, Otto A, Becher D, van Dijl JM
Published in: Virulence, Issue 18(6), 2017, Page(s) 891-907, ISSN 2150-5594
Publisher: Landes Bioscience
DOI: 10.1080/21505594.2017.1325064

Strategies to Enhance Periplasmic Recombinant Protein Production Yields in Escherichia coli

Author(s): Alexandros Karyolaimos and Jan-Willem de Gier
Published in: Front Bioeng Biotech, 2021, Page(s) 797334, ISSN 2296-4185
Publisher: Frontiers Media S.A.
DOI: 10.3389/fbioe.2021.797334

Functional association of the stress-responsive LiaH protein and the minimal TatAyCy protein translocase in Bacillus subtilis

Author(s): Bernal-Cabas M, Miethke M, Antelo-Varela M, Aguilar Suárez R, Neef J, Schön L, Gabarrini G, Otto A, Becher D, Wolf D, van Dijl JM
Published in: Biochim Biophys Acta Mol Cell Res, Issue 1867(8), 2020, Page(s) 19, ISSN 2079-6382
Publisher: Elsevier
DOI: 10.1016/j.bbamcr.2020.118719

Probing the quality control mechanism of the Escherichia coli twin-arginine translocase with folding variants of a de novo –designed heme protein

Author(s): George A. Sutherland, Katie J. Grayson, Nathan B. P. Adams, Daphne M. J. Mermans, Alexander S. Jones, Angus J. Robertson, Dirk B. Auman, Amanda A. Brindley, Fabio Sterpone, Pierre Tuffery, Philippe Derreumaux, P. Leslie Dutton, Colin Robinson, Andrew Hitchcock, C. Neil Hunter
Published in: Journal of Biological Chemistry, Issue 293/18, 2018, Page(s) 6672-6681, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1074/jbc.ra117.000880

Far-reaching cellular consequences of tat deletion in Escherichia coli revealed by comprehensive proteome analyses

Author(s): Katarzyna M. Dolata, Isabel Guerrero Montero, Wayne Miller, Susanne Sievers, Thomas Sura, Christian Wolff, Rabea Schlüter, Katharina Riedel, Colin Robinson
Published in: Microbiological Research, Issue 218, 2019, Page(s) 97-107, ISSN 0944-5013
Publisher: Elsevier BV
DOI: 10.1016/j.micres.2018.10.008

Comparative proteome analysis in an Escherichia coli CyDisCo strain identifies stress responses related to protein production, oxidative stress and accumulation of misfolded protein

Author(s): Isabel Guerrero Montero, Katarzyna Magdalena Dolata, Rabea Schlüter, Gilles Malherbe, Susanne Sievers, Daniela Zühlke, Thomas Sura, Emma Dave, Katharina Riedel, Colin Robinson
Published in: Microbial Cell Factories, Issue 18/1, 2019, ISSN 1475-2859
Publisher: BioMed Central
DOI: 10.1186/s12934-019-1071-7

The tunable pReX expression vector enables optimizing the T7-based production of membrane and secretory proteins in E. coli

Author(s): Grietje Kuipers, Alexandros Karyolaimos, Zhe Zhang, Nurzian Ismail, Gianluca Trinco, David Vikström, Dirk Jan Slotboom, Jan-Willem de Gier
Published in: Microbial Cell Factories, Issue 16/1, 2017, ISSN 1475-2859
Publisher: BioMed Central
DOI: 10.1186/s12934-017-0840-4

An ancient family of mobile genomic islands introducing cephalosporinase and carbapenemase genes in Enterobacteriaceae

Author(s): Suruchi Nepal, Florian Bonn, Stefano Grasso, Tim Stobernack, Anne de Jong, Kai Zhou, Ronald Wedema, Sigrid Rosema, Dörte Becher, Andreas Otto, John W. Rossen, Jan Maarten van Dijl, Erik Bathoorn
Published in: Virulence, Issue 9/1, 2018, Page(s) 1377-1389, ISSN 2150-5594
Publisher: Landes Bioscience
DOI: 10.1080/21505594.2018.1509666

SppI Forms a Membrane Protein Complex with SppA and Inhibits Its Protease Activity in Bacillus subtilis

Author(s): Henriques G, McGovern S, Neef J, Antelo-Varela M, Götz F, Otto A, Becher D, van Dijl JM, Jules M, Delumeau O
Published in: mSphere, Issue 5(5), 2020, Page(s) 00724-20, ISSN 2379-5042
Publisher: ASM Journals
DOI: 10.1128/msphere.00724-20

Upstream charged and hydrophobic residues impact the timing of membrane insertion of transmembrane helices

Author(s): Nicolaus, F., Ibrahimi, F., den Besten, A., & von Heijne, G
Published in: FEBS letters, Issue 10.1002, 2022, ISSN 0014-5793
Publisher: Elsevier BV
DOI: 10.1002/1873-3468.14286

Double trouble: Bacillus depends on a functional Tat machinery to avoid severe oxidative stress and starvation upon entry into a NaCl-depleted environment

Author(s): Prajapati B, Bernal-Cabas M, López-Álvarez M, Schaffer M, Bartel J, Rath H, Steil L, Becher D, Völker U, Mäder U, van Dijl JM
Published in: Biochim Biophys Acta Mol Cell Res, Issue 1868(2), 2020, Page(s) 118914, ISSN 0167-4889
Publisher: Elsevier BV
DOI: 10.1016/j.bbamcr.2020.118914

"Membrane Modulation of Super-Secreting ""midiBacillus"" Expressing the Major Staphylococcus aureus Antigen - A Mass-Spectrometry-Based Absolute Quantification Approach"

Author(s): Antelo-Varela M, Aguilar Suárez R, Bartel J, Bernal-Cabas M, Stobernack T, Sura T, van Dijl JM, Maaß S, Becher D
Published in: Front Bioeng Biotechnol, Issue 8, 2020, Page(s) 143, ISSN 2296-4185
Publisher: Frontiers Media S.A
DOI: 10.3389/fbioe.2020.00143

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