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6. Dual Action of Eeyarestatin 24 on Sec-Dependent Protein Secretion and Bacterial DNA

Author

Schäfer, Ann-Britt, primary, Steenhuis, Maurice, additional, Jim, Kin Ki, additional, Neef, Jolanda, additional, O’Keefe, Sarah, additional, Whitehead, Roger C., additional, Swanton, Eileithyia, additional, Wang, Biwen, additional, Halbedel, Sven, additional, High, Stephen, additional, van Dijl, Jan Maarten, additional, Luirink, Joen, additional, and Wenzel, Michaela, additional

Published
2023
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10. A Tale of Two Cell Factories:Heterologous protein secretion in Bacillus subtilis and Lactococcus lactis

Author

Neef, Jolanda, Neef, Jolanda, Neef, Jolanda, and Neef, Jolanda

Abstract

Bacteria, like the soil bacterium Bacillus subtilis, are often used as “cell factories” for the production of proteins with applications in food processing, detergents and the chemical industry. The application of such proteins is sustainable and cheap. A possible alternative host for protein production is the "cheese bacterium" Lactococcus lactis. The present thesis describes pro's and con's of both cell factories with focus on systems that facilitate the secretion of proteins into the growth medium. The secretion of proteins is of interest, because purification of secreted proteins is relatively easy. In addition, this thesis describes research on the improvement of both cell factories. To this end, novel protein expression systems were developed for L. lactis, and these were tested for production of proteins from the human pathogen Staphylococcus aureus, which may find future application in vaccines. To optimize protein secretion in B. subtilis a completely new approach was developed, which keeps the envelope of the bacterium clean during the production process. This involved overproduction of a protein that degrades other proteins and their remnants, thereby 'unclogging' the bacterium. In this manner, the production of a starch-degrading enzyme was no less than 10-fold increased. Further, three other bottlenecks for protein secretion were identified. Altogether, the documented studies show that it is possible to achieve considerable improvements in bacterial protein production by the analysis and subsequent elimination of bottlenecks. It is thus feasible to expand the spectrum of proteins that can be produced for applications in our daily lives, healthcare and industry.

Published
2019

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

Author

Aguilar Suárez, Rocío, Antelo-Varela, Minia, Maaß, Sandra, Neef, Jolanda, Becher, Dörte, van Dijl, Jan Maarten, University of Groningen, Microbes in Health and Disease (MHD), and Translational Immunology Groningen (TRIGR)

Subjects
Physiology, Biochemistry, Microbiology, QR1-502, genome minimization, Computer Science Applications, proteomics, Sec pathway, Modeling and Simulation, protein secretion, signal peptidase, Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Bacillus subtilis
Abstract

Genome engineering offers the possibility to create completely novel cell factories with enhanced properties for biotechnological applications. In recent years, genome minimization was extensively explored in the Gram-positive bacterial cell factory Bacillus subtilis, where up to 42% of the genome encoding dispensable functions was removed. Such studies showed that some strains with minimized genomes gained beneficial features, especially for secretory protein production. However, strains with the most minimal genomes displayed growth defects. This focused our attention on strains with less extensive genomic deletions that display close-to-wild-type growth properties while retaining the acquired beneficial traits in secretory protein production. A strain of this category is B. subtilis IIG-Bs27-47-24, here referred to as midiBacillus, which lacks 30.95% of the parental genome. To date, it was unknown how the altered genomic configuration of midiBacillus impacts cell physiology in general, and protein secretion in particular. The present study bridges this knowledge gap through comparative quantitative proteome analyses with focus on protein secretion. Interestingly, the results show that the secretion stress responses of midiBacillus, as elicited by high-level expression of the immunodominant staphylococcal antigen A, are completely different from secretion stress responses that occur in the parental strain 168. We further show that midiBacillus has an increased capacity for translation and that a variety of critical Sec secretion machinery components is present at elevated levels. Altogether, our observations demonstrate that high-level protein secretion has different consequences for wild-type and genome-engineered Bacillus strains, dictated by the altered genomic and proteomic configurations. IMPORTANCE Our present study showcases a genome-minimized nonpathogenic bacterium, the so-called midiBacillus, as a chassis for the development of future industrial strains that serve in the production of high-value difficult-to-produce proteins. In particular, we explain how midiBacillus, which lacks about one-third of the original genome, effectively secretes a protein of the major human pathogen Staphylococcus aureus that cannot be produced by the parental Bacillus subtilis strain. This is important, because the secreted S. aureus protein is exemplary for a range of targets that can be implemented in future antistaphylococcal immunotherapies. Accordingly, we anticipate that midiBacillus chassis will contribute to the development of vaccines that protect both humans and livestock against diseases caused by S. aureus, a bacterial pathogen that is increasingly difficult to fight with antibiotics, because it has accumulated resistances to essentially all antibiotics that are currently in clinical practice.

Published
2021
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18. Enhanced protein production and methods thereof

Author

Bongiorni, Cristina, Neef, Jolanda, Schmidt, Brian F., van Kimmenade, Anita, van Dijl, Jan, Microbes in Health and Disease (MHD), and Translational Immunology Groningen (TRIGR)

Abstract

The present disclosure is generally related to modified Gram-positive bacterial cells producing increased amounts of one or more protein(s) of interest. Certain embodiments of the instant disclosure are therefore directed to modified Gram-positive bacterial cells expressing an increased amount of a POI relative to unmodified (i.e., parental) Gram-positive bacterial cells, wherein the modified (i.e., daughter) bacterial cells comprise a modification which increases rasP gene expression. In certain other embodiments, the disclosure pertains to methods of modifying bacterial cells such that the modified (daughter) cells produce an increased level of a protein of interest. In other embodiments, the disclosure pertains to a protein of interest produced by fermenting a modified bacterial cell of the instant disclosure. Certain other embodiments of the disclosure are directed to one or more proteinaceous compositions comprising one or more protein(s) of interest thus made.

Published
2017

19. Novel surface display system for proteins on non-genetically modified gram-positive bacteria

Author

Bosma, Tjibbe, Kanninga, Rolf, Neef, Jolanda, Audouy, Sandrine A.L., Van Roosmalen, Maarten L., Steen, Anton, Buist, Girbe, Kok, Jan, Kuipers, Oscar P., Robillard, George, and Leenhouts, Kees

Subjects
Gram-positive bacteria -- Physiological aspects, Gram-positive bacteria -- Research, Bacterial proteins -- Properties, Polymerase chain reaction -- Analysis, Fluorescence microscopy -- Usage, Biological sciences
Abstract

A study was conducted on the highly efficient immobilization of heterologous proteins on bacterial surfaces made possible by a novel display system. It was observed that the non-living and non-genetically modified gram-positive bacterial cells are used as substrates to bind externally added heterologous proteins by means of a high affinity binding domain.

Published
2006

22. Active immunization with an octa-valent Staphylococcus aureus antigen mixture in models of S. aureus bacteremia and skin infection in mice

Author

Van Den Berg, Sanne, Koedijk, Dennis G.A.M., Back, Jaap Willem, Neef, Jolanda, Dreisbach, Annette, Van Dijl, Jan Maarten, Bakker-Woudenberg, Irma A.J.M., Buist, Girbe, Van Den Berg, Sanne, Koedijk, Dennis G.A.M., Back, Jaap Willem, Neef, Jolanda, Dreisbach, Annette, Van Dijl, Jan Maarten, Bakker-Woudenberg, Irma A.J.M., and Buist, Girbe

Published
2015

23. Versatile vector suite for the extracytoplasmic production and purification of heterologous His-tagged proteins in Lactococcus lactis

Author

MMB, UMC Utrecht, Infection & Immunity, Neef, Jolanda, Milder, Fin J., Koedijk, Danny G A M, Klaassens, Marindy, Heezius, Erik C., van Strijp, Jos A G, Otto, Andreas, Becher, Dörte, van Dijl, Jan Maarten, Buist, Girbe, MMB, UMC Utrecht, Infection & Immunity, Neef, Jolanda, Milder, Fin J., Koedijk, Danny G A M, Klaassens, Marindy, Heezius, Erik C., van Strijp, Jos A G, Otto, Andreas, Becher, Dörte, van Dijl, Jan Maarten, and Buist, Girbe

Published
2015

25. Low anti-staphylococcal IgG responses in granulomatosis with polyangiitis patients despite long-term Staphylococcus aureus exposure

Author

Glasner, Corinna, primary, van Timmeren, Mirjan M., additional, Stobernack, Tim, additional, Omansen, Till F., additional, Raangs, Erwin C., additional, Rossen, John W., additional, de Goffau, Marcus C., additional, Arends, Jan P., additional, Kampinga, Greetje A., additional, Koedijk, Denny G. A. M., additional, Neef, Jolanda, additional, Buist, Girbe, additional, Tavakol, Mehri, additional, van Wamel, Willem J. B., additional, Rutgers, Abraham, additional, Stegeman, Coen A., additional, Kallenberg, Cees G. M., additional, Heeringa, Peter, additional, and van Dijl, Jan Maarten, additional

Published
2015
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26. Pyruvate Oxidase Influences the Sugar Utilization Pattern and Capsule Production in Streptococcus pneumoniae

Author

Carvalho, Sandra M., Farshchi Andisi, Vahid, Gradstedt, Henrik, Neef, Jolanda, Kuipers, Oscar P., Neves, Ana R., Bijlsma, Jetta J. E., Carvalho, Sandra M., Farshchi Andisi, Vahid, Gradstedt, Henrik, Neef, Jolanda, Kuipers, Oscar P., Neves, Ana R., and Bijlsma, Jetta J. E.

Abstract

Pyruvate oxidase is a key function in the metabolism and lifestyle of many lactic acid bacteria and its activity depends on the presence of environmental oxygen. In Streptococcus pneumoniae the protein has been suggested to play a major role in metabolism and has been implicated in virulence, oxidative stress survival and death in stationary phase. Under semi-aerobic conditions, transcriptomic and metabolite profiling analysis of a spxB mutant grown on glucose showed minor changes compared to the wild type, apart from the significant induction of two operons involved in carbohydrate uptake and processing. This induction leads to a change in the sugar utilization capabilities of the bacterium, as indicated by the analysis of the growth profiles of the D39 parent and spxB mutant on alternative carbohydrates. Metabolic analysis and growth experiments showed that inactivation of SpxB has no effect on the glucose fermentation pattern, except under aerobic conditions. More importantly, we show that mutation of spxB results in the production of increased amounts of capsule, the major virulence factor of S. pneumoniae. Part of this increase can be attributed to induction of capsule operon (cps) transcription. Therefore, we propose that S. pneumoniae utilizes pyruvate oxidase as an indirect sensor of the oxygenation of the environment, resulting in the adaption of its nutritional capability and the amount of capsule to survive in the host.

Published
2013

31. Development of lactococcal GEM-based pneumococcal vaccines

Author

Audouy, Sandrine A.L., primary, van Selm, Saskia, additional, van Roosmalen, Maarten L., additional, Post, Eduard, additional, Kanninga, Rolf, additional, Neef, Jolanda, additional, Estevão, Silvia, additional, Nieuwenhuis, Edward E.S., additional, Adrian, Peter V., additional, Leenhouts, Kees, additional, and Hermans, Peter W.M., additional

Published
2007
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32. Pyruvate Oxidase Influences the Sugar Utilization Pattern and Capsule Production in Streptococcus pneumoniae.

Author

Carvalho, Sandra M., Farshchi Andisi, Vahid, Gradstedt, Henrik, Neef, Jolanda, Kuipers, Oscar P., Neves, Ana R., and Bijlsma, Jetta J. E.

Subjects
PYRUVATES, OXIDASES, PHARMACEUTICAL encapsulation, STREPTOCOCCUS pneumoniae, LACTIC acid bacteria, BACTERIAL metabolism, MICROBIAL virulence
Abstract

Pyruvate oxidase is a key function in the metabolism and lifestyle of many lactic acid bacteria and its activity depends on the presence of environmental oxygen. In Streptococcus pneumoniae the protein has been suggested to play a major role in metabolism and has been implicated in virulence, oxidative stress survival and death in stationary phase. Under semi-aerobic conditions, transcriptomic and metabolite profiling analysis of a spxB mutant grown on glucose showed minor changes compared to the wild type, apart from the significant induction of two operons involved in carbohydrate uptake and processing. This induction leads to a change in the sugar utilization capabilities of the bacterium, as indicated by the analysis of the growth profiles of the D39 parent and spxB mutant on alternative carbohydrates. Metabolic analysis and growth experiments showed that inactivation of SpxB has no effect on the glucose fermentation pattern, except under aerobic conditions. More importantly, we show that mutation of spxB results in the production of increased amounts of capsule, the major virulence factor of S. pneumoniae. Part of this increase can be attributed to induction of capsule operon (cps) transcription. Therefore, we propose that S. pneumoniae utilizes pyruvate oxidase as an indirect sensor of the oxygenation of the environment, resulting in the adaption of its nutritional capability and the amount of capsule to survive in the host. [ABSTRACT FROM AUTHOR]

Published
2013
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33. Pyruvate Oxidase Influences the Sugar Utilization Pattern and Capsule Production in Streptococcus pneumoniae.

Author

Carvalho, Sandra M., Farshchi Andisi, Vahid, Gradstedt, Henrik, Neef, Jolanda, Kuipers, Oscar P., Neves, Ana R., and Bijlsma, Jetta J. E.

Subjects
*PYRUVATES, *OXIDASES, *PHARMACEUTICAL encapsulation, *STREPTOCOCCUS pneumoniae, *LACTIC acid bacteria, *BACTERIAL metabolism, *MICROBIAL virulence
Abstract

Pyruvate oxidase is a key function in the metabolism and lifestyle of many lactic acid bacteria and its activity depends on the presence of environmental oxygen. In Streptococcus pneumoniae the protein has been suggested to play a major role in metabolism and has been implicated in virulence, oxidative stress survival and death in stationary phase. Under semi-aerobic conditions, transcriptomic and metabolite profiling analysis of a spxB mutant grown on glucose showed minor changes compared to the wild type, apart from the significant induction of two operons involved in carbohydrate uptake and processing. This induction leads to a change in the sugar utilization capabilities of the bacterium, as indicated by the analysis of the growth profiles of the D39 parent and spxB mutant on alternative carbohydrates. Metabolic analysis and growth experiments showed that inactivation of SpxB has no effect on the glucose fermentation pattern, except under aerobic conditions. More importantly, we show that mutation of spxB results in the production of increased amounts of capsule, the major virulence factor of S. pneumoniae. Part of this increase can be attributed to induction of capsule operon (cps) transcription. Therefore, we propose that S. pneumoniae utilizes pyruvate oxidase as an indirect sensor of the oxygenation of the environment, resulting in the adaption of its nutritional capability and the amount of capsule to survive in the host. [ABSTRACT FROM AUTHOR]

Published
2013
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34. TLR4 sensing of IsdB of Staphylococcus aureus induces a proinflammatory cytokine response via the NLRP3-caspase-1 inflammasome cascade.

Author

Gonzalez JJI, Hossain MF, Neef J, Zwack EE, Tsai C-M, Raafat D, Fechtner K, Herzog L, Kohler TP, Schlüter R, Reder A, Holtfreter S, Liu GY, Hammerschmidt S, Völker U, Torres VJ, van Dijl JM, Lillig CH, Bröker BM, and Darisipudi MN

Subjects
Humans, Caspase 1 metabolism, Inflammasomes metabolism, Iron metabolism, Bacterial Proteins immunology, Cation Transport Proteins immunology, Cytokines metabolism, Methicillin-Resistant Staphylococcus aureus immunology, NLR Family, Pyrin Domain-Containing 3 Protein genetics, NLR Family, Pyrin Domain-Containing 3 Protein metabolism, Staphylococcal Infections immunology, Toll-Like Receptor 4 metabolism
Abstract

Importance: The prevalence of multidrug-resistant Staphylococcus aureus is of global concern, and vaccines are urgently needed. The iron-regulated surface determinant protein B (IsdB) of S. aureus was investigated as a vaccine candidate because of its essential role in bacterial iron acquisition but failed in clinical trials despite strong immunogenicity. Here, we reveal an unexpected second function for IsdB in pathogen-host interaction: the bacterial fitness factor IsdB triggers a strong inflammatory response in innate immune cells via Toll-like receptor 4 and the inflammasome, thus acting as a novel pathogen-associated molecular pattern of S. aureus . Our discovery contributes to a better understanding of how S. aureus modulates the immune response, which is necessary for vaccine development against the sophisticated pathogen., Competing Interests: The authors declare no conflict of interest.

Published
2024
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