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4. Population-based Optimization for Kinetic Parameter Identification in Glycolytic Pathway in Saccharomyces cerevisiae

Author

Weglarz-Tomczak, Ewelina, Tomczak, Jakub M., Eiben, Agoston E., and Brul, Stanley

Subjects
Quantitative Biology - Biomolecules, Computer Science - Neural and Evolutionary Computing
Abstract

Models in systems biology are mathematical descriptions of biological processes that are used to answer questions and gain a better understanding of biological phenomena. Dynamic models represent the network through rates of the production and consumption for the individual species. The ordinary differential equations that describe rates of the reactions in the model include a set of parameters. The parameters are important quantities to understand and analyze biological systems. Moreover, the perturbation of the kinetic parameters are correlated with upregulation of the system by cell-intrinsic and cell-extrinsic factors, including mutations and the environment changes. Here, we aim at using well-established models of biological pathways to identify parameter values and point their potential perturbation/deviation. We present our population-based optimization framework that is able to identify kinetic parameters in the dynamic model based on only input and output data (i.e., timecourses of selected metabolites). Our approach can deal with the identification of the non-measurable parameters as well as with discovering deviation of the parameters. We present our proposed optimization framework on the example of the well-studied glycolytic pathway in Saccharomyces cerevisiae., Comment: Code at https://github.com/jmtomczak/popi

Published
2020

25. Identification and characterization of new proteins crucial for bacterial spore resistance and germination

Author

Yu, Benjamin, primary, Kanaan, Julia, additional, Shames, Hannah, additional, Wicander, James, additional, Aryal, Makunda, additional, Li, Yunfeng, additional, Korza, George, additional, Brul, Stanley, additional, Kramer, Gertjan, additional, Li, Yong-qing, additional, Nichols, Frank C., additional, Hao, Bing, additional, and Setlow, Peter, additional

Published
2023
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27. Expression of the 2Duf protein in wild-type Bacillus subtilis spores stabilizes inner membrane proteins and increases spore resistance to wet heat and hydrogen peroxide

Author

Korza, George, primary, DePratti, Sarah, additional, Fairchild, Daniel, additional, Wicander, James, additional, Kanaan, Julia, additional, Shames, Hannah, additional, Nichols, Frank C, additional, Cowan, Ann, additional, Brul, Stanley, additional, and Setlow, Peter, additional

Published
2023
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42. Model-driven approach for the production of butyrate from CO2/H2 by a novel co-culture of C. autoethanogenum and C. beijerinckii

Author

Benito-Vaquerizo, Sara, Nouse, Niels, Schaap, Peter J., Hugenholtz, Jeroen, Brul, Stanley, López-Contreras, Ana M., Martins dos Santos, Vitor A.P., Suarez-Diez, Maria, Benito-Vaquerizo, Sara, Nouse, Niels, Schaap, Peter J., Hugenholtz, Jeroen, Brul, Stanley, López-Contreras, Ana M., Martins dos Santos, Vitor A.P., and Suarez-Diez, Maria

Abstract

One-carbon (C1) compounds are promising feedstocks for the sustainable production of commodity chemicals. CO2 is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted into valuable products while reducing its atmospheric levels. Acetogens are microorganisms that can grow on CO2/H2 gas mixtures and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with other microbial species that can further process such products, can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone-butanol-ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of an acetogen and a solventogen in a consortium provides a potential platform to produce valuable chemicals from CO2. In this study, metabolic modeling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO2/H2 mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation of Clostridium beijerinckii on these substrates in batch serum bottles and subsequently in pH-controlled bioreactors. Community modeling also suggested that a novel microbial consortium consisting of the acetogen Clostridium autoethanogenum, and the solventogen C. beijerinckii would be feasible and stable. On the basis of this prediction, a co-culture was experimentally established. C. autoethanogenum grew on CO2/H2 producing acetate and traces of ethanol. Acetate was in turn, consumed by C. beijerinckii together with lactate, producing butyrate. These results show that community modeling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable reso

Published
2022

47. Identification and characterization of new proteins crucial for bacterial spore resistance and germination.

Author

Benjamin Yu, Kanaan, Julia, Shames, Hannah, Wicander, James, Aryal, Makunda, Yunfeng Li, Korza, George, Brul, Stanley, Kramer, Gertjan, Yong-qing Li, Nichols, Frank C., Bing Hao, and Setlow, Peter

Subjects
BACTERIAL spores, DRUG resistance in bacteria, BACTERIAL proteins, OPERONS, TRANSPOSONS, BACILLUS cereus, WETTING agents
Abstract

2Duf, named after the presence of a transmembrane (TM) Duf421 domain and a small Duf1657 domain in its sequence, is likely located in the inner membrane (IM) of spores in some Bacillus species carrying a transposon with an operon termed spoVA2mob. These spores are known for their extreme resistance to wet heat, and 2Duf is believed to be the primary contributor to this trait. In this study, we found that the absence of YetF or YdfS, both Duf421 domain-containing proteins and found only in wild-type (wt) B. subtilis spores with YetF more abundant, leads to decreased resistance to wet heat and agents that can damage spore core components. The IM phospholipid compositions and core water and calciumdipicolinic acid levels of YetF-deficient spores are similar to those of wt spores, but the deficiency could be restored by ectopic insertion of yetF, and overexpression of YetF increased wt spore resistance to wet heat. In addition, yetF and ydfS spores have decreased germination rates as individuals and populations with germinant receptor-dependent germinants and increased sensitivity to wet heat during germination, potentially due to damage to IM proteins. These data are consistent with a model in which YetF, YdfS and their homologs modify IM structure to reduce IM permeability and stabilize IM proteins against wet heat damage. Multiple yetF homologs are also present in other spore forming Bacilli and Clostridia, and even some asporogenous Firmicutes, but fewer in asporogenous species. The crystal structure of a YetF tetramer lacking the TM helices has been reported and features two distinct globular subdomains in each monomer. Sequence alignment and structure prediction suggest this fold is likely shared by other Duf421-containing proteins, including 2Duf. We have also identified naturally occurring 2duf homologs in some Bacilli and Clostridia species and in wt Bacillus cereus spores, but not in wt B. subtilis. Notably, the genomic organization around the 2duf gene in most of these species is similar to that in spoVA2mob, suggesting that one of these species was the source of the genes on this operon in the extremely wet heat resistant spore formers. [ABSTRACT FROM AUTHOR]

Published
2023
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48. Sa2050 REVEALING THE SIGNIFICANCE OF PURINE METABOLISM IN ACHIEVING REMISSION IN PEDIATRIC CROHN'S DISEASE THROUGH INTEGRATED OMICS ANALYSIS OF FECES, PLASMA, AND URINE.

Author

Koopman, Nienke, Jaspers, Yorrick, van Leeuwen, Pim, Chronas, Konstantinos, Diederen, Kay, Yim, Andrew Y. Li, Velde, Anje te, Roseboom, Winfried, Kindermann, Angelika, Benninga, Marc A., Kramer, Gertjan, De Jonge, Wouter J., Brul, Stanley, Levin, Evgeni, Kemp, Stephan, and Seppen, Jurgen

Published
2024
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