Article
Cell Biology
Isabella N. Brown, M. Carmen Lafita-Navarro, Maralice Conacci-Sorrell
Summary: The nucleolus plays a crucial role in protein synthesis by producing new ribosomes. In cancer, nucleolar activity is heightened due to increased demand for protein synthesis. The transcription factor MYC promotes nucleolar activity and understanding and potentially inhibiting aberrant nucleolar activity in cancer cells could lead to novel therapeutics.
Article
Cell Biology
Wen Fang, Yibing Zhu, Sen Yang, Xiaomeng Tong, Cunqi Ye
Summary: Phospholipid biosynthesis mediates communication between membranes and histone, influencing metabolic decisions. In response to nutrient deprivation, phospholipid methylation generates a starvation signal by depleting S-adenosylmethionine (SAM), causing dynamic changes in histone methylation. Our study highlights the critical role of SAM-responsive methylation of H3K36 in metabolic adaptation to nutrient starvation in Saccharomyces cerevisiae. Deficiency in H3K36 methylation leads to defects in membrane integrity and pyrimidine metabolism, and reduces viability under starvation. Modulating phospholipid synthesis effectively rewires metabolic pathways for nucleotide synthesis and enhances antioxidant production, improving the defects caused by loss of H3K36 methylation. Furthermore, we demonstrate that H3K36 methylation reciprocally regulates phospholipid synthesis by influencing redox balance. Our findings illustrate an adaptive mechanism in which phospholipid synthesis involves histone modification to reprogram metabolism for adaptation in a eukaryotic model organism.
Article
Multidisciplinary Sciences
Ibrahim E. Elsemman, Angelica Rodriguez Prado, Pranas Grigaitis, Manuel Garcia Albornoz, Victoria Harman, Stephen W. Holman, Johan van Heerden, Frank J. Bruggeman, Mark M. M. Bisschops, Nikolaus Sonnenschein, Simon Hubbard, Rob Beynon, Pascale Daran-Lapujade, Jens Nielsen, Bas Teusink
Summary: The study developed a metabolic model of yeast cells to predict proteome constraints governing metabolic strategies. Under specific conditions, unicellular organisms rewire their metabolism to adapt to growth and maintenance needs.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Ana Sanchez-Iglesias, Kellie Jenkinson, Sara Bals, Luis M. Liz-Marzan
Summary: The synthesis of gold nanorods requires the presence of symmetry-breaking and shape-directing additives, such as bromide ions and quaternary ammonium surfactants. By using hexadecyltrimethylammonium chloride (CTAC) as the principal surfactant and a low concentration of bromide, gold nanorods can be synthesized at temperatures as low as 8 degrees C, allowing for temperature-controlled aspect ratio tunability.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Review
Biochemical Research Methods
Cristal Zuniga, Juan D. Tibocha-Bonilla, Michael J. Betenbaugh
Summary: Microbial organisms engage in a variety of metabolic interactions, with transporters playing a crucial role in mediating the exchange of molecules between different organelles, cells, and the environment. Theoretical calculations about the inputs and outputs of cells via metabolic exchanges have enabled insights into intraorganismal and inter-organismal systems. Utilizing kinetic, metabolic, and statistical modeling approaches along with omics data enhances understanding of metabolic exchange and resource allocation.
CURRENT OPINION IN BIOTECHNOLOGY
(2021)
Article
Plant Sciences
Gen Sakurai, Stanley J. Miklavcic
Summary: In this study, we used a detailed whole leaf hydraulic model to investigate the local operation of three stomatal conductance models distributed on a whole leaf scale. By examining the leaf-area distributions of photosynthesis, transpiration, stomatal conductance, and guard cell turgor pressure, we quantified the behavior of these models and their responses to changes in environmental conditions. Our findings reveal that a stomatal conductance model which includes mechanical processes dependent on local variables predicts a spatial variation of physiological activity across the leaf, indicating that the leaf functions of photosynthesis and transpiration are not uniformly operative even under uniform external conditions. Our simulation experiments comparing two versions of a mechanical stomatal conductance model suggest that leaves exhibit a more complex spatial distribution pattern of both photosynthesis and transpiration rate and more complex dependencies on environmental conditions when a non-linear relationship between the stomatal aperture and guard cell and epidermal cell turgor pressures is implemented.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Kerian Thuillier, Caroline Baroukh, Alexander Bockmayr, Ludovic Cottret, Loic Pauleve, Anne Siegel
Summary: This study presents a novel approach to infer Boolean rules for metabolic regulation from time-series data and a prior knowledge network (PKN). By combining answer set programming and linear programming, candidate Boolean regulations that can reproduce the given data are generated. The quality of predictions depends on the available time-series data, such as kinetic, fluxomics or transcriptomics data.
Article
Biochemical Research Methods
Liliana Angeles-Martinez, Vassily Hatzimanikatis
Summary: This study analyzes the sensitivity of biofilm simulation to crowding conditions and finds that traditional methods may not accurately capture the diverse nature of biofilms. The modeling of crowding conditions in microbial systems can guide the selection of effective treatments for disrupting and controlling biofilms associated with chronic diseases.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Neurosciences
Zorana Kurbalija Novicic, Robert Boden, Ksenija Kozarski, Mihailo Jelic, Vladimir M. Jovanovic, Janet L. Cunningham
Summary: This study on fruit flies found that lithium has an effect on the whole-organism metabolic rate, with a subtle balance between efficacy and side effects within a narrow dose range. Additionally, lithium exposure was found to have different effects on metabolism based on mtDNA haplotypes and sex.
JOURNAL OF NEUROSCIENCE RESEARCH
(2021)
Article
Engineering, Environmental
Seow Wah How, Tadashi Shoji, Chee Keong Tan, Thomas P. Curtis, Adeline Seak May Chua
Summary: This study simulated and calibrated the low-DO OA process in tropical wastewater treatment plants based on the ASM1 model, revealing that the microbes in the low-DO OA SBR had lower growth rates and affinities, supporting the proliferation of nitrifiers under low-dissolved-oxygen conditions. The research emphasizes the importance of using suitable parameters in the design of wastewater treatment plants in tropical regions.
JOURNAL OF WATER PROCESS ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Shailee Gaur, Suresh Gupta, Amit Jain
Summary: This study investigated the kinetics and biodegradation potential of a thermophilic strain for degrading waste engine oil. The results showed that the strain had different degradation effects on different concentrations of waste engine oil, and the biosurfactant produced facilitated the degradation process.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Review
Agriculture, Dairy & Animal Science
Julie A. Hicks, Hsiao-Ching Liu
Summary: MiRNA, a class of small noncoding RNAs, regulate the majority of protein-coding genes in organisms. Disruption of miRNA function can lead to pathological conditions, with metabolism being one physiological system under tight miRNA regulation.
Article
Genetics & Heredity
Saman M. Najmi, David A. Schneider
Summary: Ribosome biogenesis in yeast requires the concerted activities of three nuclear RNA polymerases and significant cellular energy. It has been found that growing cells produce compounds that accumulate in the growth medium, inducing repression of rRNA synthesis. This repression is mediated by quorum sensing and involves the degradation of certain RNA polymerase subunits.
Article
Biotechnology & Applied Microbiology
R. P. van Rosmalen, R. W. Smith, V. A. P. Martins dos Santos, C. Fleck, M. Suarez-Diez
Summary: Constraint-based, genome-scale metabolic models are crucial for guiding metabolic engineering, but lack the time dimension and enzyme dynamics. Model reduction can bridge the gap between these models and kinetic models, allowing integration into the Design Built-Test-Learn cycle. These reduced size models can represent the dynamics of the original model and enable further exploration of dynamic responses in metabolic networks.
METABOLIC ENGINEERING
(2021)
Review
Biology
Wei Jia, Yitao Li, Kenneth C. P. Cheung, Xiaojiao Zheng
Summary: Bile acids play a crucial role in nutrient absorption and act as key regulators of lipid and glucose metabolism and immune homeostasis. They interact with receptors in all major organs, leading to organ-organ interactions that regulate both local and global metabolic processes, as well as the immune system. Targeting BA synthesis and receptor signaling is a promising strategy for the development of novel therapies for various diseases throughout the body.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Iraes Rabbers, Willi Gottstein, Adam M. Feist, Bas Teusink, Frank J. Bruggeman, Herwig Bachmann
Summary: Overflow metabolism, although often considered inefficient, can still be advantageous in promoting high growth rates and fitness. Experimental evolution of bacteria without nutrient competition showed that overflow metabolism led to an increase in cell yield despite a reduction in cell size, demonstrating that this metabolic strategy can be favorable even in the absence of nutrient competition.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Ibrahim E. Elsemman, Angelica Rodriguez Prado, Pranas Grigaitis, Manuel Garcia Albornoz, Victoria Harman, Stephen W. Holman, Johan van Heerden, Frank J. Bruggeman, Mark M. M. Bisschops, Nikolaus Sonnenschein, Simon Hubbard, Rob Beynon, Pascale Daran-Lapujade, Jens Nielsen, Bas Teusink
Summary: The study developed a metabolic model of yeast cells to predict proteome constraints governing metabolic strategies. Under specific conditions, unicellular organisms rewire their metabolism to adapt to growth and maintenance needs.
NATURE COMMUNICATIONS
(2022)
Article
Food Science & Technology
Vincent Somerville, Pranas Grigaitis, Julius Battjes, Francesco Moro, Bas Teusink
Summary: Microbes play a key role in creating safe, edible, and enriched fermented food products through their metabolism. Metabolic modeling is a valuable tool for integrating large datasets and linking genotype to phenotype, addressing challenges in food microbiology such as safety, biotransformation, and food enhancement.
CURRENT OPINION IN FOOD SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Julius Battjes, Chrats Melkonian, Sebastian N. Mendoza, Auke Haver, Kosai Al-Nakeeb, Anna Koza, Lars Schrubbers, Marijke Wagner, Ahmad A. Zeidan, Douwe Molenaar, Bas Teusink
Summary: Climate change increases sugar content in grapes, resulting in unwanted increase in ethanol content of wine. Lachancea thermotolerans ferments glucose and fructose into both ethanol and lactate, decreasing final ethanol content and positively affecting wine acidity. However, a mechanistic understanding of the lactate producing phenotype is currently lacking in Lachancea thermotolerans strains.
Article
Biotechnology & Applied Microbiology
Pranas Grigaitis, Samira L. van den Bogaard, Bas Teusink
Summary: Microbial growth requires energy investment, which is achieved through the production of proteins for energy harvesting. In this study, a resource allocation model of S. cerevisiae was used to compare metabolic strategies under different conditions. The results revealed the additional energy costs for growth of S. cerevisiae with respiratory-impaired mitochondria and highlighted the role of amino acid supplementation in rescuing growth reduction. This study highlights the importance of resource allocation modeling in addressing open questions in microbial physiology.
FEMS YEAST RESEARCH
(2023)
Article
Cell Biology
Jodie H. K. Man, Charlotte A. G. H. van Gelder, Marjolein Breur, Daniel Okkes, Douwe Molenaar, Sophie van der Sluis, Truus Abbink, Maarten Altelaar, Marjo S. van der Knaap, Marianna Bugiani
Summary: This study comprehensively analyzed the cortex of vanishing white matter (VWM) patients using high-resolution mass spectrometry-based proteomics and immunohistochemistry. The findings revealed a large number of differentially expressed proteins in the VWM cortex, forming a major protein interaction network. Gene ontology analysis further indicated enrichment for cellular metabolism, particularly mitochondrial activity. Importantly, the study identified astrocytic involvement in the cortical pathology of VWM, with morphological changes and decreased complexity observed in VWM cortical astrocytes compared to control cells. These astrocytes were found to be immature and non-reactive. These insights into cortical involvement in VWM have significant implications for the development of therapeutic strategies.
Article
Multidisciplinary Sciences
Daan H. de Groot, Age J. Tjalma, Frank J. Bruggeman, Erik van Nimwegen
Summary: Microbes in the wild adapt to changing environments by using sensory regulatory systems and gene expression noise, and recent experimental results show that phenotype-switching rates may systematically decrease with growth rate. This growth rate dependent stability (GRDS) can overcome the trade-off that limits bet-hedging, allowing for effective adaptation even when environments are diverse and change rapidly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Alan Gerber, Sander van Otterdijk, Frank J. Bruggeman, Evelina Tutucci
Summary: Gene regulatory mechanisms play a crucial role in cellular adaptation to changing environments. mRNA is a key molecule in gene expression and its quantitative measurement in single cells has greatly improved over the past decades. This article provides an overview of state-of-the-art imaging approaches for measuring and understanding gene expression, highlighting the coordination between transcription and degradation of mRNA. The article also discusses future challenges in this multidisciplinary field.
TRANSCRIPTION-AUSTIN
(2023)
Review
Biochemistry & Molecular Biology
Frank J. J. Bruggeman, Bas Teusink, Ralf Steuer
Summary: Microbial systems biology has made significant progress in understanding the relationship between microbial physiology and biochemistry. By studying model microorganisms, computational models have been developed to predict metabolic activities, protein expression, and growth. However, these models may not be applicable to different growth conditions and microorganisms. This article discusses the relationship between growth rate, limited resources, and long-term fitness, as well as the limitations of current computational models, particularly in rapidly changing and adverse environments. The authors propose a classification of microbial growth strategies based on Grimes's CSR framework.
Article
Biology
David D. van Niekerk, Erik Rust, Frank Bruggeman, Hans V. Westerhoff, Jacky L. Snoep
Summary: By analyzing models from the JWS Online and Biomodels databases, we investigated the use of the disequilibrium ratio as an estimator for the flux control of a reaction. While no functional relationship was found, the disequilibrium ratio can still be used as an estimator for the maximal flux control of a reaction step. We further expanded the analysis by incorporating the overall pathway disequilibrium ratio in the expression, leading to explicit expressions for flux control coefficients.
Article
Biotechnology & Applied Microbiology
Tamara Bendig, Andreas Ulmer, Laura Luzia, Susanne Mueller, Sven Sahle, Frank T. Bergmann, Maren Loesch, Florian Erdemann, Ahmad A. Zeidan, Sebastian N. Mendoza, Bas Teusink, Ralf Takors, Ursula Kummer, Ana Sofia Figueiredo
Summary: The fermentation process of milk to yoghurt using Lactobacillus delbrueckii subsp. bulgaricus in co-culture with Streptococcus thermophilus is characterized by lactose breakdown and acidification, which impairs metabolic activities and microbial growth. A proton-dependent computational model was developed to understand the metabolic impact of acidification, and simulation results showed a decrease in metabolic flux with acidification of the cytosol.
JOURNAL OF BIOTECHNOLOGY
(2023)
Article
Microbiology
Sieze Douwenga, Berdien van Olst, Sjef Boeren, Yanzhang Luo, Xin Lai, Bas Teusink, Jacques Vervoort, Michiel Kleerebezem, Herwig Bachmann
Summary: Bacteria like Lactococcus cremoris have a hierarchical sugar catabolism system, where they consistently prioritize the catabolization of higher-quality sugars for optimal growth rate, but also have some proteins always present for consuming certain lower-quality sugars.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
Dennis Botman, Sineka Kanagasabapathi, Philipp Savakis, Bas Teusink
Summary: The AKAR3-EV biosensor measures the activity of PKA and Sch9 kinases in single yeast cells, providing insights into the cellular adaptations of yeast to changing nutrient environments. The biosensor was able to accurately measure the phosphorylation status in intact yeast cells, with heterogeneous responses observed for different sugars. The study highlights the importance of the AKAR3-EV sensor in understanding cellular adaptation in single yeast cells.
FEMS YEAST RESEARCH
(2023)
Article
Biology
Frank J. Bruggeman, Maaike Remeijer, Maarten Droste, Luis Salinas, Meike Wortel, Robert Planque, Herbert M. Sauro, Bas Teusink, Hans Westerhoff
Summary: This paper extends the scope of metabolic control analysis (MCA) to a whole-cell context, considering metabolism in the evolutionary context of growth-rate maximisation. The study shows that elementary flux modes (EFMs) naturally emerge as optimal metabolic networks in this context, and their control properties can be derived. The paper also demonstrates the estimation of flux control coefficients from proteomics and ribosome-profiling data. The findings provide insights into the control of metabolic enzymes on growth rate and contribute to the understanding of general principles in cell biochemistry.