Understanding and mathematical modelling of cellular resource allocation in microorganisms: a comparative synthesis

Microbial markets: socio-economic perspective in studying microbial communities

Studying microbial communities through a socio-economic lens, this paper draws parallels with human economic transactions and microbes' race for resources. Extending the 'Market Economy' concept of social science to microbial ecosystems, the paper aims to contribute to comprehending the collaborative and competitive dynamics among microorganisms. Created by a multidisciplinary team of an economist, microbiologists, and mathematicians, the paper also highlights the risks involved in employing a socio-economic perspective to explain the complexities of natural ecosystems. Navigating through microbial markets offers insights into the implications of these interactions while emphasizing the need for cautious interpretation within the broader ecological context. We hope that this paper will be a fruitful source of inspiration for future studies on microbial communities.

Low and high nucleic acid content bacteria play discrepant roles in response to various carbon supply modes

Planktonic bacteria can be grouped into 'high nucleic acid content (HNA) bacteria' and 'low nucleic acid content (LNA) bacteria.' Nutrient input modes vary in environments, causing nutrient availability heterogeneity. We incubated them with equal amounts of total glucose added in a continuous/pulsed mode. The pulse-treated LNA bacteria exhibited twice the cell abundance and four times the viability of the continuous-treated LNA, while HNA did not show an adaptation to pulsed treatment. In structural equation modelling, LNA bacteria had higher path coefficients than HNA, between growth and carbon-saving metabolic pathways, intracellular ATP and the inorganic energy storage polymer, polyphosphate, indicating their low-cost growth, and flexible energy storage and utilisation. After incubation, the pulse-treated LNA bacteria contained more proteins and polysaccharides (0.00064, 0.0012 ng cell-1 ) than the continuous-treated LNA (0.00014, 0.00014 ng cell-1 ), conferring endurance and rapid response to pulses. Compared to LNA, HNA keystone taxa had stronger correlations with the primary glucose metabolism step, glycolysis, and occupied leading positions to explain the random forest model. They are essential to introduce glucose into the element cycling of the whole community under both treatments. Our work outlines a systematic bacterial response to carbon input.

Improved production of β-carotene in light-powered Escherichia coli by co-expression of Gloeobacter rhodopsin expression

BACKGROUND

Providing sufficient and usable energy for the cell factory has long been a heated issue in biosynthesis as solar energy has never been rooted out from the strategy for improvement, and turning Escherichia coli (E. coli) into a phototrophic host has multiple captivating qualities for biosynthesis. In this study, β-carotene was a stable compound for production in E. coli with the expression of four enzymes (CrtE, CrtB, CrtI, CrtY) for production due to its light-harvesting feature as an antenna pigment and as an antioxidant and important precursor for human health. The expression of Gloeobacter rhodopsin (GR) in microbial organisms was proved to have potential for application.

RESULTS

The expression of fusion protein, GR-GFP, in E. coli showed visible GFP signal under fluorescent microscopy, and its in vivo proton pumping activity signal can be detected in induced photocurrent by electrodes on the chip under intervals of illumination. To assess the phototrophic synthesis ability of the host strain compared to wild-type and vector control strain in chemostat batch with illumination, the expression of red fluorescent protein (RFP) as a target protein showed its yield improvement in protein assay and also reflected its early dominance in RFP fluorescence signal during the incubation, whereas the synthesis of β-carotene also showed yield increase by 1.36-fold and 2.32-fold compared with its wildtype and vector control strain. To investigate the effect of GR-GFP on E. coli, the growth of the host showed early rise into the exponential phase compared to the vector control strain and glucose turnover rate was elevated in increased glucose intake rate and upregulation of ATP-related genes in glycolysis (PtsG, Pgk, Pyk).

CONCLUSION

We reported the first-time potential application of GR in the form of fusion protein GR-GFP. Expression of GR-GFP in E. coli improved the production of β-carotene and RFP. Our work provides a strain of E. coli harboring phototrophic metabolism, thus paving path to a more sustainable and scalable production of biosynthesis.

Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook

In microorganisms, different from primary metabolism for cellular growth, secondary metabolism is for ecological interactions and stress responses and an important source of natural products widely used in various areas such as pharmaceutics and food additives. With advancements of sequencing technologies and bioinformatics tools, a large number of biosynthetic gene clusters of secondary metabolites have been discovered from microbial genomes. However, due to challenges from the difficulty of genome-scale pathway reconstruction and the limitation of conventional flux balance analysis (FBA) on secondary metabolism, the quantitative modeling of secondary metabolism is poorly established, in contrast to that of primary metabolism. This review first discusses current efforts on the reconstruction of secondary metabolic pathways in genome-scale metabolic models (GSMMs), as well as related FBA-based modeling techniques. Additionally, potential extensions of FBA are suggested to improve the prediction accuracy of secondary metabolite production. As this review posits, biosynthetic pathway reconstruction for various secondary metabolites will become automated and a modeling framework capturing secondary metabolism onset will enhance the predictive power. Expectedly, an improved FBA-based modeling workflow will facilitate quantitative study of secondary metabolism and in silico design of engineering strategies for natural product production.

Simple Growth–Metabolism Relations Are Revealed by Conserved Patterns of Heat Flow from Cultured Microorganisms

Quantitative analyses of cell replication address the connection between metabolism and growth. Various growth models approximate time-dependent cell numbers in culture media, but physiological implications of the parametrizations are vague. In contrast, isothermal microcalorimetry (IMC) measures with unprecedented sensitivity the heat (enthalpy) release via chemical turnover in metabolizing cells. Hence, the metabolic activity can be studied independently of modeling the time-dependence of cell numbers. Unexpectedly, IMC traces of various origins exhibit conserved patterns when expressed in the enthalpy domain rather than the time domain, as exemplified by cultures of Lactococcus lactis (prokaryote), Trypanosoma congolese (protozoan) and non-growing Brassica napus (plant) cells. The data comply extraordinarily well with a dynamic Langmuir adsorption reaction model of nutrient uptake and catalytic turnover generalized here to the non-constancy of catalytic capacity. Formal relations to Michaelis–Menten kinetics and common analytical growth models are briefly discussed. The proposed formalism reproduces the “life span” of cultured microorganisms from exponential growth to metabolic decline by a succession of distinct metabolic phases following remarkably simple nutrient–metabolism relations. The analysis enables the development of advanced enzyme network models of unbalanced growth and has fundamental consequences for the derivation of toxicity measures and the transferability of metabolic activity data between laboratories.