Biology subjects

Bruheim, P.

Publications and source records attributed to Bruheim, P..

3 recordsLinked to original sources

bioRxiv2021

Quantification of macromolecular biomass composition for constraint-based metabolic modeling

Genome-scale metabolic models (GEMs) are mathematical representations of metabolism that allow for in silico simulation of metabolic phenotypes and capabilities. A prerequisite for these predictions is an accurate representation of the biomolecular composition of the cell necessary for replication and growth, implemented in GEMs as the so-called biomass objective function (BOF). The BOF contains the metabolic precursors required for synthesis of the cellular macro- and micromolecular constituents (e.g. protein, RNA, DNA), and its composition is highly dependent on the particular organism, strain, and growth condition. Despite its critical role, the BOF is rarely constructed using specific measurements of the modeled organism, drawing the validity of this approach into question. Thus, there is a need to establish robust and reliable protocols for experimental condition-specific biomass determination. Here, we address this challenge by presenting a general pipeline for biomass quantification, evaluating its performance on Escherichia coli K-12 MG1655 sampled during balanced exponential growth under controlled conditions in a batch-fermentor set-up. We significantly improve both the coverage and molecular resolution compared to previously published workflows, quantifying 91.6% of the biomass. Our measurements display great correspondence with previously reported measurements, and we were also able to detect subtle characteristics specific to the particular E. coli strain. Using the modified E. coli GEM iML1515a, we compare the feasible flux ranges of our experimentally determined BOF with the original BOF, finding that the changes in BOF coefficients considerably affect the attainable fluxes at the genome-scale.

systems biology↗

bioRxiv2020

Cell biological studies of ethanologenic bacterium Zymomonas mobilis

Alphaproteobacterium Zymomonas mobilis exhibits extreme ethanologenic physiology, making this species a promising biofuel producer. Numerous studies have investigated its biology relevant to industrial applications and mostly at the population level. However, the organization of single cells in this industrially important, polyploid species has been largely uncharacterized. In the present study, we characterized basic cellular behaviour of Z. mobilis strain Zm6 at a single cell level. We observed that growing Z. mobilis cells often divided at non mid-cell position, which contributed to variant cell size at birth. Yet, the cell size variance was regulated by a modulation of cell cycle span, mediated by a correlation of bacterial tubulin homologue FtsZ-ring accumulation with cell growth. The Z. mobilis culture also exhibited heterogeneous cellular DNA contents among individual cells, which might have been caused by asynchronous replication of chromosome that was not coordinated to cell growth. Furthermore, slightly angled divisions might have rendered temporary curvatures of attached Z. mobilis cells. Overall, the presented study uncovered a novel bacterial cell organization in Z. mobilis, the metabolism of which is not favoured for biosynthesis to build biomass. ImportanceWith increasing environmental concerns about the exhausting use of fossil fuels, a development of sustainable biofuel production platform has been attracting significant public attention. Ethanologenic Z. mobilis species are endowed with an efficient ethanol-fermentation capacity that surpass, in several aspects, that of the bakers yeast Saccharomyces cerevisiae, the most used microorganism for ethanol productions. For a development of Z. mobilis culture-based biorefinery, an investigation of its uncharacterized cell biology is important, because bacterial cellular organization and metabolism are closely associated with each other in a single cell compartment. In addition, the current work highlights that polyploid bacterium Z. mobilis exhibits a distinctive mode of bacterial cell organization, reflecting its unique metabolism that do not prioritize incorporation of nutrients to cell growth. Thus, another significance of presented work is to advance our general understanding in the diversity of bacterial cell architecture.

microbiology↗

bioRxiv2020

PCNA has specific functions in regulation of metabolism in haematological cells

PCNAs essential roles in DNA replication and repair are well established, while its recently discovered cytosolic roles are less explored. Here we show that impairing PCNAs cytosolic scaffold functions led to massive changes in cellular signaling, and most strikingly, a strong reduction in glycolytic metabolite and nucleoside phosphate pools in haematological cancer cells. This was not detected in cells from solid tissues nor in primary monocytes from healthy donors. However, lipopolysaccharide stimulated monocytes responded to targeting PCNAs scaffold function similarly to haematological cancer cells, suggesting that cellular stress is an important factor for the observed response. Integrated transcriptome, proteome and metabolome analysis revealed that pathways involved in protein stability/folding and immune responses were affected in haematopoietic cancer cells. Altogether, our data suggests that PCNA has an important role in regulation of cytoplasmic stress via regulation of central carbon metabolism in haematological cells, which potentially can be targeted in cancer treatment. HighlightA strong reduction in glycolytic metabolites and the nucleoside phosphate pools was detected in haematological cancer cells upon inhibiting PCNA scaffold functions. These metabolic changes were not found in cancer cells from other tissues, indicating a special role of PCNA in regulation of metabolism in cells of haematological origin.

cell biology↗