Energy coupling of metabolite transport in Saccharomyces cerevisiae

In living cells, transport proteins allow for the translocation of molecules across biological membranes that are otherwise impermeable to charged and polar solutes. These membrane associated proteins play an essential role in the uptake of substrate molecules and export of metabolic products, as well as in the maintenance of electrochemical...

Unravelling the hydrolytic activity of sludge degrading aquatic worms

The overall objective of this thesis was to investigate ways to improve the extent and rate of waste activated sludge (WAS) hydrolysis by researching the WAS degrading activities and mechanisms of the aquatic worm Tubifex tubifex (T. tubifex) as a starting point. The WAS degrading aquatic worms were taken as a model “biochemical reactor” of...

Novel Evolutionary Engineering Approach to Alter Substrate Specificity of Disaccharide Transporter Mal11 in Saccharomyces cerevisiae

A major challenge in the research of transport proteins is to understand how single amino acid residues contribute to their structure and biological function. Amino acid substitutions that result in a selective advantage in adaptive laboratory evolution experiments can provide valuable hints at their role in transport proteins. In this study, we...

Integration of metabolomics with genomics: Metabolic gene prioritization using metabolomics data and genomic variant (CADD) scores

The integration of metabolomics data with sequencing data is a key step towards improving the diagnostic process for finding the disease-causing genetic variant(s) in patients suspected of having an inborn error of metabolism (IEM). The measured metabolite levels could provide additional phenotypical evidence to elucidate the degree of...

Evolutionary engineering reveals amino acid substitutions in Ato2 and Ato3 that allow improved growth of Saccharomyces cerevisiae on lactic acid

In Saccharomyces cerevisiae, the complete set of proteins involved in transport of lactic acid across the cell membrane has not been determined. In this study, we aimed to identify transport proteins not previously described to be involved in lactic acid transport via a combination of directed evolution, whole-genome resequencing and reverse...

The biodegradability of aquatic worm predated waste activated sludge: A sequential aerobic and anaerobic treatment approach

The objective of this study was to investigate the effect of waste activated sludge (WAS) predation by the aquatic worm Tubifex tubifex (T. tubifex) on the overall biodegradability of WAS. The initial WAS biodegradability potential was determined in 80 days sequential batch-fed anaerobic and aerobic treatment combinations. These treatment...

Pathway engineering strategies for improved product yield in yeast-based industrial ethanol production

Product yield on carbohydrate feedstocks is a key performance indicator for industrial ethanol production with the yeast Saccharomyces cerevisiae. This paper reviews pathway engineering strategies for improving ethanol yield on glucose and/or sucrose in anaerobic cultures of this yeast by altering the ratio of ethanol production, yeast growth...

Carbon dioxide fixation via production of succinic acid from glycerol in engineered Saccharomyces cerevisiae

Background: The microbial production of succinic acid (SA) from renewable carbon sources via the reverse TCA (rTCA) pathway is a process potentially accompanied by net-fixation of carbon dioxide (CO₂). Among reduced carbon sources, glycerol is particularly attractive since it allows a nearly twofold higher CO₂-fixation...

Energy coupling of membrane transport and efficiency of sucrose dissimilation in yeast

Proton coupled transport of α-glucosides via Mal11 into Saccharomyces cerevisiae costs one ATP per imported molecule. Targeted mutation of all three acidic residues in the active site resulted in sugar uniport, but expression of these mutant transporters in yeast did not enable growth on sucrose. We then isolated six unique transporter...

Physical and biochemical changes in sludge upon Tubifex tubifex predation

Worm predation (WP) on activated sludge leads to increased sludge degradation rates, irrespective of the type of worm used or reactor conditions employed. However, the cause of the increased sludge degradation rates remains unknown. This paper presents a comparative analysis of the physical and biochemical aspects of predated sludge,...

Unravelling the protein preference of aquatic worms during waste activated sludge degradation

Worm predation (WP) by Tubifex tubifex was investigated using waste activated sludge (WAS) as the substrate. In order to better understand the sludge degradation mechanisms during WP, the activity of five common hydrolytic enzymes was determined and compared among the initial feed activated sludge, endogenous respirated sludge and worm...

Engineering proton-coupled hexose uptake in Saccharomyces cerevisiae for improved ethanol yield

Background: In the yeast Saccharomyces cerevisiae, which is widely applied for industrial bioethanol production, uptake of hexoses is mediated by transporters with a facilitated diffusion mechanism. In anaerobic cultures, a higher ethanol yield can be achieved when transport of hexoses is proton-coupled, because of the lower net ATP yield of...

Elucidating the microbial community associated with the protein preference of sludge-degrading worms

Sludge predation by aquatic worms results in an increased sludge reduction rate, which is mainly due to the specific removal of a protein fraction from the sludge. As microorganisms play an essential role in sludge hydrolysis a better understanding of the microbial community involved in the worm predation process will provide more insight...

Optimal sediment transport for morphodynamic model validation

Although commonly used for the validation of morphological predictions, point-wise accuracy metrics, such as the root-mean-squared error (RMSE), are not well suited to demonstrate the quality of a high-variability prediction; in the presence of (often inevitable) location errors, the comparison of depth values per grid point tends to favour...

Fermentation of glucose-xylose-arabinose mixtures by a synthetic consortium of single-sugar-fermenting Saccharomyces cerevisiae strains

D-Glucose, D-xylose and L-arabinose are major sugars in lignocellulosic hydrolysates. This study explores fermentation of glucose-xylose-arabinose mixtures by a consortium of three ‘specialist’ Saccharomyces cerevisiae strains. A D-glucose- and L-arabinose-tolerant xylose specialist was constructed by eliminating hexose phosphorylation in an...