Correction to: Industrial antifoam agents impair ethanol fermentation and induce stress responses in yeast cells.

The article "Industrial antifoam agents impair ethanol fermentation and induce stress responses in yeast cells" was originally published Online First without open access. After publication in volume 101, issue 22, page 8237-8248, the author decided to opt for Open Choice and to make the article an open access publication.

Industrial antifoam agents impair ethanol fermentation and induce stress responses in yeast cells.

The Brazilian sugarcane industry constitutes one of the biggest and most efficient ethanol production processes in the world. Brazilian ethanol production utilizes a unique process, which includes cell recycling, acid wash, and non-aseptic conditions. Process characteristics, such as extensive CO generation, poor quality of raw materials, and frequent contaminations, all lead to excessive foam formation during fermentations, which is treated with antifoam agents (AFA).

Scale-down of continuous protein producing Saccharomyces cerevisiae cultivations using a two-compartment system.

In the biotechnological industry, economic decisions in investment are typically based on laboratory-scale experiments. Scale-down as a tool is therefore of high industrial importance to transfer the processes into larger production scale without loss in performance. In this study, large-scale prolonged continuous cultivations with a heterologous protein producing Saccharomyces cerevisiae strain have been scaled-down to a two-compartment scale-down reactor system.

A high-throughput method for quantifying metabolically active yeast cells.

By redesigning the established methylene blue reduction test for bacteria and yeast, we present a cheap and efficient methodology for quantitative physiology of eukaryotic cells applicable for high-throughput systems. Validation of the method in fermenters and high-throughput systems proved equivalent, displaying reduction curves that interrelated directly with CFU counts. For growth rate estimation, the methylene blue reduction test (MBRT) proved superior, since the discriminatory nature of the method allowed for the quantification of metabolically active cells only, excluding dead cells.

Large-scale bioreactor production of the herbicide-degrading Aminobacter sp. strain MSH1.

The Aminobacter sp. strain MSH1 has potential for pesticide bioremediation because it degrades the herbicide metabolite 2,6-dichlorobenzamide (BAM). Production of the BAM-degrading bacterium using aerobic bioreactor fermentation was investigated.

Comparing cellular performance of Yarrowia lipolytica during growth on glucose and glycerol in submerged cultivations.

Yarrowia lipolytica is an attractive host for sustainable bioprocesses due to its ability to utilize a variety of carbon substrates and convert them to a range of different product types (including lipids, organic acids and polyols) under specific conditions. Despite an increasing number of applications for this yeast, relatively few studies have focused on uptake and metabolism of carbon sources, and the metabolic basis for carbon flow to the different products. The focus of this work was quantification of the cellular performance of Y.

Dispersive solid phase extraction combined with ion-pair ultra high-performance liquid chromatography tandem mass spectrometry for quantification of nucleotides in Lactococcus lactis.

Analysis of intracellular metabolites in bacteria is of utmost importance for systems biology and at the same time analytically challenging due to the large difference in concentrations, multiple negative charges, and high polarity of these compounds. To challenge this, a method based on dispersive solid phase extraction with charcoal and subsequent analysis with ion-pair liquid chromatography coupled with electrospray ionization tandem mass spectrometry was established for quantification of intracellular pools of the 28 most important nucleotides. The method can handle extracts where cells leak during the quenching.

Identification of a transcription factor controlling pH-dependent organic acid response in Aspergillus niger.

Acid formation in Aspergillus niger is known to be subjected to tight regulation, and the acid production profiles are fine-tuned to respond to the ambient pH. Based on transcriptome data, putative trans-acting pH responding transcription factors were listed and through knock out studies, mutants exhibiting an oxalate overproducing phenotype were identified. The yield of oxalate was increased up to 158% compared to the wild type and the corresponding transcription factor was therefore entitled Oxalic Acid repression Factor, OafA.

Genome-scale metabolic representation of Amycolatopsis balhimycina.

Infection caused by methicillin-resistant Staphylococcus aureus (MRSA) is an increasing societal problem. Typically, glycopeptide antibiotics are used in the treatment of these infections. The most comprehensively studied glycopeptide antibiotic biosynthetic pathway is that of balhimycin biosynthesis in Amycolatopsis balhimycina.

Industrial glucoamylase fed-batch benefits from oxygen limitation and high osmolarity.

The market for glucoamylase is large and very competitive and the production process has been optimized through several decades. So far a thorough characterization of the process has not been published, but previous academic reports suggest that the process suffers from severe byproduct formation. In this study we have carried out a thorough characterization of a process as close as possible to the industrial reality.

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88.

The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A.

Differential proteomic analysis highlights metabolic strategies associated with balhimycin production in Amycolatopsis balhimycina chemostat cultivations.

Background: Proteomics was recently used to reveal enzymes whose expression is associated with the production of the glycopeptide antibiotic balhimycin in Amycolatopsis balhimycina batch cultivations. Combining chemostat fermentation technology, where cells proliferate with constant parameters in a highly reproducible steady-state, and differential proteomics, the relationships between physiological status and metabolic pathways during antibiotic producing and non-producing conditions could be highlighted.

Results: Two minimal defined media, one with low Pi (0.

Increased glycopeptide production after overexpression of shikimate pathway genes being part of the balhimycin biosynthetic gene cluster.

Amycolatopsis balhimycina produces the vancomycin-analogue balhimycin. The strain therefore serves as a model strain for glycopeptide antibiotic production. Previous characterisation of the balhimycin biosynthetic cluster had shown that the border sequences contained both, a putative 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (dahp), and a prephenate dehydrogenase (pdh) gene.

Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina.

A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially and constitutively expressed protein isoforms, which were associated with 203 ORFs in the A. balhimycina genome.

Essential pathway identification: from in silico analysis to potential antifungal targets in Aspergillus fumigatus.

Computational metabolic flux modeling has been a great aid for both understanding and manipulating microbial metabolism. A previously developed metabolic flux model for Aspergillus niger, an economically important biotechnology fungus known for protein and organic acid production, is comprised of 1190 biochemically unique reactions that are associated with 871 open reading frames. Through a systematic in silico deletion of single metabolic reactions using this model, several essential metabolic pathways were identified for A.

Disruption of the NADPH-dependent glutamate dehydrogenase affects the morphology of two industrial strains of Penicillium chrysogenum.

New morphological aspects of Penicillium chrysogenum were found during physiological characterisation of two NADPH-dependent glutamate dehydrogenase mutant strains. A morphological characterisation of the previously constructed strains, together with the two beta-lactam producing industrial recipient strains, was conducted. The reference strains showed a compact structure with highly branched hyphal elements whereas the morphology of the DeltagdhA strains consisting of long elongated hyphal elements with few branches.

NADPH-dependent glutamate dehydrogenase in Penicillium chrysogenum is involved in regulation of beta-lactam production.

The interactions between the ammonium assimilatory pathways and beta-lactam production were investigated by disruption of the NADPH-dependent glutamate dehydrogenase gene (gdhA) in two industrial beta-lactam-producing strains of Penicillium chrysogenum. The strains used were an adipoyl-7-ADCA- and a penicillin-producing strain. The gdhA gene disruption caused a decrease in maximum specific growth rate of 26 % and 35 % for the adipoyl-7-ADCA-producing strain and the penicillin-producing strain, respectively, compared to the corresponding reference strains.

Metabolic engineering of beta-lactam production.

Metabolic engineering has become a rational alternative to classical strain improvement in optimisation of beta-lactam production. In metabolic engineering directed genetic modification are introduced to improve the cellular properties of the production strains. This has resulted in substantial increases in the existing beta-lactam production processes.

Metabolic network analysis of an adipoyl-7-ADCA-producing strain of Penicillium chrysogenum: elucidation of adipate degradation.

An adipoyl-7-ADCA-producing, recombinant strain of Penicillium chrysogenum was characterized by metabolic network analysis, with special focus on the degradation of adipate and determination of the metabolic fluxes. Degradation of the side-chain precursor, adipate, causes an undesired consumption of adipate in the production of 7-ADCA. Using (13)C-labeled glucose and measurement of metabolite labeling patterns, it was shown that adipate was degraded by beta-oxidation to succinyl-CoA and acetyl-CoA.