Dataset Information

Heterogeneous oxygen availability affects the titer and topology but not the fidelity of plasmid DNA produced by Escherichia coli.

ABSTRACT:

Background

Dissolved oxygen tension (DOT) is hardly constant and homogenously distributed in a bioreactor, which can have a negative impact in the metabolism and product synthesis. However, the effects of DOT on plasmid DNA (pDNA) production and quality have not been thoroughly investigated. In the present study, the effects of aerobic (DOT ?30% air sat.), microaerobic (constant DOT = 3% air sat.) and oscillatory DOT (from 0 to 100% air sat.) conditions on pDNA production, quality and host performance were characterized.

Results

Microaerobic conditions had little effect on pDNA production, supercoiled fraction and sequence fidelity. By contrast, oscillatory DOT caused a 22% decrease in pDNA production compared with aerobic cultures. Although in aerobic cultures the pDNA supercoiled fraction was 98%, it decreased to 80% under heterogeneous DOT conditions. The different oxygen availabilities had no effect on the fidelity of the produced pDNA. The estimated metabolic fluxes indicated substantial differences at the level of the pentose phosphate pathway and TCA cycle under different conditions. Cyclic changes in fermentative pathway fluxes, as well as fast shifts in the fluxes through cytochromes, were also estimated. Model-based genetic modifications that can potentially improve the process performance are suggested.

Conclusions

DOT heterogeneities strongly affected cell performance, pDNA production and topology. This should be considered when operating or scaling-up a bioreactor with deficient mixing. Constant microaerobic conditions affected the bacterial metabolism but not the amount or quality of pDNA. Therefore, pDNA production in microaerobic cultures may be an alternative for bioreactor operation at higher oxygen transfer rates.

SUBMITTER: Jaen KE

PROVIDER: S-EPMC5496438 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Heterogeneous oxygen availability affects the titer and topology but not the fidelity of plasmid DNA produced by Escherichia coli.

Jaén Karim E KE Sigala Juan-Carlos JC Olivares-Hernández Roberto R Niehaus Karsten K Lara Alvaro R AR

BMC biotechnology 20170704 1

<h4>Background</h4>Dissolved oxygen tension (DOT) is hardly constant and homogenously distributed in a bioreactor, which can have a negative impact in the metabolism and product synthesis. However, the effects of DOT on plasmid DNA (pDNA) production and quality have not been thoroughly investigated. In the present study, the effects of aerobic (DOT ≥30% air sat.), microaerobic (constant DOT = 3% air sat.) and oscillatory DOT (from 0 to 100% air sat.) conditions on pDNA production, quality and ho ...[more]

PMID: 28676110

Similar Datasets

Project description:When exploring the impact of resource availability on perennial plants, artificial treatments often apply conditions homogeneously across space and time, even though this rarely reflects conditions in natural systems. To investigate the effects of spatially heterogeneous soil moisture on morphological and physiological responses, trembling aspen (Populus tremuloides) saplings were used in a split-pot experiment. Following the division of the root systems, saplings were established for a full year and then subjected to either heterogeneous (portion of the root system exposed to non-lethal drought) or homogeneous (whole root system exposed to non-lethal drought or well-watered) treatments. Above- and belowground growth and non-structural carbohydrate (NSC) reserves (soluble sugars and starch) were measured to determine how allocation of reserves and mass between and within organs changed in response to variation in soil moisture availability. In contrast to saplings in the homogeneous drought treatment, which experienced reduced shoot growth, leaf abscission and fine root loss, saplings exposed to the heterogeneous conditions maintained similar aboveground growth and increased root system allocation compared to well-watered saplings. Interestingly under heterogeneous soil moisture conditions, the portion of the root system that was resource limited had no root dieback and increased carbon reserve concentrations, while the portion of the root system that was not resource limited added new roots (30% increase). Overall, saplings subjected to the heterogeneous soil moisture regime over-compensated belowground, both in mass and NSC reserves. These results indicate that the differential allocation of mass or reserves between above- and belowground organs, but also within the root system can occur. While the mechanisms and processes involved in these patterns are not clear, these responses could be interpreted as adaptations and acclimations to preserve the integrity of the entire sapling and suggests that different portions of plant organs might respond autonomously to local conditions. This study provides further appreciation of the complexity of the mechanisms by which plants manage heterogeneous conditions and offers evidence that spatial and temporal variability of resource availability, particularly belowground, needs to be accounted for when extrapolating and modeling stress responses at larger temporal and spatial scales.

Project description:G-quadruplexes (G4s), a type of non-B DNA, play important roles in a wide range of molecular processes, including replication, transcription, and translation. Genome integrity relies on efficient and accurate DNA synthesis, and is compromised by various stressors, to which non-B DNA structures such as G4s can be particularly vulnerable. However, the impact of G4 structures on DNA polymerase fidelity is largely unknown. Using an in vitro forward mutation assay, we investigated the fidelity of human DNA polymerases delta (δ4, four-subunit), eta (η), and kappa (κ) during synthesis of G4 motifs representing those in the human genome. The motifs differ in sequence, topology, and stability, features that may affect DNA polymerase errors. Polymerase error rate hierarchy (δ4 < κ < η) is largely maintained during G4 synthesis. Importantly, we observed unique polymerase error signatures during synthesis of VEGF G4 motifs, stable G4s which form parallel topologies. These statistically significant errors occurred within, immediately flanking, and encompassing the G4 motif. For pol δ4, the errors were deletions, insertions and complex errors within the G4 or encompassing the G4 motif and surrounding sequence. For pol η, the errors occurred in 3' sequences flanking the G4 motif. For pol κ, the errors were frameshift mutations within G-tracts of the G4. Because these error signatures were not observed during synthesis of an antiparallel G4 and, to a lesser extent, a hybrid G4, we suggest that G4 topology and/or stability could influence polymerase fidelity. Using in silico analyses, we show that most polymerase errors are predicted to have minimal effects on predicted G4 stability. Our results provide a unique view of G4s not previously elucidated, showing that G4 motif heterogeneity differentially influences polymerase fidelity within the motif and flanking sequences. Thus, our study advances the understanding of how DNA polymerase errors contribute to G4 mutagenesis.

Dataset Information

Heterogeneous oxygen availability affects the titer and topology but not the fidelity of plasmid DNA produced by Escherichia coli.

Background

Results

Conclusions

Publications

Heterogeneous oxygen availability affects the titer and topology but not the fidelity of plasmid DNA produced by Escherichia coli.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets