Comparative Transcriptome Analysis of Bacillus subtilis Responding to Dissolved Oxygen in Adenosine Fermentation

Yu, Wen-Bang; Gao, Shuhong; Yin, Chun-Yun; Zhou, Ying; Ye, Bang‐Ce

doi:10.1371/journal.pone.0020092

Cited by 21 publications

(11 citation statements)

References 61 publications

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“…Dissolved oxygen (DO) is an important factor that significantly influences metabolism, biomass synthesis, electron transport, ATP availability, peptide folding, and product yield of C . glutamicum when it expresses recombinant protein in a bioreactor [1, 14, 15], however, due to the complexity of the relationship between oxygen supplementation and fermentation production, increasing the DO level does not guarantee increased yield [15]. Zupke et al used quantitative estimates of intracellular flux to evaluate the effect of different DO concentrations on hybridoma cells in batch culture [16], and the result showed that physiological processes could be controlled through modulation of the DO level.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome and Multivariable Data Analysis of Corynebacterium glutamicum under Different Dissolved Oxygen Conditions in Bioreactors

et al. 2016

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Dissolved oxygen (DO) is an important factor in the fermentation process of Corynebacterium glutamicum, which is a widely used aerobic microbe in bio-industry. Herein, we described RNA-seq for C. glutamicum under different DO levels (50%, 30% and 0%) in 5 L bioreactors. Multivariate data analysis (MVDA) models were used to analyze the RNA-seq and metabolism data to investigate the global effect of DO on the transcriptional distinction of the substance and energy metabolism of C. glutamicum. The results showed that there were 39 and 236 differentially expressed genes (DEGs) under the 50% and 0% DO conditions, respectively, compared to the 30% DO condition. Key genes and pathways affected by DO were analyzed, and the result of the MVDA and RNA-seq revealed that different DO levels in the fermenter had large effects on the substance and energy metabolism and cellular redox balance of C. glutamicum. At low DO, the glycolysis pathway was up-regulated, and TCA was shunted by the up-regulation of the glyoxylate pathway and over-production of amino acids, including valine, cysteine and arginine. Due to the lack of electron-acceptor oxygen, 7 genes related to the electron transfer chain were changed, causing changes in the intracellular ATP content at 0% and 30% DO. The metabolic flux was changed to rebalance the cellular redox. This study applied deep sequencing to identify a wealth of genes and pathways that changed under different DO conditions and provided an overall comprehensive view of the metabolism of C. glutamicum. The results provide potential ways to improve the oxygen tolerance of C. glutamicum and to modify the metabolic flux for amino acid production and heterologous protein expression.

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Section: Introductionmentioning

confidence: 99%

Transcriptome and Multivariable Data Analysis of Corynebacterium glutamicum under Different Dissolved Oxygen Conditions in Bioreactors

et al. 2016

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“…The pfkA , pgk , and pykF genes, encoding the three rate‐limiting glycolytic enzymes phosphofructokinase, phosphoglycerate kinase, and pyruvate kinase, were up‐regulated by 3.5‐, 5.0‐, and 4.1‐fold, respectively. These changes clearly reflect increased ATP synthesis through substrate‐level phosphorylation and the increased production of precursors for biomass synthesis (Jouhten et al, 2008; Peng and Shimizu, 2003; Yu et al, 2011).…”

Section: Resultsmentioning

confidence: 99%

Balancing redox cofactor generation and ATP synthesis: Key microaerobic responses in thermophilic fermentations

Loftie-Eaton

Taylor

Horne

et al. 2012

Biotech & Bioengineering

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ABSTRACT:Geobacillus thermoglucosidasius is a Gram-positive, thermophilic bacterium capable of ethanologenic fermentation of both C5 and C6 sugars and may have possible use for commercial bioethanol production [Tang et al., 2009;Taylor et al. (2009) Trends Biotechnol 27(7): 398-405]. Little is known about the physiological changes that accompany a switch from aerobic (high redox) to microaerobic/fermentative (low redox) conditions in thermophilic organisms. The changes in the central metabolic pathways in response to a switch in redox potential were analyzed using quantitative real-time PCR and proteomics. During low redox (fermentative) states, results indicated that glycolysis was uniformly up-regulated, the Krebs (tricarboxylic acid or TCA) cycle nonuniformly down-regulated and that there was little to no change in the pentose phosphate pathway. Acetate accumulation was accounted for by strong down-regulation of the acetate CoA ligase gene (acs) in addition to up-regulation of the pta and ackA genes (involved in acetate production), thus conserving ATP while reducing flux through the TCA cycle. Substitution of an NADH dehydrogenase (down-regulated) by an up-regulated NADH:FAD oxidoreductase and up-regulation of an ATP synthase subunit, alongside the observed shifts in the TCA cycle, suggested that an oxygen-scavenging electron transport chain likely remained active during low redox conditions. Together with the observed up-regulation of a glyoxalase and down-regulation of superoxide dismutase, thought to provide protection against the accumulation of toxic phosphorylated glycolytic intermediates and reactive oxygen species, respectively, the changes observed in G. thermoglucosidasius NCIMB 11955 under conditions of aerobic-to-microaerobic switching were consistent with responses to low pO 2 stress.

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“…We believe that the reduced precision rate of the expanded model is mostly an artifact resulted from the fact that the pathway models in MetaCyc are far from being complete. For example, we found that the following items are relevant with the target pathways but are not in MetaCyc, such as HemY (BSU10140) that is a peripheral membrane protein essential for protoheme IX synthesis [30] and may be related with the heme biosynthesis from uroporphyrinogen-III pathway in Table 1, ThiF (BSU11700) that is a thiamine biosynthesis protein [31] and may be related with the thiamin biosynthesis I pathway, and HisH (BSU34890), an imidazole glycerol phosphate synthase and HisZ (BSU34930) a histidyl-tRNA synthetase, both of which are involved in the histidine biosynthesis [32] and may be related with the histidine biosynthesis pathway, suggesting that CINPER could effectively recruit additional relevant genes into the target pathways, for which the additional experimental validation is needed.…”

Section: Resultsmentioning

confidence: 99%

CINPER: An Interactive Web System for Pathway Prediction for Prokaryotes

Mao

Chen²,

Zhang³

et al. 2012

PLoS ONE

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We present a web-based network-construction system, CINPER (CSBL INteractive Pathway BuildER), to assist a user to build a user-specified gene network for a prokaryotic organism in an intuitive manner. CINPER builds a network model based on different types of information provided by the user and stored in the system. CINPER’s prediction process has four steps: (i) collection of template networks based on (partially) known pathways of related organism(s) from the SEED or BioCyc database and the published literature; (ii) construction of an initial network model based on the template networks using the P-Map program; (iii) expansion of the initial model, based on the association information derived from operons, protein-protein interactions, co-expression modules and phylogenetic profiles; and (iv) computational validation of the predicted models based on gene expression data. To facilitate easy applications, CINPER provides an interactive visualization environment for a user to enter, search and edit relevant data and for the system to display (partial) results and prompt for additional data. Evaluation of CINPER on 17 well-studied pathways in the MetaCyc database shows that the program achieves an average recall rate of 76% and an average precision rate of 90% on the initial models; and a higher average recall rate at 87% and an average precision rate at 28% on the final models. The reduced precision rate in the final models versus the initial models reflects the reality that the final models have large numbers of novel genes that have no experimental evidences and hence are not yet collected in the MetaCyc database. To demonstrate the usefulness of this server, we have predicted an iron homeostasis gene network of Synechocystis sp. PCC6803 using the server. The predicted models along with the server can be accessed at http://csbl.bmb.uga.edu/cinper/.

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Comparative Transcriptome Analysis of Bacillus subtilis Responding to Dissolved Oxygen in Adenosine Fermentation

Cited by 21 publications

References 61 publications

Transcriptome and Multivariable Data Analysis of Corynebacterium glutamicum under Different Dissolved Oxygen Conditions in Bioreactors

Transcriptome and Multivariable Data Analysis of Corynebacterium glutamicum under Different Dissolved Oxygen Conditions in Bioreactors

Balancing redox cofactor generation and ATP synthesis: Key microaerobic responses in thermophilic fermentations

CINPER: An Interactive Web System for Pathway Prediction for Prokaryotes

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