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

Abstract

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.

Transcriptome analysis of Corynebacterium glutamicum in the process of recombinant protein expression in bioreactors

“…The harvesting of total RNA and the RNA-Seq protocol were described previously [19]. The clean reads were exported in the FASTQ format and were deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) with the accession numbers GSE77502/GSE87077.…”

“…After the alignment results passed QC, downstream analysis was performed, including gene expression level analysis, differential expression analysis, pathway enrichment analysis, and gene ontology (GO) enrichment analysis. RPKM (reads per kb per million reads) was used for the gene expression level calculation [19, 21, 22]. …”

“…MVDA was carried out by SIMCA-P 14(MKS UmetricsAB, Sweden) as the method described previously [19, 23]. …”

Application of fermentation process control to increase l‐tryptophan production in Escherichia coli

“…By massive parallel sequencing of short DNA sequences, the abundance of mRNA molecules can be estimated in a sample, with identification of precise nucleotide sequences . The transcriptome and multivariable data analysis of Corynebacterium glutamicum fermented under different DO conditions revealed large effects of DO levels on energy metabolism and cellular redox balance . Deep sequencing identified genes and pathways that changed under different DO conditions to provide a comprehensive view of the C. glutamicum metabolism .…”

“…The transcriptome and multivariable data analysis of Corynebacterium glutamicum fermented under different DO conditions revealed large effects of DO levels on energy metabolism and cellular redox balance . Deep sequencing identified genes and pathways that changed under different DO conditions to provide a comprehensive view of the C. glutamicum metabolism . In addition, as for E. coli , the transcriptional levels of the genes ( pck A and pps A, respectively) encoding phosphoenolpyruvate (PEP) carboxykinase and PEP synthase are higher at high DO level, and this contributes to an increased PEP supply and biosynthesis of aromatic compounds …”