A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum

Abstract

Corynebacterium glutamicum is the major host for the industrial production of amino acids and has become one of the best studied model organisms in microbial biotechnology. Rational strain construction has led to an improvement of producer strains and to a variety of novel producer strains with a broad substrate and product spectrum. A key factor for the success of these approaches is detailed knowledge of transcriptional regulation in C. glutamicum. Here, we present a large compendium of 927 manually curated microarray-based transcriptional profiles for wild-type and engineered strains detecting genome-wide expression changes of the 3,047 annotated genes in response to various environmental conditions or in response to genetic modifications. The replicates within the 927 experiments were combined to 304 microarray sets ordered into six categories that were used for differential gene expression analysis. Hierarchical clustering confirmed that no outliers were present in the sets. The compendium provides a valuable resource for future fundamental and applied research with C. glutamicum and contributes to a systemic understanding of this microbial cell factory. Measurement(s) Gene Expression Analysis Technology Type(s) Two Color Microarray Factor Type(s) WT condition A vs. WT condition B • Plasmid-based gene overexpression in parental strain vs. parental strain with empty vector control • Deletion mutant vs. parental strain Sample Characteristic - Organism Corynebacterium glutamicum Sample Characteristic - Environment laboratory environment Sample Characteristic - Location Germany

Beyond rational—biosensor-guided isolation of 100 independently evolved bacterial strain variants and comparative analysis of their genomes

“…S10). Even though its position and cps itself are highly conserved in many Corynebacterium species, we could not find any significant regulation of this gene in the compendium of 927 microarray-based transcriptional profiles available for C. glutamicum ATCC 13032 [ 56 ]. However, modulation of the putative NRPS activity may also benefit l -histidine production by an alteration of the cell wall composition.…”

“…Located upstream is mutT , potentially involved in DNA repair, and in close proximity a N -acetylmuramoyl- l -alanine amidase encoding gene, which is involved in cell wall synthesis (ERGO systems biology informatics toolkit, Igenbio Inc., Chicago, IL, USA). In the compendium of expression profile data, we found no significant regulation of this gene [ 56 ]. According to the AlphaFold structure prediction, the identified NCgl2981 -D735G substitution is located in a loop on the protein surface close to a C-terminal transmembrane helix (Additional file 1 : Fig.…”

Biosynthesis of Apigenin Glucosides in Engineered Corynebacterium glutamicum

“…The Gram-positive, facultatively anaerobic, non-sporulating soil bacteria, C. glutamicum , has been a major producer of amino acids such as L-glutamate and L-leucine ever since its discovery in the late 1950s in Japan [ 25 , 26 ]. Due to its status as GRAS (generally regarded as safe) bacteria, C. glutamicum has been preferred for the large-scale fermentation of valuable compounds such as hyaluronic acid, glutathione, and amino acids for the pharmaceutical, cosmetic, and food industries [ 27 , 28 ].…”

“…Due to its status as GRAS (generally regarded as safe) bacteria, C. glutamicum has been preferred for the large-scale fermentation of valuable compounds such as hyaluronic acid, glutathione, and amino acids for the pharmaceutical, cosmetic, and food industries [ 27 , 28 ]. Additionally, the product spectrum of C. glutamicum has greatly increased to include biofuels such as ethanol, carotenoids, muconic acid, and isobutanol [ 25 , 29 - 33 ]. On top of the numerous advantages, C. glutamicum has been successful in white biotechnology due to its ease of cultivation, high substrate susceptibility, its ability to use different sugars as carbon sources, and the availability of strategies for metabolic engineering [ 34 , 35 ].…”

Biosynthesis of apigenin glucosides in engineered Corynebacterium glutamicum

“…The Gram-positive, facultatively anaerobic, non-sporulating soil bacteria, C. glutamicum, has been a major producer of amino acids such as L-glutamate and L-leucine ever since its discovery in the late 1950s in Japan [25,26]. Due to its status as GRAS (generally regarded as safe) bacteria, C. glutamicum has been preferred for the large-scale fermentation of valuable compounds such as hyaluronic acid, glutathione and amino acids for the pharmaceutical, cosmetic and food industries [27,28].…”