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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.

SUBMITTER: Kranz A

PROVIDER: S-EPMC9526701 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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

Kranz Angela A Polen Tino T Kotulla Christian C Arndt Annette A Bosco Graziella G Bussmann Michael M Chattopadhyay Ava A Cramer Annette A Davoudi Cedric-Farhad CF Degner Ursula U Diesveld Ramon R Freiherr von Boeselager Raphael R Gärtner Kim K Gätgens Cornelia C Georgi Tobias T Geraths Christian C Haas Sabine S Heyer Antonia A Hünnefeld Max M Ishige Takeru T Kabus Armin A Kallscheuer Nicolai N Kever Larissa L Klaffl Simon S Kleine Britta B Kočan Martina M Koch-Koerfges Abigail A Kraxner Kim J KJ Krug Andreas A Krüger Aileen A Küberl Andreas A Labib Mohamed M Lange Christian C Mack Christina C Maeda Tomoya T Mahr Regina R Majda Stephan S Michel Andrea A Morosov Xenia X Müller Olga O Nanda Arun M AM Nickel Jens J Pahlke Jennifer J Pfeifer Eugen E Platzen Laura L Ramp Paul P Rittmann Doris D Schaffer Steffen S Scheele Sandra S Spelberg Stephanie S Schulte Julia J Schweitzer Jens-Eric JE Sindelar Georg G Sorger-Herrmann Ulrike U Spelberg Markus M Stansen Corinna C Tharmasothirajan Apilaasha A Ooyen Jan van JV van Summeren-Wesenhagen Philana P Vogt Michael M Witthoff Sabrina S Zhu Lingfeng L Eikmanns Bernhard J BJ Oldiges Marco M Schaumann Georg G Baumgart Meike M Brocker Melanie M Eggeling Lothar L Freudl Roland R Frunzke Julia J Marienhagen Jan J Wendisch Volker F VF Bott Michael M

Scientific data 20221001 1

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 ma ...[more]

PMID: 36182956

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Project description:BackgroundThe nitrogen containing aromatic compound indole is known for its floral odor typical of jasmine blossoms. Due to its characteristic scent, it is frequently used in dairy products, tea drinks and fine fragrances. The demand for natural indole by the flavor and fragrance industry is high, yet, its abundance in essential oils isolated from plants such as jasmine and narcissus is low. Thus, there is a strong demand for a sustainable method to produce food-grade indole.ResultsHere, we established the biotechnological production of indole upon L-tryptophan supplementation in the bacterial host Corynebacterium glutamicum. Heterologous expression of the tryptophanase gene from E. coli enabled the conversion of supplemented L-tryptophan to indole. Engineering of the substrate import by co-expression of the native aromatic amino acid permease gene aroP increased whole-cell biotransformation of L-tryptophan to indole by two-fold. Indole production to 0.2 g L-1 was achieved upon feeding of 1 g L-1 L-tryptophan in a bioreactor cultivation, while neither accumulation of side-products nor loss of indole were observed. To establish an efficient and robust production process, new tryptophanases were recruited by mining of bacterial sequence databases. This search retrieved more than 400 candidates and, upon screening of tryptophanase activity, nine new enzymes were identified as most promising. The highest production of indole in vivo in C. glutamicum was achieved based on the tryptophanase from Providencia rettgeri. Evaluation of several biological aspects identified the product toxicity as major bottleneck of this conversion. In situ product recovery was applied to sequester indole in a food-grade organic phase during the fermentation to avoid inhibition due to product accumulation. This process enabled complete conversion of L-tryptophan and an indole product titer of 5.7 g L-1 was reached. Indole partitioned to the organic phase which contained 28 g L-1 indole while no other products were observed indicating high indole purity.ConclusionsThe bioconversion production process established in this study provides an attractive route for sustainable indole production from tryptophan in C. glutamicum. Industrially relevant indole titers were achieved within 24 h and indole was concentrated in the organic layer as a pure product after the fermentation.

Project description:MotivationThe interactions among various types of cells play critical roles in cell functions and the maintenance of the entire organism. While cell-cell interactions are traditionally revealed from experimental studies, recent developments in single-cell technologies combined with data mining methods have enabled computational prediction of cell-cell interactions, which have broadened our understanding of how cells work together, and have important implications in therapeutic interventions targeting cell-cell interactions for cancers and other diseases. Despite the importance, to our knowledge, there is no database for systematic documentation of high-quality cell-cell interactions at the cell type level, which hinders the development of computational approaches to identify cell-cell interactions.ResultsWe develop a publicly accessible database, CITEdb (Cell-cell InTEraction database, https://citedb.cn/), which not only facilitates interactive exploration of cell-cell interactions in specific physiological contexts (e.g. a disease or an organ) but also provides a benchmark dataset to interpret and evaluate computationally derived cell-cell interactions from different tools. CITEdb contains 728 pairs of cell-cell interactions in human that are manually curated. Each interaction is equipped with structured annotations including the physiological context, the ligand-receptor pairs that mediate the interaction, etc. Our database provides a web interface to search, visualize and download cell-cell interactions. Users can search for cell-cell interactions by selecting the physiological context of interest or specific cell types involved. CITEdb is the first attempt to catalogue cell-cell interactions at the cell type level, which is beneficial to both experimental, computational and clinical studies of cell-cell interactions.Availability and implementationCITEdb is freely available at https://citedb.cn/ and the R package implementing benchmark is available at https://github.com/shanny01/benchmark.Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

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

Publications

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

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