Kinoshita, S., Udaka, S. & Shimono, M. Studies on the amino acid fermentation. Part 1. Production of L-glutamic acid by various microorganisms. The Journal of General and Applied Microbiology 3, 193–205, https://doi.org/10.2323/jgam.3.193 (1957).
Eggeling, L. & Bott, M. A giant market and a powerful metabolism: L-lysine provided by Corynebacterium glutamicum. Appl Microbiol Biotechnol 99, 3387–3394, https://doi.org/10.1007/s00253-015-6508-2 (2015).
van Ooyen, J., Noack, S., Bott, M., Reth, A. & Eggeling, L. Improved L-lysine production with Corynebacterium glutamicum and systemic insight into citrate synthase flux and activity. Biotechnol Bioeng 109, 2070–2081, https://doi.org/10.1002/bit.24486 (2012).
Becker, J., Zelder, O., Häfner, S., Schröder, H. & Wittmann, C. From zero to hero – design-based systems metabolic engineering of Corynebacterium glutamicumfor L-lysine production. Metab Eng 13, 159–168, https://doi.org/10.1016/j.ymben.2011.01.003 (2011).
Jin, C. & Bao, J. Lysine Production by Dry Biorefining of Wheat Straw and Cofermentation of Corynebacterium glutamicum. J Agric Food Chem 69, 1900–1906, https://doi.org/10.1021/acs.jafc.0c07902 (2021).
Wendisch, V. F. Metabolic engineering advances and prospects for amino acid production. Metab Eng 58, 17–34, https://doi.org/10.1016/j.ymben.2019.03.008 (2020).
Vogt, M. et al. Pushing product formation to its limit: metabolic engineering of Corynebacterium glutamicum for L-leucine overproduction. Metab Eng 22, 40–52, https://doi.org/10.1016/j.ymben.2013.12.001 (2014).
Vogt, M. et al. The contest for precursors: channelling L-isoleucine synthesis in Corynebacterium glutamicum without byproduct formation. Appl Microbiol Biotechnol 99, 791–800, https://doi.org/10.1007/s00253-014-6109-5 (2015).
Mahr, R. et al. Biosensor-driven adaptive laboratory evolution of l-valine production in Corynebacterium glutamicum. Metab Eng 32, 184–194, https://doi.org/10.1016/j.ymben.2015.09.017 (2015).
Blombach, B., Arndt, A., Auchter, M. & Eikmanns, B. J. L-valine production during growth of pyruvate dehydrogenase complex-deficient Corynebacterium glutamicum in the presence of ethanol or by inactivation of the transcriptional regulator SugR. Appl Environ Microbiol 75, 1197–1200, https://doi.org/10.1128/AEM.02351-08 (2009).
Han, G. et al. Improvement of l-Valine Production by Atmospheric and Room Temperature Plasma Mutagenesis and High-Throughput Screening in Corynebacterium glutamicum. ACS Omega 5, 4751–4758, https://doi.org/10.1021/acsomega.9b02747 (2020).
Wiechert, J., Gätgens, C., Wirtz, A. & Frunzke, J. Inducible Expression Systems Based on Xenogeneic Silencing and Counter-Silencing and Design of a Metabolic Toggle Switch. ACS Synth Biol 9, 2023–2038, https://doi.org/10.1021/acssynbio.0c00111 (2020).
Jiang, Y., Sheng, Q., Wu, X. Y., Ye, B. C. & Zhang, B. l-arginine production in Corynebacterium glutamicum: manipulation and optimization of the metabolic process. Crit Rev Biotechnol 41, 172–185, https://doi.org/10.1080/07388551.2020.1844625 (2021).
Schwentner, A. et al. Modular systems metabolic engineering enables balancing of relevant pathways for l-histidine production with Corynebacterium glutamicum. Biotechnol Biofuels 12, 65, https://doi.org/10.1186/s13068-019-1410-2 (2019).
Kulis-Horn, R. K., Persicke, M. & Kalinowski, J. Corynebacterium glutamicum ATP-phosphoribosyl transferases suitable for L-histidine production–Strategies for the elimination of feedback inhibition. J Biotechnol 206, 26–37, https://doi.org/10.1016/j.jbiotec.2015.04.001 (2015).
Ikeda, M. & Nakagawa, S. The Corynebacterium glutamicum genome: features and impacts on biotechnological processes. Appl Microbiol Biotechnol 62, 99–109, https://doi.org/10.1007/s00253-003-1328-1 (2003).
Kalinowski, J. et al. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J Biotechnol 104, 5–25, https://doi.org/10.1016/s0168-1656(03)00154-8 (2003).
Wieschalka, S., Blombach, B., Bott, M. & Eikmanns, B. J. Bio-based production of organic acids with Corynebacterium glutamicum. Microb Biotechnol 6, 87–102, https://doi.org/10.1111/1751-7915.12013 (2013).
Kallscheuer, N. & Marienhagen, J. Corynebacterium glutamicum as platform for the production of hydroxybenzoic acids. Microb Cell Fact 17, 70, https://doi.org/10.1186/s12934-018-0923-x (2018).
Kogure, T., Suda, M., Hiraga, K. & Inui, M. Protocatechuate overproduction by Corynebacterium glutamicum via simultaneous engineering of native and heterologous biosynthetic pathways. Metab Eng 65, 232–242, https://doi.org/10.1016/j.ymben.2020.11.007 (2021).
Jojima, T. et al. Metabolic engineering for improved production of ethanol by Corynebacterium glutamicum. Appl Microbiol Biotechnol 99, 1165–1172, https://doi.org/10.1007/s00253-014-6223-4 (2015).
Hasegawa, S., Jojima, T., Suda, M. & Inui, M. Isobutanol production in Corynebacterium glutamicum: Suppressed succinate by-production by pckA inactivation and enhanced productivity via the Entner-Doudoroff pathway. Metab Eng 59, 24–35, https://doi.org/10.1016/j.ymben.2020.01.004 (2020).
Blombach, B. & Eikmanns, B. J. Current knowledge on isobutanol production with Escherichia coli, Bacillus subtilis and Corynebacterium glutamicum. Bioeng Bugs 2, 346–350, https://doi.org/10.4161/bbug.2.6.17845 (2011).
Vogt, M., Brüsseler, C., Ooyen, J. V., Bott, M. & Marienhagen, J. Production of 2-methyl-1-butanol and 3-methyl-1-butanol in engineered Corynebacterium glutamicum. Metab Eng 38, 436–445, https://doi.org/10.1016/j.ymben.2016.10.007 (2016).
Heider, S. A. & Wendisch, V. F. Engineering microbial cell factories: Metabolic engineering of Corynebacterium glutamicum with a focus on non-natural products. Biotechnol J 10, 1170–1184, https://doi.org/10.1002/biot.201400590 (2015).
Kallscheuer, N. et al. Construction of a Corynebacterium glutamicum platform strain for the production of stilbenes and (2S)-flavanones. Metab Eng 38, 47–55, https://doi.org/10.1016/j.ymben.2016.06.003 (2016).
Milke, L., Aschenbrenner, J., Marienhagen, J. & Kallscheuer, N. Production of plant-derived polyphenols in microorganisms: current state and perspectives. Appl Microbiol Biotechnol 102, 1575–1585, https://doi.org/10.1007/s00253-018-8747-5 (2018).
Wolf, S. et al. Advances in metabolic engineering of Corynebacterium glutamicum to produce high-value active ingredients for food, feed, human health, and well-being. Essays Biochem 65, 197–212, https://doi.org/10.1042/EBC20200134 (2021).
Freudl, R. Beyond amino acids: Use of the Corynebacterium glutamicum cell factory for the secretion of heterologous proteins. J Biotechnol 258, 101–109, https://doi.org/10.1016/j.jbiotec.2017.02.023 (2017).
Bakkes, P. J. et al. Improved pEKEx2-derived expression vectors for tightly controlled production of recombinant proteins in Corynebacterium glutamicum. Plasmid 112, 102540, https://doi.org/10.1016/j.plasmid.2020.102540 (2020).
Kirchner, O. & Tauch, A. Tools for genetic engineering in the amino acid-producing bacterium Corynebacterium glutamicum. J Biotechnol 104, 287–299, https://doi.org/10.1016/s0168-1656(03)00148-2 (2003).
Kortmann, M., Kuhl, V., Klaffl, S. & Bott, M. A chromosomally encoded T7 RNA polymerase-dependent gene expression system for Corynebacterium glutamicum: construction and comparative evaluation at the single-cell level. Microb Biotechnol 8, 253–265, https://doi.org/10.1111/1751-7915.12236 (2015).
Li, C., Swofford, C. A., Rückert, C. & Sinskey, A. J. Optimizing recombineering in Corynebacterium glutamicum. Biotechnol Bioeng, https://doi.org/10.1002/bit.27737 (2021).
Tenhaef, N., Stella, R., Frunzke, J. & Noack, S. Automated Rational Strain Construction Based on High-Throughput Conjugation. ACS Synth Biol https://doi.org/10.1021/acssynbio.0c00599 (2021).
Kjeldsen, K. R. & Nielsen, J. In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network. Biotechnol Bioeng 102, 583–597, https://doi.org/10.1002/bit.22067 (2009).
Brinkrolf, K., Brune, I. & Tauch, A. The transcriptional regulatory network of the amino acid producer Corynebacterium glutamicum. J Biotechnol 129, 191–211, https://doi.org/10.1016/j.jbiotec.2006.12.013 (2007).
Toyoda, K. & Inui, M. Regulons of global transcription factors in Corynebacterium glutamicum. Appl Microbiol Biotechnol 100, 45–60, https://doi.org/10.1007/s00253-015-7074-3 (2016).
Schröder, J. & Tauch, A. Transcriptional regulation of gene expression in Corynebacterium glutamicum: the role of global, master and local regulators in the modular and hierarchical gene regulatory network. FEMS Microbiol Rev 34, 685–737, https://doi.org/10.1111/j.1574-6976.2010.00228.x (2010).
Bott, M. & Brocker, M. Two-component signal transduction in Corynebacterium glutamicum and other corynebacteria: on the way towards stimuli and targets. Appl Microbiol Biotechnol 94, 1131–1150, https://doi.org/10.1007/s00253-012-4060-x (2012).
Pátek, M. & Nesvera, J. Sigma factors and promoters in Corynebacterium glutamicum. J Biotechnol 154, 101–113, https://doi.org/10.1016/j.jbiotec.2011.01.017 (2011).
Myers, K. S., Park, D. M., Beauchene, N. A. & Kiley, P. J. Defining bacterial regulons using ChIP-seq. Methods 86, 80–88, https://doi.org/10.1016/j.ymeth.2015.05.022 (2015).
Harada, R. & Nepveu, A. Chromatin affinity purification. Methods Mol Biol 809, 237–253, https://doi.org/10.1007/978-1-61779-376-9_16 (2012).
Parise, M. T. D. et al. CoryneRegNet 7, the reference database and analysis platform for corynebacterial gene regulatory networks. Sci Data 7, 142, https://doi.org/10.1038/s41597-020-0484-9 (2020).
Heyer, A. et al. The two-component system ChrSA is crucial for haem tolerance and interferes with HrrSA in haem-dependent gene regulation in Corynebacterium glutamicum. Microbiology (Reading) 158, 3020–3031, https://doi.org/10.1099/mic.0.062638-0 (2012).
Koçan, M. et al. Two-component systems of Corynebacterium glutamicum: deletion analysis and involvement of the PhoS-PhoR system in the phosphate starvation response. J Bacteriol 188, 724–732, https://doi.org/10.1128/JB.188.2.724-732.2006 (2006).
Keppel, M. et al. HrrSA orchestrates a systemic response to heme and determines prioritization of terminal cytochrome oxidase expression. Nucleic Acids Res 48, 6547–6562, https://doi.org/10.1093/nar/gkaa415 (2020).
Kleine, B. et al. The three-component system EsrISR regulates a cell envelope stress response in Corynebacterium glutamicum. Mol Microbiol 106, 719–741, https://doi.org/10.1111/mmi.13839 (2017).
Busche, T., Šilar, R., Pičmanová, M., Pátek, M. & Kalinowski, J. Transcriptional regulation of the operon encoding stress-responsive ECF sigma factor SigH and its anti-sigma factor RshA, and control of its regulatory network in Corynebacterium glutamicum. BMC Genomics 13, 445, https://doi.org/10.1186/1471-2164-13-445 (2012).
Taniguchi, H. et al. Physiological roles of sigma factor SigD in Corynebacterium glutamicum. BMC Microbiol 17, 158, https://doi.org/10.1186/s12866-017-1067-6 (2017).
Dostálová, H. et al. Overlap of Promoter Recognition Specificity of Stress Response Sigma Factors SigD and SigH in Corynebacterium glutamicum ATCC 13032. Front Microbiol 9, 3287, https://doi.org/10.3389/fmicb.2018.03287 (2018).
Baumbach, J., Brinkrolf, K., Czaja, L. F., Rahmann, S. & Tauch, A. CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics 7, 24, https://doi.org/10.1186/1471-2164-7-24 (2006).
Faith, J. J. et al. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5, e8, https://doi.org/10.1371/journal.pbio.0050008 (2007).
Yousef, M., Kumar, A. & Bakir-Gungor, B. Application of Biological Domain Knowledge Based Feature Selection on Gene Expression Data. Entropy (Basel) 23, https://doi.org/10.3390/e23010002 (2020).
Toro-Dominguez, D. et al. A survey of gene expression meta-analysis: methods and applications. Brief Bioinform https://doi.org/10.1093/bib/bbaa019 (2020).
Frawley, W. J., Piatetsky-Shapiro, G., & Matheus, C. J. Knowledge Discovery in Databases: An Overview. AI Magazine 13 (1992).
Polen, T. & Wendisch, V. F. Genomewide expression analysis in amino acid-producing bacteria using DNA microarrays. Appl Biochem Biotechnol 118, 215–232, https://doi.org/10.1385/abab:118:1-3:215 (2004).
Brazma, A. Minimum Information About a Microarray Experiment (MIAME)–successes, failures, challenges. ScientificWorldJournal 9, 420–423, https://doi.org/10.1100/tsw.2009.57 (2009).
Wilkinson, M. D. et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 3, 160018, https://doi.org/10.1038/sdata.2016.18 (2016).
Wilkinson, M. D. et al. Addendum: The FAIR Guiding Principles for scientific data management and stewardship. Sci Data 6, 6, https://doi.org/10.1038/s41597-019-0009-6 (2019).
Gao, B. & Gupta, R. S. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria. Microbiol Mol Biol Rev 76, 66–112, https://doi.org/10.1128/MMBR.05011-11 (2012).
Turkarslan, S. et al. A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. Sci Data 2, 150010, https://doi.org/10.1038/sdata.2015.10 (2015).
Schäfer, A. et al. Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145, 69–73, https://doi.org/10.1016/0378-1119(94)90324-7 (1994).
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6, 343–345, https://doi.org/10.1038/nmeth.1318 (2009).
Bertani, G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 62, 293–300, https://doi.org/10.1128/JB.62.3.293-300.1951 (1951).
Keilhauer, C., Eggeling, L. & Sahm, H. Isoleucine synthesis in Corynebacterium glutamicum: molecular analysis of the ilvB–ilvN–ilvC operon. J Bacteriol 175, 5595–5603, https://doi.org/10.1128/jb.175.17.5595-5603.1993 (1993).
van der Rest, M. E., Lange, C. & Molenaar, D. A heat shock following electroporation induces highly efficient transformation of Corynebacterium glutamicum with xenogeneic plasmid DNA. Appl Microbiol Biotechnol 52, 541–545, https://doi.org/10.1007/s002530051557 (1999).
Hemmerich, J. et al. Screening of a genome-reduced Corynebacterium glutamicum strain library for improved heterologous cutinase secretion. Microb Biotechnol 13, 2020–2031, https://doi.org/10.1111/1751-7915.13660 (2020).
Litsanov, B., Brocker, M. & Bott, M. Toward homosuccinate fermentation: metabolic engineering of Corynebacterium glutamicum for anaerobic production of succinate from glucose and formate. Appl Environ Microbiol 78, 3325–3337, https://doi.org/10.1128/AEM.07790-11 (2012).
Michel, A., Koch-Koerfges, A., Krumbach, K., Brocker, M. & Bott, M. Anaerobic growth of Corynebacterium glutamicum via mixed-acid fermentation. Appl Environ Microbiol 81, 7496–7508, https://doi.org/10.1128/AEM.02413-15 (2015).
Wendisch, V. F. et al. Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays. Anal Biochem 290, 205–213, https://doi.org/10.1006/abio.2000.4982 (2001).
Lange, C., Rittmann, D., Wendisch, V. F., Bott, M. & Sahm, H. Global expression profiling and physiological characterization of Corynebacterium glutamicum grown in the presence of L-valine. Appl Environ Microbiol 69, 2521–2532, https://doi.org/10.1128/aem.69.5.2521-2532.2003 (2003).
Frunzke, J., Engels, V., Hasenbein, S., Gätgens, C. & Bott, M. Co-ordinated regulation of gluconate catabolism and glucose uptake in Corynebacterium glutamicum by two functionally equivalent transcriptional regulators, GntR1 and GntR2. Mol Microbiol 67, 305–322, https://doi.org/10.1111/j.1365-2958.2007.06020.x (2008).
Polen, T., Krämer, M., Bongaerts, J., Wubbolts, M. & Wendisch, V. F. The global gene expression response of Escherichia coli to L-phenylalanine. J Biotechnol 115, 221–237, https://doi.org/10.1016/j.jbiotec.2004.08.017 (2005).
Kranz, A., Polen, T. & Bott, M. A compendium of expression profiles for Corynebacterium glutamicum ATCC13032. GEO https://identifiers.org/geo:GSE169361 (2022).
Kranz, A., Polen, T. & Bott, M. A compendium of expression profiles for Corynebacterium glutamicum. Zenodo. https://doi.org/10.5281/zenodo.6842664 (2022).
Baumgart, M. et al. Corynebacterium glutamicum Chassis C1*: Building and Testing a Novel Platform Host for Synthetic Biology and Industrial Biotechnology. ACS Synth Biol 7, 132–144, https://doi.org/10.1021/acssynbio.7b00261 (2018).
Frunzke, J., Bramkamp, M., Schweitzer, J. E. & Bott, M. Population Heterogeneity in Corynebacterium glutamicum ATCC 13032 caused by prophage CGP3. J Bacteriol 190, 5111–5119, https://doi.org/10.1128/JB.00310-08 (2008).
Jurischka, S. et al. A secretion biosensor for monitoring Sec-dependent protein export in Corynebacterium glutamicum. Microb Cell Fact 19, 11, https://doi.org/10.1186/s12934-019-1273-z (2020).
van Dam, S., Võsa, U., van der Graaf, A., Franke, L. & de Magalhães, J. P. Gene co-expression analysis for functional classification and gene-disease predictions. Brief Bioinform 19, 575–592, https://doi.org/10.1093/bib/bbw139 (2018).
Parise, D. et al. On the Consistency between Gene Expression and the Gene Regulatory Network of Corynebacterium glutamicum. Netw Syst Med 4, 51–59, https://doi.org/10.1089/nsm.2020.0014 (2021).
Molina Mora, J. A. et al. A first perturbome of Pseudomonas aeruginosa: Identification of core genes related to multiple perturbations by a machine learning approach. Biosystems 205, 104411, https://doi.org/10.1016/j.biosystems.2021.104411 (2021).

