Identifying the Growth Modulon of Corynebacterium glutamicum

Haas T, Graf M, Niess A, Busche T, Kalinowski J, Blombach B, Takors R (2019)
FRONTIERS IN MICROBIOLOGY 10: 974.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Autor*in
Haas, Thorsten; Graf, Michaels; Niess, Alexander; Busche, TobiasUniBi; Kalinowski, JörnUniBi; Blombach, Bastian; Takors, Ralf
Abstract / Bemerkung
The growth rate (mu) of industrially relevant microbes, such as Corynebacterium glutamicum, is a fundamental property that indicates its production capacity. Therefore, understanding the mechanism underlying the growth rate is imperative for improving productivity and performance through metabolic engineering. Despite recent progress in the understanding of global regulatory interactions, knowledge of mechanisms directing cell growth remains fragmented and incomplete. The current study investigated RNA-Seq data of three growth rate transitions, induced by different pre-culture conditions, in order to identify transcriptomic changes corresponding to increasing growth rates. These transitions took place in minimal medium and ranged from 0.02 to 0.4 h(-1) mu. This study enabled the identification of 447 genes as components of the growth modulon. Enrichment of genes within the growth modulon revealed 10 regulons exhibiting a significant effect over growth rate transition. In summary, central metabolism was observed to be regulated by a combination of metabolic and transcriptional activities orchestrating control over glycolysis, pentose phosphate pathway, and the tricarboxylic acid cycle. Additionally, major responses to changes in the growth rate were linked to iron uptake and carbon metabolism. In particular, genes encoding glycolytic enzymes and the glucose uptake system showed a positive correlation with the growth rate.
Stichworte
Corynebacterium glutamicum; growth rate; growth modulon; transcript; analysis; gene regulatory network; growth rate transition
Erscheinungsjahr
2019
Zeitschriftentitel
FRONTIERS IN MICROBIOLOGY
Band
10
Art.-Nr.
974
ISSN
1664-302x
eISSN
1664-302X
Page URI
https://pub.uni-bielefeld.de/record/2935870

Zitieren

Haas T, Graf M, Niess A, et al. Identifying the Growth Modulon of Corynebacterium glutamicum. FRONTIERS IN MICROBIOLOGY. 2019;10: 974.
Haas, T., Graf, M., Niess, A., Busche, T., Kalinowski, J., Blombach, B., & Takors, R. (2019). Identifying the Growth Modulon of Corynebacterium glutamicum. FRONTIERS IN MICROBIOLOGY, 10, 974. doi:10.3389/fmicb.2019.00974
Haas, T., Graf, M., Niess, A., Busche, T., Kalinowski, J., Blombach, B., and Takors, R. (2019). Identifying the Growth Modulon of Corynebacterium glutamicum. FRONTIERS IN MICROBIOLOGY 10:974.
Haas, T., et al., 2019. Identifying the Growth Modulon of Corynebacterium glutamicum. FRONTIERS IN MICROBIOLOGY, 10: 974.
T. Haas, et al., “Identifying the Growth Modulon of Corynebacterium glutamicum”, FRONTIERS IN MICROBIOLOGY, vol. 10, 2019, : 974.
Haas, T., Graf, M., Niess, A., Busche, T., Kalinowski, J., Blombach, B., Takors, R.: Identifying the Growth Modulon of Corynebacterium glutamicum. FRONTIERS IN MICROBIOLOGY. 10, : 974 (2019).
Haas, Thorsten, Graf, Michaels, Niess, Alexander, Busche, Tobias, Kalinowski, Jörn, Blombach, Bastian, and Takors, Ralf. “Identifying the Growth Modulon of Corynebacterium glutamicum”. FRONTIERS IN MICROBIOLOGY 10 (2019): 974.

66 References

Daten bereitgestellt von Europe PubMed Central.

RamA and RamB are global transcriptional regulators in Corynebacterium glutamicum and control genes for enzymes of the central metabolism.
Auchter M, Cramer A, Huser A, Ruckert C, Emer D, Schwarz P, Arndt A, Lange C, Kalinowski J, Wendisch VF, Eikmanns BJ., J. Biotechnol. 154(2-3), 2010
PMID: 20620178
Metabolic flux engineering of L-lysine production in Corynebacterium glutamicum--over expression and modification of G6P dehydrogenase.
Becker J, Klopprogge C, Herold A, Zelder O, Bolten CJ, Wittmann C., J. Biotechnol. 132(2), 2007
PMID: 17624457
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404
Enhanced H2 Production and Redirected Metabolic Flux via Overexpression of fhlA and pncB in Klebsiella HQ-3 Strain.
Jawed M, Pi J, Xu L, Zhang H, Hakeem A, Yan Y., Appl. Biochem. Biotechnol. 178(6), 2015
PMID: 26590848
Modification of histidine biosynthesis pathway genes and the impact on production of L-histidine in Corynebacterium glutamicum.
Cheng Y, Zhou Y, Yang L, Zhang C, Xu Q, Xie X, Chen N., Biotechnol. Lett. 35(5), 2013
PMID: 23355034
Reserve Flux Capacity in the Pentose Phosphate Pathway Enables Escherichia coli's Rapid Response to Oxidative Stress.
Christodoulou D, Link H, Fuhrer T, Kochanowski K, Gerosa L, Sauer U., Cell Syst 6(5), 2018
PMID: 29753645
Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth.
Dai X, Zhu M, Warren M, Balakrishnan R, Patsalo V, Okano H, Williamson JR, Fredrick K, Wang YP, Hwa T., Nat Microbiol 2(), 2016
PMID: 27941827
Siderophore-mediated iron transport in Bacillus subtilis and Corynebacterium glutamicum.
Dertz EA, Stintzi A, Raymond KN., J. Biol. Inorg. Chem. 11(8), 2006
PMID: 16912897
Adaptive laboratory evolution -- principles and applications for biotechnology.
Dragosits M, Mattanovich D., Microb. Cell Fact. 12(), 2013
PMID: 23815749
Group 2 sigma factor SigB of Corynebacterium glutamicum positively regulates glucose metabolism under conditions of oxygen deprivation.
Ehira S, Shirai T, Teramoto H, Inui M, Yukawa H., Appl. Environ. Microbiol. 74(16), 2008
PMID: 18567683
rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli.
Gourse RL, Gaal T, Bartlett MS, Appleman JA, Ross W., Annu. Rev. Microbiol. 50(), 1996
PMID: 8905094
Beyond growth rate 0.6: Corynebacterium glutamicum cultivated in highly diluted environments.
Grunberger A, van Ooyen J, Paczia N, Rohe P, Schiendzielorz G, Eggeling L, Wiechert W, Kohlheyer D, Noack S., Biotechnol. Bioeng. 110(1), 2012
PMID: 22890752
Engineering of Corynebacterium glutamicum for growth and production of L-ornithine, L-lysine, and lycopene from hexuronic acids.
Hadiati A., Krahn I., Lindner S., Wendisch V.., 2014
Expression of Corynebacterium glutamicum glycolytic genes varies with carbon source and growth phase.
Han SO, Inui M, Yukawa H., Microbiology (Reading, Engl.) 153(Pt 7), 2007
PMID: 17600063
Industrial production of amino acids by coryneform bacteria.
Hermann T., J. Biotechnol. 104(1-3), 2003
PMID: 12948636
ReadXplorer 2-detailed read mapping analysis and visualization from one single source.
Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A., Bioinformatics 32(24), 2016
PMID: 27540267
Reengineering of a Corynebacterium glutamicum L-arginine and L-citrulline producer.
Ikeda M, Mitsuhashi S, Tanaka K, Hayashi M., Appl. Environ. Microbiol. 75(6), 2009
PMID: 19139237
The Corynebacterium glutamicum genome: features and impacts on biotechnological processes.
Ikeda M, Nakagawa S., Appl. Microbiol. Biotechnol. 62(2-3), 2003
PMID: 12743753
The phosphate starvation stimulon of Corynebacterium glutamicum determined by DNA microarray analyses.
Ishige T, Krause M, Bott M, Wendisch VF, Sahm H., J. Bacteriol. 185(15), 2003
PMID: 12867461
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
Studies on the amino acid fermentation. Part 1. Production of L-glutamic acid by various microorganisms.
Kinoshita S, Udaka S, Shimono M., J. Gen. Appl. Microbiol. 50(6), 2004
PMID: 15965888
Histidine biosynthesis, its regulation and biotechnological application in Corynebacterium glutamicum.
Kulis-Horn RK, Persicke M, Kalinowski J., Microb Biotechnol 7(1), 2013
PMID: 23617600
The Actinobacterium Corynebacterium glutamicum, an Industrial Workhorse.
Lee JY, Na YA, Kim E, Lee HS, Kim P., J. Microbiol. Biotechnol. 26(5), 2016
PMID: 26838341
Requirement of chelating compounds for the growth of Corynebacterium glutamicum in synthetic media.
Liebl W., Klamer R., Schleifer K.., 1989
Expression of recombinant protein using Corynebacterium Glutamicum: progress, challenges and applications.
Liu X, Yang Y, Zhang W, Sun Y, Peng F, Jeffrey L, Harvey L, McNeil B, Bai Z., Crit. Rev. Biotechnol. 36(4), 2015
PMID: 25714007
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Love MI, Huber W, Anders S., Genome Biol. 15(12), 2014
PMID: 25516281
Roles of export genes cgmA and lysE for the production of L-arginine and L-citrulline by Corynebacterium glutamicum.
Lubitz D, Jorge JM, Perez-Garcia F, Taniguchi H, Wendisch VF., Appl. Microbiol. Biotechnol. 100(19), 2016
PMID: 27350619
Promoter activity dynamics in the lag phase of Escherichia coli.
Madar D, Dekel E, Bren A, Zimmer A, Porat Z, Alon U., BMC Syst Biol 7(), 2013
PMID: 24378036
Regulation of ribosome biosynthesis in Escherichia coli and saccharomyces cerevisiae: diversity and common GUEST COMMENTARY regulation of ribosome biosynthesis in Escherichia coli and Saccharomyces cerevisiae: diversity and common principles.
Nomura M.., 2014
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.
Nueda MJ, Tarazona S, Conesa A., Bioinformatics 30(18), 2014
PMID: 24894503
Application of metabolic engineering for the biotechnological production of L-valine.
Oldiges M, Eikmanns BJ, Blombach B., Appl. Microbiol. Biotechnol. 98(13), 2014
PMID: 24816722
Sigma factors and promoters in Corynebacterium glutamicum.
Patek M, Nesvera J., J. Biotechnol. 154(2-3), 2011
PMID: 21277915
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.
Pauling J, Rottger R, Tauch A, Azevedo V, Baumbach J., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22080556
Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique.
Pfeifer-Sancar K, Mentz A, Ruckert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24341750
Effect of pyruvate kinase overproduction on glucose metabolism of Lactococcus lactis.
Ramos A, Neves AR, Ventura R, Maycock C, Lopez P, Santos H., Microbiology (Reading, Engl.) 150(Pt 4), 2004
PMID: 15073320
Causes and consequences of DNA repair activity modulation during stationary phase in Escherichia coli.
Saint-Ruf C, Pesut J, Sopta M, Matic I., Crit. Rev. Biochem. Mol. Biol. 42(4), 2007
PMID: 17687668
Stress and survival of aging Escherichia coli rpoS colonies.
Saint-Ruf C, Taddei F, Matic I., Genetics 168(1), 2004
PMID: 15454563

Sambrook J.., 2001
Dynamics of the Escherichia coli proteome in response to nitrogen starvation and entry into the stationary phase.
Sanchuki HB, Gravina F, Rodrigues TE, Gerhardt EC, Pedrosa FO, Souza EM, Raittz RT, Valdameri G, de Souza GA, Huergo LF., Biochim Biophys Acta Proteins Proteom 1865(3), 2016
PMID: 27939605
The RamA regulon: complex regulatory interactions in relation to central metabolism in Corynebacterium glutamicum.
Shah A, Blombach B, Gauttam R, Eikmanns BJ., Appl. Microbiol. Biotechnol. 102(14), 2018
PMID: 29804137
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T., Genome Res. 13(11), 2003
PMID: 14597658
DNA microarray analysis of the nitrogen starvation response of Corynebacterium glutamicum.
Silberbach M, Huser A, Kalinowski J, Puhler A, Walter B, Kramer R, Burkovski A., J. Biotechnol. 119(4), 2005
PMID: 15935503
Phosphoglycerate mutase is a highly efficient enzyme without flux control in Lactococcus lactis.
Solem C, Petranovic D, Koebmann B, Mijakovic I, Jensen PR., J. Mol. Microbiol. Biotechnol. 18(3), 2010
PMID: 20530968
Engineering of Corynebacterium glutamicum with an NADPH-generating glycolytic pathway for L-lysine production.
Takeno S, Murata R, Kobayashi R, Mitsuhashi S, Ikeda M., Appl. Environ. Microbiol. 76(21), 2010
PMID: 20851994
Iron and oxidative stress in bacteria.
Touati D., Arch. Biochem. Biophys. 373(1), 2000
PMID: 10620317
Reactions upstream of glycerate-1,3-bisphosphate drive Corynebacterium glutamicum (D)-lactate productivity under oxygen deprivation.
Tsuge Y, Yamamoto S, Suda M, Inui M, Yukawa H., Appl. Microbiol. Biotechnol. 97(15), 2013
PMID: 23712891
Beyond growth rate 0.6: What drives Corynebacterium glutamicum to higher growth rates in defined medium.
Unthan S, Grunberger A, van Ooyen J, Gatgens J, Heinrich J, Paczia N, Wiechert W, Kohlheyer D, Noack S., Biotechnol. Bioeng. 111(2), 2013
PMID: 23996851
The DtxR regulon of Corynebacterium glutamicum.
Wennerhold J, Bott M., J. Bacteriol. 188(8), 2006
PMID: 16585752

Wickham H.., 2016
Classification and clustering of sequencing data using a poisson model.
Witten D.., 2011
Overexpression of genes encoding glycolytic enzymes in Corynebacterium glutamicum enhances glucose metabolism and alanine production under oxygen deprivation conditions.
Yamamoto S, Gunji W, Suzuki H, Toda H, Suda M, Jojima T, Inui M, Yukawa H., Appl. Environ. Microbiol. 78(12), 2012
PMID: 22504802

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