Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase

Alkhateeb R, Vorhölter F-J, Steffens T, Rückert C, Ortseifen V, Hublik G, Niehaus K, Pühler A (2018)
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 102(15): 6613-6625.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
The E -proteobacterium pound Xanthomonas campestris pv. campestris (Xcc) is the producer of the biopolymer xanthan, a polysaccharide which is used as a thickener in numerous industrial applications. In this study, we present a global transcriptome profiling of two Xcc strain B100 cultures obtained from fermentation during the growth phase and the subsequent stationary phase associated with xanthan biosynthesis. During the xanthan production phase, highly abundant transcripts belonged to genes encoding for small RNAs, glycogen biosynthesis, and xanthan export. A total of 1850 (40%) genes were differentially transcribed during the stationary phase where 924 were transcriptionally up-regulated and 926 genes were down-regulated. An overview of differentially transcribed genes includes a significant down-regulation of genes involved in transcription, translation, and amino acid biosynthesis pathways. A group of up-regulated genes was involved in cellular response against oxidative stress, such as those coding for superoxide dismutase and catalase. Genes encoding enzymes involved in nucleotide sugar precursor synthesis of xanthan biosynthesis, such as xanA, galU, and ugd, exhibited a transcription pattern that did not change during the growth and stationary phase. Regarding the transcription pattern of the gum gene cluster that govern xanthan biosynthesis, a significant up-regulation of the genes gumB, gumC, and gumD was observed, while the transcript pools of the genes gumG, gumH, gumI, and gumJ were reduced and those of genes gumE, gumF, gumK, gumL, and gumM remained un-changed during the stationary phase compared to the growth phase. The obtained data represents the first analysis of gene expression patterns under xanthan production conditions and provides the bases for future studies aiming at enhancing xanthan yield.
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APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
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102
Ausgabe
15
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6613-6625
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Alkhateeb R, Vorhölter F-J, Steffens T, et al. Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY. 2018;102(15):6613-6625.
Alkhateeb, R., Vorhölter, F. - J., Steffens, T., Rückert, C., Ortseifen, V., Hublik, G., Niehaus, K., et al. (2018). Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 102(15), 6613-6625. doi:10.1007/s00253-018-9106-2
Alkhateeb, R., Vorhölter, F. - J., Steffens, T., Rückert, C., Ortseifen, V., Hublik, G., Niehaus, K., and Pühler, A. (2018). Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 102, 6613-6625.
Alkhateeb, R., et al., 2018. Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 102(15), p 6613-6625.
R. Alkhateeb, et al., “Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase”, APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, vol. 102, 2018, pp. 6613-6625.
Alkhateeb, R., Vorhölter, F.-J., Steffens, T., Rückert, C., Ortseifen, V., Hublik, G., Niehaus, K., Pühler, A.: Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY. 102, 6613-6625 (2018).
Alkhateeb, Rabeaa, Vorhölter, Frank-Jörg, Steffens, Tim, Rückert, Christian, Ortseifen, Vera, Hublik, Gerd, Niehaus, Karsten, and Pühler, Alfred. “Comparative transcription profiling of two fermentation cultures of Xanthomonas campestris pv. campestris B100 sampled in the growth and in the stationary phase”. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 102.15 (2018): 6613-6625.

74 References

Daten bereitgestellt von Europe PubMed Central.

Refined annotation of the complete genome of the phytopathogenic and xanthan producing Xanthomonas campestris pv. campestris strain B100 based on RNA sequence data.
Alkhateeb RS, Ruckert C, Rupp O, Pucker B, Hublik G, Wibberg D, Niehaus K, Puhler A, Vorholter FJ., J. Biotechnol. 253(), 2017
PMID: 28506932
High-resolution transcriptional analysis of the regulatory influence of cell-to-cell signalling reveals novel genes that contribute to Xanthomonas phytopathogenesis.
An SQ, Febrer M, McCarthy Y, Tang DJ, Clissold L, Kaithakottil G, Swarbreck D, Tang JL, Rogers J, Dow JM, Ryan RP., Mol. Microbiol. 88(6), 2013
PMID: 23617851
Structural basis for transcription regulation by alarmone ppGpp.
Artsimovitch I, Patlan V, Sekine S, Vassylyeva MN, Hosaka T, Ochi K, Yokoyama S, Vassylyev DG., Cell 117(3), 2004
PMID: 15109491
Hydrogen peroxide effects in Escherichia coli cells.
Asad NR, Asad LM, Silva AB, Felzenszwalb I, Leitao AC., Acta Biochim. Pol. 45(3), 1998
PMID: 9918494
Xanthan gum biosynthesis and application: a biochemical/genetic perspective.
Becker A, Katzen F, Puhler A, Ielpi L., Appl. Microbiol. Biotechnol. 50(2), 1998
PMID: 9763683
Plant carbohydrate scavenging through tonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria.
Blanvillain S, Meyer D, Boulanger A, Lautier M, Guynet C, Denance N, Vasse J, Lauber E, Arlat M., PLoS ONE 2(2), 2007
PMID: 17311090
The relationship between glycogen synthesis, biofilm formation and virulence in salmonella enteritidis.
Bonafonte MA, Solano C, Sesma B, Alvarez M, Montuenga L, Garcia-Ros D, Gamazo C., FEMS Microbiol. Lett. 191(1), 2000
PMID: 11004396

MR, 1987

M, 1996
The roles of peroxide protective regulons in protecting Xanthomonas campestris pv. campestris from sodium hypochlorite stress.
Charoenlap N, Sornchuer P, Piwkam A, Srijaruskul K, Mongkolsuk S, Vattanaviboon P., Can. J. Microbiol. 61(5), 2015
PMID: 25825971
The Xanthomonas campestris gumD gene required for synthesis of xanthan gum is involved in normal pigmentation and virulence in causing black rot.
Chou FL, Chou HC, Lin YS, Yang BY, Lin NT, Weng SF, Tseng YH., Biochem. Biophys. Res. Commun. 233(1), 1997
PMID: 9144435
Advances in bacterial transcriptome and transposon insertion-site profiling using second-generation sequencing.
Febrer M, McLay K, Caccamo M, Twomey KB, Ryan RP., Trends Biotechnol. 29(11), 2011
PMID: 21764162
Xanthan gum: production, recovery, and properties.
Garcia-Ochoa F, Santos VE, Casas JA, Gomez E., Biotechnol. Adv. 18(7), 2000
PMID: 14538095

NE, 1995
ReadXplorer--visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
PMID: 24790157

G, 2012
Expression, purification and crystallization of the outer membrane lipoprotein GumB from Xanthomonas campestris.
Jacobs M, Salinas SR, Bianco MI, Ielpi L., Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68(Pt 10), 2012
PMID: 23027761
Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range.
Jalan N, Kumar D, Andrade MO, Yu F, Jones JB, Graham JH, White FF, Setubal JC, Wang N., BMC Genomics 14(), 2013
PMID: 23941402
Structure of extracellular polysaccharide from Xanthomonas campestris.
Jansson PE, Kenne L, Lindberg B., Carbohydr. Res. 45(), 1975
PMID: 1212669
Promoter analysis of the Xanthomonas campestris pv. campestris gum operon directing biosynthesis of the xanthan polysaccharide.
Katzen F, Becker A, Zorreguieta A, Puhler A, Ielpi L., J. Bacteriol. 178(14), 1996
PMID: 8763965

AUTHOR UNKNOWN, 0
Superoxide accelerates DNA damage by elevating free-iron levels.
Keyer K, Imlay JA., Proc. Natl. Acad. Sci. U.S.A. 93(24), 1996
PMID: 8942986
Novel roles of ohrR-ohr in Xanthomonas sensing, metabolism, and physiological adaptive response to lipid hydroperoxide.
Klomsiri C, Panmanee W, Dharmsthiti S, Vattanaviboon P, Mongkolsuk S., J. Bacteriol. 187(9), 2005
PMID: 15838057
Fast gapped-read alignment with Bowtie 2.
Langmead B, Salzberg SL., Nat. Methods 9(4), 2012
PMID: 22388286
Specificity in two-component signal transduction pathways.
Laub MT, Goulian M., Annu. Rev. Genet. 41(), 2007
PMID: 18076326
Functional specialization within the Fur family of metalloregulators.
Lee JW, Helmann JD., Biometals 20(3-4), 2007
PMID: 17216355
Applying DNA affinity chromatography to specifically screen for sucrose-related DNA-binding transcriptional regulators of Xanthomonas campestris.
Leßmeier L, Alkhateeb RS, Schulte F, Steffens T, Loka TP, Puhler A, Niehaus K, Vorholter FJ., J. Biotechnol. 232(), 2016
PMID: 27060555
The influence of metabolic network structures and energy requirements on xanthan gum yields.
Letisse F, Chevallereau P, Simon JL, Lindley N., J. Biotechnol. 99(3), 2002
PMID: 12385717
Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae.
Liang H, Zhao YT, Zhang JQ, Wang XJ, Fang RX, Jia YT., BMC Genomics 12(), 2011
PMID: 21276262

AUTHOR UNKNOWN, 0
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
Enhanced symbiotic performance by Rhizobium tropici glycogen synthase mutants.
Marroqui S, Zorreguieta A, Santamaria C, Temprano F, Soberon M, Megias M, Downie JA., J. Bacteriol. 183(3), 2001
PMID: 11208782
Glycogen production by different Salmonella enterica serotypes: contribution of functional glgC to virulence, intestinal colonization and environmental survival.
McMeechan A, Lovell MA, Cogan TA, Marston KL, Humphrey TJ, Barrow PA., Microbiology (Reading, Engl.) 151(Pt 12), 2005
PMID: 16339941
Structural elucidation of the O-chain of the lipopolysaccharide from Xanthomonas campestris strain 8004.
Molinaro A, Silipo A, Lanzetta R, Newman MA, Dow JM, Parrilli M., Carbohydr. Res. 338(3), 2003
PMID: 12543561
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B., Nat. Methods 5(7), 2008
PMID: 18516045
Dynamic protein phosphorylation during the growth of Xanthomonas campestris pv. campestris B100 revealed by a gel-based proteomics approach.
Musa YR, Basell K, Schatschneider S, Vorholter FJ, Becher D, Niehaus K., J. Biotechnol. 167(2), 2013
PMID: 23792782
TonB-dependent transporters: regulation, structure, and function.
Noinaj N, Guillier M, Barnard TJ, Buchanan SK., Annu. Rev. Microbiol. 64(), 2010
PMID: 20420522
Bacterial glycogen synthesis and its regulation.
Preiss J., Annu. Rev. Microbiol. 38(), 1984
PMID: 6093684
Lipopolysaccharide endotoxins.
Raetz CR, Whitfield C., Annu. Rev. Biochem. 71(), 2001
PMID: 12045108
The TetR family of transcriptional repressors.
Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R., Microbiol. Mol. Biol. Rev. 69(2), 2005
PMID: 15944459

T, Curr Microbiol 21(), 1990

ZZ, Hem Ind 71(), 2017
Establishment, in silico analysis, and experimental verification of a large-scale metabolic network of the xanthan producing Xanthomonas campestris pv. campestris strain B100.
Schatschneider S, Persicke M, Watt SA, Hublik G, Puhler A, Niehaus K, Vorholter FJ., J. Biotechnol. 167(2), 2013
PMID: 23395674
Metabolic flux pattern of glucose utilization by Xanthomonas campestris pv. campestris: prevalent role of the Entner-Doudoroff pathway and minor fluxes through the pentose phosphate pathway and glycolysis.
Schatschneider S, Huber C, Neuweger H, Watt TF, Puhler A, Eisenreich W, Wittmann C, Niehaus K, Vorholter FJ., Mol Biosyst 10(10), 2014
PMID: 25072918
Small RNA sX13: a multifaceted regulator of virulence in the plant pathogen Xanthomonas.
Schmidtke C, Abendroth U, Brock J, Serrania J, Becker A, Bonas U., PLoS Pathog. 9(9), 2013
PMID: 24068933
Nutritional Studies on Xanthan Production by Xanthomonas campestris NRRL B1459.
Souw P, Demain AL., Appl. Environ. Microbiol. 37(6), 1979
PMID: 16345398
The influence of a modified lipopolysaccharide O-antigen on the biosynthesis of xanthan in Xanthomonas campestris pv. campestris B100.
Steffens T, Vorholter FJ, Giampa M, Hublik G, Puhler A, Niehaus K., BMC Microbiol. 16(), 2016
PMID: 27215401
8-oxoguanine (8-hydroxyguanine) DNA glycosylase and its substrate specificity.
Tchou J, Kasai H, Shibutani S, Chung MH, Laval J, Grollman AP, Nishimura S., Proc. Natl. Acad. Sci. U.S.A. 88(11), 1991
PMID: 2052552
The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli.
Traxler MF, Summers SM, Nguyen HT, Zacharia VM, Hightower GA, Smith JT, Conway T., Mol. Microbiol. 68(5), 2008
PMID: 18430135
Evidence for a role for the gumB and gumC gene products in the formation of xanthan from its pentasaccharide repeating unit by Xanthomonas campestris.
Vojnov AA, Zorreguieta A, Dow JM, Daniels MJ, Dankert MA., Microbiology (Reading, Engl.) 144 ( Pt 6)(), 1998
PMID: 9639919
Expression of the gum operon directing xanthan biosynthesis in Xanthomonas campestris and its regulation in planta.
Vojnov AA, Slater H, Daniels MJ, Dow JM., Mol. Plant Microbe Interact. 14(6), 2001
PMID: 11386372
The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
Vorholter FJ, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Ruckert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Puhler A., J. Biotechnol. 134(1-2), 2008
PMID: 18304669

PH, Plant Dis 64(), 1980

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