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

Abstract

The ɣ-proteobacterium 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.

Two forms of phosphomannomutase in gammaproteobacteria: The overlooked membrane‐bound form of AlgC is required for twitching motility of Lysobacter enzymogenes

“…S5). In addition to L. enzymogenes , transcribed RNAs from the 5′ regions of the respective ORFs have been found in the SRA entries for various Xanthomonas spp., including X. campestris strains 8004 and B100 (Bonomi et al ., ; Wang et al ., ; Alkhateeb et al ., ), X. citri (Jalan et al ., ), and X. oryzae (Kim et al ., ), as well as S. maltophilia strain FLR (Gallagher et al ., ) and Xylella fastidiosa strain ‘Temecula’ (Parker et al ., ), see Supporting Information Table S4. A similar picture, showing expression of the full‐length AlgC‐type PMM, was observed in P. aeruginosa strains PAO1 and PA14 (Supporting Information Fig.…”

Two forms of phosphomannomutase in gammaproteobacteria: The overlooked membrane-bound form of AlgC is required for twitching motility ofLysobacter enzymogenes

“…enzymogenes , transcribed RNAs from the 5’ regions of the respective ORFs have been found in the SRA entries for various Xanthomonas spp., including X . campestris strains 8004 and B100 (Bonomi et al ., 2016; Wang et al ., 2017; Alkhateeb et al ., 2018), X . citri (Jalan et al ., 2013), and X .…”

Comprehensive Proteome Profiling of a Xanthomonas campestris pv. Campestris B100 Culture Grown in Minimal Medium with a Specific Focus on Nutrient Consumption and Xanthan Biosynthesis

“…A similar observation was made in earlier studies for the transcription rates of the corresponding encoding genes in Xcc . Most transcripts for genes associated with sugar nucleotide synthesis were unaffected or lower in the stationary phase than in the exponential phase [ 27 ]. Post-translational modifications might play a role in the activity of this pathway instead.…”

“…The unraveling of the complete genome of Xcc B100, along with an improved annotation using RNA sequence data [ 14 , 26 ], provided an opportunity for further research into proteome and metabolome under relevant conditions. For example, differences in gene expression between exponential growth and stationary phase have been investigated [ 27 ]. In a 2D-gel electrophoresis-based proteome analysis of Xcc , 281 proteins were identified, which could be attributed to 81 distinct metabolic pathways [ 28 ].…”

“…Several proteome studies have focused on the interaction between Xcc and its host plants [ 30 , 31 , 32 ]. Recently, liquid chromatography–mass spectrometry (LC-MS)-based techniques have led to a significant improvement in the analysis of the Xcc proteome, with a much higher coverage of the predicted total proteome compared to 2D gel-based approaches [ 27 , 33 ].…”