Project description:Welan gum is mainly produced by Sphingomonas sp. ATCC 31555 and has broad applications in industry such as that in cement production. Both carbon and nitrogen sources are essential for welan production. However, how nitrogen sources affect the metabolism and gene transcription of welan remains elusive. Here, we used next-generation sequencing RNA-seq to analyze the transcriptome of Sphingomonas sp. ATCC 31555 in the presence of inorganic or organic nitrogen sources. Enriched gene expression and pathway analysis suggest that organic nitrogen sources significantly enhanced the expression of genes in central metabolic pathways of Sphingomonas sp. ATCC 31555 and those critical for welan synthesis compared to that observed using inorganic nitrogen sources. The present study improves our understanding of the molecular mechanism underlying the use of nitrogen in welan synthesis in Sphingomonas sp., as well as provides an important transcriptome resource for Sphingomonas sp. in relation to nitrogen sources.
Project description:Welan gum is mainly produced by Sphingomonas sp. ATCC 31555 and has broad applications in industry such as that in cement production. Both carbon and nitrogen sources are essential for welan production. However, how nitrogen sources affect the metabolism and gene transcription of welan remains elusive. Here, we used next-generation sequencing RNA-seq to analyze the transcriptome of Sphingomonas sp. ATCC 31555 in the presence of inorganic or organic nitrogen sources. Enriched gene expression and pathway analysis suggest that organic nitrogen sources significantly enhanced the expression of genes in central metabolic pathways of Sphingomonas sp. ATCC 31555 and those critical for welan synthesis compared to that observed using inorganic nitrogen sources. The present study improves our understanding of the molecular mechanism underlying the use of nitrogen in welan synthesis in Sphingomonas sp., as well as provides an important transcriptome resource for Sphingomonas sp. in relation to nitrogen sources. Sphingomonas sp. ATCC 31555 strain (stored in our laboratory) was first seeded in an inoculum medium (20 g/L glucose, 3 g/L yeast extract, 3 g/L malt extract, and 5 g/L fish meal protein peptone, pH 7.0), and then cultured in a fermentation medium containing 40 g/L sucrose, 4.0 g/L nitrogen source, 0.6 g/L KH2PO4, and 0.2 g/L MgSO4.7H2O at 37°C. The nitrogen sources used in the present study were as follows: NaNO3 (4.0 g/L) as inorganic nitrogen (IN), beef extract (4.0 g/L) as organic nitrogen (ON), and NaNO3 (1.5 g/L) + beef extract (2.5 g/L) as complex nitrogen (CN). All cultivations were conducted in flasks with constant rotary shaking at 400â??1,000 rpm and 37°C.
Project description:The mechanisms of heavy metal accumulation in primary producers and the damage and stress response induced by heavy metals is not well understood. We used UHTS to analyze the transcriptomic response of Elodea nuttallii to heavy metal pollution. We exposed shoots of E. nuttallii for 24 h to increasing concentrations of Hg and Cd. Using Illumina RNA-Seq, we have generated over 50 million 54 nt paired end reads and 14 million single end reads, which we used for de novo assembly of the E. nuttallii transcriptome.
Project description:Investigation of whole genome gene expression level in motile strain of Sphingomonas. sp A1 All flagellar genes in motile strain of Sphingomonas. sp A1 are highly transcribed.
