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:The outer-membrane c-type cytochrome Cyc2 is generally considered to be the initial electron acceptor in iron respiratory chain of Acidithiobacillus ferrooxidans ATCC 23270, a model microorganism in acidophilic bioleaching environment. In our work, however, the knockout of cyc2 did not result in impaired Fe(II) consumption or growth capacity. To screen the potential genes for alternative initial electron acceptors other than Cyc2, RNA-Seq was employed to compare global gene expressions in the A. ferrooxidans ATCC 23270 wild type and the Δcyc2 mutant grown on Fe(II) or switched energy source from S0 to Fe(II). The data focused on 29 up-regulated and 19 down-regulated genes in the mutant under both conditions, among which AFE_1428 was the most highest one. in-silico analysis also suggested that the product of AFE_1428 might act as an alternative initial electron acceptor when Cyc2 was absent, which needs to be further validated.
Project description:Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis contrary to the significant down-regulation of the majority motility-related genes. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed.
Project description:Acidithiobacillus ferrooxidans (A. ferrooxidans) ATCC 23270 is a model bacteria for bioleaching research. Because of the use of extractant in metal extraction industry, A. ferrooxidans needs to cope with the water-organic two-phase system. To get insight into the molecular response of A. ferrooxidans to organic solvent, global gene expression pattern was examined in A. ferrooxidans ATCC 23270 cells subjected to Lix984n (an organic extractant) using the method of whole-genome DNA microarray. The data suggested that the global response of A. ferrooxidans to Lix984n stress was characterized by the up-regulation of genes involved in pentose phosphate pathway, fatty acid and glutamate biosynthesis contrary to the significant down-regulation of the majority motility-related genes. In further study, compared to heterotrophic bacteria in dealing with short-time stress, A. ferrooxidans has a special strategy of continuously enhancing the expression of genes encoding proteins involved in electron transport, such as petI, petII, cyo and cyd. Besides, acrAB-tolC operon encoding organic solvent efflux pump and its positive regulator gene ostR were addressed. In this work, the whole-genome array was employed to conduct the time-course transcriptome analysis of A. ferrooxidans ATCC 23270 in response to 1% (v/v) Lix984n for 5, 20, 40, and 80 min.
