Dataset Information

Analyze key proteins in Syntrophus aciditrophicus

ABSTRACT: Pure cultures of S. aciditrophicus grown in 250 ml of 20 mM crotonate medium in 500-ml Schott bottles were used for proteomic analysis after 2-dimensional (2-D) PAGE.

ORGANISM(S): Syntrophus Aciditrophicus Sb

SUBMITTER: Joseph Loo

PROVIDER: PXD011100 | JPOST Repository | Mon Apr 29 00:00:00 BST 2019

REPOSITORIES: jPOST

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Dataset's files

Source:

			Action	DRS
	050120syntroph11cmA2.wiff	Wiff
	050120syntroph11cmA3.wiff	Wiff
	050120syntroph11cmA4.wiff	Wiff
	050120syntroph11cmA5.wiff	Wiff
	050120syntroph11cmA6.wiff	Wiff

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Publications

Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids.

James Kimberly L KL Kung Johannes W JW Crable Bryan R BR Mouttaki Housna H Sieber Jessica R JR Nguyen Hong H HH Yang Yanan Y Xie Yongming Y Erde Jonathan J Wofford Neil Q NQ Karr Elizabeth A EA Loo Joseph A JA Ogorzalek Loo Rachel R RR Gunsalus Robert P RP McInerney Michael J MJ

Environmental microbiology 20190501 5

Syntrophy is essential for the efficient conversion of organic carbon to methane in natural and constructed environments, but little is known about the enzymes involved in syntrophic carbon and electron flow. Syntrophus aciditrophicus strain SB syntrophically degrades benzoate and cyclohexane-1-carboxylate and catalyses the novel synthesis of benzoate and cyclohexane-1-carboxylate from crotonate. We used proteomic, biochemical and metabolomic approaches to determine what enzymes are used for fat ...[more]

PMID: 30895699

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Project description:Purpose: To understand how D654Y mutated RpoB affect gene expression under either normal or osmotic stress conditions in Escherichia coli . Methods: RNA-seq libraries were constructed for four samples, including (I) The parental strain Suc-T110 grown at normal condition (5%w/v glucose); (II)RpoB mutant RpoBD645Y [Suc-T110::rpoB (D654Y), RNA-seq library named NZ-502] grown at normal condition;(III) Suc-T110 grown at osmotic stress condition(12%w/v glucose);(IV) NZ-502 grown at osmotic stress condition. For preparation of RNA samples, Fresh colonies were picked from New NBS mineral salts plates containing 20 g liter-1 glucose, inoculated into 250 ml flasks containing 30 ml NBS mineral salts medium with 20 g liter-1 glucose, and grown at 37°C and 250 rpm for 12 h. Cultures were then transferred to a 500 ml fermentation vessel containing 250 ml NBS mineral salts medium with either 5%w/v or 12%w/v glucose. After 48 h, 1 ml culture was harvested by centrifugation, frozen in liquid nitrogen and sent to Beijing Genomics Institute (BGI, Shenzhen, China). The four 90-nt paired-end RNA-seq libraries were generated commercially at Beijing Genomics Institute by using the HiSeq™ 2000 platform. Sequencing data was handled essentially with Bowtie2, NOIseq. Expression levels are presented as Reads Per Kilobase of transcript per Million mapped reads (RPKM). Results: we first comparative accessed expression levels of Suc-T110 and NZ-502 under normal condition. Among the 4200 predicted genes, 128 genes were found altered their expression in NZ502 compared with Suc-T110; with 38 targets specific up-regulated while 90 targets down-regulated. Genes engaged in biological function of amino acid metabolism (P-value=4.60E-05) were significantly enriched among in induced gene set. Under osmotic stress condition, 244 differential expressed genes were identified in NZ-502 when compared with Suc-T110, with 132 targets specific up-regulated while 112 targets down-regulated, Functional enrichment of 132 up regulated genes showed the most significantly enriched physiological function of NZ-502 upon hyperosmotic stress was associated with carbon source transportation (FunCat term: 20.01.03 C-compound and carbohydrate transport, P-value=9.51E-05), which containing a group of genes encoding diverse sugar transporters. Conclusions: Transcriptome profiling suggested that derepression of sugar transporters might be the primary cause for NZ-502 to resist osmotic stress.