Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

KCl Stress in Desulfovibrio vulgaris Hildenborough (Series 1)

ABSTRACT: Increased salinity constitutes an important and frequent fluctuation faced by D. vulgaris in its natural habitat. Using data from microarray experiments, we investigated the effects of excess KCl on D. vulgaris. Keywords: stress response, time course Comparison of cells treated with 250mM KCl to untreated cells at times of 0, 30, 60, 120, and 240 min. See also Series GSE4447: http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GSE4447

ORGANISM(S): Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough

SUBMITTER: Adam Arkin

PROVIDER: E-GEOD-4515 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach.

Mukhopadhyay Aindrila A He Zhili Z Alm Eric J EJ Arkin Adam P AP Baidoo Edward E EE Borglin Sharon C SC Chen Wenqiong W Hazen Terry C TC He Qiang Q Holman Hoi-Ying HY Huang Katherine K Huang Rick R Joyner Dominique C DC Katz Natalie N Keller Martin M Oeller Paul P Redding Alyssa A Sun Jun J Wall Judy J Wei Jing J Yang Zamin Z Yen Huei-Che HC Zhou Jizhong J Keasling Jay D JD

Journal of bacteriology 20060601 11

The ability of Desulfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. Increased salinity is an important and frequent fluctuation faced by D. vulgaris in its natural habitat. In liquid culture, exposure to excess salt resulted in striking elongation of D. vulgaris cells. Using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profil ...[more]

PMID: 16707698

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Project description:Background. Desulfovibrio vulgaris Hildenborough is a sulfate-reducing bacterium (SRB) that is intensively studied in the context of metal corrosion and heavy-metal bioremediation, and SRB populations are commonly observed in pipe and subsurface environments as surface-associated populations. In order to elucidate physiological changes associated with biofilm growth at both the transcript and protein level, transcriptomic and proteomic analyses were done on mature biofilm cells and compared to both batch and reactor planktonic populations. The biofilms were cultivated with lactate and sulfate in a continiouslly fed biofilm reactor, and compared to both batch and reactor planktonic populations. The functional genomic analysis demonstrated that biofilm cells were different compared to planktonic cells, and the majority of altered abundances for genes and proteins were annotated as hypothetical (unknown function), energy conservation, amino acid metabolism, and signal transduction. Genes and proteins that showed similar trends in detected levels were particularly involved in energy conservation such as increases in an annotated ech hydrogenase, formate dehydrogenase, pyruvate:ferredoxin oxidoreductase, and rnf oxidoreductase, and the biofilm cells had elevated formate dehydrogenase activity. Several other hydrogenases and formate dehydrogenases also showed an increased protein level, while decreased transcript and protein levels were observed for putative coo hydrogenases as well as a lactate permease and hyp hydrogenases for biofilm cells. Genes annotated for amino acid synthesis and nitrogen utilization were also predominant changers within the biofilm state. Ribosomal transcripts and proteins were notably decreased within the biofilm cells compared to exponential-phase cells but were not as low as levels observed in planktonic, stationary-phase cells. Several putative, extracellular proteins (DVU1012, 1545) were also detected in the extracellular fraction from biofilm cells. Even though both the planktonic and biofilm cells were oxidizing lactate and reducing sulfate, the biofilm cells were physiologically distinct compared to planktonic growth states due to altered abundances of genes/proteins involved in carbon/energy flow and extracellular structures. In addition, average expression values for multiple rRNA transcripts and respiratory activity measurements indicated that biofilm cells were metabolically more similar to exponential-phase cells although biofilm cells are structured differently. The characterization of physiological advantages and constraints of the biofilm growth state for sulfate-reducing bacteria will provide insight into bioremediation applications as well as microbially-induced metal corrosion. Biofilms grown in reactors were compared to reference samples of reactor, planktonic and batch, planktonic. Each sample had a biological triplicate.

Dataset Information

KCl Stress in Desulfovibrio vulgaris Hildenborough (Series 1)

Publications

Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach.

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