Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Global response of Silicibacter pomeroyi strain DSS3 to dimethyl sulfoniopropionate (DMSP)

ABSTRACT: Dimethylsufoniopropionate (DMSP) is an important and abundant organic sulfur compound and an important substrate for marine bacterioplankton. The Roseobacter clade of marine alpha-proteobacteria, including Silicibacter pomeroyi strain DSS3, are known to be a key phylogenetic group involved in DMSP degradaton. The fate of DMSP has important implications for the global sulfur cycle, but the genes involved in this process and their regulation are largely unknown. S. pomeroyi is capable of performing two major pathways of DMSP degradation, making it an interesting model organism. Based on the full genome sequence of this strain we designed an oligonucleotide-based microarray for the detection of transcripts of nearly all genes. The array was used to study the transcriptional response of S. pomeroyi cultures to additions of DMSP or Acetate in a time series experiment. We identified a number of DMSP-upregulated genes that could be assigned to potential roles in the metabolization of DMSP. DMSP also affected the transcription of other groups of genes, including genes for transport and metabolization of peptides, amino-acids and polyamines. High DMSP concentrations may be a chemical signal indicating phytoplankton abundance and elicit a regulatory response aimed at making maximum use of the available nutrients under these conditions. Keywords: Microarray, marine bacterium, messenger RNA, transcription, sulfur metabolism The array design is based on the complete genome sequence of S. pomeroyi strain DSS 3 and available from Genbank (Accession numbers CP000031 and CP000032). Probes for all identified potential genes were designed by Combimatrix using proprietary software. A total of 4161 genes out of the 4348 identified potential genes on the S. pomeroyi genome are represented on the array. When possible, two probes per gene were designed.

ORGANISM(S): Ruegeria pomeroyi

SUBMITTER: Shulei Sun

PROVIDER: E-GEOD-5480 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Transcriptional response of Silicibacter pomeroyi DSS-3 to dimethylsulfoniopropionate (DMSP).

Bürgmann Helmut H Howard Erinn C EC Ye Wenying W Sun Feng F Sun Shulei S Napierala Sarah S Moran Mary Ann MA

Environmental microbiology 20071101 11

Dimethylsufoniopropionate (DMSP) is an abundant organic sulfur compound in the ocean and an important substrate for marine bacterioplankton. The Roseobacter clade of marine alphaproteobacteria, including Silicibacter pomeroyi strain DSS-3, are known to be involved in DMSP degradation in situ. The fate of DMSP has important implications for the global sulfur cycle, but the genes involved in this process and their regulation are largely unknown. S. pomeroyi is capable of performing two major pathw ...[more]

PMID: 17922758

Similar Datasets

Project description:In order to study the function of the Campylobacter jejuni Cj0667 gene, a series of experiments were carried out. Two strains were constructed: a Cj0667 knockout strain and a strain with a second copy over-expressing Cj0667 from an fdxA promoter. The transcriptomes of these were all compared to the wild-type strain. The arrays are all from RNA isolated in mid-exponential growth. Batch cultures of Campylobacter jejuni NCTC 11168 were grown in 50 ml volumes of Brucella broth in 70cm tissue culture flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (5% Oxygen, 10% Carbon dioxide, 85% Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 37 M-BM-:C. RNA was extracted from C. jejuni cultures grown to an OD600 of approximately 0.4. Briefly, 0.1 volume of 5% phenol in ethanol was mixed with the broth culture, and after centrifugation RNA was isolated with Tri Reagent (Sigma) and chloroform. RNA was further purified using the RNeasy kit (Qiagen) according to the manufacturerM-bM-^@M-^Ys instructions. The RNA was treated with Turbo DNA-free (Ambion) to remove any residual DNA according to the manufacturerM-bM-^@M-^Ys instructions. RNA concentration was determined using the Nanodrop Spectrophotometer NS-1000 (Thermo Scientific). RNA preparations of each sample type were labelled and hybridized to custom-designed Agilent microarrays. Equal quantities of RNA from test and control cultures were labelled by using nucleotide homologues of dUTP containing either Cy3 or Cy5 fluorescent dye (Perkin Elmer). For each microarray slide, the test strain was labelled with Cy3-dUTP, while the wild-type sample was labelled with Cy5-dUTP. RNA (15 M-BM-5g) was primed with 5 M-BM-5g pd(N)6 random hexamers (Amersham Biosciences). The Affinity Script kit (GE Healthcare) was used to produce cDNA, and hybridized (Agilent Hi-RPM Gene Expression Hybridization Kit) to the microarray slide according to the manufacturerM-bM-^@M-^Ys instructions. Microarrays were scanned at 5 M-BM-5m using an Axon 4000A scanner, and images were acquired using GenePix Pro 3.0 software (Axon). Related analysis reference: Holmes K., Mulholland F., Pearson B. M., Pin C., McNicholl-Kennedy J., Ketley J. M., Wells J. M. (2005) Campylobacter jejuni gene expression in response to iron limitation and the role of Fur Microbiology-SGM 151 243-257 (PMID 15632442).

Project description:In order to study the function of the Campylobacter jejuni Cj1103 gene, a series of experiments were carried out. Three strains were constructed: a Cj1103 knockout strain, a strain where the Cj1103 knockout was complemented in trans, and a strain with a second copy over-expressing Cj1103 from an metK promoter. The transcriptomes of these were all compared to the wild-type strain. The arrays are all from RNA isolated in mid-exponential growth from independent biological replicates. Batch cultures of Campylobacter jejuni NCTC 11168 were grown in 50 ml volumes of Brucella broth in 70cm tissue culture flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (5% Oxygen, 10% Carbon dioxide, 85% Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 37 M-BM-:C. RNA was extracted from C. jejuni cultures grown to an OD600 of approximately 0.4. Briefly, 0.1 volume of 5% phenol in ethanol was mixed with the broth culture, and after centrifugation RNA was isolated with Tri Reagent (Sigma) and chloroform. RNA was further purified using the RNeasy kit (Qiagen) according to the manufacturerM-bM-^@M-^Ys instructions. The RNA was treated with Turbo DNA-free (Ambion) to remove any residual DNA according to the manufacturerM-bM-^@M-^Ys instructions. RNA concentration was determined using the Nanodrop Spectrophotometer NS-1000 (Thermo Scientific). Two or three independent RNA preparations (biological replicates) of each sample type were labelled and hybridized to custom-designed Agilent microarrays. Equal quantities of RNA from test and control cultures were labelled by using nucleotide homologues of dUTP containing either Cy3 or Cy5 fluorescent dye (Perkin Elmer). For each microarray slide, the test strain was labelled with Cy3-dUTP, while the wild-type sample was labelled with Cy5-dUTP. RNA (15 M-BM-5g) was primed with 5 M-BM-5g pd(N)6 random hexamers (Amersham Biosciences). The Affinity Script kit (GE Healthcare) was used to produce cDNA, and hybridized (Agilent Hi-RPM Gene Expression Hybridization Kit) to the microarray slide according to the manufacturerM-bM-^@M-^Ys instructions. Microarrays were scanned at 5 M-BM-5m using an Axon 4000A scanner, and images were acquired using GenePix Pro 3.0 software (Axon). Related analysis reference: Holmes K., Mulholland F., Pearson B. M., Pin C., McNicholl-Kennedy J., Ketley J. M., Wells J. M. (2005) Campylobacter jejuni gene expression in response to iron limitation and the role of Fur Microbiology-SGM 151 243-257 (PMID 15632442).

Project description:In order to study the function of the Campylobacter jejuni Cj0138 gene, a series of experiments were carried out. Three strains were constructed: a Cj0138 knockout strain, a strain where the Cj0138 knockout was complemented in trans, and a strain with a second copy over-expressing Cj0138 from an fdxA promoter. The transcriptomes of these were all compared to the wild-type strain. The arrays are all from RNA isolated in mid-exponential growth from independent biological replicates. Batch cultures of Campylobacter jejuni NCTC 11168 were grown in 50 ml volumes of Brucella broth in 70cm tissue culture flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (5% Oxygen, 10% Carbon dioxide, 85% Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 37 M-BM-:C. RNA was extracted from C. jejuni cultures grown to an OD600 of approximately 0.4. Briefly, 0.1 volume of 5% phenol in ethanol was mixed with the broth culture, and after centrifugation RNA was isolated with Tri Reagent (Sigma) and chloroform. RNA was further purified using the RNeasy kit (Qiagen) according to the manufacturerM-bM-^@M-^Ys instructions. The RNA was treated with Turbo DNA-free (Ambion) to remove any residual DNA according to the manufacturerM-bM-^@M-^Ys instructions. RNA concentration was determined using the Nanodrop Spectrophotometer NS-1000 (Thermo Scientific). RNA preparations of each sample type were labelled and hybridized to custom-designed Agilent microarrays. Equal quantities of RNA from test and control cultures were labelled by using nucleotide homologues of dUTP containing either Cy3 or Cy5 fluorescent dye (Perkin Elmer). For each microarray slide, the test strain was labelled with Cy3-dUTP, while the wild-type sample was labelled with Cy5-dUTP. RNA (15 M-BM-5g) was primed with 5 M-BM-5g pd(N)6 random hexamers (Amersham Biosciences). The Affinity Script kit (GE Healthcare) was used to produce cDNA, and hybridized (Agilent Hi-RPM Gene Expression Hybridization Kit) to the microarray slide according to the manufacturerM-bM-^@M-^Ys instructions. Microarrays were scanned at 5 M-BM-5m using an Axon 4000A scanner, and images were acquired using GenePix Pro 3.0 software (Axon). Related analysis reference: Holmes K., Mulholland F., Pearson B. M., Pin C., McNicholl-Kennedy J., Ketley J. M., Wells J. M. (2005) Campylobacter jejuni gene expression in response to iron limitation and the role of Fur Microbiology-SGM 151 243-257 (PMID 15632442).

Project description:In order to study the function of the Campylobacter jejuni Cj1501 gene, a series of experiments were carried out. Three strains were constructed: a Cj1501 knockout strain, a strain where the Cj1501 knockout was complemented in trans, and a strain with a second copy over-expressing Cj1501 from an fdxA promoter. The transcriptomes of these were all compared to the wild-type strain. The arrays are all from RNA isolated in mid-exponential growth from independent biological replicates. Batch cultures of Campylobacter jejuni NCTC 11168 were grown in 50 ml volumes of Brucella broth in 70cm tissue culture flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (5% Oxygen, 10% Carbon dioxide, 85% Nitrogen) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 37 M-BM-:C. RNA was extracted from C. jejuni cultures grown to an OD600 of approximately 0.4. Briefly, 0.1 volume of 5% phenol in ethanol was mixed with the broth culture, and after centrifugation RNA was isolated with Tri Reagent (Sigma) and chloroform. RNA was further purified using the RNeasy kit (Qiagen) according to the manufacturerM-bM-^@M-^Ys instructions. The RNA was treated with Turbo DNA-free (Ambion) to remove any residual DNA according to the manufacturerM-bM-^@M-^Ys instructions. RNA concentration was determined using the Nanodrop Spectrophotometer NS-1000 (Thermo Scientific). Two or three independent RNA preparations (biological replicates) of each sample type were labelled and hybridized to custom-designed Agilent microarrays. Equal quantities of RNA from test and control cultures were labelled by using nucleotide homologues of dUTP containing either Cy3 or Cy5 fluorescent dye (Perkin Elmer). For each microarray slide, the test strain was labelled with Cy3-dUTP, while the wild-type sample was labelled with Cy5-dUTP. RNA (15 M-BM-5g) was primed with 5 M-BM-5g pd(N)6 random hexamers (Amersham Biosciences). The Affinity Script kit (GE Healthcare) was used to produce cDNA, and hybridized (Agilent Hi-RPM Gene Expression Hybridization Kit) to the microarray slide according to the manufacturerM-bM-^@M-^Ys instructions. Microarrays were scanned at 5 M-BM-5m using an Axon 4000A scanner, and images were acquired using GenePix Pro 3.0 software (Axon). Related analysis reference: Holmes K., Mulholland F., Pearson B. M., Pin C., McNicholl-Kennedy J., Ketley J. M., Wells J. M. (2005) Campylobacter jejuni gene expression in response to iron limitation and the role of Fur Microbiology-SGM 151 243-257 (PMID 15632442).

Dataset Information

Global response of Silicibacter pomeroyi strain DSS3 to dimethyl sulfoniopropionate (DMSP)

Publications

Transcriptional response of Silicibacter pomeroyi DSS-3 to dimethylsulfoniopropionate (DMSP).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure