12 k microarray slides  (CustomArray Inc)

Journal: Frontiers in Microbiology

Article Title: Transcriptional Changes Underlying Elemental Stoichiometry Shifts in a Marine Heterotrophic Bacterium

doi: 10.3389/fmicb.2012.00159

Figure Lengend Snippet: Schematic of microarray data analysis . Probe counts are shown in italicized font and gene counts are in bold font. (A) Significant Analysis of Microarray (SAM) was used to analyze the microarray data (pairwise SAM comparisons with 5,000 permutations and a false discovery rate ≤ 2%). From these results, probes significantly different in all three comparisons to the other treatments (that is, falling into the three-way overlap region of each Venn diagram) were selected for further analyses. (B) From the normalized fluorescence values, the fold-change for each probe was calculated as the median value between all limitation-to-excess pairwise comparisons and genes whose fold-change was ≥ 3 were retained.

Article Snippet: The CustomArray 12 K microarray slides for R. pomeroyi DSS-3 used in this study were described in detail by Bürgmann et al. ( ).

Techniques: Microarray, Fluorescence

Journal: The Journal of Biological Chemistry

Article Title: Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli *

doi: 10.1074/jbc.M109.089755

Figure Lengend Snippet: Schematic organization of the fnrS chromosomal region and conservation of the promoter region. A, genetic organization of the E. coli region encoding fnrS is shown. Arrows indicate the direction of transcription, and stem-loop structures of the predicted ρ-independent terminator are indicated by a lollipop. The fnrS gene is highly conserved in a wide range of enterobacteria. B, alignment of the fnrS promoter region of E. coli K-12 (ECO), Klebsiella pneumoniae (KPN), Salmonella typhimurium (STY), Citrobacter rodentium (CRO), Sodalis glossinidius (SGL), Yersinia pestis (YPE), Edwardsiella (EDW), Serratia marcescens (SMA), Dickeya dadantii (DDA), Enterobacter sakazakii (ESA), Cronobacter turicensis (CTU), Proteus mirabilis (PMI), Photorhabdus asymbiotica (PHO), and Providencia stuartii (PST) by the ClustalW program. The −10 promoter element and the FNR DNA binding site are highlighted in gray. The transcription start site of the E. coli fnrS gene is indicated by an arrow.

Article Snippet: Transcriptome Analysis Global gene expression analysis was carried out using E. coli glass-slide microarrays ( E. coli K-12 V2 OciChip, Ocimum Biosolutions) as previously described ( 20 ).

Techniques: Binding Assay

Journal: The Journal of Biological Chemistry

Article Title: Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli *

doi: 10.1074/jbc.M109.089755

Figure Lengend Snippet: Transcriptional regulation of fnrS. A, shown is anaerobic regulation of FnrS RNA expression. Wild-type (WT) strain SØ928 and isogenic derivatives containing a chromosomal deletion of fnr, crp, or arcA, respectively, were grown with aeration in LB medium at 37 °C to exponential growth phase (A450 ∼ 0.3). Samples were taken before (lane 1; 0 min) and after (lanes 1–3; 10, 20, 30 min) anaerobic incubation. The levels of FnrS were determined using Northern blot analysis. B, the transcription start site of the E. coli fnrS gene was determined by primer extension analysis with total RNA isolated from SØ928 grown under anaerobic growth conditions (rightmost lane). C, shown is the predicted secondary structure for E. coli FnrS from Mfold (67). The conserved segment of the sRNA that possesses sequence complementarity to the translational initiation region of target mRNAs as well as the predicted binding site for Hfq is marked by a filled line.

Article Snippet: Transcriptome Analysis Global gene expression analysis was carried out using E. coli glass-slide microarrays ( E. coli K-12 V2 OciChip, Ocimum Biosolutions) as previously described ( 20 ).

Techniques: RNA Expression, Incubation, Northern Blot, Isolation, Sequencing, Binding Assay

Journal: The Journal of Biological Chemistry

Article Title: Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli *

doi: 10.1074/jbc.M109.089755

Figure Lengend Snippet: FnrS-mediated repression of sodB expression and roles of Hfq. A, strains SØ928ΔfnrS/pNDM220, SØ928ΔfnrS/pNDM220-fnrS, SØ928Δhfq/pNDM220, and SØ928 Δhfq/pNDM220-fnrS were grown aerobically in LB media to an A450 of 0.4 and then induced by the addition of IPTG (final concentration 1 mm). Samples were taken before (time 0), and 10 min after induction and total RNA was extracted. The sodB mRNA and FnrS RNA levels were analyzed by Northern blot. B, shown is accumulation of sodB mRNA in the absence and presence of FnrS RNA upon a sudden shift from aerobic to anaerobic growth. Aerobically grown cells of SØ928 and SØ928ΔfnrS were shifted to anoxia at time 0. Samples were taken at the indicated times, and RNA was extracted and probed for sodB mRNA and FnrS RNA. C, shown is putative base pairing between FnrS RNA and sodB mRNA. The translation start site is indicated. D, Hfq cooperates in RNA-RNA interaction. Samples containing 5′ end-labeled FnrS RNA (2 nm) and increasing amounts of unlabeled sodB′ RNA substrate (from −53 to + 97 relative to the translation start site) were incubated in the absence (lanes 1–4) or in the presence of Hfq (lanes 5–8), and complex formation was monitored in a electrophoretic mobility shift experiment. sodB′ RNA concentrations were as indicated, and the Hfq “hexamer” concentration was 0.33 μm. Unbound FnrS RNA and complexes corresponding to Hfq-FnrS RNA and FnrS RNA-Hfq-sodB′ RNA are indicated by arrows. E, target validation by translational sodB::gfp fusion is shown. In one experiment E. coli strains SØ928 and SØ928 ΔfnrS carrying the target fusion plasmid were grown anaerobically in LB media for at least six generations (A450 ∼ 0.4) (lanes 1 and 2). In another experiment the ΔfnrS/pNDM220 and ΔfnrS/pNDM220-fnrS strains carrying target fusion plasmid were grown aerobically to an A450 of 0.4 in the presence of IPTG (1 mm final concentration) (lanes 3 and 4). For both experiments cells samples were subjected to Western blot analysis with monoclonal α-GFP antibodies (upper panel) and to Northern blot analysis of gfp-fusion mRNA and FnrS RNA (second and third panels). GroEL and 5S were used as loading control for Western and Northern blots, respectively.

Article Snippet: Transcriptome Analysis Global gene expression analysis was carried out using E. coli glass-slide microarrays ( E. coli K-12 V2 OciChip, Ocimum Biosolutions) as previously described ( 20 ).

Techniques: Expressing, Concentration Assay, Northern Blot, Labeling, Incubation, Electrophoretic Mobility Shift Assay, Biomarker Discovery, Plasmid Preparation, Western Blot, Control

Journal: The Journal of Biological Chemistry

Article Title: Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli *

doi: 10.1074/jbc.M109.089755

Figure Lengend Snippet: FnrS-mediated repression of cydDC mRNA expression. A, shown is primer extension analysis of cydDC 5′ end transcript. fnrS deletion strains containing an empty control vector (pNDM220) or pNDM220-fnrS were grown aerobically in LB medium at 37 °C to exponential growth phase (A450 ∼ 0.3). Samples were taken before (lanes 1 and 3; 0 min) and after (lanes 2 and 4; 10 min) FnrS induction by 1 mm IPTG. Wild-type and fnrS deletion strains were grown aerobically in LB medium at 37 °C to exponential growth phase (A450 ∼ 0.3). Samples were taken before (lanes 5 and 7; 0 min) and after (lanes 6 and 8; 30 min) of anaerobic incubation. B, the transcription start site (black arrow) was mapped to a position 33 bp downstream of the start site reported by Cook et al. (61) (gray arrow) (i.e. start site reassigned from position 930254 to 930221 of the E. coli chromosome). Putative −10 and −35 boxes are underlined. C, shown is validation of post-transcriptional regulation of the yobA-yebZY message by a translational yobA::gfp reporter fusion. The experiment as in Fig. 4E but with the pXG10-yobA′::gfp reporter plasmid.

Article Snippet: Transcriptome Analysis Global gene expression analysis was carried out using E. coli glass-slide microarrays ( E. coli K-12 V2 OciChip, Ocimum Biosolutions) as previously described ( 20 ).

Techniques: Expressing, Control, Plasmid Preparation, Incubation, Biomarker Discovery

Journal: The Journal of Biological Chemistry

Article Title: Translational Regulation of Gene Expression by an Anaerobically Induced Small Non-coding RNA in Escherichia coli *

doi: 10.1074/jbc.M109.089755

Figure Lengend Snippet: Effect of FnrS expression on the protein pattern of E. coli. A, the figure shows the relevant part of two-dimensional gels of strains ΔfnrS/pNDM220 (control) and ΔfnrS/pNDM220-fnrS. Cells were grown to log phase in minimal medium supplemented with glucose and then induced with 0.5 mm IPTG for 30 min at 37 °C. After this the cultures were labeled with [35S]methionine for 2 min and concentrated by centrifugation, and their proteins were analyzed by standard two-dimensional gel electrophoresis and autoradiography. The arrows indicate the position of proteins whose net synthesis rate was markedly altered upon FnrS expression. B, left panel, FnrS mediated repression of sodA expression. Strains SØ928ΔfnrS/pNDM220 (control) and SØ928ΔfnrS/pNDM220-fnrS were grown aerobically in LB media to an A450 of 0.4 and then induced by addition of IPTG (final concentration 1 mm). Samples were taken before (time 0) and 10 min after induction, and total RNA was extracted. The sodA mRNA and FnrS RNA levels were analyzed by Northern. B, right panel, shown is the effect of fnrS deletion on sodA expression. Aerobically grown cells of SØ928 and SØ928ΔfnrS were shifted to anoxia at time 0. Samples were taken at the indicated times, and RNA was extracted and probed for sodA mRNA and FnrS RNA. C, Hfq cooperates in RNA-RNA interaction. Samples containing 5′ end-labeled FnrS RNA (2 nm) and increasing amounts of unlabeled sodA1–150 substrate (covering the transcription start site to 97 nucleotides downstream of the translation start site) were incubated in the absence (lanes 1–4) or in the presence of Hfq (lanes 5–8), and complex formation was monitored in a electrophoretic mobility shift experiment. sodA′ RNA concentrations were as indicated, and the Hfq hexamer concentration was 0.33 μm. Unbound FnrS RNA and complexes corresponding to Hfq-FnrS RNA and FnrS RNA-Hfq-sodA′ RNA are indicated by arrows. D, shown is validation of post-transcriptional regulation of sodA expression by a translational sodA::gfp reporter fusion. The experiment was as in Fig. 4E but with the pXG10-sodA′::gfp reporter plasmid. E, the experiment was the same as D but with pXG10-metE′::gfp reporter plasmid.

Article Snippet: Transcriptome Analysis Global gene expression analysis was carried out using E. coli glass-slide microarrays ( E. coli K-12 V2 OciChip, Ocimum Biosolutions) as previously described ( 20 ).

Techniques: Expressing, Control, Labeling, Centrifugation, Two-Dimensional Gel Electrophoresis, Electrophoresis, Autoradiography, Concentration Assay, Northern Blot, Incubation, Electrophoretic Mobility Shift Assay, Biomarker Discovery, Plasmid Preparation