Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression analysis of the wild-type (N3433) and pcnB mutant (IBPC903) using custom microarrays

ABSTRACT: The experiments were aimed at comparison of gene expression patterns of Escherichia coli pcnB mutant (IBPC903) lacking functional poly(A) polymerase I with its isogenic wild-type (N3433) strain grown in Luria-Bertani (LB) by using custom microarrays with improved detection of E. coli sRNAs.

INSTRUMENT(S): G2565CA DNA microarray scanner (Agilent) for scanning., Chamber type: SureHyb hybridization chamber (Agilent).

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Vladimir Kaberdin

PROVIDER: E-MTAB-5433 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A new custom microarray for sRNA profiling in Escherichia coli.

Ruiz-Larrabeiti Olatz O Plágaro Ander Hernández AH Gracia Celine C Sevillano Elena E Gallego Lucía L Hajnsdorf Eliane E Kaberdin Vladimir R VR

FEMS microbiology letters 20160517 13

Bacterial small RNAs (sRNAs) play essential roles in the post-transcriptional control of gene expression. To improve their detection by conventional microarrays, we designed a custom microarray containing a group of probes targeting known and some putative Escherichia coli sRNAs. To assess its potential in detection of sRNAs, RNA profiling experiments were performed with total RNA extracted from E. coli MG1655 cells exponentially grown in rich (Luria-Bertani) and minimal (M9/glucose) media. We f ...[more]

PMID: 27190161

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Project description:Pelagic aggregates function as hotspots for microbial activity and biological carbon pumps for exporting OM fixed by photoautotrophs to sediments in lakes and oceans. In iron-rich (ferruginous) lakes, photoferrotrophic or chemolithoautotrophic bacteria appear to contribute to CO2 fixation by oxidizing reduced iron which leads to the formation of iron-rich pelagic aggregates called iron-snow. In acidic lakes, iron snow is colonized mainly by acidophilic iron-cycling microbes that can trigger interspecies aggregation mechanisms. However, the significance of iron oxidizers in carbon fixation, their general role in iron snow functioning, and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis with a 13CO2 metabolic labeling approach to determine general metabolic activities. Protein-based stable isotope probing (protein-SIP) was used to trace the 13CO2 incorporation in iron snow microcosms over time under both oxic and anoxic conditions. Analysis of our mRNA-derived metatranscriptome data identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6%-85.7%) in iron snow encoding a variety of ecologically relevant pathways, including carbon fixation, polysaccharide biosynthesis, and flagellar-based motility. We did not detect transcriptional activity for carbon fixation from archaea or eukaryotes. The largest numbers of expressed genes (3008, 2991, 2936) matched to the genomes of our previously obtained iron snow isolates (Acidithrix sp. C25, Acidiphilium sp. C61, Acidocella sp. C78) separately. 13CO2 incorporation studies identified Leptospirillum and Ferrovum, as the main active chemolithoautotrophs under oxic conditions, and Ferrovum was the main active organism under anoxic conditions as well. Small amounts of labeled 13C (Relative isotope abundance: 1.0%-5.3%) were found in the heterotrophic Acidiphilium and Acidocella. Overall, our data show that iron oxidizers play an important role in the formation of iron minerals and CO2 fixation, but the majority of fixed C apparently did not reach other iron snow microbes. This finding suggests that most of the fixed C will be directly exported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

Dataset Information

Gene expression analysis of the wild-type (N3433) and pcnB mutant (IBPC903) using custom microarrays

Publications

A new custom microarray for sRNA profiling in Escherichia coli.

Similar Datasets

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