Comment[ArrayExpressAccession] E-GEOD-66443 MAGE-TAB Version 1.1 Public Release Date 2015-03-03 Investigation Title Transcriptional control in Candidatus Pelagibacter ubique and other marine bacterial taxa Comment[Submitted Name] Transcriptional control in Candidatus Pelagibacter ubique and other marine bacterial taxa Experiment Description Bacteria respond to stimuli in the environment using transcriptional control, but this may not be the case for most marine bacteria having small, streamlined genomes. Candidatus Pelagibacter ubique, a cultivated representative of the SAR11 clade, which is the most abundant clade in the oceans 4, has a small, streamlined genome and possesses an unusually small number of transcriptional regulators. This observation leads to the hypothesis that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. However, the extent of transcriptional control in Pelagibacter is unknown. Here we show that transcriptional control is extremely low in Pelagibacter and another oligotroph (SAR92) compared to two marine copiotrophic bacterial taxa, Polaribacter MED152 and Ruegeria pomeroyi. We found that ~0.1% of protein-encoding genes in Pelagibacter are under transcriptional control compared to >10% of genes in other marine bacteria. Regardless of the growth condition, the same genes were highly expressed while most genes were always expressed at very low levels. Quantitative RNA sequencing revealed that abundances of most Pelagibacter transcripts were <0.01 copies per cell whereas transcript abundances were 1 to 10 copies per cell in some other bacteria. Our results demonstrate that Pelagibacter can change growth without shifts in transcript levels, suggesting that transcriptional control plays a minimal role in the adaptive strategy for one of the most successful organisms in the biosphere. Bacteria were grown in batch culture and sampled twice during the initial, rapid phase of exponential growth and twice during the phase of slower growth that followed. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Cottrell Cottrell Kirchman Person First Name Matthew Matthew David Person Mid Initials T L Person Email mattcott@udel.edu Person Affiliation University of Delaware Person Phone 302 645 4383 Person Address University of Delaware, 700 Pilottown Rd, Lewes, USA Person Roles submitter Protocol Name P-GSE66443-3 P-GSE66443-2 P-GSE66443-1 Protocol Description HiSeq Control Software Rockhopper software (http://cs.wellesley.edu/~btjaden/Rockhopper/) Genome_build: Candidatus Pelagibacter ubique HTCC1062, complete genome (NC_007205.1), Polaribacter sp. MED152, complete genome (CP004349.1), Ruegeria pomeroyi DSS-3, complete genome (NC_003911.12), Ruegeria pomeroyi DSS-3 megaplasmid (NC_006569.1), marine gamma proteobacterium HTCC2207 scaffolds (NZ_CH672400,NZ_CH672399,NZ_CH672398,NZ_CH672397,NZ_CH672396) Supplementary_files_format_and_content: Excel file containing Rockhopper output Bacterial biomass was collected by vacuum filtration using 0.2 µm-pore-size Durapore filters. The filters were stored at -80°C in RLT buffer until DNA and RNA were extracted using the AllPrep DNA/RNA (Qiagen) kit following the manufacturer's instructions. RNA libraries were prepared for sequencing using Ribo-Zero rRNA Removal Kit (Bacteria) and TruSeq RNA Sample Prep Kit following Illumina protocols Batch culture, 19°C, aerated in darkness Protocol Type normalization data transformation protocol nucleic acid library construction protocol growth protocol Experimental Factor Name strain growth phase organism Experimental Factor Type strain growth phase organism Comment[SecondaryAccession] GSE66443 Comment[GEOReleaseDate] 2015-03-03 Comment[ArrayExpressSubmissionDate] 2015-03-03 Comment[GEOLastUpdateDate] 2015-03-04 Comment[AEExperimentType] RNA-seq of coding RNA Comment[AdditionalFile:Data1] GSE66443_Processed_Data_Matrix_for_Pelagibacter_SAR92_MED152_Ruegeria.xlsx Comment[SecondaryAccession] SRP055747 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR1823734-SRR1823777 SDRF File E-GEOD-66443.sdrf.txt