1887

Abstract

The discovery of non-coding RNA (ncRNA) has been mainly limited to laboratory model systems and human pathogenic bacteria. In this study, we begin to explore the ncRNA diversity in four recently sequenced environmental species ( 40B, 1DA3, VM573 and BAA-1116) by performing searches using Infernal and Rfam for the identification of putative ncRNA-encoding genes. This search method resulted in the identification of 31–38 putative ncRNA genes per species and the total ncRNA catalogue spanned an assortment of regulatory mechanisms (riboswitches, -encoded ncRNAs, -encoded ncRNAs, modulators of protein activity, ribonucleoproteins, transcription termination ncRNAs and unknown). We chose to experimentally validate the identifications for BAA-1116 using a microarray-based expression profiling strategy. Transcript hybridization to tiled probes targeting annotated BAA-1116 intergenic regions revealed that 21 of the 38 predicted ncRNA genes were expressed in mid-exponential-phase cultures grown in nutrient-rich medium. The microarray findings were confirmed by testing a subset of three highly expressed (6S, tmRNA and TPP-2) and three moderately expressed (CsrB, GcvB and purine) ncRNAs via reverse transcription PCR. Our findings provide new information on the diversity of ncRNA in environmental vibrios while simultaneously promoting a more accurate annotation of genomic intergenic regions.

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2010-08-01
2020-01-19
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Primers used in the RT-PCR experiments [ Excel file] (33 kb) ncRNAs found in the four genomes [ Excel file] (288 kb) [ .txt file] (5 kb) [ .txt file] (3 kb) [ .txt file] (5 kb) [ .txt file] (2 kb) [ .txt file] (6 kb) [ .txt file] (2 kb) [ .txt file] (5 kb) [ .txt file] (2 kb)

EXCEL

Primers used in the RT-PCR experiments [ Excel file] (33 kb) ncRNAs found in the four genomes [ Excel file] (288 kb) [ .txt file] (5 kb) [ .txt file] (3 kb) [ .txt file] (5 kb) [ .txt file] (2 kb) [ .txt file] (6 kb) [ .txt file] (2 kb) [ .txt file] (5 kb) [ .txt file] (2 kb)

EXCEL

Primers used in the RT-PCR experiments [ Excel file] (33 kb) ncRNAs found in the four genomes [ Excel file] (288 kb) [ .txt file] (5 kb) [ .txt file] (3 kb) [ .txt file] (5 kb) [ .txt file] (2 kb) [ .txt file] (6 kb) [ .txt file] (2 kb) [ .txt file] (5 kb) [ .txt file] (2 kb)

TEXT

Primers used in the RT-PCR experiments [ Excel file] (33 kb) ncRNAs found in the four genomes [ Excel file] (288 kb) [ .txt file] (5 kb) [ .txt file] (3 kb) [ .txt file] (5 kb) [ .txt file] (2 kb) [ .txt file] (6 kb) [ .txt file] (2 kb) [ .txt file] (5 kb) [ .txt file] (2 kb)

TEXT

Primers used in the RT-PCR experiments [ Excel file] (33 kb) ncRNAs found in the four genomes [ Excel file] (288 kb) [ .txt file] (5 kb) [ .txt file] (3 kb) [ .txt file] (5 kb) [ .txt file] (2 kb) [ .txt file] (6 kb) [ .txt file] (2 kb) [ .txt file] (5 kb) [ .txt file] (2 kb)

TEXT

Primers used in the RT-PCR experiments [ Excel file] (33 kb) ncRNAs found in the four genomes [ Excel file] (288 kb) [ .txt file] (5 kb) [ .txt file] (3 kb) [ .txt file] (5 kb) [ .txt file] (2 kb) [ .txt file] (6 kb) [ .txt file] (2 kb) [ .txt file] (5 kb) [ .txt file] (2 kb)

TEXT

Primers used in the RT-PCR experiments [ Excel file] (33 kb) ncRNAs found in the four genomes [ Excel file] (288 kb) [ .txt file] (5 kb) [ .txt file] (3 kb) [ .txt file] (5 kb) [ .txt file] (2 kb) [ .txt file] (6 kb) [ .txt file] (2 kb) [ .txt file] (5 kb) [ .txt file] (2 kb)

TEXT

Primers used in the RT-PCR experiments [ Excel file] (33 kb) ncRNAs found in the four genomes [ Excel file] (288 kb) [ .txt file] (5 kb) [ .txt file] (3 kb) [ .txt file] (5 kb) [ .txt file] (2 kb) [ .txt file] (6 kb) [ .txt file] (2 kb) [ .txt file] (5 kb) [ .txt file] (2 kb)

TEXT

Primers used in the RT-PCR experiments [ Excel file] (33 kb) ncRNAs found in the four genomes [ Excel file] (288 kb) [ .txt file] (5 kb) [ .txt file] (3 kb) [ .txt file] (5 kb) [ .txt file] (2 kb) [ .txt file] (6 kb) [ .txt file] (2 kb) [ .txt file] (5 kb) [ .txt file] (2 kb)

TEXT

Primers used in the RT-PCR experiments [ Excel file] (33 kb) ncRNAs found in the four genomes [ Excel file] (288 kb) [ .txt file] (5 kb) [ .txt file] (3 kb) [ .txt file] (5 kb) [ .txt file] (2 kb) [ .txt file] (6 kb) [ .txt file] (2 kb) [ .txt file] (5 kb) [ .txt file] (2 kb)

TEXT
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