Abstract
BackgroundHerbaspirillum seropedicae is a diazotrophic bacterium from the β-proteobacteria class that colonizes endophytically important gramineous species, promotes their growth through phytohormone-dependent stimulation and can express nif genes and fix nitrogen inside plant tissues. Due to these properties this bacterium has great potential as a commercial inoculant for agriculture. The H. seropedicae SmR1 genome is completely sequenced and annotated but despite the availability of diverse structural and functional analysis of this genome, studies involving small non-coding RNAs (sRNAs) has not yet been done. We have conducted computational prediction and RNA-seq analysis to select and confirm the expression of sRNA genes in the H. seropedicae SmR1 genome, in the presence of two nitrogen independent sources and in presence of naringenin, a flavonoid secreted by some plants.ResultsThis approach resulted in a set of 117 sRNAs distributed in riboswitch, cis-encoded and trans-encoded categories and among them 20 have Rfam homologs. The housekeeping sRNAs tmRNA, ssrS and 4.5S were found and we observed that a large number of sRNAs are more expressed in the nitrate condition rather than the control condition and in the presence of naringenin. Some sRNAs expression were confirmed in vitro and this work contributes to better understand the post transcriptional regulation in this bacterium.ConclusionsH. seropedicae SmR1 express sRNAs in the presence of two nitrogen sources and/or in the presence of naringenin. The functions of most of these sRNAs remains unknown but their existence in this bacterium confirms the evidence that sRNAs are involved in many different cellular activities to adapt to nutritional and environmental changes.
Highlights
Herbaspirillum seropedicae is a diazotrophic bacterium from the β-proteobacteria class that colonizes endophytically important gramineous species, promotes their growth through phytohormone-dependent stimulation and can express nif genes and fix nitrogen inside plant tissues
Were analysed three RNA sequencing (RNA-seq) data conditions obtained during the exponential growth phase of the bacterium: (i) control (CRT) - bacteria grown in NFbHPN medium containing NH4Cl as nitrogen source, (ii) presence of naringenin (NAR) - bacteria cultured in NFbHPN medium containing NH4Cl and the flavonoid naringenin, and (iii) nitrate (NIT) - bacteria grown in NFbHP medium containing KNO3 as nitrogen source
Using the coverage criterion which established a minimum coverage ≥5 as a confidence level to select Small non-coding RNA (sRNA) in at least one of the three culture conditions we were able to verify the expression of 117 sRNAs transcripts in H. seropedicae SmR1 which have been termed Hsnc001 to Hsnc117 (Additional file 1)
Summary
Herbaspirillum seropedicae is a diazotrophic bacterium from the β-proteobacteria class that colonizes endophytically important gramineous species, promotes their growth through phytohormone-dependent stimulation and can express nif genes and fix nitrogen inside plant tissues. Due to these properties this bacterium has great potential as a commercial inoculant for agriculture. Herbaspirillum seropedicae SmR1 is a diazotrophic and endophytic bacterium that belongs to the β-proteobacteria This microorganism fixes nitrogen under microaerobic conditions inside the plant tissues of the economically. This microorganism can catabolize naringenin probably to obtain carbon and energy [18]
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