TY - JOUR
T1 - In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1
AU - Dobrzanski, Tatiane
AU - Pobre, Vânia
AU - Moreno, Leandro Ferreira
AU - Barbosa, Helba Cirino De Souza
AU - Monteiro, Rose Adele
AU - De Oliveira Pedrosa, Fábio
AU - De Souza, Emanuel Maltempi
AU - Arraiano, Cecília Maria
AU - Steffens, Maria Berenice Reynaud
PY - 2020/2/10
Y1 - 2020/2/10
N2 - Background: 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. 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. Results: This 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. Conclusions: H. 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.
AB - Background: 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. 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. Results: This 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. Conclusions: H. 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.
KW - Bacterial plant interaction
KW - Diazotrophic bacterium
KW - Herbaspirillum seropedicae SmR1
KW - Nitrogen fixation
KW - Regulatory RNA
KW - sRNA
UR - http://www.scopus.com/inward/record.url?scp=85079110967&partnerID=8YFLogxK
U2 - 10.1186/s12864-019-6402-x
DO - 10.1186/s12864-019-6402-x
M3 - Article
C2 - 32039705
AN - SCOPUS:85079110967
SN - 1471-2164
VL - 21
JO - BMC Genomics
JF - BMC Genomics
IS - 1
M1 - 134
ER -