Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná (UFPR), Av. Coronel. Francisco H. dos Santos, 210, PoBox 19046, Curitiba, 81.531-980, Paraná, Brazil.
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal.
BMC Genomics. 2020 Feb 10;21(1):134. doi: 10.1186/s12864-019-6402-x.
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.
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.
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.
Herbaspirillum seropedicae 是一种从β变形菌纲分离出来的固氮菌，它定殖于重要的禾本科内共生体，通过依赖植物激素的刺激促进其生长，并能在植物组织内表达 nif 基因和固定氮。由于这些特性，该细菌具有作为农业商业接种剂的巨大潜力。H. seropedicae SmR1 基因组已完全测序和注释，但尽管对该基因组进行了多样化的结构和功能分析，涉及小非编码 RNA (sRNA) 的研究尚未进行。我们已经进行了计算预测和 RNA-seq 分析，以选择和确认 H. seropedicae SmR1 基因组中 sRNA 基因的表达，这些基因存在于两种独立的氮源和柚皮素（一些植物分泌的一种类黄酮）存在的情况下。
这种方法产生了一组分布在核糖体开关、顺式编码和反式编码类别中的 117 个 sRNA，其中 20 个具有 Rfam 同源物。发现了管家 sRNA tmRNA、ssrS 和 4.5S，我们观察到大量 sRNA 在硝酸盐条件下的表达高于对照条件下的表达，并且在柚皮素存在的情况下表达更多。一些 sRNA 的表达在体外得到了证实，这项工作有助于更好地理解该细菌中转录后调控。
H. seropedicae SmR1 在存在两种氮源和/或柚皮素的情况下表达 sRNA。这些 sRNA 中的大多数功能仍然未知，但它们在该细菌中的存在证实了 sRNA 参与许多不同的细胞活动以适应营养和环境变化的证据。
