Small RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs has been carried out in various plant growth-promoting bacteria and they have been shown to help the cells cope up with environmental stress. No study has been carried out to uncover these regulatory molecules in the diazotrophic alpha-proteobacterium Azospirillum brasilense Sp245 to date. Expression-based sRNA identification (RNA-seq) revealed the first list of ~ 468 sRNA candidate genes in A. brasilense Sp245 that were differentially expressed in nitrogen starvation versus non-starved conditions. In parallel, in silico tools also identified 2 of the above as candidate sRNAs. Altogether, putative candidates were stringently curated from RNA-seq data based on known sRNA parameters (size, location, secondary structure, and abundance). In total, ~ 59 significantly expressed sRNAs were identified in this study of which 53 are potentially novel sRNAs as they have no Rfam and BSRD homologs. Sixteen sRNAs were randomly selected and validated for differential expression, which largely was found to be in congruence with the RNA-seq data. Differential expression of 468 A. brasilense sRNAs was indicated by RNA-seq data, a subset of which was confirmed by expression analysis. Four of the significantly expressed sRNAs were not observed in nitrogen starvation while 16 sRNAs were found to be exclusively expressed in nitrogen depletion. Putative candidate sRNAs identified have potential mRNA targets primarily involved in stress (abiotic and biotic) adaptability; regulation of bacterial cellular, biological and molecular pathways such as nitrogen fixation, polyhydroxybutyrate synthesis, chemotaxis, biofilm formation and transcriptional regulation. In addition to directly influencing bacteria, some of these sRNAs also have targets influencing plant-microbe interactions through adhesion of bacteria to plant roots directly, suppressing host response, inducing plant defence and signalling.

中文翻译：

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全基因组鉴定固氮螺菌 Sp245 小 RNA 对氮饥饿的响应并可能参与植物-微生物相互作用


小RNA (sRNA) 是非编码RNA，已知可调节多种细菌的各种生物功能，例如应激适应、代谢、毒力以及致病性，主要通过控制mRNA 稳定或调节翻译。 sRNA 的鉴定和功能表征已在多种植物促生长细菌中进行，并且已被证明可以帮助细胞应对环境压力。迄今为止，尚未开展任何研究来揭示固氮α-变形菌巴西固氮螺菌 Sp245 中的这些调节分子。基于表达的 sRNA 鉴定 (RNA-seq) 首次揭示了 A. brasilense Sp245 中大约 468 个 sRNA 候选基因的列表，这些基因在氮饥饿和非饥饿条件下表达存在差异。与此同时，计算机模拟工具也将上述 2 种识别为候选 sRNA。总而言之，假定的候选者是根据已知的 sRNA 参数（大小、位置、二级结构和丰度）从 RNA-seq 数据中严格筛选出来的。本研究总共鉴定出约 59 种显着表达的 sRNA，其中 53 种可能是新型 sRNA，因为它们没有 Rfam 和 BSRD 同源物。随机选择并验证了 16 个 sRNA 的差异表达，结果发现它们很大程度上与 RNA-seq 数据一致。 RNA-seq 数据表明了 468 个 A. brasilense sRNA 的差异表达，其中一部分通过表达分析得到了证实。 4 个显着表达的 sRNA 在氮饥饿中未观察到，而 16 个 sRNA 被发现仅在氮耗尽中表达。 已确定的假定候选 sRNA 具有主要涉及应激（非生物和生物）适应性的潜在 mRNA 靶点；调节细菌细胞、生物和分子途径，例如固氮、聚羟基丁酸酯合成、趋化性、生物膜形成和转录调节。除了直接影响细菌外，其中一些 sRNA 还具有通过细菌直接粘附到植物根部、抑制宿主反应、诱导植物防御和信号传导来影响植物-微生物相互作用的目标。