Although bacterial small noncoding RNAs (sRNAs) are known to play a critical role in various cellular processes, including pathogenesis, the identity and action of such sRNAs are still poorly understood in many organisms. Here we have performed a genome‐wide screen and functional analysis of the sRNAs in Xanthomonas campestris pv. campestris (Xcc), an important phytopathogen. The 50–500‐nt RNA fragments isolated from the wild‐type strain grown in a virulence gene‐inducing condition were sequenced and a total of 612 sRNA candidates (SRCs) were identified. The majority (82%) of the SRCs were derived from mRNA, rather than specific sRNA genes. A representative panel of 121 SRCs were analysed by northern blotting; 117 SRCs were detected, supporting the contention that the overwhelming majority of the 612 SRCs identified are indeed sRNAs. Phenotypic analysis of strains overexpressing different candidates showed that a particular sRNA, RsmU, acts as a negative regulator of virulence, the hypersensitive response, and cell motility in Xcc. In vitro electrophoretic mobility shift assay and in vivo coimmunoprecipitation analyses indicated that RsmU interacted with the global posttranscriptional regulator RsmA, although sequence analysis displayed that RsmU is not a member of the sRNAs families known to antagonize RsmA. Northern blotting analyses demonstrated that RsmU has two isoforms that are processed from the 3′‐untranslated region of the mRNA of XC1332 predicted to encode ComEA, a periplasmic protein required for DNA uptake in bacteria. This work uncovers an unexpected major sRNA biogenesis strategy in bacteria and a hidden layer of sRNA‐mediated virulence regulation in Xcc.

中文翻译：

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Xanthomonas中的全基因组筛选和功能分析揭示了大量的mRNA衍生sRNA，包括新型RsmA-后代RsmU。

尽管已知细菌小的非编码RNA（sRNA）在包括发病在内的各种细胞过程中都起着关键作用，但在许多生物中仍不清楚这种sRNA的身份和作用。在这里，我们对Xanthomonas campestris pv中的sRNA进行了全基因组筛选和功能分析。桔梗（Xcc），一种重要的植物病原体。从在致病性基因诱导条件下生长的野生型菌株中分离的50-500nt核苷酸片段进行了测序，共鉴定出612个sRNA候选物（SRC）。大多数（82％）SRC来自mRNA，而不是特定的sRNA基因。通过Northern印迹分析了代表性的121个SRC。检测到117个SRC，支持以下论点：确定的612个SRC中绝大多数是sRNA。对过度表达不同候选菌株的表型分析表明，特定的sRNA RsmU在Xcc中充当毒力，超敏反应和细胞运动的负调节剂。体外电泳迁移率变动分析和体内共免疫沉淀分析表明，RsmU与全局转录后调节剂RsmA相互作用，尽管序列分析显示RsmU不是已知可拮抗RsmA的sRNAs家族的成员。Northern印迹分析表明，RsmU具有两种同工型，它们是从mRNA的3'非翻译区加工而来的。XC1332预计将编码ComEA，一种细菌DNA摄取所需的周质蛋白。这项工作揭示了细菌中意想不到的主要sRNA生物发生策略，以及Xcc中sRNA介导的毒力调节的隐藏层。