title: The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501.
abstract: Unlike most Pseudomonas, the root-associated bacterium Pseudomonas stutzeri A1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. A genome-wide search for small noncoding RNAs (ncRNAs) in P. stutzeri A1501 identified the novel P. stutzeri-specific ncRNA NfiS in the core genome, whose synthesis was significantly induced under nitrogen fixation or sorbitol stress conditions. The expression of NfiS was RNA chaperone Hfq-dependent and activated by the sigma factor RpoN/global nitrogen activator NtrC/nif-specific activator NifA regulatory cascade. The nfiS-deficient mutant displayed reduced nitrogenase activity, as well as increased sensitivity to multiple stresses, such as osmotic and oxidative stresses. Secondary structure prediction and complementation studies confirmed that a stem-loop structure was essential for NfiS to regulate the nitrogenase gene nifK mRNA synthesis and thus nitrogenase activity. Microscale thermophoresis and physiological analysis showed that NfiS directly pairs with nifK mRNA and ultimately enhances nitrogenase activity by increasing the translation efficiency and the half-life of nifK mRNA. Our data also suggest structural and functional divergence of NfiS evolution in diazotrophic and nondiazotrophic backgrounds. It is proposed that NfiS was recruited by nifK mRNA as a novel regulator to integrate the horizontally acquired nif island into host global networks.
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Zhan
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Yongliang
authors.initials: Y
authors.lastname: Yan
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Deng
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Wei
authors.initials: W
authors.lastname: Lu
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Chao
authors.initials: C
authors.lastname: Lu
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Liguo
authors.initials: L
authors.lastname: Shang
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Zhimin
authors.initials: Z
authors.lastname: Yang
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Wei
authors.initials: W
authors.lastname: Zhang
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Yun
authors.initials: Y
authors.lastname: Li
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Qi
authors.initials: Q
authors.lastname: Ke
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Jiasi
authors.initials: J
authors.lastname: Lu
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Yuquan
authors.initials: Y
authors.lastname: Xu
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Liwen
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China;
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Xie
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
authors.forename: Qi
authors.initials: Q
authors.lastname: Cheng
authors.affiliation: Institut Pasteur, Paris 75724 Cedex 15, France.
authors.forename: Claudine
authors.initials: C
authors.lastname: Elmerich
authors.affiliation: National Key Facility for Crop Gene Resources and Genetic Improvement, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; linmin57@vip.163.com.
authors.forename: Min
authors.initials: M
authors.lastname: Lin
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D020029:Base Pairing / Q000235:genetics*; D001483:Base Sequence; D015964:Gene Expression Regulation, Bacterial; D009154:Mutation; D009586:Nitrogen Fixation / Q000235:genetics*; D009591:Nitrogenase / Q000235:genetics* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D044223:Pseudomonas stutzeri / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D001426:Bacterial Proteins; D012333:RNA, Messenger; D022661:RNA, Untranslated; D009591:Nitrogenase
keywords: NfiS; Pseudomonas stutzeri; nifK mRNA; nitrogen fixation; regulatory ncRNA