Genome Transcriptome Analysis and Functional Characterization of a Nitrogen‐Fixation Island in Root‐Associated
            <i>Pseudomonas stutzeri</i>

Yan, Yongliang; Lu, Wei; Chen, Ming; Wang, Jin; Zhang, Wei; Zhang, Yunhua; Ping, Shuzhen; Elmerich, Claudine; Lin, Min

doi:10.1002/9781118297674.ch80

Cited by 5 publications

(9 citation statements)

References 61 publications

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“…A band corresponding to the migration of a 250-nt molecule was detected by Northern blot analysis in the WT strain A1501, but it was not detected when the analysis was performed with RNA extracted from deletion mutants for rpoN, ntrC, or nifA under nitrogen fixation conditions (Fig. 1A, Inset, lanes 1-4), which are involved in the regulation of nitrogen fixation (17,18,24,25). The band intensity was decreased when the analysis was performed with RNA extracted from an rpoS deletion mutant, known in other systems as the RNA polymerase sigma factor of the general stress response (30) (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…In contrast, their expression was remarkably enhanced by overproduction of NfiS. In particular, nifA, coding for the transcriptional activator of all nif operons (18,24,25), showed a threefold increase, and glnK, coding for a PII family protein (31,32), showed a sixfold increase (Fig. S4A).…”

Section: Nfis Contributes To the Global And Positive Regulation Of Nimentioning

confidence: 99%

“…They play important roles in the nitrogen and carbon cycles (16). However, the biological nitrogen fixation ability, a process by which bacteria reduce molecular N 2 gas to ammonia, is rarely encountered in this genus (16)(17)(18). It is now established that nitrogen-fixing strains can be found within the P. stutzeri species.…”

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confidence: 99%

“…It is now established that nitrogen-fixing strains can be found within the P. stutzeri species. Determination of the P. stutzeri A1501, DSM4166, and BAL398 genome nucleotide sequences led to the identification of a conserved, 49-kb nitrogen-fixing island acquired by horizontal gene transfer (HGT) in these three strains (17)(18)(19)(20). A recent in silico analysis revealed that the island is also conserved in other available genomes of nitrogen-fixing P. stutzeri (ref.…”

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confidence: 99%

“…Thus, the regulatory network controlling nitrogen fixation in A1501 may result from regulatory systems of different evolutionary origins. Colonization of the plant rhizosphere implies that nitrogen-fixing P. stutzeri strains adapt to a range of physiological conditions, such as environmental stresses and nutrient availability (18,23,26). Despite the identification of a number of genes potentially involved in rhizosphere competence in the A1501 genome, little is known about the mechanisms of adaptation and survival in the rhizosphere (17).…”

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confidence: 99%

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The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501

Zhan

Yan

Deng

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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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 Hfqdependent and activated by the sigma factor RpoN/global nitrogen activator NtrC/nif-specific activator NifA regulatory cascade. The nfiSdeficient 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.nitrogen fixation | Pseudomonas stutzeri | regulatory ncRNA | NfiS | nifK mRNA

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Section: Resultsmentioning

confidence: 99%

Section: Nfis Contributes To the Global And Positive Regulation Of Nimentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501

Zhan

Yan

Deng

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions

et al. 2017

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The multicellular communities of microorganisms known as biofilms are of high significance in agricultural setting, yet it is largely unknown about the biofilm formed by nitrogen-fixing bacteria. Here we report the biofilm formation by Pseudomonas stutzeri A1501, a free-living rhizospheric bacterium, capable of fixing nitrogen under microaerobic and nitrogen-limiting conditions. P. stutzeri A1501 tended to form biofilm in minimal media, especially under nitrogen depletion condition. Under such growth condition, the biofilms formed at the air-liquid interface (termed as pellicles) and the colony biofilms on agar plates exhibited nitrogenase activity in air. The two kinds of biofilms both contained large ovoid shape 'cells' that were multiple living bacteria embedded in a sac of extracellular polymeric substances (EPSs). We proposed to name such large 'cells' as A1501 cyst. Our results suggest that the EPS, especially exopolysaccharides enabled the encased bacteria to fix nitrogen while grown under aerobic condition. The formation of A1501 cysts was reversible in response to the changes of carbon or nitrogen source status. A1501 cyst formation depended on nitrogen-limiting signaling and the presence of sufficient carbon sources, yet was independent of an active nitrogenase. The pellicles formed by Azospirillum brasilense, another free-living nitrogen-fixing rhizobacterium, which also exhibited nitrogenase activity and contained the large EPS-encapsuled A1501 cyst-like 'cells'. Our data imply that free-living nitrogen-fixing bacteria could convert the easy-used carbon sources to exopolysaccharides in order to enable nitrogen fixation in a natural aerobic environment.

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Small RNAs Involved in Regulation of Nitrogen Metabolism

Prasse

Schmitz

2018

Regulating With RNA in Bacteria and Archaea

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Genome Transcriptome Analysis and Functional Characterization of a Nitrogen‐Fixation Island in Root‐Associated Pseudomonas stutzeri

Cited by 5 publications

References 61 publications

The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501

The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501

Biofilm formation enables free-living nitrogen-fixing rhizobacteria to fix nitrogen under aerobic conditions

Small RNAs Involved in Regulation of Nitrogen Metabolism

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