ArticleBMC genomics2010
Global transcriptional analysis of nitrogen fixation and ammonium repression in root-associated Pseudomonas stutzeri A1501.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 89 citations in OpenAlex.
- Enhancing biological nitrogen fixation in rice paddy ecosystems: challenges, opportunities, and sustainable strategies.Frontiers in microbiology · 2026Review
- Nitrogen-fixing microbes gain genes in diverse types of living environments.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Biofertilizer Industry and Research Developments in China: A Mini-Review.Microbial biotechnology · 2025Review
- Biological Activity of Silicon Nitride Ceramics: A Critical Review.Materials (Basel, Switzerland) · 2024Review
- Article
- Nitrogen-fixing bacterial communities differ between perennial agroecosystem crops.FEMS microbiology ecology · 2024Article
- Reconstruction and metabolic profiling of the genome-scale metabolic network model ofSynthetic and systems biotechnology · 2023Article
- Mechanisms for Generating Low Potential Electrons across the Metabolic Diversity of Nitrogen-Fixing Bacteria.Applied and environmental microbiology · 2023Review
- Systematic identification of endogenous strong constitutive promoters from the diazotrophic rhizosphere bacterium Pseudomonas stutzeri DSM4166 to improve its nitrogenase activity.Microbial cell factories · 2023Article
- Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes iniScience · 2022Article
- Characterization of symbiotic and nitrogen fixing bacteria.AMB Express · 2022Review
- A regulatory network involving Rpo, Gac and Rsm for nitrogen-fixing biofilm formation by Pseudomonas stutzeri.NPJ biofilms and microbiomes · 2021Article
- Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions inFrontiers in microbiology · 2021Article
- Genome-Wide Analyses of Proteome and Acetylome inFrontiers in microbiology · 2021Article
- Microbial community successions and their dynamic functions during harmful cyanobacterial blooms in a freshwater lake.Water research · 2020Article
- Control of nitrogen fixation in bacteria that associate with cereals.Nature microbiology · 2020Article
- NfiR, a New Regulatory Noncoding RNA (ncRNA), Is Required in Concert with the NfiS ncRNA for Optimal Expression of Nitrogenase Genes in Pseudomonas stutzeri A1501.Applied and environmental microbiology · 2019Article
- Substrate cross-feeding affects the speed and trajectory of molecular evolution within a synthetic microbial assemblage.BMC evolutionary biology · 2019Article
- Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit.Biochemical Society transactions · 2019Review
- Global investigation of an engineered nitrogen-fixing Escherichia coli strain reveals regulatory coupling between host and heterologous nitrogen-fixation genes.Scientific reports · 2018Article
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Authors and funding
18 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBiological nitrogen fixation is highly controlled at the transcriptional level by regulatory networks that respond to the availability of fixed nitrogen. In many diazotrophs, addition of excess ammonium in the growth medium results in immediate repression of nif gene transcription. Although the regulatory cascades that control the transcription of the nif genes in proteobacteria have been well investigated, there are limited data on the kinetics of ammonium-dependent repression of nitrogen fixation.
resultsHere we report a global transcriptional profiling analysis of nitrogen fixation and ammonium repression in Pseudomonas stutzeri A1501, a root-associated and nitrogen-fixing bacterium. A total of 166 genes, including those coding for the global nitrogen regulation (Ntr) and Nif-specific regulatory proteins, were upregulated under nitrogen fixation conditions but rapidly downregulated as early as 10 min after ammonium shock. Among these nitrogen fixation-inducible genes, 95 have orthologs in each of Azoarcus sp. BH72 and Azotobacter vinelandii AvoP. In particular, a 49-kb expression island containing nif and other associated genes was markedly downregulated by ammonium shock. Further functional characterization of pnfA, a new NifA-sigma54-dependent gene chromosomally linked to nifHDK, is reported. This gene encodes a protein product with an amino acid sequence similar to that of five hypothetical proteins found only in diazotrophic strains. No noticeable differences in the transcription of nifHDK were detected between the wild type strain and pnfA mutant. However, the mutant strain exhibited a significant decrease in nitrogenase activity under microaerobic conditions and lost its ability to use nitrate as a terminal electron acceptor for the support of nitrogen fixation under anaerobic conditions.
conclusionsBased on our results, we conclude that transcriptional regulation of nif gene expression in A1501 is mediated by the nif-specific and ntr gene regulatory systems. Furthermore, microarray and mutational analyses revealed that many genes of unknown function may play some essential roles in controlling the expression or activity of nitrogenase. The findings presented here establish the foundation for further studies on the physiological function of nitrogen fixation-inducible genes.
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