ArticlePLoS genetics2014
Comparative genomic analysis of N2-fixing and non-N2-fixing Paenibacillus spp.: organization, evolution and expression of the nitrogen fixation genes.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
72 citing papers in PubMed, 141 citations in OpenAlex.
- Enhancement of Nitrogenase Activity in Recombinant Escherichia coli by Replacing Upstream Region of nif Operon from Paenibacillus Species.Chembiochem : a European journal of chemical biology · 2026Article
- Ecological constraints and evolutionary trade-offs shape nitrogen fixation across habitats.ISME communications · 2026Article
- NMicroorganisms · 2025Article
- 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
- Discovery of α-glucosidase inhibitors from Paenibacillus sp. JNUCC 31 via genome mining, fatty acid profiling, and in silico analysis.Scientific reports · 2025Article
- Microbial communities in the rhizosphere of tropical soils cultivated with maize as a function of nitrogen and phosphorus fertilizers.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Characterization of toxin systems of Paenibacillus strains isolated from honeybees.Scientific reports · 2025Article
- Regulation of the Ald gene encoding alanine dehydrogenase and its induction of ammonium-tolerant nitrogen fixation in Paenibacillus polymyxa WLY78.Microbial cell factories · 2025Article
- Novel gut bacteria species Paenibacillus ilasis with phosphorus degrading and soluble starch hydrolysis abilities isolated from fresh feces of rhinoceros.Scientific reports · 2025Article
- Biofertilizer Industry and Research Developments in China: A Mini-Review.Microbial biotechnology · 2025Review
- Role of horizontal gene transfer and cooperation in rhizosphere microbiome assembly.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Review
- Four Decades ofMicroorganisms · 2025Article
- The ever-evolving world of microbes: the current state of microbial taxonomy, genome evolutionary dynamics, and the potential impact on the future of agricultural microbials risk assessment.Frontiers in bioengineering and biotechnology · 2025Review
- NifFinder: improved Nif protein prediction using SWeeP vectors and neural networks.Bioinformatics advances · 2025Article
- Nitrogen-FixingMicroorganisms · 2024Article
- Friends and Foes: Bacteria of the Hydroponic Plant Microbiome.Plants (Basel, Switzerland) · 2024Review
- Integrated Proteomics and Metabolomics Reveal Altered Metabolic Regulation ofACS applied materials & interfaces · 2024Article
- Glutamine synthetase and GlnR regulate nitrogen metabolism inApplied and environmental microbiology · 2023Article
- Paenibacillus plantiphilus sp. nov. from the plant environment of Zea mays.Antonie van Leeuwenhoek · 2023Article
- Whole-Genome Sequence of Paenibacillus marchantiae Isolated from the Liverwort Marchantia polymorpha subsp.Microbiology resource announcements · 2023Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We provide here a comparative genome analysis of 31 strains within the genus Paenibacillus including 11 new genomic sequences of N2-fixing strains. The heterogeneity of the 31 genomes (15 N2-fixing and 16 non-N2-fixing Paenibacillus strains) was reflected in the large size of the shell genome, which makes up approximately 65.2% of the genes in pan genome. Large numbers of transposable elements might be related to the heterogeneity. We discovered that a minimal and compact nif cluster comprising nine genes nifB, nifH, nifD, nifK, nifE, nifN, nifX, hesA and nifV encoding Mo-nitrogenase is conserved in the 15 N2-fixing strains. The nif cluster is under control of a σ(70)-depedent promoter and possesses a GlnR/TnrA-binding site in the promoter. Suf system encoding [Fe-S] cluster is highly conserved in N2-fixing and non-N2-fixing strains. Furthermore, we demonstrate that the nif cluster enabled Escherichia coli JM109 to fix nitrogen. Phylogeny of the concatenated NifHDK sequences indicates that Paenibacillus and Frankia are sister groups. Phylogeny of the concatenated 275 single-copy core genes suggests that the ancestral Paenibacillus did not fix nitrogen. The N2-fixing Paenibacillus strains were generated by acquiring the nif cluster via horizontal gene transfer (HGT) from a source related to Frankia. During the history of evolution, the nif cluster was lost, producing some non-N2-fixing strains, and vnf encoding V-nitrogenase or anf encoding Fe-nitrogenase was acquired, causing further diversification of some strains. In addition, some N2-fixing strains have additional nif and nif-like genes which may result from gene duplications. The evolution of nitrogen fixation in Paenibacillus involves a mix of gain, loss, HGT and duplication of nif/anf/vnf genes. This study not only reveals the organization and distribution of nitrogen fixation genes in Paenibacillus, but also provides insight into the complex evolutionary history of nitrogen fixation.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.