NodMutDB: a database for genes and mutants involved in symbiosis

@article{Mao2005NodMutDBAD,
  title={NodMutDB: a database for genes and mutants involved in symbiosis},
  author={Chunhong Mao and Jing Qiu and Chunxia Wang and Trevor C. Charles and Bruno W. S. Sobral},
  journal={Bioinformatics},
  year={2005},
  volume={21 12},
  pages={
          2927-9
        }
}
UNLABELLED Functional genomics research is producing large amounts of data on the functions of individual genes related to symbiosis. We have developed a relational database, NodMutDB (Nodulation Mutant Database), to provide a comprehensive resource for depositing, organizing and retrieving information on symbiosis-related genes, mutants and published literature. NodMutDB brings together new studies and existing mutant-based literature to facilitate our understanding of how genes function in… 

Figures and Tables from this paper

Evolution of Symbiosis Genes: Vertical and Horizontal Gene Transfer

TLDR
The evolutionary history of nitrogen fixation genes can be disassociated from that of nodulation genes (Fig. 6.1), indicating potential replacement of transferred nif genes by indigenous ones.

Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations

TLDR
It is suggested that faithfully vertical genes were rare compared with those with history of recombination including lateral gene transfer, although rhizobial adaptations to symbiotic interactions and other environmental conditions extensively recruited lineage-specific shell genes under direct or indirect control through the speciation process.

Coordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii

TLDR
The importance of integrative regulation of hierarchical core/accessory components in the multipartite genome of bacteria during niche adaptation and in shaping the prokaryotic pangenome in the long run is highlighted.

Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts

TLDR
Comparative genomics demonstrated horizontal gene transfer exclusively at the plasmid level, leading to expanded diversity of bean-nodulating Rhizobium strains and suggested symbiosis with other indigenous legumes and loss of originally symbiotic regions or non-symbionts before the introduction of common bean into China.

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

TLDR
The extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity of S. meliloti strains AK83 and BL225C, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains.

Metabolic Analyses of Nitrogen Fixation in the Soybean Microsymbiont Sinorhizobium fredii Using Constraint-Based Modeling

TLDR
This work presents the first metabolic network reconstruction of S. fredii as an example of a useful tool for exploring the potential benefits of microsymbionts to sustainable agriculture and the ecosystem and predicted a higher nitrogen fixation capacity in cultivated soybean.

Replicon-Dependent Differentiation of Symbiosis-Related Genes in Sinorhizobium Strains Nodulating Glycine max

TLDR
Taking together, genes from different replicons of rhizobia might be involved in the establishment of symbiosis with legumes, but these symbiosis-related genes might have evolved differently according to their corresponding replicons.

Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters

TLDR
Results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.

In Silico Insights into the Symbiotic Nitrogen Fixation in Sinorhizobium meliloti via Metabolic Reconstruction

TLDR
The manually curated model iHZ565 provides an overview of the major metabolic properties of the SNF bioprocess in S. meliloti 1021 and can be used as a knowledge-based framework for better understanding the symbiotic relationship between rhizobia and legumes.

References

SHOWING 1-10 OF 10 REFERENCES

Six nonnodulating plant mutants defective for Nod factor-induced transcriptional changes associated with the legume-rhizobia symbiosis.

  • R. MitraS. ShawS. Long
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 2004
TLDR
46 sequences that are differentially expressed in plants exposed for 24 h to WT Sinorhizobium meliloti or to the invasion defective S. Meliloti mutant, exoA are identified, including nucleolar proteins, which are implicated in ribosome biogenesis and several previously uncharacterized genes.

The Composite Genome of the Legume Symbiont Sinorhizobium meliloti

TLDR
The annotated DNA sequence of the α-proteobacteriumSinorhizobium meliloti, the symbiont of alfalfa, is presented, indicating that all three elements contribute, in varying degrees, to symbiosis and reveals how this genome may have emerged during evolution.

A receptor kinase gene regulating symbiotic nodule development

TLDR
The cloning of a gene from Medicago sativa that is essential for Nod-factor perception in alfalfa is described, and by genetic analogy, in the related legumes Medicago truncatula and Pisum sativum, and the identified ‘nodulation receptor kinase’, NORK, is predicted to function in the Nod -factor perception/transduction system (the NORK system) that initiates a signal cascade leading to nodulation.

Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid

TLDR
The complete 1,354,226-nt sequence of pSymA, which contains genes likely to be involved in nitrogen and carbon metabolism, transport, stress, and resistance responses, and other functions that give S. meliloti an advantage in its specialized niche.

Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021

TLDR
The presence in this replicon of a large number of nucleotide cyclases with a peculiar structure, as well as of genes homologous to virulence determinants of animal and plant pathogens, opens perspectives in the study of this bacterium both as a free-living soil microorganism and as a plant symbiont.

The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti

Analysis of the 1,683,333-nt sequence of the pSymB megaplasmid from the symbiotic N2-fixing bacterium Sinorhizobium meliloti revealed that the replicon has a high gene density with a total of 1,570

A Nonsymbiotic Root Hair Tip Growth Phenotype in NORK-Mutated Legumes: Implications for Nodulation Factor–Induced Signaling and Formation of a Multifaceted Root Hair Pocket for Bacteria

TLDR
It is reported that NORK-mutated legumes of three species show an enhanced touch response to experimental handling, which results in a nonsymbiotic root hair phenotype.

Proc

  • Natl Acad. Sci. USA, 98, 9877–9882.
  • 1021