Abstract
Symbiotic nitrogen fixation in legumes is mediated by an interplay of signaling processes between plant hosts and rhizobial symbionts. In legumes, several secreted protein families have undergone expansions and play key roles in nodulation. Thus, identifying lineage-specific expansions (LSEs) of nodulation-associated genes can be a strategy to discover candidate gene families. Using bioinformatic tools, we identified 13 LSEs of nodulation-related secreted protein families, each unique to either Glycine, Arachis or Medicago lineages. In the Medicago lineage, nodule-specific Polycystin-1, Lipoxygenase, Alpha Toxin (PLAT) domain proteins (NPDs) expanded to five members. We examined NPD function using CRISPR/Cas9 multiplex genome editing to create Medicago truncatula NPD knockout lines, targeting one to five NPD genes. Mutant lines with differing combinations of NPD gene inactivations had progressively smaller nodules, earlier onset of nodule senescence, or ineffective nodules compared to the wild-type control. Double- and triple-knockout lines showed dissimilar nodulation phenotypes but coincided in upregulation of a DHHC-type zinc finger and an aspartyl protease gene, possible candidates for the observed disturbance of proper nodule function. By postulating that gene family expansions can be used to detect candidate genes, we identified a family of nodule-specific PLAT domain proteins and confirmed that they play a role in successful nodule formation.
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Claims 6
Claim · model-written summary
Thirteen lineage-specific expansions of nodulation-related secreted protein families were identified across the Glycine, Arachis, and Medicago lineages.
GlycineOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we identified 13 LSEs of nodulation-related secreted protein families, each unique to either Glycine, Arachis or Medicago lineages”
Claim · model-written summary
Nodule-specific PLAT domain proteins expanded to five members in the Medicago lineage.
- Gene
- nodule-specific Polycystin-1, Lipoxygenase, Alpha Toxin (PLAT) domain proteins (NPDs)e0
- Outcome
- expanded to five memberse0
- Value
- five memberse0
MedicagoOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“In the Medicago lineage, nodule-specific Polycystin-1, Lipoxygenase, Alpha Toxin (PLAT) domain proteins (NPDs) expanded to five members”
Claim · model-written summary
Medicago truncatula NPD knockout combinations produced progressively smaller nodules than wild type.
- Taxon
- Medicago truncatula
Medicago truncatulat0 - Treatment
- NPD gene inactivationse0
- Gene
- NPDe0
- Outcome
- nodulese0
- Direction
- progressively smallere0
- Comparator
- wild-type controle0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Mutant lines with differing combinations of NPD gene inactivations had progressively smaller nodules, earlier onset of nodule senescence, or ineffective nodules compared to the wild-type control”
t0“Medicago truncatula”
Claim · model-written summary
Medicago truncatula NPD knockout combinations had earlier nodule senescence than wild type.
- Taxon
- Medicago truncatulaMedicago truncatulat0
- Treatment
- NPD gene inactivationse0
- Gene
- NPDe0
- Outcome
- nodule senescencee0
- Direction
- earlier onsete0
- Comparator
- wild-type controle0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Mutant lines with differing combinations of NPD gene inactivations had progressively smaller nodules, earlier onset of nodule senescence, or ineffective nodules compared to the wild-type control”
t0“Medicago truncatula”
Claim · model-written summary
Some Medicago truncatula NPD knockout combinations produced ineffective nodules.
- Taxon
- Medicago truncatulaMedicago truncatulat0
- Treatment
- NPD gene inactivationse0
- Gene
- NPDe0
- Outcome
- ineffective nodulese0
- Comparator
- wild-type controle0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Mutant lines with differing combinations of NPD gene inactivations had progressively smaller nodules, earlier onset of nodule senescence, or ineffective nodules compared to the wild-type control”
t0“Medicago truncatula”
Claim · model-written summary
Double and triple NPD knockout lines shared upregulation of a DHHC-type zinc finger and an aspartyl protease gene despite differing nodulation phenotypes.
- Taxon
- Medicago truncatulaMedicago truncatulat0
- Material
- Double- and triple-knockout linese0
- Gene
- a DHHC-type zinc finger and an aspartyl protease genee0
- Outcome
- upregulatione0
- Direction
- upregulatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Double- and triple-knockout lines showed dissimilar nodulation phenotypes but coincided in upregulation of a DHHC-type zinc finger and an aspartyl protease gene”
t0“Medicago truncatula”