Abstract
Salicylic acid (SA) has an essential role in the responses of plants to pathogens. SA initiates defence signalling via binding to proteins. NPR1 is a transcriptional co-activator and a key target of SA binding. Many other proteins have recently been shown to bind SA. Amongst these proteins are important enzymes of primary metabolism. This fact could stand behind SA’s ability to control energy fluxes in stressed plants. Nevertheless, only sparse information exists on the role and mechanisms of such binding. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was previously demonstrated to bind SA both in human and plants. Here, we detail that the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM, as shown in surface plasmon resonance experiments. Besides, we show that SA inhibits its GAPDH activity in vitro. To gain some insight into the underlying molecular interactions and binding mechanism, we combined in silico molecular docking experiments and molecular dynamics simulations on the free protein and protein–ligand complex. The molecular docking analysis yielded to the identification of two putative binding pockets for SA. A simulation in water of the complex between SA and the protein allowed us to determine that only one pocket—a surface cavity around Asn35—would efficiently bind SA in the presence of solvent. In silico mutagenesis and simulations of the ligand/protein complexes pointed to the importance of Asn35 and Arg81 in the binding of SA to GAPA1. The importance of this is further supported through experimental biochemical assays. Indeed, mutating GAPA1 Asn35 into Gly or Arg81 into Leu strongly diminished the ability of the enzyme to bind SA. The very same cavity is responsible for the NADP+ binding to GAPA1. More precisely, modelling suggests that SA binds to the very site where the pyrimidine group of the cofactor fits. NADH inhibited in a dose-response manner the binding of SA to GAPA1, validating our data.
Abstract from the paper’s OpenAlex record; open copy licensed cc-by. Read at the source ↗
The text the model read, with the source record’s inline markup (italics, sub- and superscripts) rendered and its character entities decoded; quote offsets refer to the raw text.
Claims 9
Claim · model-written summary
GAPA1 from Arabidopsis thaliana binds salicylic acid with a KD of 16.7 nM.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM”
Claim · model-written summary
Salicylic acid inhibits GAPDH activity in vitro.
- Taxon
- Arabidopsis thaliana
Arabidopsis thalianae0 - Treatment
- SAe1
- Gene
- GAPDHe1
- Outcome
- GAPDH activitye1
- Direction
- inhibitse1
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM”
e1“we show that SA inhibits its GAPDH activity in vitro”
Claim · model-written summary
Mutating GAPA1 Asn35 into Gly or Arg81 into Leu strongly diminished the ability of GAPA1 to bind SA.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae0
- Treatment
- mutating GAPA1 Asn35 into Gly or Arg81 into Leue2
- Gene
- GAPA1e2
- Outcome
- ability of the enzyme to bind SAe2
- Direction
- strongly diminishede2
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM”
e2“mutating GAPA1 Asn35 into Gly or Arg81 into Leu strongly diminished the ability of the enzyme to bind SA”
Claim · model-written summary
NADH inhibited in a dose-response manner the binding of SA to GAPA1.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae0
- Treatment
- NADHe3
- Outcome
- the binding of SA to GAPA1e3
- Direction
- inhibitede3
- Qualifier
- dose-response mannere3
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM”
e3“NADH inhibited in a dose-response manner the binding of SA to GAPA1”
Claim · model-written summary
Modelling suggests that SA binds to the same site where the pyrimidine group of the NADP+ cofactor fits.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae0
- Outcome
- the very sitee4
- Qualifier
- pyrimidine group of the cofactore4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM”
e4“modelling suggests that SA binds to the very site where the pyrimidine group of the cofactor fits”
Claim · model-written summary
The molecular docking analysis identified two putative binding pockets for SA on GAPA1.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae0
- Outcome
- two putative binding pockets for SAe5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM”
e5“The molecular docking analysis yielded to the identification of two putative binding pockets for SA”
Claim · model-written summary
Only one surface cavity around Asn35 would efficiently bind SA in the presence of solvent.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae0
- Outcome
- a surface cavity around Asn35e6
- Qualifier
- in the presence of solvente6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM”
e6“only one pocket—a surface cavity around Asn35—would efficiently bind SA in the presence of solvent”
Claim · model-written summary
In silico mutagenesis and simulations pointed to the importance of Asn35 and Arg81 in binding SA to GAPA1.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae0
- Gene
- GAPA1e7
- Outcome
- importance of Asn35 and Arg81 in the binding of SA to GAPA1e7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM”
e7“pointed to the importance of Asn35 and Arg81 in the binding of SA to GAPA1”
Claim · model-written summary
The same cavity that binds SA is responsible for NADP+ binding to GAPA1.
- Taxon
- Arabidopsis thalianaArabidopsis thalianae0
- Compound
- NADP+e6
- Outcome
- NADP+ binding to GAPA1e6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a KD of 16.7 nM”
e6“The very same cavity is responsible for the NADP+ binding to GAPA1”