Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC–MS Techniques

Straube, Henryk; Witte, Claus-Peter; Herde, Marco

doi:10.3390/cells10030689

Cited by 19 publications

(8 citation statements)

References 127 publications

(207 reference statements)

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“…Measurements failing the quality criteria for retention time, qualifier to quantifier ratio or with a signal to noise ratio below 10 were called “not detected”. The quantification of nucleotides was performed as recently described 14 , 37 .…”

Section: Methodsmentioning

confidence: 99%

Initiation of cytosolic plant purine nucleotide catabolism involves a monospecific xanthosine monophosphate phosphatase

et al. 2021

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In plants, guanosine monophosphate (GMP) is synthesized from adenosine monophosphate via inosine monophosphate and xanthosine monophosphate (XMP) in the cytosol. It has been shown recently that the catabolic route for adenylate-derived nucleotides bifurcates at XMP from this biosynthetic route. Dephosphorylation of XMP and GMP by as yet unknown phosphatases can initiate cytosolic purine nucleotide catabolism. Here we show that Arabidopsis thaliana possesses a highly XMP-specific phosphatase (XMPP) which is conserved in vascular plants. We demonstrate that XMPP catalyzes the irreversible entry reaction of adenylate-derived nucleotides into purine nucleotide catabolism in vivo, whereas the guanylates enter catabolism via an unidentified GMP phosphatase and guanosine deaminase which are important to maintain purine nucleotide homeostasis. We also present a crystal structure and mutational analysis of XMPP providing a rationale for its exceptionally high substrate specificity, which is likely required for the efficient catalysis of the very small XMP pool in vivo.

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Section: Methodsmentioning

confidence: 99%

Initiation of cytosolic plant purine nucleotide catabolism involves a monospecific xanthosine monophosphate phosphatase

et al. 2021

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“…We also observed an interesting phenomenon in which most amino acids, nucleotides and their derivatives significantly increased in abundance in G160 sugarcane, which exhibits low resistance to smut disease. Amino acids are the raw materials for protein synthesis in plants and other organisms, and nucleotides are the basic constituents of DNA and RNA [ 50 , 51 ]. The higher concentration of amino acids, nucleotides and their derivatives in G160 sugarcane than in Zhongzhe 1 sugarcane may explain why pathogenic microorganisms are more amenable to infestation in the former, thus leading to disease susceptibility.…”

Section: Discussionmentioning

confidence: 99%

Cytogenetic Characterization and Metabolomic Differences of Full-Sib Progenies of Saccharum spp.

Wang

Chen

2023

Plants

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Sugarcane smut is a worldwide fungal disease. Disease resistance breeding is the most economical and effective measure to prevent and control sugarcane smut. The cytogenetic characteristics and metabolomic differences of sugarcane F1s are closely related to disease resistance. Zhongzhe 1 and G160 sugarcane from the same parents (ROC25 and Yunzhe89-7) were used; the plants were grown in accordance with the barrel method. When the seedlings had 4–5 leaves, genomic in situ hybridization (GISH) was performed; digoxigenin (DIG)-labeled female parental (ROC25)DNA and biotin-labeled male parental (Yunzhe89-7) DNA were used as probes, and the karyotypes of two hybrids were analyzed. The new sugarcane smut-resistant variety (Zhongzhe 1) and the susceptible variety (G160) derived from the same parent were analyzed via gas chromatography‒mass spectrometry technology (GC‒MS) to compare the metabolomic differences between them. GISH analysis revealed that the chromosome ploidy number of Zhongzhe 1 sugarcane and G160 sugarcane were 114 and 110, respectively. However, the two contain different numbers of chromosomes from the female (ROC25) and male (Yunzhe89-7) parents. Moreover, 258 significantly changed metabolites were identified in smut-resistant Zhongzhe 1, as compared with the smut-susceptible G160 sugarcane: 56 flavonoids, 52 phenolic acids, 30 lipids, 26 organic acids, 26 amino acids and derivatives, 19 nucleotides and derivatives, 5 alkaloids, 9 terpenoids, and 35 others. Multivariate statistical analysis revealed a distinct difference in metabolic pathways between Zhongzhe 1 sugarcane and G160, and both of these varieties had unique functional metabolites. Differences in chromosome composition may constitute the genetic basis for the difference in resistance to smut disease between Zhongzhe 1 sugarcane and G160 sugarcane, and a high accumulation of flavonoids, lipids, terpenoids and tannins may constitute the basis of resistance to smut disease for the Zhongzhe 1 variety.

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“…Absolute quantitation of ADP and ATP by LC-MS was carried out according to previous reports (Straube et al, 2021) with slight modifications. Briefly, approximately 25-mg roots or 50-mg leaf discs were collected and immediately snap-frozen in liquid nitrogen.…”

Section: Analyses Of Nucleotides By Lc-srm-msmentioning

confidence: 99%

ENOD93 interacts with cytochrome c oxidase altering respiratory ATP production and root growth in plants

Lee

Gawryluk

et al. 2023

Preprint

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The early nodulin 93 (ENOD93) gene family in plants can regulate biological nitrogen fixation in legumes and nitrogen use efficiency in cereals but its molecular function is unknown. We show profile hidden Markov models define ENOD93 as a distant homolog of the N-terminal domain of RESPIRATORY SUPERCOMPLEX FACTOR 2 (RCF2). RCF2 is reported to regulate cytochrome oxidase (CIV) influencing the generation of a mitochondria proton motive force in yeast. Knockout of enod93 in Arabidopsis leads to a short root phenotype. ENOD93 is associated with a protein complex the size of CIV in isolated mitochondria but neither CIV abundance nor its activity in ruptured organelles changed in enod93. However, a progressive loss of ADP-dependent respiration rate was observed in enod93 mitochondria which could be fully recovered in complemented lines. Mitochondrial membrane potential was higher in enod93 but ATP synthesis and ADP depletion rates progressively decreased. Respiration rate of whole enod93 seedlings was elevated and root ADP content was nearly double that in WT without a change in ATP content. These altered energetic states correlated with elevated respiratory substrate levels in roots of enod93 compared to WT and complemented lines. Overexpression of ENOD93 lowered ATP content in roots and increased the abundance of a range of amino acids in both roots and leaves. We propose that two previously unconnected gene families in plants, ENOD93 and HYPOXIA INDUCED GENE DOMAIN, are the functional equivalent of yeast RCF2 but have remained undiscovered in many eukaryotic lineages because they are encoded in two separate genes.

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Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC–MS Techniques

Cited by 19 publications

References 127 publications

Initiation of cytosolic plant purine nucleotide catabolism involves a monospecific xanthosine monophosphate phosphatase

Initiation of cytosolic plant purine nucleotide catabolism involves a monospecific xanthosine monophosphate phosphatase

Cytogenetic Characterization and Metabolomic Differences of Full-Sib Progenies of Saccharum spp.

ENOD93 interacts with cytochrome c oxidase altering respiratory ATP production and root growth in plants

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