Determination of total ribonucleotide pool in plant materials by high-pH anion-exchange high-performance liquid chromatography following extraction with potassium hydroxide

Riondet, Christophe; Morel, Sylvain; Alcaraz, Gérard

doi:10.1016/j.chroma.2005.04.036

Cited by 14 publications

(8 citation statements)

References 19 publications

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“…Our recent work confirmed that, at least for the duration of the extraction, NTs and Ns are acid-stable with good recoveries [2]. Although, more studies have used acidic conditions for NT extraction, there are protocols for the determination of rNTs in Nicotiana tabacum, Arabidopsis thaliana, and Solanum lycopersicum using quenching with a high pH, which also led to excellent recoveries [32]. At high pH, NTs were reported to be stable even when stored for 3 days at room temperature [32].…”

Section: Extraction Of Nts and Ns From Plant Samplessupporting

confidence: 72%

“…Although, more studies have used acidic conditions for NT extraction, there are protocols for the determination of rNTs in Nicotiana tabacum, Arabidopsis thaliana, and Solanum lycopersicum using quenching with a high pH, which also led to excellent recoveries [32]. At high pH, NTs were reported to be stable even when stored for 3 days at room temperature [32]. In general, frozen nucleotide solutions are stable for a prolonged time if the acid from the quenching step is removed or neutralized [33].…”

Section: Extraction Of Nts and Ns From Plant Samplesmentioning

confidence: 99%

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

Straube

Witte

Herde

2021

Cells

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Nucleotides fulfill many essential functions in plants. Compared to non-plant systems, these hydrophilic metabolites have not been adequately investigated in plants, especially the less abundant nucleotide species such as deoxyribonucleotides and modified or damaged nucleotides. Until recently, this was mainly due to a lack of adequate methods for in-depth analysis of nucleotides and nucleosides in plants. In this review, we focus on the current state-of-the-art of nucleotide analysis in plants with liquid chromatography coupled to mass spectrometry and describe recent major advances. Tissue disruption, quenching, liquid–liquid and solid-phase extraction, chromatographic strategies, and peculiarities of nucleotides and nucleosides in mass spectrometry are covered. We describe how the different steps of the analytical workflow influence each other, highlight the specific challenges of nucleotide analysis, and outline promising future developments. The metabolite matrix of plants is particularly complex. Therefore, it is likely that nucleotide analysis methods that work for plants can be applied to other organisms as well. Although this review focuses on plants, we also discuss advances in nucleotide analysis from non-plant systems to provide an overview of the analytical techniques available for this challenging class of metabolites.

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Section: Extraction Of Nts and Ns From Plant Samplessupporting

confidence: 72%

Section: Extraction Of Nts and Ns From Plant Samplesmentioning

confidence: 99%

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

Straube

Witte

Herde

2021

Cells

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“…Free NTPs were extracted from young leaves of N . benthamiana and cassava by using a previously described method (Riondet et al, 2005). Extracts were immediately injected into a Vanquish UHPLC system equipped with a Q Exactive Focus Orbitrap spectrometry detector (Thermo Fisher Scientific).…”

Section: Methodsmentioning

confidence: 99%

Maf/ham1-like pyrophosphatases of non-canonical nucleotides are host-specific partners of viral RNA-dependent RNA polymerases

Vallí

López

Ribaya

et al. 2021

Preprint

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Cassava brown streak disease (CBSD), dubbed the Ebola of plants, is a serious threat for food security in Africa caused by two viruses of the family Potyviridae: cassava brown streak virus (CBSV) and Ugandan (U)CBSV. Intriguingly, U/CBSV, along with another member of this family and one secoviridae, are the only known RNA viruses in nature encoding a protein of the Maf/ham1-like family, a group of widespread pyrophosphatase of non-canonical nucleotides (ITPase) expressed by all living organisms. Despite the socio-economic impact of CDSD, the relevance and role of this atypical viral factor has not been yet established. Here, using an infectious cDNA clone and reverse genetics, we demonstrate that UCBSV requires the ITPase activity in cassava, but not in the model plant Nicotiana benthamiana. HPLC-MS/MS experiments show that, quite likely, this host-specific constraint is due to an unexpected high concentration of non-canonical nucleotides in cassava. Finally, protein analyses and experimental evolution of mutant viruses indicate that keeping a fraction of the yielded UCBSV ITPase covalently bound to the viral RNA-dependent RNA polymerase (RdRP) optimizes viral fitness, and this seems to be a feature shared by the other members of the Potyviridae family expressing Maf/ham1-like proteins. All in all, our work (i) reveals that the over-accumulation of non-canonical nucleotides in the host might have a key role in antiviral defense, and (ii) provides the first example of an RdRP-ITPase partnership, reinforcing the idea that RNA viruses are incredibly inventive at adaptation to different host setups.

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“…Anion-exchange chromatography has also been a common method for analysis for other types of nucleotides and nucleotide derivatives [26][27][28], however, it is not a very suitable method when coupled with mass spectrometry. More sensitive and versatile methods have been developed for the analysis of AppCCl 2 p utilizing ion-pair high-performance liquid chromatography (HPLC) and tandem mass spectrometry, which allows detection of several metabolites in a single chromatographic run [29,30].…”

mentioning

confidence: 99%

Analysis of endogenous ATP analogs and mevalonate pathway metabolites in cancer cell cultures using liquid chromatography–electrospray ionization mass spectrometry

Jauhiainen

Mönkkönen

Räikkönen

et al. 2009

Journal of Chromatography B

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Determination of total ribonucleotide pool in plant materials by high-pH anion-exchange high-performance liquid chromatography following extraction with potassium hydroxide

Cited by 14 publications

References 19 publications

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

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

Maf/ham1-like pyrophosphatases of non-canonical nucleotides are host-specific partners of viral RNA-dependent RNA polymerases

Analysis of endogenous ATP analogs and mevalonate pathway metabolites in cancer cell cultures using liquid chromatography–electrospray ionization mass spectrometry

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