Detection of ribose-methylated nucleotides in Pyrodictium occultum tRNA by liquid chromatography--frit-fast atom bombardment mass spectrometry

Detection and Analysis of RNA Ribose 2'-O-Methylations: Challenges and Solutions

Ribose 2'-O-methylation is certainly one of the most common RNA modifications found in almost any type of cellular RNA. It decorates transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), small nuclear RNAs (snRNAs) (and most probably small nucleolar RNAs, snoRNAs), as well as regulatory RNAs like microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), and finally, eukaryotic messenger RNAs (mRNAs). Due to this exceptional widespread of RNA 2'-O-methylation, considerable efforts were made in order to precisely map these numerous modifications. Extensive studies of RNA 2'-O-methylation were also stimulated by the discovery of C/D-box snoRNA-guided machinery, which insures site-specific modification of hundreds 2'-O-methylated residues in archaeal and eukaryotic rRNAs and some other RNAs. In this brief review we discussed both traditional approaches of RNA biochemistry and also modern deep sequencing-based methods, used for detection/mapping and quantification of RNA 2'-O-methylations.

RNA ribose methylation (2'-O-methylation): Occurrence, biosynthesis and biological functions

Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life domains. This modification was extensively studied for decades in rRNAs and tRNAs, but recent data revealed the presence of 2'-O-methyl groups also in low abundant RNAs, like mRNAs. Ribose methylation is formed in RNA by two alternative enzymatic mechanisms: either by stand-alone protein enzymes or by complex assembly of proteins associated with snoRNA guides (sno(s)RNPs). In that case one catalytic subunit acts at various RNA sites, the specificity is provided by base pairing of the sno(s)RNA guide with the target RNA. In this review we compile available information on 2'-OH ribose methylation in different RNAs, enzymatic machineries involved in their biosynthesis and dynamics, as well as on the physiological functions of these modified residues.

Draft Genome Sequence of Pyrodictium occultum PL19T, a Marine Hyperthermophilic Species of Archaea That Grows Optimally at 105°C

We report here the draft genome sequence of Pyrodictium occultum PL19(T), a marine hyperthermophilic archaeon. The genome provides insights into molecular and cellular adaptation mechanisms to life in extreme environments and the evolution of early organisms on Earth.

Investigation of the use of immobilised metal affinity chromatography for the on-line sample clean up and pre-concentration of nucleotides prior to their determination by ion pair liquid chromatography-electrospray mass spectrometry: a pilot study

This study explored an alternative way to enrich and pre-purify biological samples containing nucleoside mono-, di- and triphosphates. These compounds were trapped by immobilised metal affinity chromatography (IMAC) on a Poros 20 MC IMAC-column, which was conditioned with Fe3+. The IMAC-column was implemented in a column switching set-up separating nucleoside mono-, di- and triphosphates on a Hypersil ODS 35 mm x 0.3 mm capillary column hyphenated to electrospray mass spectrometry resulting in the first miniaturised column switching liquid chromatography-mass spectrometry (LC-MS) system for nucleotides.

RNA metabolism in uremic patients: accumulation of modified ribonucleosides in uremic serum. Technical note

To determine the metabolism of ribonucleic acid (RNA) in uremia, serum and urine levels of ribonucleosides in uremic patients were analyzed using reversed-phase high-performance liquid chromatography. The serum levels of xanthosine and all modified ribonucleosides were increased in undialyzed patients with chronic renal failure (CRF), and patients undergoing hemodialysis (HD) and continuous ambulatory peritoneal dialysis (CAPD). The serum level of pseudouridine was markedly increased in all the uremic patients especially CAPD patients (32 times higher than normal). By contrast, the serum level of adenosine did not show any significant change in the uremic patients. Interestingly, the serum and urine levels of inosine were significantly decreased in all the uremic patients, suggesting that the production of inosine is decreased in uremic patients. The serum level of uridine was significantly elevated only in the HD patients. The serum levels of all ribonucleosides except inosine and uridine decreased significantly after HD. The urinary excretion of inosine, 1-methyladenosine, 1-methylguanosine, N2,N2-dimethylguanosine and N4-acetylcytidine was significantly decreased in the CRF patients, leading to the accumulation of these modified ribonucleosides in the uremic serum. CAPD patients showed markedly increased serum levels of modified ribonucleosides such as pseudouridine, 1-methylinosine, and N2,N2-dimethylguanosine and N4-acetylcytidine as compared with the HD patients. These results demonstrate that there was an altered metabolism of RNA in uremic patients with marked accumulation of modified ribonucleosides.

Mass spectrometry in the search for uremic toxins

This article reviews the literature on the mass spectrometry (MS) that has been used in the research of uremic toxins. Gas chromatography/mass spectrometry (GC/MS) has been most often used for the analysis of low-molecular-weight compounds in uremic blood such as organic acids, phenols, and polyols. However, it cannot be used for the analysis of middle- to high-molecular-weight substances or for involatile compounds. The development of fast atom bombardment (FAB) and liquid secondary ion mass spectrometry (LSIMS) has made possible the analysis of middle-molecules and involatile low-molecular-weight substances such as peptides and nucleosides. The development of atmospheric pressure chemical ionization (APCI) has also lead to the analysis of involatile low-molecular-weight substances. The recent advances in ionization methods, such as electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI), have permitted the MS analysis of high-molecular-weight substances such as beta 2-microglobulin, a major component of dialysis amyloid. Liquid chromatography/mass spectrometry (LC/MS), using ESI, APCI, or FAB as an ionization method, is currently the preferred method for the analysis of low- to high-molecular-weight substances in uremic blood. ESI-LC/MS and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOFMS) are useful for elucidating the structure of post-translationally modified proteins obtained from the blood and tissues of uremic patients. Post-translational modification such as the formation of advanced glycation end-products and carbamoylation is enhanced in uremic patients, and is considered to be responsible for some uremic symptoms. Laser microprobe MS is unique in its capability for the two-dimensional detection of atoms such as aluminum in a tissue section obtained from uremic patients. This review focuses on the mainstream research for discovering uremic toxins, specific uremic toxins identified or quantified using MS, and the MS analysis of post-translationally modified proteins in uremia. These studies have provided ample evidence that MS has played an important role in the search for uremic toxins.