What are Nucleosides?
A sugar molecule and a nitrogenous base are the two main parts of a nucleoside. Adenine (A), cytosine (C), guanine (G), or uracil (U) for RNA, and thymine (T) for DNA, are the four nucleobases that can serve as the nitrogenous base. Nucleosides include either ribose or deoxyribose as the sugar molecule, depending on whether they are components of RNA or DNA, respectively.
Nucleoside vs. Nucleotide
While a sugar molecule and a nitrogenous base make up a nucleoside, a phosphate group or groups are added to the sugar molecule to make a nucleotide. Energy transmission, enzymatic processes, and the production of nucleic acids are just a few of the critical functions that phosphate groups in nucleotides confer. Energy carriers for cellular functions include nucleotides like adenosine triphosphate (ATP) and guanosine triphosphate (GTP).
| Nucleosides | Nucleotides | |
|---|---|---|
| Structure | Nitrogenous base + Sugar molecule | Nitrogenous base + Sugar molecule + Phosphate group(s) |
| Components | Nitrogenous base and sugar molecule | Nitrogenous base, sugar molecule, and phosphate group(s) |
| Phosphate Group | Absent | Present |
| Function | Building blocks of nucleic acids | Essential for nucleic acid synthesis, energy metabolism, enzymatic reactions, and cell signaling |
| Examples | Adenosine, Guanosine, Cytidine, Thymidine | Adenosine triphosphate (ATP), Guanosine triphosphate (GTP), Cytidine triphosphate (CTP) |
Nucleoside Metabolism
Nucleoside metabolism occurs primarily in the cytoplasm of cells. The cytoplasm is the fluid-filled region between the cell membrane and the nucleus and serves as the site for numerous metabolic processes, including nucleoside metabolism. Within the cytoplasm, various enzymes and pathways are involved in the synthesis, degradation, and interconversion of nucleosides.
De Novo Synthesis: The de novo synthesis of nucleosides begins with the assembly of a nitrogenous base and a sugar molecule. Enzymes in the cytoplasm catalyze the stepwise addition of these components to form nucleosides. The nitrogenous bases, such as adenine, guanine, cytosine, thymine, and uracil, are derived from precursor molecules, and they combine with ribose or deoxyribose sugars to form nucleosides like adenosine, guanosine, cytidine, thymidine, and uridine.
Salvage Pathways: Nucleosides can be salvaged and recycled in the cytoplasm through salvage pathways. Salvage pathways utilize specific enzymes to convert free bases or nucleosides derived from the breakdown of nucleotides or from external sources back into nucleotides. This recycling process helps conserve energy and reduce the demand for de novo synthesis.
Nucleoside Degradation: Nucleosides can be degraded in the cytoplasm through enzymatic reactions. Nucleoside phosphorylases and nucleosidases are involved in breaking down nucleosides into their constituent parts, including nitrogenous bases and sugars. These breakdown products can then be further metabolized or utilized in other cellular processes.
Nucleoside Kinases: Nucleoside kinases are enzymes present in the cytoplasm that catalyze the phosphorylation of nucleosides. Phosphorylation of nucleosides is an important step in the conversion of nucleosides into nucleotides, as it involves the addition of phosphate groups to the sugar molecule. This phosphorylation reaction is necessary for nucleosides to participate in nucleotide synthesis or other cellular functions.
Pyrimidine nucleoside and/or nucleotide metabolism in mammalian cells (Balzarini et al., 2012).
How is Nucleoside Metabolism Regulated?
To keep the balance of nucleosides, guarantee the availability of nucleotides for DNA and RNA synthesis, and manage cellular signaling activities, nucleoside metabolism is strictly regulated in cells. Numerous processes regulate the synthesis, salvage, degradation, and interconversion of nucleosides as part of the regulation of nucleoside metabolism. Here are a few significant regulatory systems:
Enzyme Regulation: Enzymes involved in nucleoside metabolism are subject to regulation at the level of gene expression, post-translational modifications, and allosteric regulation. The expression of enzymes can be regulated by transcription factors and other regulatory proteins in response to cellular needs and environmental cues. Post-translational modifications such as phosphorylation, acetylation, or ubiquitination can modulate enzyme activity. Allosteric regulation occurs when certain metabolites or nucleotides bind to the enzyme, causing a conformational change that affects its activity.
Feedback Inhibition: In the regulation of nucleoside metabolism, feedback inhibition frequently occurs. It entails the suppression of enzyme function by metabolic pathway by-products. Nucleosides and nucleotides have the ability to bind to particular enzymes in a pathway and stop their activity when their concentration reaches a certain level. This feedback inhibition stops the overproduction or depletion of nucleotides and maintains the equilibrium of nucleosides.
Substrate Availability: The pathway can also be regulated by the availability of substrates for nucleoside metabolism. The production of nucleosides requires the availability of precursor molecules such as nitrogenous bases and ribose or deoxyribose sugars. Nutrient availability, cellular energy status, and metabolic flux are only a few examples of the variables that may have an impact on the availability of these substrates.
Hormonal and Signaling Pathways: Hormones and signaling molecules can regulate nucleoside metabolism. For example, insulin and glucagon can affect nucleoside metabolism by modulating enzyme activity or gene expression. Signaling pathways activated by growth factors or stress can also influence nucleoside metabolism, coordinating it with other cellular processes.
Cell Cycle Regulation: Nucleoside metabolism is tightly linked to the cell cycle, particularly during DNA replication and cell division. The regulation of nucleoside metabolism is integrated with cell cycle checkpoints and mechanisms that ensure the availability of nucleotides for DNA synthesis during S phase. Regulatory proteins such as cyclins and cyclin-dependent kinases (CDKs) play important roles in coordinating nucleotide availability with cell cycle progression.
Epigenetic Regulation: Epigenetic alterations, such as DNA methylation and histone modifications, can impact nucleoside metabolism by influencing the expression of pathway genes. Changes in the epigenetic landscape can have an effect on nucleotide availability and metabolism, which can help with cellular homeostasis and adaptability to environmental stimuli.
These regulatory systems collaborate to maintain nucleoside balance, coordinate nucleotide supply with cellular demands, and guarantee proper nucleic acid synthesis, cellular signaling, and other nucleoside-dependent functions.
Functions of Nucleosides
Nucleosides have diverse functions in cellular processes, beyond their role as building blocks of nucleic acids. Some important functions of nucleosides include:
Precursors for Nucleotide Synthesis
Nucleosides serve as precursors for nucleotide synthesis. They can be phosphorylated to form nucleotides through the action of nucleoside kinases. The resulting nucleotides are vital for DNA and RNA synthesis and play essential roles in genetic information storage and transmission.
Energy Metabolism
Certain nucleosides, such as adenosine and guanosine, have a role in energy metabolism. Adenosine triphosphate (ATP) is a vital chemical in cellular energy transport and storage. ATP is the cell's "energy currency" and is used in a variety of energy-demanding functions.
Cell Signaling
In cellular communication, nucleosides operate as signaling molecules. Adenosine, for example, regulates a variety of physiological processes, such as neurotransmission, immunological response, and vascular tone. Adenosine receptors are found on the cell surface, and adenosine evokes particular signaling pathways upon binding.
Medicinal Applications
Nucleosides and their derivatives have significant therapeutic applications. Many antiviral and anticancer drugs are nucleoside analogs that interfere with nucleic acid synthesis in pathogens or cancer cells. Nucleoside analogs can inhibit DNA or RNA replication, making them valuable in the treatment of viral infections and certain types of cancer.
Analytical Techniques for Nucleoside Analysis
Nucleosides are crucial biomolecules involved in various cellular processes and play important roles in nucleic acid synthesis, energy metabolism, and signaling pathways. Analyzing nucleosides and their related metabolites provides valuable insights into cellular metabolism, disease mechanisms, and therapeutic interventions. Mass spectrometry-based analytical techniques have emerged as powerful tools for nucleoside analysis in metabolomics studies. These techniques enable sensitive and comprehensive detection, identification, and quantification of nucleosides and their modified forms in complex biological samples.
Liquid Chromatography-Mass Spectrometry (LC-MS):
LC-MS is a widely used technique for nucleoside analysis. It combines the separation capabilities of liquid chromatography with the high sensitivity and selectivity of mass spectrometry. LC-MS allows the separation of nucleosides based on their physicochemical properties, such as polarity, hydrophobicity, and size. It offers excellent resolution and sensitivity, enabling the detection and quantification of nucleosides even at low concentrations in complex biological matrices.
Schematic representation of a typical workflow for the analysis of nucleotides and nucleosides in plants (Straube et al., 2021)
Gas Chromatography-Mass Spectrometry (GC-MS):
GC-MS is another powerful technique for nucleoside analysis. It involves the separation of volatile or derivatized nucleosides by gas chromatography followed by their detection and identification using mass spectrometry. GC-MS provides high-resolution separation and sensitive detection, particularly for volatile and thermally stable nucleosides. It is commonly used for the analysis of modified nucleosides and stable isotope-labeled nucleoside analogs.
High-Resolution Mass Spectrometry (HRMS):
HRMS offers enhanced mass accuracy and resolution, enabling the precise determination of nucleosides and their isotopologues. HRMS techniques such as Fourier transform ion cyclotron resonance (FT-ICR) and Orbitrap mass spectrometry provide exceptional mass measurement accuracy and high resolving power. These techniques are well-suited for the identification and characterization of nucleosides in complex samples, including structural elucidation of modified nucleosides.
Tandem Mass Spectrometry (MS/MS):
MS/MS plays a crucial role in nucleoside analysis by providing structural information about nucleosides and their modified forms. MS/MS techniques, such as collision-induced dissociation (CID) and higher-energy collision dissociation (HCD), involve the fragmentation of nucleoside ions to generate characteristic fragment ions. The resulting fragmentation patterns aid in the identification and confirmation of nucleosides and their modifications.
Targeted and Untargeted Approaches:
Nucleoside analysis can be performed using targeted or untargeted approaches. Targeted analysis focuses on specific nucleosides or their modified forms and employs selected reaction monitoring (SRM) or multiple reaction monitoring (MRM) methods for quantification. Untargeted analysis, on the other hand, aims to comprehensively detect and identify nucleosides and their metabolites without prior knowledge of their specific identities. Untargeted approaches utilize high-resolution mass spectrometry and data processing techniques to identify and annotate nucleosides based on accurate mass measurements and fragmentation patterns.
References
- Balzarini, Jan, et al. "Introduction of a fluorine atom at C3 of 3-deazauridine shifts its antimetabolic activity from inhibition of CTP synthetase to inhibition of orotidylate decarboxylase, an early event in the de novo pyrimidine nucleotide biosynthesis pathway." Journal of Biological Chemistry 287.36 (2012): 30444-30454.
- Straube, Henryk, Claus-Peter Witte, and Marco Herde. "Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC–MS Techniques." Cells 10.3 (2021): 689.
You may be interested in:
