GO:0044208 'de novo' AMP biosynthetic process | Genes & Methods

The 'de novo' AMP biosynthetic process (GO:0044208) is a metabolic pathway that produces adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP). This process is a critical branch of the larger de novo purine biosynthesis pathway, which generates the purine nucleotides required for DNA and RNA synthesis, energy metabolism, and cellular signaling. Researchers study this pathway to understand how cells maintain nucleotide homeostasis and how its dysregulation contributes to diseases such as cancer and inborn errors of metabolism [1,5]. The pathway involves two key enzymes: adenylosuccinate synthetase (ADSS) and adenylosuccinate lyase (ADSL). ADSS catalyzes the formation of adenylosuccinate from IMP and aspartate, and ADSL then cleaves adenylosuccinate to release AMP and fumarate. Because AMP is a precursor for ATP and other adenine nucleotides, its de novo synthesis is tightly regulated to meet cellular demands. Recent studies have highlighted the importance of this pathway in tumor immune evasion, where ADSL-generated fumarate can inhibit STING signaling. Understanding the molecular details of de novo AMP biosynthesis provides a foundation for developing therapeutic strategies targeting nucleotide metabolism [1,5].

According to the Gene Ontology, GO:0044208 'de novo' AMP biosynthetic process is defined as the chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from inosine 5'-monophosphate (IMP). This definition encompasses the two enzymatic steps that convert IMP to AMP, which are part of the broader de novo purine biosynthetic pathway.

The de novo AMP biosynthetic process is essential for maintaining cellular adenine nucleotide pools, which are required for DNA and RNA synthesis, energy transfer, and signal transduction. Dysregulation of this pathway has been implicated in cancer, where altered purine metabolism supports rapid cell proliferation [1,5]. Moreover, mutations in ADSL cause adenylosuccinate lyase deficiency, a rare neurometabolic disorder characterized by psychomotor retardation and epilepsy. Understanding this pathway also provides insights into immune regulation, as ADSL-generated fumarate can inhibit STING, promoting tumor immune evasion.

The following genes encode enzymes and regulators directly involved in the 'de novo' AMP biosynthetic process.

The 'de novo' AMP biosynthetic process is regulated at multiple levels. ADSS is feedback-inhibited by AMP and requires GTP as a cofactor, linking AMP synthesis to cellular energy status. The pathway is also subject to transcriptional regulation in response to growth factors and nutrient availability. Additionally, ADSL activity can be affected by mutations that alter its catalytic efficiency or stability. In cancer cells, oncogenic signaling pathways such as mTOR can upregulate purine biosynthesis to support proliferation. Furthermore, the pathway intersects with immune signaling, as ADSL-generated fumarate inhibits STING, thereby modulating innate immune responses.

Mutations in ADSL cause adenylosuccinate lyase deficiency, an autosomal recessive neurometabolic disorder characterized by psychomotor retardation, epilepsy, and autistic features. The disease is associated with accumulation of succinylpurines in body fluids, which are neurotoxic. Diagnosis is typically made by detecting elevated succinyladenosine and SAICAR in urine.

Altered purine metabolism, including the de novo AMP biosynthetic process, is a hallmark of cancer. Many cancer cells upregulate purine biosynthesis to meet the demands of rapid proliferation. Targeting this pathway, for example with inhibitors of ADSS or ADSL, is a potential therapeutic strategy. Additionally, ADSL-generated fumarate can promote tumor immune evasion by inhibiting STING.

ADSL produces fumarate as a byproduct of AMP synthesis, and fumarate can bind and inhibit STING, thereby suppressing innate immune responses. This mechanism contributes to tumor immune evasion and suggests that targeting ADSL could enhance anti-tumor immunity. The cGAS-STING pathway is also a target for de novo designed inhibitors, highlighting the importance of this axis in disease.

Metabolomics using mass spectrometry can quantify AMP, IMP, adenylosuccinate, and other purine intermediates to assess pathway activity. Stable isotope tracing with 13C-labeled substrates can measure flux through the de novo AMP biosynthetic process.

ADSS and ADSL enzyme activities can be measured in cell lysates using spectrophotometric or HPLC-based assays. These assays are useful for characterizing mutant enzymes and testing inhibitors.

Genome-wide CRISPR knockout or activation screens can identify genes that are essential for de novo AMP biosynthesis or that confer resistance to inhibitors. Such screens have been used to uncover metabolic vulnerabilities in cancer.

X-ray crystallography and cryo-EM can provide structural insights into ADSS and ADSL catalysis and regulation. These methods aid in the design of small-molecule inhibitors.

Researchers studying 'de novo' AMP biosynthetic process-related genes often need to determine whether a candidate gene is causally involved in pathway regulation, disease progression, or therapeutic response. Precise genetic models are essential to validate findings from metabolomic and transcriptomic studies. EDITGENE provides a comprehensive suite of CRISPR services to accelerate this research.

The 'de novo' AMP biosynthetic process (GO:0044208) is a fundamental metabolic pathway that converts IMP to AMP through the sequential actions of ADSS and ADSL. Its tight regulation ensures balanced nucleotide pools for DNA, RNA, and energy metabolism. Dysregulation of this pathway is implicated in cancer, immune evasion, and inherited metabolic disorders [1,5]. Advances in CRISPR-based genetic models and metabolomic technologies are accelerating our understanding of this pathway and its therapeutic potential.