Abstract

Cell fate is determined not only by signaling cascades composed of receptors, kinases, and transcription factors, but also by two more fundamental regulatory processes. Metabolic enzymes control the direction and rate of nutrient conversion, thereby determining the energy, biosynthetic precursors, and reducing capacity available to the cell. Proteases and protein degradation systems control protein processing, activation, and clearance, thereby determining the abundance, activity, and lifespan of functional proteins.

These two systems do not operate independently. Metabolic states influence protein synthesis, folding, and degradation, whereas protein turnover reshapes metabolic flux by altering the abundance of metabolic enzymes, transcription factors, and organelles. By examining metabolic flux, protein degradation, and their bidirectional regulation, this article explains how these two systems jointly determine cell proliferation, stress adaptation, and cell death.

1 Metabolic Enzymes and Proteases Do Not Constitute a Single Signaling Pathway

1.1 What Do These Two Types of Enzymes Control?

According to the enzyme classification principles of the International Union of Biochemistry and Molecular Biology, enzymes are classified on the basis of the chemical reactions they catalyze. Metabolic enzymes catalyze the synthesis, degradation, and interconversion of small molecules, whereas proteases, in the strict sense, catalyze the hydrolysis of peptide bonds.

“Metabolic enzymes/proteases” do not constitute a linear pathway with a fixed starting point, endpoint, and order of signal transmission. Instead, they represent two interconnected cellular regulatory systems:

Metabolic enzymes primarily determine “what the cell is able to use,” whereas protein degradation systems primarily determine “what the cell retains and executes.” Cell fate results from the coordinated action of these two regulatory systems.

1.2 Protein Degradation Is Not Equivalent to Protease Activity

Protein degradation is not independently completed by a single protease. In the ubiquitin–proteasome system, for example, a substrate must undergo recognition, ubiquitin tagging, delivery, unfolding, and hydrolysis. The autophagy–lysosome system additionally requires cargo selection, autophagosome formation, membrane fusion, and lysosomal hydrolysis.

The regulation of protein fate discussed in this article includes both proteases that directly catalyze peptide-bond cleavage and the complete protein degradation systems that determine whether a protein is recognized, tagged, delivered, and degraded.

2 How Metabolic Enzymes Alter Cellular State Through Metabolic Flux

2.1 Metabolic Flux Is Different from Metabolite Abundance

Metabolite abundance describes how much of a particular substance is present in a cell at a given time, whereas metabolic flux describes the rate at which material passes through a metabolic reaction per unit time.

If the production and consumption of a metabolite accelerate simultaneously, its intracellular abundance may remain largely unchanged even though the flux through that metabolite has increased. Conversely, metabolite accumulation may result either from increased production or from impaired downstream consumption. Static metabolomics alone therefore cannot determine the direction or rate of metabolic reactions and usually needs to be combined with stable-isotope tracing and metabolic flux analysis.

To understand the function of a metabolic enzyme, three questions should be addressed in sequence:

① What reaction does the enzyme catalyze?

② Which metabolic branch is altered by that reaction?

③ How does the change in metabolic flux affect energy production, biosynthetic precursors, or redox homeostasis?

2.2 Energy Production and Biosynthesis Must Both Be Supported

Glycolysis is an important pathway through which cells obtain energy and metabolic intermediates. Without detailing the individual intermediate reactions, its net reaction can be expressed as:

Glucose + 2 NAD⁺ + 2 ADP + 2 Pi → 2 pyruvate + 2 NADH + 2 H⁺ + 2 ATP + 2 H₂O

Here, NAD⁺ is oxidized nicotinamide adenine dinucleotide, ADP is adenosine diphosphate, Pi is inorganic phosphate, and ATP is adenosine triphosphate.

Pyruvate produced through glycolysis can be reduced to lactate or transported into mitochondria, where it is converted to acetyl coenzyme A and enters the tricarboxylic acid cycle. Intermediates of glucose metabolism can also be diverted into branches such as the pentose phosphate pathway, serine biosynthesis, and glycerolipid synthesis.

This illustrates that the role of a metabolic network is not limited to ATP production. Proliferating cells also require:

① Nucleotides for DNA and RNA synthesis;

② Amino acids for protein synthesis;

③ Fatty acids and cholesterol for the formation of membrane structures;

④ Reducing equivalents for biosynthesis and antioxidant reactions.

The maintenance of high glycolytic activity in rapidly proliferating cells does not necessarily indicate a loss of mitochondrial function. Increased glucose uptake and glycolytic flux can also support the diversion of metabolic intermediates into biosynthetic pathways. Consequently, after a metabolic enzyme is inhibited, a cell may stop proliferating because of insufficient nucleotide, lipid, or amino acid supply even before a marked decline in intracellular ATP becomes detectable.

2.3 Redox Metabolism Determines Whether Cells Can Limit Damage

Reactive oxygen species (ROS) are generated during mitochondrial respiration and various redox reactions. Moderate levels of ROS can participate in signal regulation, whereas excessive ROS can oxidize proteins, nucleic acids, and membrane lipids.

Cells rely mainly on reduced nicotinamide adenine dinucleotide phosphate (NADPH), reduced glutathione (GSH), and related antioxidant enzymes to maintain redox homeostasis. Glutathione peroxidase 4 (GPX4) uses GSH to reduce phospholipid hydroperoxides in cellular membranes to the corresponding phospholipid alcohols.

Phospholipid hydroperoxide + 2 molecules of GSH

→ catalyzed by GPX4 →

Phospholipid alcohol + GSSG + water

That is:

PLOOH + 2 GSH → PLOH + GSSG + H₂O

Catalyzing enzyme: GPX4

Where:

① PLOOH represents a phospholipid hydroperoxide, a damaging product of lipid peroxidation;

② PLOH represents a phospholipid alcohol, the reduced product of PLOOH;

③ GSH represents reduced glutathione;

④ GSSG represents oxidized glutathione;

⑤ H₂O represents water.

When GPX4 activity is inhibited, intracellular GSH supply is insufficient, or NADPH-dependent reducing systems are unable to sustain GSH regeneration, phospholipid hydroperoxides may not be removed efficiently. Peroxidation reactions can then propagate through membrane phospholipids containing polyunsaturated fatty acids, damaging membrane structure and function. Once the damage reaches a critical threshold, it can induce an iron-dependent form of regulated cell death known as ferroptosis.

RSL3 can covalently inhibit GPX4 activity and promote the accumulation of phospholipid peroxides. It is therefore commonly used to investigate GPX4-dependent defenses against lipid peroxidation and the process of ferroptosis.

This reaction demonstrates a direct connection between metabolic enzymes and cell fate. Metabolic regulation not only affects the rate of cell growth but also determines whether a cell can withstand specific forms of oxidative damage.

2.4 Metabolites Also Participate in Protein Modification and Gene Regulation

Some metabolites serve not only as substrates in metabolic reactions but also as donors or cofactors required for protein and chromatin modifications. For example:

① Acetyl coenzyme A provides acetyl groups for acetylation reactions;

② S-adenosylmethionine provides methyl groups for methylation reactions;

③ α-Ketoglutarate participates in reactions catalyzed by multiple dioxygenases;

④ NAD⁺ participates in reactions catalyzed by certain deacetylases and poly(ADP-ribose) polymerases.

Metabolic states can therefore influence protein activity, chromatin states, and gene expression by altering the availability of modification substrates and the conditions required for enzymatic reactions. In this way, metabolic networks constitute an important regulatory layer linking nutrient status to cellular function.

3 How Proteases and Protein Degradation Systems Control Protein Fate

3.1 The Ubiquitin–Proteasome System Mediates Selective Protein Degradation

The ubiquitin–proteasome system (UPS) is one of the major pathways responsible for selective intracellular protein degradation. It primarily removes short-lived regulatory proteins, misfolded proteins, and damaged proteins. Ubiquitin tagging is generally completed sequentially by the ubiquitin-activating enzyme E1, ubiquitin-conjugating enzyme E2, and ubiquitin ligase E3.

Step 1: E1 Uses ATP to Activate Ubiquitin

Ubiquitin + ATP + E1

→ ubiquitin-bound E1 + AMP + pyrophosphate

E1 uses ATP to activate ubiquitin and forms a high-energy thioester bond with ubiquitin.

Step 2: Ubiquitin Is Transferred from E1 to E2

Ubiquitin-bound E1 + E2

→ E1 + ubiquitin-bound E2

Ubiquitin is transferred from E1 to E2 and forms a thioester bond with the active site of E2.

Step 3: E3 Promotes the Conjugation of Ubiquitin to the Substrate Protein

Ubiquitin-bound E2 + substrate protein

→ through the action of E3 →

ubiquitinated substrate protein + E2

E3 is primarily responsible for recognizing specific substrates and promoting the conjugation of ubiquitin to those substrates. The carboxyl group of the C-terminal glycine of ubiquitin usually forms an isopeptide bond with the amino group of a lysine side chain in the substrate. Additional ubiquitin molecules can be conjugated sequentially to form different types of polyubiquitin chains.

The 26S Proteasome Completes Substrate Recognition, Unfolding, and Hydrolysis

Polyubiquitinated proteins carrying appropriate degradation signals can be recognized by the 26S proteasome. The 26S proteasome consists of one 20S catalytic core and one or two 19S regulatory particles.

Process of Substrate Degradation by the 26S Proteasome

Polyubiquitinated substrate is recognized by the 19S regulatory particle

→ the ubiquitin chain is removed and recycled

→ ATP drives substrate unfolding

→ the unfolded substrate is translocated into the 20S catalytic core

→ the 20S catalytic core hydrolyzes peptide bonds and generates short peptides

The 19S regulatory particle is responsible for substrate recognition, deubiquitination, unfolding, and translocation, whereas the 20S catalytic core is responsible for proteolysis.

Ubiquitination is not equivalent to protein degradation. K48-linked polyubiquitin chains are common signals for proteasomal degradation. K11-linked chains and K11/K48-branched ubiquitin chains can also participate in proteasome-dependent degradation. Other ubiquitin chain types can regulate protein localization, signaling-complex assembly, DNA-damage responses, and membrane trafficking.

Whether a substrate is ultimately degraded depends on the structure and length of its ubiquitin chain, whether the substrate contains an initiation region that can enter the proteasome, and the recognition and processing state of the proteasome.

3.2 The Autophagy–Lysosome System Mediates Large-Scale Clearance and Recycling

Because substrates must first be unfolded before entering the catalytic chamber of the proteasome, the proteasome is not suitable for directly processing intact organelles or large protein aggregates. Such cargo is mainly cleared by the autophagy–lysosome system.

During macroautophagy, cytoplasmic cargo is enclosed by a double-membrane structure to form an autophagosome. The autophagosome subsequently fuses with a lysosome. Cathepsins and other acidic hydrolases within the lysosome degrade the cargo, and the resulting amino acids, fatty acids, and other small molecules can be reused.

Autophagy can process:

① Long-lived proteins and protein aggregates;

② Damaged mitochondria and other organelles;

③ Certain lipid droplets and membrane structures;

④ Pathogens that have invaded the intracellular environment.

The proteasome and the autophagy–lysosome system are not simply interchangeable. The proteasome is better suited to the rapid and precise regulation of individual proteins or relatively small substrates. The autophagy–lysosome system is better suited to processing large complexes, aggregates, and organelles and also performs an important nutrient-recycling function.

3.3 Limited Proteolysis Activates and Executes Signaling Programs

Proteolysis does not necessarily result in the complete elimination of a substrate. Many proteases cleave substrates only at specific sites, converting inactive precursors into active proteins or releasing fragments with new functions. This process is known as limited proteolysis.

Limited proteolysis participates in:

① Zymogen activation;

② Maturation of hormones and cytokines;

③ Blood coagulation;

④ Processing of receptors and transcription factors;

⑤ Cell-death processes such as apoptosis and pyroptosis.

Cysteine-dependent aspartate-specific proteases, or caspases, are typical examples. Initiator caspases are generally recruited to multiprotein complexes and activated through proximity-induced dimerization. Initiator caspases subsequently cleave and activate executioner caspases. Executioner caspases then cleave cytoskeletal proteins, DNA-repair proteins, and other critical substrates, thereby driving the apoptotic program to completion.

4 How Metabolic Flux and Protein Degradation Regulate Each Other

4.1 Metabolic State Determines the Capacity to Maintain Protein Homeostasis

Protein synthesis, folding, transport, and degradation all require metabolic support.

① Ubiquitin activation consumes ATP, and the AAA+ ATPases in the proteasome require ATP to drive substrate unfolding and translocation. When cellular energy is insufficient, protein quality-control capacity may become limited.

② Redox imbalance increases protein damage. Excessive ROS can oxidize amino acid side chains, cause protein misfolding, and disrupt protein complexes, thereby increasing the burden on molecular chaperones, proteasomes, and autophagy systems.

③ Nutrient and metabolite availability affects protein modifications such as glycosylation, acetylation, and methylation. These modifications may alter protein conformation, localization, interactions, and degradation rates.

Metabolic stress therefore does more than reduce energy or precursor availability. It can also disrupt protein homeostasis by increasing the burden of damaged proteins and weakening the capacity for their clearance.

4.2 Protein Turnover Reshapes Metabolic Flux

Metabolic enzymes are themselves proteins that require continuous renewal. Changes in the degradation rate of a key metabolic enzyme may directly alter the catalytic capacity and metabolic flux of the corresponding reaction.

Protein degradation can also reshape metabolism through the following mechanisms:

① Regulating metabolic enzyme abundance by altering the half-lives of rate-limiting enzymes or key branch-point enzymes;

② Regulating transcription factors and kinases, thereby simultaneously changing the expression or activity of multiple metabolic enzymes;

③ Removing damaged organelles, because mitochondrial quality control directly affects oxidative phosphorylation, fatty acid oxidation, and ROS production;

④ Recycling amino acids, because amino acids released by proteolysis can be reused for protein synthesis or enter energy metabolism and biosynthetic pathways.

The outcome of protein degradation is therefore not limited to “a reduction in the abundance of a particular protein.” It may also result in redistribution across the entire metabolic network.

4.3 AMPK and mTORC1 Coordinate Synthesis and Degradation

AMP-activated protein kinase (AMPK) and mechanistic target of rapamycin complex 1 (mTORC1) are major regulators that connect energy status, nutrient availability, and protein homeostasis.

When cellular energy is insufficient, AMPK activity increases. AMPK promotes catabolic pathways that support ATP restoration and inhibits certain energy-intensive biosynthetic processes. AMPK can also promote autophagy by phosphorylating the autophagy-initiating kinase ULK1.

When amino acids, energy, and growth factors are abundant, mTORC1 generally promotes protein synthesis and cell growth while inhibiting autophagy initiation. During nutrient deprivation or when mTORC1 is inhibited, autophagy is more readily activated.

The central relationships can be summarized as follows:

Adequate nutrients and energy

→ mTORC1 activation

→ promotion of protein synthesis and inhibition of autophagy initiation

Energy deficiency

→ AMPK activation

→ inhibition of energy-intensive biosynthesis and promotion of catabolism and autophagy

This coordinated mechanism enables cells to adjust the balance between “synthesizing new material” and “degrading existing material” according to resource availability.

4.4 Protein Degradation Can Also Be Regulated Upstream of the Proteasome

Neural precursor cell expressed, developmentally downregulated 8 (NEDD8) is a ubiquitin-like protein. NEDD8 modification of cullin proteins enhances the activity of Cullin–RING ubiquitin ligases (CRLs), thereby promoting the ubiquitination of specific substrates.

MLN4924, also known as pevonedistat, inhibits the NEDD8-activating enzyme (NAE), reduces cullin neddylation and CRL activity, and causes the accumulation of certain CRL substrates.

This mechanism demonstrates that altering protein degradation does not necessarily require direct inhibition of the proteasome. Substrate recognition, ubiquitin-like modifications, and E3 ligase activity are also important regulatory points.

5 How the Two Systems Jointly Determine Cell Fate

5.1 Cell Proliferation Requires Coordination Between Metabolic Supply and Protein Turnover

For a cell to complete one round of division, two conditions must be met simultaneously.

On the one hand, the metabolic network must provide ATP, nucleotides, lipids, and amino acids. On the other hand, cyclins, replication-licensing factors, and checkpoint proteins must be produced and removed in the correct temporal sequence.

If metabolic resources are insufficient, the cell cannot complete biomass duplication even if growth signals remain active. If protein turnover is disrupted, the cell cycle may arrest or abnormal replication may occur even when sufficient precursors are available.

Cell proliferation is therefore not simply switched on by a particular growth-signaling pathway. It depends on the coordination of biosynthetic capacity, metabolic supply, and protein turnover.

5.2 Stress Adaptation Depends on Reducing Consumption and Increasing Recycling

During short-term nutrient deprivation, hypoxia, or protein damage, cells commonly first reduce energy-intensive biosynthetic activity while increasing material recycling and quality-control capacity.

Major changes during this phase include:

① Reduced protein and lipid synthesis;

② Mobilization of glycogen, lipids, amino acids, or other stored resources;

③ Recycling of cellular components through autophagy;

④ Increased antioxidant capacity and damage-repair activity;

⑤ Removal of damaged proteins and organelles.

If the stress is resolved, cellular homeostasis may be restored. If energy deficiency, lipid peroxidation, or protein damage continues to worsen, adaptive responses may fail, and the cell may enter arrest, senescence, or death.

5.3 Imbalances at Different Regulatory Nodes Can Cause Different Forms of Cell Death

Reduced cell viability is only an endpoint phenotype and does not identify the specific mechanism of cell death. Dysregulation of metabolic enzymes and proteolytic systems can cause cell death through different pathways.

Different forms of regulated cell death can interact with one another. Reliable identification of a death mechanism cannot be based solely on cell morphology or a single biomarker. Instead, the mechanism should be established on the basis of essential molecular events, pharmacological rescue experiments, and genetic evidence.

6 How to Establish Reliable Experimental Evidence

6.1 Studies of Metabolic Enzymes Must Demonstrate Changes in Metabolic Flux

An increase or decrease in the expression of a metabolic enzyme does not prove that the rate of the corresponding metabolic reaction changes in the same direction.

Enzyme activity is also influenced by:

Substrate and cofactor availability;

Allosteric regulation;

Post-translational modifications;

Subcellular localization;

Feedback inhibition;

Compensation by isoenzymes.

A complete body of evidence should include three levels:

6.2 Studies of Protein Degradation Must Distinguish Synthesis from Clearance

Protein abundance is jointly determined by the rates of protein synthesis and degradation. An increase in the abundance of a protein after treatment may result from:

① Increased transcription;

② Enhanced translation;

③ Prolonged protein half-life;

④ Altered subcellular localization;

⑤ Changes in protein-complex formation or modification state.

Demonstrating a protein-degradation mechanism usually requires assessing:

① Whether the protein half-life changes;

② Whether proteasome or lysosome inhibition prevents the decline in protein abundance;

③ Whether the substrate undergoes ubiquitination or other degradation-associated modifications;

④ Whether a candidate E3 ligase, deubiquitinase, or protease is involved;

⑤ Whether mutation of a degradation site or recognition sequence stabilizes the protein;

⑥ Whether stabilization of the protein restores the downstream phenotype.

A relatively complete causal relationship can be established only when the change in degradation of the target protein is shown to occur before the phenotype and when blocking that degradation produces functional rescue.

6.3 Small-Molecule Tools Should Be Combined with Genetic and Rescue Experiments

2-DG can cause glycolytic stress, interfere with N-linked glycosylation, and induce endoplasmic reticulum stress. Its effects therefore cannot be explained simply as the result of glycolytic inhibition.

Reliable mechanistic studies should integrate three mutually supportive forms of evidence:

Pharmacological intervention + genetic intervention + functional rescue and direct biochemical measurements

Small-molecule treatments allow rapid control over the timing and dose of an intervention but may produce multi-target effects. Gene knockdown or knockout provides clearer target specificity but may induce long-term compensatory responses. Functional rescue experiments are used to determine whether the target molecule truly lies within the causal pathway.

6.4 Temporal Order Is Essential for Establishing Causality

Metabolic changes, disruption of protein homeostasis, and cell death generally do not occur simultaneously. A common sequence is:

Change in target activity

→ change in metabolite abundance or protein half-life

→ disruption of energy balance, redox homeostasis, or protein homeostasis

→ cell-cycle, stress-response, and cell-death phenotypes

Examining only a single late time point can lead to the misinterpretation of secondary changes as initiating mechanisms. Experiments should therefore include early, intermediate, and late time points to distinguish initiating events, adaptive responses, secondary damage, and irreversible cell-death processes.

7 Classification and Research Applications of Representative Compounds Related to the Regulation of Cell Fate by Metabolic Enzymes and Proteases

Table 1. Metabolic Flux, Mitochondrial Bioenergetics, and Nutrient Sensing

Table 2. Redox Homeostasis and Ferroptosis

Table 3. Ubiquitin–Proteasome System and Ubiquitin-Like Modifications

Table 4. Autophagy–Lysosome System and Intracellular Proteases

Table 5. Caspases and Extracellular Matrix Proteases

Note: The products listed above are representative Aladdin products intended for scientific research and formulation studies. Additional product specifications, grades, and certificate of analysis information can be retrieved from the Aladdin website using the product name, CAS number, or catalog number.

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