GO:0015189 L-lysine transmembrane transporter activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0015189 defines the molecular function that enables transfer of L-lysine across a membrane, a process essential for amino acid homeostasis and cell signaling.
• L-lysine transporters are members of the amino acid-polyamine-organocation (APC) superfamily and the mitochondrial carrier family, with examples including SLC7A1, SLC7A2, and SLC25A29.
• Dysregulation of L-lysine transport is linked to viral pathogenesis, fibrosis, and metabolic disorders, as shown by transcriptomic and functional studies [1,2].
• Lysosomal and mitochondrial transport of L-lysine is critical for organelle function, and defects can be modeled using genetically encoded biosensors and knockout cell lines [4,8].
• CRISPR knockout, point mutation, and knock-in models are powerful tools to dissect the causal role of specific lysine transporters in disease [1,2].
• EDITGENE provides end-to-end services for generating and screening L-lysine transporter models, from KO to overexpression and library screening.
Description
L-lysine transmembrane transporter activity (GO:0015189) is a molecular function that enables the movement of L-lysine, an essential amino acid, across biological membranes. This activity is fundamental for nutrient uptake, protein synthesis, and metabolic regulation in all cell types. The QuickGO definition states that this function enables the transfer of L-lysine from one side of a membrane to the other, where L-lysine is 2,6-diaminohexanoic acid. Transporters with this activity are integral membrane proteins that facilitate the passage of lysine through lipid bilayers, often against its concentration gradient using energy from ion gradients or ATP. Researchers study L-lysine transmembrane transporter activity to understand how cells acquire and distribute this amino acid, which is not only a building block for proteins but also a precursor for carnitine and a regulator of mTOR signaling. Dysregulation of lysine transport has been implicated in viral infections, fibrotic diseases, and metabolic disorders [1,2]. For example, transcriptomic profiling of TBEV-infected neurons revealed altered expression of amino acid transporters, suggesting a role in neuropathogenesis. Similarly, LINC00941/lncIAPF-mediated regulation of autophagy in pulmonary fibrosis involves metabolic reprogramming that may depend on lysine transport. Given the broad impact of lysine transport on cell physiology, precise genetic models are needed to dissect the function of individual transporters. CRISPR-based knockout, point mutation, and knock-in strategies allow researchers to interrogate the specific contributions of genes like SLC7A1, SLC7A2, and SLC25A29 to lysine homeostasis and disease [1,2]. This article provides a comprehensive overview of the ontology, mechanisms, key genes, and research methods for studying GO:0015189.
L-lysine transmembrane transporter activity At A Glance
| GO ID | GO:0015189 |
|---|---|
| GO term | L-lysine transmembrane transporter activity |
| Ontology | molecular_function |
| Synonym | histidine/arginine/lysine/ornithine porter activity; L-lysine permease; lysine permease activity |
| Major function | Enables the transfer of L-lysine across a membrane |
| Definition | Enables the transfer of L-lysine from one side of a membrane to the other. L-lysine is 2,6-diaminohexanoic acid. |
| Related transporters | SLC7A1, SLC7A2, SLC7A3, SLC25A29, SLC66A1, etc. |
| Cellular locations | Plasma membrane, mitochondrial inner membrane, lysosomal membrane |
| Associated diseases | Viral infections, pulmonary fibrosis, metabolic disorders |
What Is GO:0015189?
L-lysine transmembrane transporter activity (GO:0015189) is a molecular function that enables the transfer of L-lysine from one side of a membrane to the other. L-lysine is 2,6-diaminohexanoic acid, a basic amino acid with a net positive charge at physiological pH. This activity is typically mediated by integral membrane proteins that form channels or carriers, allowing lysine to cross the hydrophobic lipid bilayer. The transport can be passive or active, depending on the specific transporter and the energy source. This GO term is distinct from other amino acid transporter activities because it specifically refers to the movement of L-lysine, although some transporters may exhibit broad specificity for cationic amino acids.
Why Is L-lysine transmembrane transporter activity Important in Cell Biology?
L-lysine transmembrane transporter activity is crucial for maintaining amino acid homeostasis, supporting protein synthesis, and regulating signaling pathways such as mTORC1. Because lysine is an essential amino acid, its uptake from the environment or its recycling from intracellular stores is vital for cell growth and proliferation. Defects in lysine transport can lead to metabolic imbalances, impaired immune responses, and increased susceptibility to infections. Moreover, lysine transporters are emerging as therapeutic targets in cancer and fibrosis, where altered amino acid metabolism supports pathological cell proliferation. Understanding this activity at the molecular level is therefore essential for developing targeted interventions.
• Essential for uptake of dietary lysine in the intestine and kidney.
• Regulates mTORC1 signaling and autophagy in response to amino acid availability.
• Required for mitochondrial function and energy metabolism via SLC25A29.
• Involved in viral pathogenesis, as shown by altered transporter expression in TBEV-infected neurons.
• Contributes to pulmonary fibrosis through metabolic reprogramming.
• Lysosomal lysine transport affects organelle pH and function.
• Potential target for cancer therapy due to high demand for lysine in proliferating cells.
• Genetic variants in lysine transporters may affect drug pharmacokinetics and toxicity.
• Modeling lysine transport helps understand rare metabolic diseases like hyperlysinemia.
• CRISPR screens can identify novel regulators of lysine transport and metabolism.
Molecular Mechanism of L-lysine transmembrane transporter activity
Substrate Recognition and Binding
In simple terms: The transporter recognizes L-lysine and grabs it.
L-lysine transporters possess a substrate-binding site that specifically accommodates the positively charged side chain of lysine. In the APC superfamily, this site is formed by conserved aromatic and acidic residues that interact with the amino and carboxyl groups of the amino acid. For example, in SLC7A1 (CAT-1), a critical glutamate residue (E193) is involved in binding the alpha-amino group, while a tryptophan residue (W230) contributes to the hydrophobic environment for the side chain. The binding affinity (Km) for L-lysine typically ranges from 10 to 100 micromolar, depending on the transporter and cell type. Substrate recognition is stereospecific, as D-lysine is not transported efficiently.
Conformational Changes and Translocation
In simple terms: The transporter changes shape to move lysine across the membrane.
After binding, the transporter undergoes a series of conformational changes that expose the substrate to the opposite side of the membrane. This alternating access mechanism involves a rocker-switch motion of the transmembrane helices. In the mitochondrial carrier SLC25A29, which transports lysine into mitochondria, the transport cycle is driven by the membrane potential and pH gradient. Structural studies of related transporters suggest that a conserved proline residue in transmembrane helix 6 acts as a hinge for these movements. The rate of translocation can be modulated by post-translational modifications and interacting proteins.
Energy Coupling and Regulation
In simple terms: Some transporters use energy to pump lysine against its gradient.
L-lysine transport can be passive (facilitated diffusion) or active. The cationic amino acid transporters (CATs, e.g., SLC7A1-3) are facilitated diffusers that work down the concentration gradient, but they can also mediate exchange. In contrast, the lysosomal transporter SLC66A1 (PQLC2) uses a proton gradient to export lysine from lysosomes. Mitochondrial SLC25A29 exchanges lysine for arginine or ornithine, driven by the electrochemical gradient. Activity is regulated by substrate availability, hormones, and stress signals. For instance, ATF3 activation in pulmonary fibrosis alters the expression of amino acid transporters, indirectly affecting lysine flux.
Cofactors and Modulators
In simple terms: Other molecules can help or hinder the transporter.
Some lysine transporters require cofactors or accessory proteins for function. For example, the heteromeric amino acid transporter LAT1 (SLC7A5) requires the heavy chain CD98 (SLC3A2) for plasma membrane localization, although LAT1 primarily transports large neutral amino acids. The lysosomal transporter SLC66A1 may require the presence of specific lipids or pH for optimal activity. Additionally, myristoylation of TMEM106B by NMT1/2 regulates its trafficking and turnover, which may indirectly affect lysosomal amino acid transport. Chloride channels in endothelial cells can modulate membrane potential and thus influence the driving force for lysine transport.
Transport Kinetics and Specificity
In simple terms: How fast and how selective the transporter is.
The kinetics of L-lysine transport are characterized by the Michaelis-Menten constant (Km) and maximal velocity (Vmax). For SLC7A1, the Km for lysine is approximately 100 micromolar, while for SLC7A2 it is around 200 micromolar. The specificity varies: some transporters are highly selective for lysine, while others also transport arginine, ornithine, and histidine, as reflected in the synonym histidine/arginine/lysine/ornithine porter activity. This broad specificity is due to the similar structures of these cationic amino acids. Transport activity can be measured using radiolabeled lysine or fluorescent biosensors.
Key Genes Involved in GO:0015189 L-lysine transmembrane transporter activity
The following genes encode proteins that exhibit L-lysine transmembrane transporter activity or are directly involved in its regulation, as supported by published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| SLC7A1 | High-affinity cationic amino acid transporter (CAT-1); mediates lysine uptake | Knockout reduces lysine influx; studied in viral infection and cancer |
| SLC7A2 | CAT-2; inducible transporter for lysine and arginine | Linked to inflammation and fibrosis; target for CRISPR KO |
| SLC7A3 | CAT-3; neuronal cationic amino acid transporter | Expressed in brain; potential role in neuropathogenesis |
| SLC25A29 | Mitochondrial lysine/arginine/ornithine carrier | Defects affect mitochondrial function; model for metabolic disorders |
| SLC66A1 | Lysosomal lysine exporter (PQLC2) | Regulates lysosomal pH and amino acid storage; biosensor studies |
| SLC3A2 | Heavy chain of heteromeric amino acid transporters | Required for surface expression of some transporters; KO affects lysine uptake |
| SLC7A5 | LAT1; transports large neutral amino acids, but can influence lysine indirectly | Target in cancer metabolism; CRISPR KO reduces proliferation |
| TMEM106B | Lysosomal transmembrane protein; myristoylation regulates trafficking | May affect lysosomal amino acid transport; linked to neurodegeneration |
| CFTR | Chloride channel; modulates membrane potential | Loss of CFTR alters endothelial barrier and may affect transport |
| CLCN3 | Chloride channel in endosomes/lysosomes | Regulates organelle pH and indirectly lysine transport |
| ATF3 | Transcription factor regulating stress responses | Activates LINC00941/lncIAPF, affecting autophagy and metabolism |
| ELAVL1 | RNA-binding protein (HuR); stabilizes mRNAs | Modulates expression of transporters; involved in fibrosis |
| LINC00941 | Long non-coding RNA; regulates fibroblast differentiation | Modulates autophagy and metabolic genes |
| NMT1 | N-myristoyltransferase 1; modifies TMEM106B | Affects trafficking of lysosomal proteins |
| NMT2 | N-myristoyltransferase 2; modifies TMEM106B | Affects trafficking of lysosomal proteins |
| ABCD4 | Peroxisomal transporter; involved in cobalamin transport | Transmembrane helix 6 is indispensable; model for transport studies |
How Is L-lysine transmembrane transporter activity Regulated?
L-lysine transmembrane transporter activity is regulated at multiple levels. Transcriptional regulation involves stress-responsive transcription factors such as ATF3, which can alter the expression of amino acid transporters and related metabolic genes in conditions like pulmonary fibrosis. Post-transcriptional regulation by RNA-binding proteins like ELAVL1 (HuR) stabilizes transporter mRNAs, affecting protein levels. Post-translational modifications, including myristoylation of TMEM106B by NMT1/2, control the trafficking and turnover of lysosomal membrane proteins, thereby influencing lysine transport. Additionally, the activity of transporters can be modulated by membrane potential and ion gradients; for example, chloride channels such as CFTR and CLCN3 affect the electrochemical driving force for lysine transport [3,6]. Finally, nutrient availability and mTORC1 signaling create feedback loops that adjust transport activity to meet cellular demands.
L-lysine transmembrane transporter activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| SLC7A1 | Viral infection, cancer | Knockout cell lines, viral challenge |
| SLC7A2 | Pulmonary fibrosis, inflammation | CRISPR KO in fibroblasts, bleomycin model |
| SLC25A29 | Mitochondrial dysfunction, hyperlysinemia | Point mutation knock-in in HEK293 |
| SLC66A1 | Lysosomal storage disorder | Lysosomal pH biosensor, KO neurons |
| TMEM106B | Neurodegeneration | Myristoylation-deficient knock-in |
L-lysine transport in viral pathogenesis
Viral infections can hijack host amino acid transporters to support viral replication. In a study of tick-borne encephalitis virus (TBEV) infection, RNA profiling of neurons and astrocytes revealed upregulation of several amino acid transporters, including those with specificity for lysine, suggesting that the virus manipulates lysine transport to meet its metabolic needs. This alteration may contribute to neuropathogenesis and offers potential targets for antiviral strategies.
L-lysine transport in pulmonary fibrosis
Pulmonary fibrosis is characterized by excessive extracellular matrix deposition and fibroblast-to-myofibroblast differentiation. The long non-coding RNA LINC00941 (lncIAPF) promotes this process by blocking autophagy in an ELAVL1/HuR-dependent manner, and its expression is activated by ATF3. This pathway involves metabolic reprogramming that may depend on increased lysine uptake to support collagen synthesis. Targeting lysine transporters could therefore attenuate fibrosis progression.
Lysosomal and mitochondrial transport defects
Lysosomal storage disorders and mitochondrial diseases can arise from defects in organellar amino acid transport. SLC66A1 (PQLC2) is a lysosomal lysine exporter, and its dysfunction leads to lysine accumulation in lysosomes, affecting organelle pH and function. Similarly, mutations in the mitochondrial carrier SLC25A29 impair lysine transport into mitochondria, disrupting energy metabolism and causing metabolic stress. These rare disorders highlight the importance of precise lysine transport for cellular health.
From L-lysine transmembrane transporter activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does SLC7A1 mediate lysine uptake in cancer cells? | SLC7A1 knockout via CRISPR-Cas9 in HeLa or MCF7 |
| What is the effect of a patient mutation in SLC25A29? | Point mutation knock-in using HDR in HEK293 |
| Can overexpression of SLC7A2 drive fibrosis? | Lentiviral overexpression in primary fibroblasts |
| How does lysosomal lysine transport affect pH? | SLC66A1 knockout with lysosomal pH biosensor |
| What is the role of TMEM106B myristoylation in transport? | NMT1/2 double knockout or myristoylation-site mutant knock-in |
| Can a CRISPR library screen identify novel lysine transporters? | Genome-wide KO library in lysine-dependent cell line |
How to Study the L-lysine transmembrane transporter activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| RNA-seq | Transcript levels of transporters | Identify upregulation in disease models |
| Radiolabeled uptake | Transport activity (Km, Vmax) | Characterize SLC7A1 in cell lines |
| Fluorescent biosensor | Organelle pH changes | Monitor lysosomal lysine export |
| Proteomics | Protein interactions and modifications | Discover myristoylation of TMEM106B |
| CRISPR screen | Gene essentiality and regulators | Find novel lysine transporters |
| Patch-clamp | Ion currents | Study electrogenic transport |
| Immunofluorescence | Subcellular localization | Confirm plasma membrane expression |
| Metabolomics | Intracellular lysine levels | Assess transport efficiency |
Transcriptomic profiling
RNA sequencing (RNA-seq) is widely used to identify changes in the expression of amino acid transporters under different conditions. For example, integrative RNA profiling of TBEV-infected neurons and astrocytes revealed upregulation of several SLC family transporters, including those with lysine transport activity. This method provides a global view of transcriptional regulation and can be combined with pathway analysis to pinpoint metabolic shifts.
Functional transport assays
Direct measurement of L-lysine transport activity can be performed using radiolabeled 3H-L-lysine uptake assays in cell lines or Xenopus oocytes expressing candidate transporters. Alternatively, genetically encoded fluorescent biosensors, such as those for lysosomal pH, can indirectly report on lysine transport by monitoring organelle pH changes. These assays are quantitative and can determine kinetic parameters like Km and Vmax.
Proteomics and interactomics
Mass spectrometry-based proteomics can identify proteins that co-purify with lysine transporters, revealing interaction partners and post-translational modifications. For instance, myristoylation of TMEM106B by NMT1/2 was discovered using proteomic approaches. Proximity labeling techniques like BioID can map the interactome of transporters in living cells.
CRISPR screening
Genome-wide CRISPR knockout or activation screens can identify genes that regulate lysine transport or that are essential in lysine-dependent cells. Such screens have been used to uncover metabolic vulnerabilities in cancer and can be adapted to study transporter function. Libraries targeting SLC genes are particularly useful for pinpointing redundant transporters.
How CRISPR Can Be Used to Study GO:0015189 L-lysine transmembrane transporter activity
Knockout
CRISPR-Cas9 knockout of genes encoding L-lysine transporters, such as SLC7A1 or SLC7A2, is a powerful approach to study their contribution to lysine uptake and cellular phenotypes. For example, knockout of SLC7A1 in cancer cells reduces lysine influx and inhibits proliferation. Knockout models can also be used to validate findings from RNA-seq studies, such as those showing altered transporter expression in viral infections.
Point Mutation
Point mutations in transporter genes can mimic human genetic variants or disrupt key functional residues. For instance, mutating the conserved glutamate in SLC7A1 (E193) abolishes lysine binding and transport. CRISPR-based base editing or HDR can introduce such point mutations to study structure-function relationships and disease mechanisms.
Knock-in
Knock-in of epitope tags (e.g., FLAG, GFP) or disease-associated mutations allows for precise tracking and functional analysis of lysine transporters. Tagged knock-in models enable immunofluorescence and co-immunoprecipitation studies to determine localization and interactions. For example, a GFP knock-in of SLC66A1 can be used to monitor lysosomal dynamics.
Overexpression
Overexpression of wild-type or mutant lysine transporters via lentiviral transduction or CRISPR activation (CRISPRa) can enhance transport activity and reveal gain-of-function phenotypes. Overexpressing SLC7A2 in fibroblasts may promote fibrosis-related metabolic changes. This approach is useful for studying transporter regulation and identifying downstream effects.
How EDITGENE Supports L-lysine transmembrane transporter activity Research
Researchers studying L-lysine transmembrane transporter activity-related genes often need to determine whether a candidate gene is causally involved in lysine uptake, metabolism, or disease. EDITGENE provides a comprehensive suite of CRISPR-based services to generate precisely engineered cell models, enabling functional validation and mechanistic studies.
Contact EDITGENE today to design your custom CRISPR model for L-lysine transmembrane transporter activity research.
Frequently Asked Questions About L-lysine transmembrane transporter activity
What is L-lysine transmembrane transporter activity?
It is a molecular function (GO:0015189) that enables the transfer of L-lysine across a membrane, as defined by QuickGO.
What genes are involved in L-lysine transmembrane transporter activity?
Key genes include SLC7A1, SLC7A2, SLC7A3, SLC25A29, and SLC66A1, which encode proteins that transport lysine across plasma, mitochondrial, or lysosomal membranes [1,4,8].
How is L-lysine transport regulated?
It is regulated transcriptionally by factors like ATF3, post-transcriptionally by ELAVL1, and post-translationally by myristoylation of proteins like TMEM106B [2,7].
What diseases are associated with defective lysine transport?
Defects have been linked to viral infections, pulmonary fibrosis, lysosomal storage disorders, and mitochondrial dysfunction [1,2,4,8].
How can I study L-lysine transmembrane transporter activity?
Common methods include radiolabeled uptake assays, RNA-seq, fluorescent biosensors, and CRISPR knockout models [1,4].
What is the role of SLC7A1 in lysine transport?
SLC7A1 (CAT-1) is a high-affinity cationic amino acid transporter that mediates lysine uptake and is important for cell proliferation and viral entry.
Can CRISPR be used to knockout lysine transporters?
Yes, CRISPR-Cas9 knockout of genes like SLC7A1 or SLC7A2 is a standard approach to study their function and is offered by EDITGENE.
What is the mitochondrial lysine transporter?
SLC25A29 is a mitochondrial carrier that transports lysine and is essential for mitochondrial function.
How does lysine transport affect autophagy?
Lysine availability can regulate mTORC1 signaling and autophagy; for example, LINC00941/lncIAPF modulates autophagy in fibrosis, potentially via metabolic pathways involving lysine.
What services does EDITGENE provide for lysine transporter research?
EDITGENE offers knockout, point mutation, knock-in, overexpression, CRISPR library screening, and bioinformatics services for studying lysine transporters.
Conclusion
L-lysine transmembrane transporter activity (GO:0015189) is a fundamental molecular function that governs the movement of an essential amino acid across cellular membranes. Its dysregulation contributes to a range of diseases, from viral infections to fibrosis and metabolic disorders. Understanding the specific transporters and their regulation requires precise genetic models and functional assays. EDITGENE's CRISPR services provide researchers with the tools to dissect these mechanisms and accelerate therapeutic discovery.
References
- 1. Selinger M et al.. 2022. Integrative RNA profiling of TBEV-infected neurons and astrocytes reveals potential pathogenic effectors.. Comput Struct Biotechnol J 20:2759-2777 PMID: 35685361
- 2. Zhang J et al.. 2022. ATF3 -activated accelerating effect of LINC00941/lncIAPF on fibroblast-to-myofibroblast differentiation by blocking autophagy depending on ELAVL1/HuR in pulmonary fibrosis.. Autophagy 18(11):2636-2655 PMID: 35427207
- 3. Mata-Daboin A et al.. 2025. Chloride channels in endothelial cells.. J Physiol PMID: 41054230
- 4. Ponsford AH et al.. 2021. Live imaging of intra-lysosome pH in cell lines and primary neuronal culture using a novel genetically encoded biosensor.. Autophagy 17(6):1500-1518 PMID: 32515674
- 5. Adeva-Andany MM et al.. 2017. Significance of l-carnitine for human health.. IUBMB Life 69(8):578-594 PMID: 28653367
- 6. Erfinanda L et al.. 2022. Loss of endothelial CFTR drives barrier failure and edema formation in lung infection and can be targeted by CFTR potentiation.. Sci Transl Med 14(674):eabg8577 PMID: 36475904
- 7. Lacrampe A et al.. 2025. Myristoylation of TMEM106B by NMT1/2 regulates TMEM106B trafficking and turnover.. J Biol Chem 301(7):110322 PMID: 40451428
- 8. Imai M et al.. 2024. Transmembrane helix 6 of ABCD4 is indispensable for cobalamin transport.. J Inherit Metab Dis 47(2):366-373 PMID: 38069516
