GO:0016859 cis-trans isomerase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0016859 cis-trans isomerase activity describes catalysis of the interconversion of cis and trans isomers, a fundamental stereochemical reaction in biology.
• Peptidyl-prolyl cis/trans isomerases (PPIases) are the best-characterized enzymes in this class and accelerate the slow cis-trans isomerization of proline-containing peptide bonds.
• PPIase activity is not limited to protein folding; it can also act as a chaperone-like activity during refolding of client proteins such as creatine kinase.
• Pin1 is a phosphorylation-dependent PPIase that interacts with viral and host regulatory proteins, linking cis-trans isomerization to host-pathogen interactions and immune signaling.
• Cell-surface PPIase activity correlates with extracellular matrix development, indicating roles beyond the cytosol.
• Plant cis/cis/trans-beta-carotene isomerases such as D27-LIKE1 show that cis-trans isomerase activity also operates in carotenoid and strigolactone biosynthesis.
Description
cis-trans isomerase activity (GO:0016859) is a molecular function defined as the catalysis of a reaction that interconverts cis and trans isomers, where atoms or groups are termed cis or trans when they lie respectively on the same or opposite sides of a reference plane common among stereoisomers. This activity is essential because many biological molecules, especially peptides containing proline, can exist as distinct cis and trans conformers whose spontaneous interconversion is extremely slow. Enzymes with cis-trans isomerase activity lower the energy barrier for this interconversion, thereby controlling the timing and outcome of conformational transitions in proteins and other substrates. The best-studied examples are the peptidyl-prolyl cis/trans isomerases (PPIases), which catalyze rotation about the peptide bond preceding proline residues and are involved in protein folding, trafficking, and signaling. Beyond proline isomerization, cis-trans isomerase activity also participates in the metabolism of carotenoids and other small molecules, as shown for the Arabidopsis D27-LIKE1 enzyme that acts as a cis/cis/trans-beta-carotene isomerase in strigolactone biosynthesis. For researchers, GO:0016859 provides a precise functional annotation that connects stereochemical catalysis to diverse cellular processes, including host-pathogen interactions, immune regulation, and extracellular matrix development. Understanding this activity is therefore critical for dissecting mechanisms of protein folding, viral infection, and plant hormone biosynthesis.
cis-trans isomerase activity At A Glance
| GO ID | GO:0016859 |
|---|---|
| GO term | cis-trans isomerase activity |
| Ontology | molecular_function |
| Synonym | None listed in QuickGO |
| Major function | Catalysis of the interconversion of cis and trans isomers |
| Definition source | QuickGO definition based on stereochemical reference planes |
| Representative enzymes | Peptidyl-prolyl cis/trans isomerases (PPIases), Pin1, D27-LIKE1 |
| Biological context | Protein folding, host-pathogen interactions, carotenoid biosynthesis, extracellular matrix development |
What Is GO:0016859?
In simple terms, cis-trans isomerase activity is the ability of an enzyme to flip a molecule between its cis and trans forms, which are mirror-related arrangements around a double bond or a rigid bond such as the peptide bond preceding proline. The official GO definition states that this activity catalyzes a reaction that interconverts cis and trans isomers, where atoms or groups are termed cis or trans to one another when they lie respectively on the same or on opposite sides of a reference plane identifiable as common among stereoisomers. This activity is classified as a molecular_function in the Gene Ontology and is fundamental to stereochemical control in biological systems.
Why Is cis-trans isomerase activity Important in Cell Biology?
cis-trans isomerase activity is important because it controls rate-limiting conformational switches that cannot occur spontaneously on biologically relevant timescales, particularly the cis-trans isomerization of proline-containing peptide bonds. By accelerating these switches, PPIases and related enzymes influence protein folding, trafficking, and signaling, and they are implicated in host-pathogen interactions and immune regulation. The activity also extends to small-molecule metabolism, as illustrated by plant cis/cis/trans-beta-carotene isomerases that contribute to strigolactone biosynthesis and affect abscisic acid levels. Moreover, cell-surface PPIase activity has been linked to extracellular matrix development, suggesting roles in tissue remodeling and cell-matrix communication. Because of these diverse roles, cis-trans isomerase activity is a focal point for understanding both normal physiology and disease mechanisms, and it offers opportunities for therapeutic intervention and for engineering plant traits.
• Controls slow cis-trans isomerization of proline-containing peptide bonds, a rate-limiting step in protein folding.
• PPIases can exhibit chaperone-like activity during refolding of client proteins such as creatine kinase.
• Pin1, a phosphorylation-dependent PPIase, interacts with viral proteins and host signaling molecules, linking isomerization to infection and immunity.
• Cell-surface PPIase activity correlates with extracellular matrix development, implicating the activity in tissue remodeling.
• Plant cis/cis/trans-beta-carotene isomerases such as D27-LIKE1 contribute to strigolactone biosynthesis and negatively impact ABA levels.
• Inhibitors of peptidyl-prolyl cis/trans isomerase activity, such as thioxo tetrapeptide-4-nitroanilides, are valuable chemical probes.
• Dysregulation of PPIase activity is associated with cancer, neurodegeneration, and infectious diseases through effects on signaling and folding.
• The activity is a target for immunosuppressive and antiviral strategies because of its role in host-pathogen interactions.
• Cis-trans isomerization of carotenoids is critical for hormone biosynthesis in plants, affecting growth and stress responses.
• Understanding GO:0016859 supports the development of selective modulators for basic research and therapeutic applications.
What Happens During cis-trans isomerase activity?
Substrate recognition and binding
In simple terms: The enzyme first grabs the molecule that needs to be flipped.
cis-trans isomerases recognize specific substrates, often peptides containing proline, and bind them in a conformation that positions the target bond for rotation. For PPIases, the substrate is typically a peptidyl-prolyl bond, and binding specificity can be influenced by phosphorylation of residues near the proline, as seen for Pin1. In plants, D27-LIKE1 recognizes carotenoid substrates such as cis/cis/trans-beta-carotene.
Catalysis of cis-trans interconversion
In simple terms: The enzyme twists the bond so the molecule can switch between its cis and trans shapes.
The catalytic step lowers the activation energy for rotation about a rigid bond, allowing interconversion of cis and trans isomers. For PPIases, this involves rotation about the peptide bond preceding proline, a process that is otherwise very slow. The reaction is reversible and does not necessarily favor one isomer; instead, it accelerates equilibration. In carotenoid isomerases, the enzyme catalyzes cis-to-trans isomerization steps in the biosynthetic pathway.
Release and functional consequences
In simple terms: Once flipped, the molecule is released and can now do its job in the cell.
After isomerization, the product is released and can participate in downstream processes such as protein folding, signaling, or hormone biosynthesis. For example, PPIase activity can facilitate the refolding of denatured proteins, as shown for creatine kinase. In host-pathogen interactions, isomerization of viral or host proteins can modulate immune recognition and infection efficiency.
Regulation by phosphorylation and localization
In simple terms: The enzyme's activity can be switched on or off by chemical tags and by where it sits in the cell.
Some cis-trans isomerases, such as Pin1, are regulated by phosphorylation of their substrates, which creates a binding motif for the enzyme. Localization also matters: PPIase activity has been detected on the cell surface, where it correlates with extracellular matrix development. This spatial regulation allows the same enzymatic activity to serve different functions in different cellular compartments.
Key Genes Involved in GO:0016859 cis-trans isomerase activity
The following genes and proteins represent major experimental models for studying cis-trans isomerase activity (GO:0016859).
| Gene | Major Role | Research Relevance |
|---|---|---|
| PIN1 | Phosphorylation-dependent PPIase that isomerizes phospho-Ser/Thr-Pro motifs | Links cis-trans isomerization to cell cycle, immune signaling, and viral infection |
| PPIA (Cyclophilin A) | Peptidyl-prolyl cis/trans isomerase with chaperone-like activity | Model for protein folding and host-pathogen interactions |
| PPIB (Cyclophilin B) | PPIase involved in collagen folding and extracellular matrix development | Cell-surface PPIase activity correlates with ECM development |
| FKBP1A | FK506-binding protein with PPIase activity | Target for immunosuppressive drugs and folding studies |
| D27-LIKE1 (Arabidopsis) | cis/cis/trans-beta-carotene isomerase | Contributes to strigolactone biosynthesis and ABA regulation |
| D27 (Arabidopsis) | Carotenoid isomerase in strigolactone pathway | Model for plant hormone biosynthesis |
| CYP1 (Arabidopsis) | Cyclophilin-type PPIase | Studied for roles in plant development and stress |
| PPID (Cyclophilin D) | Mitochondrial PPIase | Regulates mitochondrial permeability transition |
| PPIE | PPIase with RNA-binding properties | Implicated in splicing and gene expression |
| PPIF | Mitochondrial cyclophilin | Involved in cell death pathways |
| PPIG | Nuclear PPIase | Associated with spliceosome function |
| PPIH | PPIase in the spliceosome | Essential for pre-mRNA splicing |
| PPIL1 | PPIase-like protein | Component of the spliceosome |
| SUR1 (Arabidopsis) | PPIase-like protein | Role in plant immunity |
| PIN1L | Pin1-like protein | Potential regulator of phospho-Pro motifs |
| CypA (viral interactor) | Host PPIase targeted by viral proteins | Model for host-pathogen interactions |
How Is cis-trans isomerase activity Regulated?
cis-trans isomerase activity is regulated at multiple levels. Phosphorylation of substrate proteins can create binding motifs for phosphorylation-dependent PPIases such as Pin1, thereby controlling when and where isomerization occurs. Localization also plays a key role: cell-surface PPIase activity is distinct from intracellular pools and correlates with extracellular matrix development, suggesting compartment-specific regulation. In plants, the expression and activity of carotenoid isomerases such as D27-LIKE1 are integrated with hormone biosynthesis pathways, affecting strigolactone and ABA levels. Additionally, inhibitor studies using substrate analogs like thioxo tetrapeptide-4-nitroanilides demonstrate that PPIase activity can be chemically modulated, providing tools to probe regulation.
cis-trans isomerase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| PIN1 | Cancer, viral infection, immune signaling | Knockout and point-mutation cell lines to test phospho-substrate binding |
| PPIA | Host-pathogen interactions, protein folding | Overexpression and KO models for folding and infection assays |
| PPIB | Extracellular matrix development, fibrosis | Cell-surface PPIase activity assays in ECM models |
| D27-LIKE1 | Plant hormone biosynthesis (strigolactone, ABA) | Arabidopsis knockout and knock-in lines for hormone profiling |
| FKBP1A | Immunosuppression, folding | CRISPR KO to study drug sensitivity and folding |
cis-trans isomerase activity in cancer and cell cycle control
Pin1, a phosphorylation-dependent PPIase, regulates cell cycle progression and is often overexpressed in cancers, where it contributes to oncogenic signaling. Its ability to isomerize phospho-Ser/Thr-Pro motifs in regulatory proteins makes it a potential therapeutic target. Inhibitors of PPIase activity, such as thioxo tetrapeptide analogs, have been explored as chemical probes for such targets.
Roles in host-pathogen interactions and infectious disease
PPIases are critical in host-pathogen interactions, as highlighted by their involvement in viral infection and immune evasion. For example, Pin1 interacts with early regulatory proteins of human cytomegalovirus, suggesting that cis-trans isomerization modulates viral gene expression. These findings position PPIases as potential antiviral targets.
Neurodegeneration and protein misfolding
Because cis-trans isomerization of proline bonds is a rate-limiting step in protein folding, PPIases may influence the accumulation of misfolded proteins in neurodegenerative diseases. Chaperone-like activity of PPIases during refolding of client proteins such as creatine kinase supports a protective role in maintaining proteostasis. Dysregulation of this activity could contribute to protein aggregation pathologies.
Plant hormone biosynthesis and agricultural traits
In plants, cis/cis/trans-beta-carotene isomerases such as D27-LIKE1 contribute to strigolactone biosynthesis and negatively impact ABA levels, linking cis-trans isomerase activity to growth regulation and stress responses. This makes these enzymes candidates for crop improvement through targeted editing.
From cis-trans isomerase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of PPIase activity affect protein folding? | Knockout cell lines for PPIA or PPIB |
| How does phosphorylation regulate Pin1 substrate binding? | Point-mutation knock-in of phospho-null or phospho-mimetic residues |
| Can cis-trans isomerase activity be monitored on the cell surface? | Tagged knock-in with extracellular epitope for activity assays |
| What is the role of D27-LIKE1 in hormone biosynthesis? | Arabidopsis knockout and overexpression lines |
| Does PPIase inhibition alter viral infection? | Overexpression and KO cells infected with HCMV |
| Can chemical inhibitors selectively block PPIase activity? | In vitro assays with purified enzyme and thioxo peptide analogs |
How to Study the cis-trans isomerase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Chromogenic PPIase assay | Rate of cis-trans isomerization of peptide substrates | Kinetic characterization and inhibitor testing |
| Protein refolding assay | Chaperone-like activity during refolding | Studying PPIase function in proteostasis |
| Co-immunoprecipitation | Protein-protein interactions | Identifying substrates of Pin1 and other PPIases |
| Cell-surface activity assay | Extracellular PPIase activity | Correlating activity with ECM development |
| LC-MS/HPLC | Isomer ratios of carotenoids | Measuring D27-LIKE1 activity in plants |
| CRISPR knockout | Loss-of-function phenotypes | Testing essential roles of PPIases |
| Phospho-mimetic knock-in | Effect of phosphorylation on substrate binding | Dissecting Pin1 regulation |
| Transcriptomics | Gene expression changes | Identifying downstream pathways affected by PPIase loss |
Enzymatic activity assays
cis-trans isomerase activity is commonly measured using chromogenic or fluorogenic peptide substrates that change absorbance or fluorescence upon isomerization. These assays allow kinetic characterization of PPIases and testing of inhibitors such as thioxo tetrapeptide-4-nitroanilides. For carotenoid isomerases, activity can be inferred from changes in isomer ratios using HPLC or LC-MS.
Protein folding and chaperone assays
Chaperone-like activity of PPIases can be assessed by monitoring the refolding of denatured client proteins such as creatine kinase. These assays distinguish isomerase-dependent folding acceleration from general chaperone effects. They are useful for studying the functional consequences of PPIase knockout or inhibition.
Interaction and localization studies
Co-immunoprecipitation, pull-down, and proximity labeling can identify substrates and interaction partners of cis-trans isomerases. Cell-surface PPIase activity can be detected using impermeant substrates or tagged enzymes, linking activity to extracellular matrix development. Imaging approaches can reveal subcellular localization of PPIases.
Genetic and CRISPR-based perturbation
CRISPR knockout, point mutation, and knock-in models enable causal testing of specific residues and domains in cis-trans isomerases. Overexpression models can reveal gain-of-function phenotypes, while knockout models uncover essential roles. These approaches are complemented by transcriptomic and proteomic profiling to identify downstream effects.
How CRISPR Can Be Used to Study GO:0016859 cis-trans isomerase activity
Knockout
CRISPR knockout of genes encoding cis-trans isomerases, such as PIN1 or PPIA, allows researchers to test loss-of-function phenotypes in cell models. Knockout studies can reveal roles in protein folding, viral infection, and cell cycle progression. These models are essential for validating whether a candidate isomerase is causally involved in a given process.
Point Mutation
Point mutations can be introduced into catalytic residues or regulatory phosphorylation sites of cis-trans isomerases to dissect mechanism. For example, mutating the phospho-Thr-Pro motif in Pin1 substrates can test the importance of phosphorylation-dependent isomerization. Such models provide precise structure-function insights.
Knock-in
Knock-in of tagged or reporter versions of cis-trans isomerases enables localization and activity studies in native contexts. Tagged knock-in models can be used to measure cell-surface PPIase activity and its correlation with extracellular matrix development. In plants, knock-in of D27-LIKE1 variants can test their role in strigolactone biosynthesis.
Overexpression
Overexpression of cis-trans isomerases such as Pin1 or cyclophilins can reveal gain-of-function phenotypes, including enhanced folding capacity or altered signaling. Overexpression models are useful for testing whether increased isomerase activity is sufficient to drive specific outcomes, such as viral replication or hormone production.
How EDITGENE Supports cis-trans isomerase activity Research
Researchers studying cis-trans isomerase activity-related genes often need to determine whether a candidate gene is causally involved in a specific biological process, and CRISPR-based models provide the most direct way to test this. By combining knockout, point mutation, knock-in, and overexpression strategies, it is possible to dissect the contribution of catalytic activity, regulatory sites, and protein interactions. EDITGENE offers a comprehensive suite of services to accelerate such studies.
Contact EDITGENE today to design your custom CRISPR model for cis-trans isomerase activity research.
Frequently Asked Questions About cis-trans isomerase activity
What is cis-trans isomerase activity?
cis-trans isomerase activity (GO:0016859) is a molecular function that catalyzes the interconversion of cis and trans isomers, often accelerating slow conformational changes in peptides and other molecules.
What genes are involved in cis-trans isomerase activity?
Key genes include PIN1, PPIA, PPIB, FKBP1A, and plant D27-LIKE1, among others.
How is cis-trans isomerase activity measured?
It is commonly measured using chromogenic peptide substrates, protein refolding assays, and LC-MS for carotenoid isomers.
Why is cis-trans isomerase activity important in disease?
It regulates protein folding and signaling pathways implicated in cancer, viral infection, and neurodegeneration.
What is the role of Pin1 in cis-trans isomerase activity?
Pin1 is a phosphorylation-dependent PPIase that isomerizes phospho-Ser/Thr-Pro motifs and interacts with viral and host regulatory proteins.
Can cis-trans isomerase activity be inhibited?
Yes, substrate analog inhibitors such as thioxo tetrapeptide-4-nitroanilides can block PPIase activity.
What is the difference between cis-trans isomerase and chaperone activity?
Some PPIases possess both isomerase and chaperone-like activities, as shown during creatine kinase refolding.
How does cis-trans isomerase activity affect plants?
Plant cis/cis/trans-beta-carotene isomerases like D27-LIKE1 contribute to strigolactone biosynthesis and influence ABA levels.
Is cis-trans isomerase activity found on the cell surface?
Yes, cell-surface PPIase activity has been detected and correlates with extracellular matrix development.
What CRISPR models are used to study cis-trans isomerase activity?
Knockout, point mutation, knock-in, and overexpression models are used to dissect gene function and mechanism.
Conclusion
cis-trans isomerase activity (GO:0016859) is a fundamental molecular function that controls stereochemical transitions critical for protein folding, signaling, and small-molecule metabolism. Its roles span host-pathogen interactions, immune regulation, plant hormone biosynthesis, and extracellular matrix development, making it a rich area for both basic and translational research. CRISPR-based models and biochemical assays provide powerful tools to dissect the mechanisms and disease relevance of this activity.
References
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- 3. Lin W et al.. 2019. Peptidyl prolyl cis/trans isomerase activity on the cell surface correlates with extracellular matrix development.. Commun Biol 2:58 PMID: 30775459
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