GO:0097435 supramolecular fiber organization: Components, Assembly and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0097435 supramolecular fiber organization describes the cellular assembly, arrangement, and disassembly of supramolecular fibers, which are polymers of protein or protein-complex subunits.
• Supramolecular fibers include chromatin fibers, cytoskeletal filaments, and amyloid-like fibrils, and their organization is critical for genome function and cellular architecture.
• The 10-nm chromatin fiber is a classic example, where nucleosome arrays fold into higher-order structures that influence gene expression.
• Lipid organization in fiber-cell plasma membranes, such as in the eye lens, represents a specialized supramolecular fiber environment.
• Defects in supramolecular fiber organization are linked to congenital cataract and other protein-aggregation diseases.
• Research methods include live-cell imaging, cryo-electron microscopy, and CRISPR-based knockout or knock-in models to dissect fiber assembly.
Description
Supramolecular fiber organization (GO:0097435) is a biological process that encompasses the assembly, arrangement, and disassembly of supramolecular fibers, which are polymers formed by the polymerization of protein or protein-complex subunits into fiber-shaped structures. This term captures a wide range of cellular events, from the formation of the 10-nm chromatin fiber to the organization of lipid-rich membranes in specialized cells. Understanding this process is essential because supramolecular fibers provide structural support, compartmentalize biochemical reactions, and regulate access to genetic information. For researchers, GO:0097435 offers a framework to study how cells build and remodel these large-scale assemblies and how their dysfunction contributes to disease.
supramolecular fiber organization At A Glance
| GO ID | GO:0097435 |
|---|---|
| GO term | supramolecular fiber organization |
| Ontology | biological_process |
| Synonym | extracellular fibril organisation, extracellular fibril organization, extracellular fibril organization and biogenesis, fibril organisation, fibril organization |
| Major function | Assembly, arrangement, or disassembly of supramolecular fibers composed of protein or protein complex subunits |
| Cellular location | Cellular level; can occur in cytoplasm, nucleus, or extracellular space |
| Example | 10-nm chromatin fiber organization |
| Related disease | Congenital cataract |
What Is GO:0097435?
According to the Gene Ontology, GO:0097435 supramolecular fiber organization is a process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure. In simpler terms, it is how cells build, organize, and break down long, fiber-like structures made from many protein building blocks.
Why Is supramolecular fiber organization Important in Cell Biology?
Supramolecular fiber organization is fundamental to cellular architecture and function, as it governs the formation of structures such as chromatin fibers, cytoskeletal elements, and amyloid fibrils. These fibers are not static; their dynamic assembly and disassembly are essential for processes like cell division, gene regulation, and stress responses. Dysregulation of fiber organization can lead to pathological aggregation, as seen in congenital cataract and neurodegenerative conditions. Therefore, studying GO:0097435 provides insights into both normal physiology and disease mechanisms, and it is a key area for therapeutic intervention.
• Maintains genome integrity by organizing chromatin into higher-order fibers.
• Regulates gene expression through dynamic changes in chromatin fiber compaction.
• Provides structural support and mechanical stability to cells and tissues.
• Enables specialized functions such as light refraction in the eye lens.
• Dysfunction is linked to congenital cataract and protein aggregation diseases.
• Involved in the regulation of proteasome supramolecular organization.
• Serves as a target for supramolecular therapeutics and biomaterials.
• Offers a model system for studying self-assembly and polymer physics in cells.
• Critical for understanding extracellular matrix fibril formation.
• Provides a basis for CRISPR-based screens to identify regulators of fiber assembly.
What Happens During supramolecular fiber organization?
Nucleation and early assembly
In simple terms: The first step is like starting a chain: a few protein subunits come together to form a seed.
Supramolecular fiber organization begins with nucleation, where a small number of protein or protein-complex subunits associate to form a stable seed. This step is often rate-limiting and can be regulated by post-translational modifications or cofactors. For example, in chromatin fiber formation, nucleosome arrays must be properly positioned to initiate higher-order folding.
Elongation and polymerization
In simple terms: Once the seed is formed, more subunits add on, making the fiber longer.
Elongation proceeds as additional subunits polymerize onto the growing fiber end. This process is driven by non-covalent interactions and can be influenced by the local environment, such as lipid composition in membranes. In the case of supramolecular polymers, coordination-induced self-assembly can lead to complex fiber structures.
Arrangement and higher-order organization
In simple terms: The fiber is not just a straight line; it can fold, bundle, or arrange into larger structures.
After elongation, fibers undergo arrangement into higher-order structures. For instance, the 10-nm chromatin fiber can fold into 30-nm fibers and further into interphase chromosome territories. Similarly, lipid organization in fiber-cell plasma membranes creates specialized domains that affect fiber function.
Disassembly and turnover
In simple terms: Fibers can be taken apart when they are no longer needed or to recycle subunits.
Disassembly is an active process that allows cells to remodel supramolecular fibers. This can occur through depolymerization or enzymatic cleavage, and it is essential for dynamic processes like cell division and stress recovery. Metabolically regulated proteasome supramolecular organization exemplifies how disassembly is controlled in situ.
Regulation by metabolic and signaling cues
In simple terms: The cell uses signals to decide when to build or break down fibers.
Supramolecular fiber organization is regulated by metabolic status and signaling pathways. For example, proteasome supramolecular organization is metabolically regulated, linking fiber assembly to cellular energy states. Additionally, out-of-equilibrium supramolecular gels demonstrate how external triggers can control fiber formation.
Key Genes Involved in GO:0097435 supramolecular fiber organization
The following genes and proteins are key players in supramolecular fiber organization, based on published literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| HIST1H1C | Linker histone H1, involved in chromatin fiber compaction | Studying 10-nm chromatin fiber organization |
| HIST2H2BE | Core histone H2B, component of nucleosome arrays | Chromatin fiber assembly and gene regulation |
| LMNA | Lamin A/C, forms nuclear lamina fibers | Nuclear envelope organization and disease models |
| VIM | Vimentin, intermediate filament protein | Cytoskeletal fiber organization and cell mechanics |
| TUBB | Beta-tubulin, microtubule subunit | Microtubule fiber dynamics |
| ACTB | Beta-actin, microfilament subunit | Actin fiber organization and cell motility |
| CRYAA | Alpha-crystallin A, lens fiber protein | Congenital cataract and lens fiber organization |
| CRYAB | Alpha-crystallin B, chaperone for lens fibers | Protein aggregation and cataract |
| GJA8 | Connexin 50, gap junction protein in lens fibers | Lens fiber cell communication |
| MIP | Major intrinsic protein, lens fiber membrane protein | Lens fiber cell membrane organization |
| BFSP1 | Beaded filament structural protein 1 | Lens fiber cell cytoskeleton |
| BFSP2 | Beaded filament structural protein 2 | Lens fiber cell architecture |
| PSMD1 | Proteasome 26S subunit, non-ATPase 1 | Proteasome supramolecular organization |
| PSMC2 | Proteasome 26S subunit, ATPase 2 | Proteasome fiber assembly |
| BTA | Benzene-1,3,5-tricarboxamide, synthetic supramolecular fiber | Model for coordination-induced self-assembly |
| COL1A1 | Collagen type I alpha 1, extracellular fibril | Extracellular matrix fiber organization |
| FBN1 | Fibrillin 1, microfibril component | Extracellular fibril organization |
How Is supramolecular fiber organization Regulated?
Supramolecular fiber organization is regulated at multiple levels, including metabolic cues, post-translational modifications, and signaling pathways. For instance, proteasome supramolecular organization is metabolically regulated, meaning that cellular energy status can influence how proteasomes assemble into fibers. Additionally, the assembly of synthetic supramolecular polymers can be controlled by chalcogen bonding and out-of-equilibrium conditions, providing insights into regulatory principles. In biological systems, chromatin fiber organization is regulated by histone modifications and chromatin remodelers. Lipid composition in fiber-cell plasma membranes also plays a role in organizing membrane-associated fibers.
supramolecular fiber organization and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| CRYAA | Congenital cataract | Knockout mouse or lens epithelial cell line |
| CRYAB | Congenital cataract and myopathy | Point mutation knock-in in iPSCs |
| GJA8 | Congenital cataract | Knock-in of patient mutations in zebrafish |
| BFSP1 | Congenital cataract | Knockout in lens fiber cells |
| PSMD1 | Proteasome dysfunction | Inducible knockout in cancer cell lines |
Congenital cataract and lens fiber disorganization
Congenital cataract is a common eye disease characterized by opacification of the lens, often due to mutations in genes encoding lens fiber proteins such as CRYAA, CRYAB, GJA8, BFSP1, and BFSP2. These proteins are essential for maintaining the organized supramolecular fiber structure of the lens, and their dysfunction leads to protein aggregation and loss of transparency. The organization of lipids in fiber-cell plasma membranes is also critical for lens function, and disruptions can contribute to cataract formation.
Neurodegeneration and protein aggregation
Aberrant supramolecular fiber organization is a hallmark of neurodegenerative diseases, where proteins such as amyloid-beta and tau form fibrillar aggregates. Although specific citations for neurodegeneration are not provided in the verified list, the general principle that fiber disorganization leads to pathology is supported by studies on proteasome supramolecular organization and chromatin fiber dynamics. These findings suggest that maintaining proper fiber organization is crucial for neuronal health.
Cancer and chromatin fiber dysregulation
Alterations in chromatin fiber organization can affect gene expression and contribute to cancer. The 10-nm chromatin fiber and its relationship to interphase chromosome organization are key to understanding how changes in fiber compaction influence oncogene expression and genome stability. Targeting the machinery that regulates chromatin fiber organization is a potential therapeutic strategy.
From supramolecular fiber organization-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| What is the role of a gene in chromatin fiber organization? | CRISPR knockout of histone genes in HeLa cells |
| How do point mutations in CRYAA affect lens fiber assembly? | Knock-in of CRYAA mutations in iPSC-derived lens cells |
| Can we visualize supramolecular fiber dynamics in live cells? | Tagged knock-in of fiber proteins with fluorescent markers |
| What is the effect of overexpression of proteasome subunits on fiber formation? | Overexpression of PSMD1 in HEK293T cells |
| How do lipid environments influence fiber organization? | Knockout of lipid-modifying enzymes in lens epithelial cells |
| What genes regulate supramolecular fiber assembly? | Genome-wide CRISPR library screening |
How to Study the supramolecular fiber organization Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Cryo-electron microscopy | High-resolution structure of fibers | Visualizing chromatin fiber and amyloid fibrils |
| Super-resolution microscopy | Nanoscale organization of fibers in cells | Live-cell imaging of cytoskeletal fibers |
| Mass spectrometry | Protein composition and modifications | Identifying proteasome fiber components |
| Chromatin conformation capture | 3D genome organization | Studying 10-nm chromatin fiber interactions |
| CRISPR knockout screening | Gene function in fiber assembly | Identifying regulators of supramolecular fibers |
| Native gel electrophoresis | Supramolecular complex size | Analyzing proteasome fiber assembly |
| Molecular dynamics simulation | Fiber dynamics and stability | Modeling synthetic supramolecular polymers |
| Fluorescence recovery after photobleaching | Fiber turnover dynamics | Measuring chromatin fiber mobility |
Imaging supramolecular fibers
Advanced imaging techniques such as cryo-electron microscopy, super-resolution fluorescence microscopy, and live-cell imaging are essential to visualize supramolecular fiber organization. These methods allow researchers to observe the assembly, arrangement, and disassembly of fibers in real time. For example, the 10-nm chromatin fiber has been studied using electron microscopy and chromatin conformation capture techniques.
Biochemical and proteomic approaches
Biochemical fractionation and mass spectrometry-based proteomics can identify the protein components of supramolecular fibers and their post-translational modifications. Proteasome supramolecular organization has been dissected using native gel electrophoresis and mass spectrometry. These methods help determine the stoichiometry and interaction partners of fiber subunits.
Genetic screens and CRISPR-based perturbations
CRISPR-Cas9 knockout, knock-in, and overexpression models enable functional dissection of genes involved in supramolecular fiber organization. Genome-wide CRISPR screens can identify novel regulators of fiber assembly. For instance, knocking out candidate genes in cell lines followed by imaging or biochemical assays can reveal their roles in fiber formation.
Computational modeling and bioinformatics
Computational models and bioinformatics tools predict fiber structures and simulate assembly dynamics. These approaches complement experimental data and can guide hypothesis-driven research. For example, molecular dynamics simulations of supramolecular polymers provide insights into the forces driving fiber formation.
How CRISPR Can Be Used to Study GO:0097435 supramolecular fiber organization
Knockout
CRISPR knockout is used to eliminate genes encoding fiber components or regulators, allowing researchers to observe the consequences for supramolecular fiber organization. For example, knocking out histone genes can disrupt chromatin fiber formation and alter gene expression. Knockout of proteasome subunits can impair proteasome supramolecular organization.
Point Mutation
Point mutations can be introduced via CRISPR to model disease-associated missense mutations in genes such as CRYAA or CRYAB, which affect lens fiber organization and cause congenital cataract. These models help determine how specific amino acid changes impact fiber assembly and stability.
Knock-in
Knock-in of fluorescent tags or reporter genes allows real-time visualization of supramolecular fiber dynamics. For instance, tagging endogenous histone proteins with GFP enables tracking of chromatin fiber organization in live cells. Knock-in of patient mutations into iPSCs provides disease models for studying fiber disorganization.
Overexpression
Overexpression of fiber-forming proteins or their regulators can drive excessive fiber assembly or disrupt stoichiometry. Overexpressing proteasome subunits can lead to altered supramolecular organization and affect protein degradation. This approach is useful for gain-of-function studies.
How EDITGENE Supports supramolecular fiber organization Research
Researchers studying supramolecular fiber organization-related genes often need to determine whether a candidate gene is causally involved in fiber assembly, arrangement, or disassembly. EDITGENE provides a comprehensive suite of CRISPR services to accelerate this research, from knockout to knock-in and library screening.
Contact EDITGENE today to design your custom CRISPR model for supramolecular fiber organization research.
Frequently Asked Questions About supramolecular fiber organization
What is GO:0097435 supramolecular fiber organization?
GO:0097435 is a Gene Ontology biological process term that describes the assembly, arrangement, or disassembly of supramolecular fibers, which are polymers of protein or protein-complex subunits.
What genes are involved in supramolecular fiber organization?
Key genes include histones (e.g., HIST1H1C), lens crystallins (CRYAA, CRYAB), proteasome subunits (PSMD1, PSMC2), and cytoskeletal proteins (LMNA, VIM, TUBB, ACTB).
How is supramolecular fiber organization related to disease?
Disruption of fiber organization is linked to congenital cataract, neurodegeneration, and cancer, through mechanisms such as protein aggregation and chromatin dysregulation.
What methods are used to study supramolecular fiber organization?
Common methods include cryo-electron microscopy, super-resolution imaging, mass spectrometry, chromatin conformation capture, and CRISPR-based screens.
What is the 10-nm chromatin fiber?
The 10-nm chromatin fiber is a supramolecular fiber formed by nucleosome arrays, and its organization influences interphase chromosome structure and gene expression.
How does the proteasome form supramolecular fibers?
Proteasome subunits can self-assemble into supramolecular fibers in a metabolically regulated manner, affecting protein degradation.
Can CRISPR be used to study supramolecular fiber organization?
Yes, CRISPR knockout, knock-in, and overexpression models enable functional studies of genes involved in fiber assembly and disassembly.
What are the synonyms for GO:0097435?
Synonyms include extracellular fibril organisation, extracellular fibril organization, extracellular fibril organization and biogenesis, fibril organisation, and fibril organization.
What is the role of lipids in supramolecular fiber organization?
Lipids in fiber-cell plasma membranes, such as in the eye lens, contribute to the organization and function of supramolecular fibers.
How can I model congenital cataract using CRISPR?
CRISPR knock-in of patient mutations in CRYAA, CRYAB, or GJA8 in iPSCs or cell lines can model lens fiber disorganization and cataract.
Conclusion
Supramolecular fiber organization (GO:0097435) is a fundamental biological process that governs the assembly, arrangement, and disassembly of protein-based fibers critical for cellular structure and function. Its dysregulation is implicated in diseases ranging from congenital cataract to cancer, making it a vital area of research. By leveraging CRISPR-based models and advanced imaging, researchers can dissect the molecular mechanisms and identify therapeutic targets. EDITGENE provides the tools and expertise to accelerate these discoveries.
References
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- 2. Subczynski WK et al.. 2017. Organization of lipids in fiber-cell plasma membranes of the eye lens.. Exp Eye Res 156:79-86 PMID: 26988627
- 3. Zeng R et al.. 2020. Chalcogen-Bonding Supramolecular Polymers.. J Org Chem 85(13):8397-8404 PMID: 32515600
- 4. Bianco S et al.. 2024. Forging out-of-equilibrium supramolecular gels.. Nat Synth 3(12):1481-1489 PMID: 39664796
- 5. Pichi F et al.. 2016. Genetics of Congenital Cataract.. Dev Ophthalmol 57:1-14 PMID: 27043388
- 7. Wu B et al.. 2022. Complex supramolecular fiber formed by coordination-induced self-assembly of benzene-1,3,5-tricarboxamide (BTA).. J Colloid Interface Sci 608(Pt 2):1297-1307 PMID: 34739992
- 8. Hansen JC et al.. 2018. The 10-nm chromatin fiber and its relationship to interphase chromosome organization.. Biochem Soc Trans 46(1):67-76 PMID: 29263138
