Atypical Organelles and Condensates Flashcards
Compartment Separation without membranes
liquid-liquid phase separation (lava lamps, vinaigrette salad dressing, nucleoli) - one liquid within another liquid, 2 immiscible liquids = apply force of shaking and one in background of the other (cannot dissolve sitting), dynamic in size, shape, number, can occur in nucleus and cytoplasm
Nucleolus as an example of compartment separation without membranes
different compartment in nucleus (liquid-liquid separation), no membrane, phase separated by membrane less organelles, during mitosis it disperses then reorganizes, more dynamic than membrane bound
Membrane structuring of membrane less organelles
protein component, metastability, and glass/gel and fiber
Protein component of membrane structure
can move in and out (more dynamic than membrane organelles)
Metastability
fine and normal (reversible) - come in and out and change shape
glass/gel and fiber
pathology when contents move onto higher organization order - detrimental
membrane less organelle function
associated with cell division, chromatin remodeling, gene transcription, synapse function, virus assembly
membrane less organelle structure
include P-body and nucleolus (disassembly/reassembly with cell division) but variable in different cells
membrane less diversity
diverse contents, duration and size (any cellular process probably has membrane less organelles associated)
Examples of membrane less organelle diversity
virus factory = COVID, HPV, etc. assemble progeny virus, Tp53 aggregation (variability of what membrane less organelles are in cells)
P-body
processing/breakdown of RNA, may arise or disperse in different cell types
what do membrane less organelles do?
generate new compartments - variable based on size, what they do, in their content; reorganize existing compartments = separating out components (not nucleoli) for self-association and organization - subnuclear (liquid-liquid); vary in time, location and size
nucleoli fusion
dynamic nucleoli fuse (no membrane, only RNA protein composition)
compare and contrast membrane-bound and membraneless organization
optimized function (specialized subcompartment), lysosome = acid hydrolase efficiency, mitochondria = electron transport, H+ gradients, P-body = (processing body) RNA decay
compare and contrast membrane bound and membrane less organelles size and shape
nucleus = 5-10 um diameter, nucleolus = 0.5-2.5 um diameter, other = less than 0.5 in frequency but are -20 um which is rare
membrane bound “organizer”
phospholipid bilayer, boundary from aqueous cytoplasm, for specialization
membrane less “organizer”
protein biochemistry, characteristics more likely to self-interact than interact with aqueous cytoplasm, protein phase separate from environment (not compatible protein biochemistry), partnered proteins associate, leaving out proteins less likely to interact
Membraneless organelles formation
liquid-liquid phase separation - dissolved protein interact with each other, and possibly RNA to coalesce (de-mix) from surrounding homogeneous pictures of diverse macromolecules in cytoplasm or nucleoplasm (dispersion into nuclear shadow), reversible depending on stimulus = compare to separation (re-mixing oil and water) and vary variable time (nuclear shadow excluded and dispersed rapidly but can organize back)
Membrane less organelle diverse examples
cajal nuclear bodies - varied content and function (partially regulate transcription and process RNA for spliceosome assembly which increases efficiency of nuclear events), PML nuclear bodies - replication suppressor, about 100 possible partner proteins in different PML bodies for varied function (apoptosis, telomere elongation)
Liquid-liquid phase separation concepts
protein condensation leads to reaction crucible, sequestration, and organizational hub
Reaction crucible
more efficient processing (post transitional modifications), concentrated subset of molecules enhances reactions (processing enzyme), liquid organization aids entry/exit, phase separated, processor for precursor to product, increased efficiency
Sequestration
storage for later processing or secretion (deposit/reservoir), reduces response time to extracellular signals (physiological response decreases lag time), secreted and processed at later event, premade proteins in preparation for physiological change
Organizational hub
normal condensation of proteins to focus interaction/polymerization of partner proteins (microtubule stability), 2 or more proteins physically associate to build structure to increase cell, advance cell, more efficient if physical components inside membrane less organelle, physical association
Scaffold proteins
can drive liquid-liquid protein separation on their own, enriched for domain repeats (multivalent) and little 3D structure (disordered), sufficient concentration will condense and separate from surrounding cytoplasm or nuclear plasm
Client proteins
proteins can interact with scaffold proteins, compatible with liquid-liquid protein synthesis of partner proteins, typically insufficient for liquid-liquid protein separation on their own
protein characteristics for liquid-liquid phase separation
multivalent - repeated subdomains = repeated sites for interactions, drives condensation of membrane less organelles, scaffold for partner protein, SOS and Grb2; disordered - no rigid 3D “lock and key type” conformation, high content of polar and charged amino acids to keep protein in extended shape, low content of hydrophobic AA so less likely to fold up to reduce interaction with water
Phase separation of liquid-liquid protein separation extracellular conditions
pH, osmolarity, etc., stressors like toxins (environmental stress), take homogeneous proteins - cause some to come out and phase separate, change extracellular to get response inside cell
Phase separation of liquid-liquid protein separation intracellular conditions
protein concentration, ion concentration, partners (other proteins, RNA or DNA), ATP (as charged molecule; not as energy source), post-translational modifications (increasing p-tau that increases separation so more microtubule depolymerization), for some proteins causes possible disease-specific mutation
Phase transition
liquid-liquid phase transition = may occur abruptly after liquid-liquid phase separation, excessive interactions among components, uncertain reversibility so uncertain consequences
Aggregation
may occur independently or following liquid-liquid phase transition, disrupts normal cell function, abnormal and often disease-associated so typically irreversible
Interaction beyond liquid-liquid phase separation bad news
function goes to dysfunction, can occur in lots of different cell types in lots of different cells, aggregation and nucleation, likely irreversible nature of assembly (amyloid) and insoluble
Dispersion to aggregation
Disperse to liquid-liquid phase separation to liquid-liquid phase transition to aggregation; condensation from excess interactions = generates “solid” structure, insoluble, fibrous “amyloid”, fibrils and tangles are associated with many degenerative diseases
Nucleation
aggregated proteins serve as condensation foci for proteins that would otherwise remain in liquid-liquid protein transition or move back to liquid-liquid protein separation
Example pathologies and dysfunctional protein
amyotrophic lateral sclerosis (ALS, lou gehrig’s disease) = TAR DNA binding protein-43, alzheimer’s disease (AD) = microtubule-associated tau, parkinson’s disease (PD) = a-synuclein amyloid fibrils from LLPT –> amyloid clumps
A-synuclein normal role
vesicle delivery to cell termini, neurotransmitter deliver and release at synapse, found in cytoplasm under membrane at synapse (in nucleus), undefined role in nucleus, normal day to day functioning delivering neurotransmitters, issue when transition to aggregation phase (amyloid fiber clumps - parkinson’s disease), several proteins associate to new neuron
A-synuclein example
potential to clump into amyloid fibers, normal function - self-associating, delivering to synapse, individuals proteins - liquid-liquid protein separation then increased self-interaction then liquid-liquid protein transition (forms aggregate) then aggregates then amyloid fibrils (disruption of neurotransmitters and dysfunction of neuron); Parkinson’s disease, decreased vesicle trafficking, disrupted transmitter release, timing and progression varies
Liquid-liquid phase separation and transition dysfunction
nucleus and cytoplasm - possible impact on many cell functions and therefore many diseases
Membrane less Organelle and liquid-liquid phase separation and transition dysfunction types
insufficient interaction for liquid liquid phase separation and therefore no “reaction crucible, storage, or hub”, excess interaction driving liquid liquid phase transition (multivalent with self or partner), partner excess or missing, wrong type or timing of post transitional modification
Resulting diverse pathologies of membrane less organelles and liquid-liquid phase separation/transition
neurodegeneration (TAR43, p-tau, a-synuclein), hyperplasia/cancer (p53, myc, p53), other tissue degeneration
Neurodegeneration therapeutic interventions
protein aggregates driving drug discovery, variations of ZPD, small molecule compound (pre-clinical drug) = inhibit nucleation and aggregation (prevent late phase only if you get to it in time), inhibits aggregation and promotes disassembly (reverse phase transition), simplifying ZPD chemistry - that interacts with a-synuclein protein to make more compatible with clinical use
Exploring therapeutic interventions
drug interaction with protein = facilitates liquid-liquid protein separation for reaction crucible, sequestration, organizational hub; reduces liquid-liquid protein separation that might be precursor or liquid-liquid phase transition or aggregate (disperse to more compatible with normal cell physiology), drug regulation of modifier = regulate post-translational modification for desired effect (protein dispersion)
