Both prokaryotes and eukaryotes have organelles, though the types they carry and how those organelles are built differ in ways that textbooks have historically oversimplified. Eukaryotic cells are famously packed with membrane-bound compartments like mitochondria, the nucleus, and the endoplasmic reticulum. Prokaryotes were long described as “simple” cells lacking internal compartments, but research over the past two decades has uncovered a surprising roster of prokaryotic organelles, from protein-shelled metabolic chambers to membrane-enclosed magnetic sensors to liquid-phase condensates that look a lot like their eukaryotic counterparts.
What Counts as an Organelle
The word “organelle” literally means “little organ,” and its definition has expanded as biologists have discovered new kinds of intracellular structures. In the traditional sense, an organelle is a membrane-bound compartment inside a cell that carries out a specialized function. That definition neatly fits the mitochondria, Golgi apparatus, and lysosomes found in eukaryotic cells. But cells also contain structures that create distinct biochemical environments without using a lipid membrane at all. Non-membrane-bound organelles achieve many of the same advantages of compartmentalization by organizing and concentrating specific sets of molecules so that reactions proceed efficiently.1PubMed Central. On the origin of non-membrane-bound organelles, and their physiological function In eukaryotic cells, these include structures like the nucleolus, Cajal bodies, P-bodies, and stress granules, which form as liquid droplets through a process called liquid-liquid phase separation.2PubMed Central. The molecular language of membraneless organelles
Prokaryotes, meanwhile, have their own versions of both membrane-bound and non-membrane-bound organelles. Some are enclosed by lipid membranes, some are wrapped in protein shells, and some are held together by nothing more than the physical chemistry of phase separation. All of them serve the same fundamental purpose: creating a distinct chemical environment inside the cell where specific reactions can happen without interference from everything else going on in the cytoplasm.3PubMed Central. Principles and functions of metabolic compartmentalization
The Classic Eukaryotic Toolkit
Eukaryotic cells are defined in part by their extensive collection of membrane-bound organelles. The nucleus houses the genome. Mitochondria generate most of a cell’s chemical energy. The endoplasmic reticulum and Golgi apparatus handle protein folding, modification, and shipping. Lysosomes and peroxisomes manage waste breakdown. In plant cells and algae, chloroplasts capture light energy to drive photosynthesis. Each of these compartments is surrounded by at least one lipid bilayer membrane that acts as both a physical barrier and a surface for specialized chemistry.4PubMed Central. Morphology and function of membrane-bound organelles
On top of the membrane-bound set, eukaryotic cells also harbor a growing list of membraneless organelles that form through phase separation. The nucleolus, which assembles ribosomes, is found across the entire eukaryotic domain. Cajal bodies, which help process certain types of RNA, appear to be similarly ancient, though they are not strictly essential for survival.5PubMed Central. Keeping up with the condensates: The retention, gain, and loss of nuclear membrane-less organelles These condensates assemble and dissolve dynamically in response to cellular signals, giving the cell a rapid, reversible way to reorganize its internal chemistry without building or dismantling permanent structures.
Prokaryotic Membrane-Bound Organelles
The textbook claim that prokaryotes lack membrane-bound organelles is outdated. Several groups of bacteria and archaea build internal compartments enclosed by lipid membranes, and these compartments serve functions every bit as specialized as their eukaryotic counterparts.
Magnetotactic bacteria produce magnetosomes, which are among the most intricate structures found in any bacterial cell. Each magnetosome is a membrane-bound organelle containing a nanoscale crystal of a magnetic iron mineral, and these organelles typically line up in tidy chains that function as a built-in compass, allowing the bacterium to navigate along Earth’s magnetic field lines in aquatic habitats.6PubMed. Biosynthesis and function of magnetic organelles in magnetotactic bacteria The membrane around each magnetosome is derived from the cell’s own inner membrane but has a distinct protein and lipid composition, much like eukaryotic organelles have distinct molecular identities.
Anammox bacteria take compartmentalization even further. These organisms, which carry out anaerobic ammonium oxidation, contain the anammoxosome, a membrane-enclosed compartment that is the site of their energy metabolism. The anammoxosome functions as a genuine prokaryotic organelle evolved specifically for generating energy, enclosed by a contiguous membrane that separates it from the rest of the cytoplasm.7Biochemical Society Transactions. The ultrastructure of the compartmentalized anaerobic ammonium-oxidizing bacteria is linked to their energy metabolism This is remarkable because it challenges the idea that energy-generating compartments are exclusive to eukaryotes.
Cyanobacteria harbor thylakoid membranes, the same type of photosynthetic membrane found inside chloroplasts. These specialized internal membranes convert sunlight into chemical energy and are thought to have originated in ancient photosynthetic bacteria, probably in connection with the evolution of the oxygen-producing type of photosynthesis that transformed Earth’s atmosphere.8PubMed. Biogenesis and origin of thylakoid membranes The thylakoid membranes inside modern chloroplasts are direct descendants of these cyanobacterial structures.9PubMed Central. Structure, biogenesis, and evolution of thylakoid membranes
Then there are the planctomycetes, a phylum of bacteria that have long puzzled cell biologists. Species in the genus Gemmata possess internal membrane systems that create what appears to be genuine compartmentalization within the cell. Research on the protein composition of isolated membrane fractions from Gemmata supports the idea that these internal membranes are not simply folds of the outer cell membrane but separate the cell into distinct compartments with different types of membranes, somewhat analogous to the nuclear envelope in eukaryotes.10PLOS ONE. Nuclear Pore-Like Structures in a Compartmentalized Bacterium
Protein-Shelled Organelles
Some of the most widespread prokaryotic organelles are not wrapped in lipid membranes at all but in shells made entirely of protein. These bacterial microcompartments, or BMCs, function analogously to eukaryotic organelles by sequestering enzymatic reactions away from the cytoplasm, but their outer barrier is a protein coat rather than a lipid bilayer.11Nature Communications. Biogenesis of a bacterial metabolosome for propanediol utilization
The best-studied BMC is the carboxysome, found in cyanobacteria. Carboxysomes concentrate the enzymes responsible for carbon fixation inside a protein shell, boosting efficiency by keeping the substrates and enzymes together and shielding them from competing reactions in the cytoplasm.12PubMed. Spatially ordered dynamics of the bacterial carbon fixation machinery Researchers have shown that carboxysomes are modular enough to be produced in bacteria that do not normally carry them. When the roughly ten genes encoding a carboxysome are transferred into E. coli, the recipient cells assemble functional protein-shelled compartments.13PubMed Central. Modularity of a carbon-fixing protein organelle That kind of portability hints at how easily these structures might be adapted for industrial or medical purposes.
Gas vesicles are another widespread protein-based organelle. These are hollow, gas-filled nanocompartments found in a diverse range of bacteria and archaea, including cyanobacteria and salt-loving archaea. Their protein shells are permeable to gases by diffusion, and they provide buoyancy, allowing cells to float toward the surface of a water column to access light or oxygen.14PubMed Central. Gas vesicle genes identified in Bacillus megaterium and functional expression in Escherichia coli Recent structural work has revealed the molecular architecture: the main shell protein self-assembles into hollow helical cylinders capped by cone-shaped tips, a design that can withstand substantial pressure while remaining lighter than water.15Cell. Structural basis of gas vesicle assembly and cellular buoyancy In at least one group of gut-dwelling bacteria, gas vesicle production is regulated by quorum sensing, meaning the cells coordinate their buoyancy behavior based on how many neighbors are nearby.16PubMed Central. A quorum-sensing molecule acts as a morphogen controlling gas vesicle organelle biogenesis and adaptive flotation in an enterobacterium
Liquid Condensates in Bacteria
Phase-separated membraneless organelles were once thought to be a eukaryotic specialty. That assumption has been overturned. Bacteria form liquid condensates that behave remarkably like the stress granules and P-bodies found in eukaryotic cells. When researchers used high-resolution microscopy to study bacterial aggresomes, which are intracellular assemblies of proteins that form under stress, they found that the proteins inside were mobile and underwent dynamic turnover, consistent with a liquid state rather than a solid aggregate. The observations matched what you would expect from phase-separated liquid droplets forming under thermal equilibrium and nucleating after proteins collide by diffusion in the cytoplasm.17PubMed Central. Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness
These bacterial condensates are not just curiosities. They have been found in multiple species, and the research showed they increase bacterial fitness by helping cells tolerate environmental stresses.17PubMed Central. Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness The finding that phase separation operates as a compartmentalization strategy across both prokaryotes and eukaryotes suggests it is probably one of the oldest organizational principles in biology, predating the evolution of membrane-bound compartments.
Acidocalcisomes, an Organelle Conserved Across All Domains
If you want a single example that demolishes the idea that organelles belong only to eukaryotes, acidocalcisomes are it. These are electron-dense, acidic, calcium- and polyphosphate-rich organelles that have been identified in bacteria, archaea, and eukaryotes, from simple soil microbes to human cells. They are the only organelle shown to have been conserved during evolution all the way from prokaryotes to multicellular organisms.18PubMed. Acidocalcisomes – conserved from bacteria to man Their presence in all three domains of life suggests that they originated very early in evolutionary history, before the split between prokaryotes and eukaryotes. In both bacteria and eukaryotic cells, acidocalcisomes play roles in storing phosphate and calcium, maintaining pH, and managing osmotic stress.
How Eukaryotic Organelles Got Their Start
The relationship between prokaryotic and eukaryotic organelles runs deeper than analogy. Mitochondria and chloroplasts, two of the most important eukaryotic organelles, were once free-living prokaryotes. Endosymbiotic theory, which has been around for over a century, explains the striking similarity between these organelles and bacteria by proposing that an ancient host cell engulfed a prokaryotic partner, and over time the two became interdependent.19PubMed. Endosymbiotic theory for organelle origins
The details have been refined considerably. The hydrogen hypothesis, for instance, proposes that the ancestral partnership leading to mitochondria was an anaerobic relationship: a hydrogen-dependent archaeal host living in close association with a bacterial partner that could either use its electron transport chain or produce hydrogen through fermentation. That flexibility directly explains why some modern eukaryotes still have organelles that function anaerobically, such as hydrogenosomes, as well as the more familiar oxygen-using mitochondria. A separate event brought a cyanobacterium into the partnership, eventually becoming the plastid (chloroplast) lineage.20PubMed Central. Endosymbiotic theories for eukaryote origin
This history means that what we call “eukaryotic organelles” are, in an evolutionary sense, domesticated prokaryotes. Some researchers have taken this argument to its logical end, arguing that because there is no clear natural boundary between a bacterium and a semiautonomous organelle, mitochondria and plastids should still be classified as bacteria.21PubMed Central. In the beginning was the word: How terminology drives our understanding of endosymbiotic organelles Most biologists do not go that far, but the point stands that the line between “prokaryotic cell” and “eukaryotic organelle” is blurrier than most people realize.
When Prokaryotic Organelles Cause Disease
Bacterial microcompartments are not just metabolic curiosities; some of them are directly linked to how pathogens cause disease. A growing body of research ties BMC-dependent metabolism to bacterial virulence in the human gut and beyond.
Fusobacterium nucleatum, a bacterium associated with adverse pregnancy outcomes and colorectal cancer, uses BMCs to metabolize ethanolamine, a nutrient available in human tissues. When researchers deleted the genes encoding BMC shell proteins, the mutant bacteria lost their ability to form microcompartments and struggled to metabolize ethanolamine. More critically, a shell-protein mutant was defective at inducing preterm birth in a mouse model, establishing that BMC-mediated metabolism is directly required for this bacterium’s virulence.22PubMed Central. Ethanolamine-induced assembly of microcompartments is required for Fusobacterium nucleatum virulence
A similar story plays out in the gut. Strains of E. coli linked to Crohn’s disease use ethanolamine and propanediol microcompartments to fuel growth on nutrients available in inflamed intestinal mucus. The metabolic flexibility these compartments provide helps the bacteria transition from harmless gut residents to disease-causing agents.23PubMed Central. Mucosal metabolites fuel the growth and virulence of E. coli linked to Crohn’s disease Bilophila wadsworthia, another gut bacterium associated with inflammatory bowel disease, depends on microcompartment genes for gut colonization. Transmission electron microscopy of bacteria recovered from mouse intestines revealed structures consistent with BMCs, and genes encoding the microcompartment shell were among the most essential for survival in the gut environment.24Nature Communications. Bacterial microcompartments and energy metabolism drive gut colonization by Bilophila wadsworthia
These findings are shifting how microbiologists think about treating infections. If a pathogen’s virulence depends on a specific organelle, disrupting the assembly or function of that organelle could be a novel antibiotic strategy, one that targets bacterial physiology without the broad collateral damage of conventional antibiotics.
Engineering Prokaryotic Organelles for Biotechnology
Because BMCs are made entirely of protein, they are natural targets for genetic engineering. You can redesign a protein shell in a way that is fundamentally harder with a lipid membrane. Researchers have already shown that BMCs can be modified to encapsulate non-native enzymes, effectively turning them into programmable nanoreactors for custom metabolic pathways.25PubMed Central. Engineered bacterial microcompartments: apps for programming metabolism
Why would you want to do this? Compartmentalization improves catalytic efficiency. Modeling work has shown that enclosing the enzymes of a synthetic pathway inside a compartment leads to improved reaction kinetics, especially when the substrates diffuse slowly or the enzymes are present in variable amounts.26PubMed. Stochastic reaction-diffusion simulation of enzyme compartmentalization reveals improved catalytic efficiency for a synthetic metabolic pathway That makes BMC-based engineering particularly attractive for industrial fermentation, where you want bacteria to churn out a product efficiently without the intermediate chemicals leaking into the cytoplasm and slowing the cell down or poisoning it.
Potential applications extend into medicine as well. The idea of reengineered microcompartments serving as drug-delivery vehicles or nanoscale diagnostic tools is still in early stages, but the modularity of these protein shells makes the concept plausible.27PubMed Central. Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering Gas vesicles, for their part, are already being explored as contrast agents for ultrasound imaging, since their hollow protein shells scatter sound waves in a way that produces a detectable signal.
The Prokaryotic Cytoskeleton and Spatial Order
Organelles do not float around randomly. In eukaryotes, the cytoskeleton moves and positions organelles with precision. Prokaryotes were once assumed to lack a cytoskeleton entirely, but they have their own versions of cytoskeletal proteins that play roles in cell division, maintaining cell shape, and even partitioning DNA and plasmids.28PubMed Central. The bacterial cytoskeleton In magnetotactic bacteria, cytoskeletal filaments are responsible for lining up magnetosomes into their characteristic chains. In cyanobacteria, carboxysomes are distributed evenly throughout the cell in an orderly pattern that depends on cytoskeletal-like mechanisms. The point is that prokaryotic organelles are not just present; they are spatially organized, sometimes with a level of order that rivals what you see in eukaryotic cells.
This spatial organization matters because it undermines the last refuge of the “prokaryotes are simple” narrative. Even if you accepted that prokaryotes had a handful of internal structures, you might still argue they lacked the sophisticated internal logistics of eukaryotes. The discovery of bacterial cytoskeletal systems that position organelles suggests the gap between prokaryotic and eukaryotic cellular organization is narrower than anyone thought a few decades ago.