Coral-Algae Symbiosis: How Lysosomal Co-Option Hijacks Host Cells and Overturns Decades of Assumptions

This finding aligns with a stony coral cell atlas that described the dinoflagellate symbiont as residing within a "lysosomal-like organelle inside the host cell" . The atlas showed that these compartments, rather than being inert, are tied to digestive pathways.

The Breakthrough: Co-Option of Lysosomal Machinery and CRISPR Evidence

The most direct test of this hypothesis came from a 2025 pre-print (not yet a published Cell paper) from UC Berkeley and collaborating institutions . Using the sea anemone Aiptasia — a well-established model for coral symbiosis — the researchers generated a high-quality proteome of the symbiosome.

What they found was striking: the symbiosome was enriched in lysosomal proteins. They visualized lysosomal fusion with the symbiosome. And critically, when they used CRISPR/Cas9 to knock down lysosomal genes — including a bicarbonate/sulfate transporter — symbiosis was significantly reduced . This provided the first direct genetic evidence that the lysosomal identity of the symbiosome is functionally important.

The Genetic Mechanism in Galaxea fascicularis

The UC Berkeley-led work did not use CRISPR directly in the coral Galaxea fascicularis, but G. fascicularis has been studied extensively in related work. A transcriptome profiling study found deep metabolic integration between the coral host and its Symbiodinium symbionts, involving vitamins, cofactors, amino acids, fatty acids, and secondary metabolites . Another study established G. fascicularis as a promising new model system for symbiosis research, showing that bleached adults can reestablish symbiosis with non-native symbionts .

More broadly, the lysosomal-hijacking hypothesis fits with other known mechanisms. A 2022 study showed that coral host cells use Rhesus-like channels on the symbiosome membrane to control nitrogen delivery to algae, with the protein trafficking to and from the symbiosome membrane over the course of the day . A 2019 study found that nutrient-dependent mTORC1 signaling, a pathway linked to lysosomal function, operates in coral-algal symbiosis .

How Lysosomal Hijacking Explains Broad Host Infectivity

The discovery that algae inhabit a lysosomal-like compartment has major implications for understanding how these symbionts can infect a wide range of hosts — from jellyfish to stony corals to sea anemones.

If the symbiosome is essentially a repurposed digestive compartment, then the key to successful infection is not avoiding digestion altogether, but controlling it. Algae use the acidic, enzyme-rich environment to their advantage — triggering the release of sugars from their own cell walls (via cellulases activated at low pH) and receiving a steady supply of nitrogen and carbon from the host .

This also explains why some algae are more successful symbionts than others. Studies show that the establishment of symbiosis is not random: corals selectively take up certain algal types, and the molecular machinery on the symbiosome membrane determines which algae stay and which get digested .

Implications for Coral Bleaching Research

Coral bleaching — the breakdown of symbiosis under heat stress — has long been a mystery at the cellular level. The new lysosomal-hijacking model offers a potential explanation. If the symbiosome's lysosomal identity is maintained by a delicate balance of host and algal signals, then environmental stressors like elevated temperature could tip that balance, turning a managed lysosome into a destructive one.

Evidence for this includes a 2023 study that found a strong negative correlation between lipid content and symbiosome membrane fluorescence during bleaching stress, suggesting that the loss of symbiosis is linked to changes in the symbiosome membrane . Other work has identified specific immune and stress-response pathways that are activated in symbiosis and dysbiosis .

What Remains Unconfirmed

It is important to note that the specific claims about a published Cell paper from UC Berkeley using CRISPR in Galaxea fascicularis could not be verified from the available sources . The CRISPR work was performed in Aiptasia and reported in a bioRxiv pre-print. No published Cell article matching that exact description was found in the provided sources.

However, the convergence of evidence — from jellyfish, sea anemones, multiple coral species, and single-cell atlases — strongly supports the model that co-option of lysosomal machinery is a fundamental mechanism of cnidarian-algal symbiosis.

Bottom Line

The 'symbiosome' is not a simple safe house. It is a dynamic, lysosomal-like compartment that coral host cells actively manage to support their photosynthetic partners. This revised understanding, backed by proteomics, CRISPR, and cell biology, has direct implications for why some algae are compatible with many hosts, and why climate change-driven thermal stress can break the partnership — leading to the coral bleaching events that threaten reefs worldwide.