Small viruses point to two-way evolution between viral shells and cellular compartments
University of Miami researchers report identifying previously unknown viruses with HK97-fold protein shells that share features with both viruses and encapsulins, cellular protein compartments. Their analysis supports repeated evolutionary transitions between the two, rather than a one-way origin of encapsulins from viruses. The work was published in Nature Communications.
The story
Researchers at the University of Miami reported a group of previously unknown viruses that may help explain the relationship between viruses and encapsulins—protein compartments in bacteria and archaea that enclose biochemical reactions. Both encapsulins and some viruses use proteins with an HK97-fold, a three-dimensional structure that assembles into a shell. In viruses, these shells can store and protect genetic material; in encapsulins, they enclose cellular reactions. The newly identified viruses have smaller, simpler genomes than other known viruses that build HK97-fold shells and share characteristics with both types of compartment. The researchers interpret those similarities as evidence that viruses and encapsulins have evolved from one another repeatedly over evolutionary time, challenging a model in which encapsulins simply evolved from viruses. The team searched structural and sequence information in databases containing billions of DNA sequences from globally collected soil, seawater, wastewater, human-gut and other samples. It combined bioinformatics, biophysical modelling, protein language models and AlphaFold. The paper also proposes that procapsids, immature viral shells, could enable transitions between genomic and metabolic roles. The findings were published as “Small viruses reveal bidirectional evolution between HK97-fold viruses and encapsulins via procapsids” in Nature Communications.
Why it matters
The proposed two-way relationship changes the questions researchers can ask about protein shells: not only how viruses package genomes, but also whether viral-like particles can support biochemical reactions. It also provides computational candidates for targeted follow-up studies of uncultured viruses, whose hosts are often unknown. The work does not establish a direct application, but its methods may be transferable to studies of viral evolution and emerging viruses, as the researchers note.
Evidence and context
HK97-fold proteins are relevant to origin-of-life research because they can separate and contain two basic biological functions: chemical reactions and inheritable genetic information. Encapsulins occur in cellular lineages including bacteria and archaea, while viral capsids use related shells to contain genomes. Many viruses cannot be grown in laboratories, leaving their hosts and biological roles unresolved. Large DNA-sequence repositories offer another route to study them, but sequence data alone must be interpreted using structural and evolutionary models. In this study, the reported bridge between viral and cellular compartments comes from that combination of database mining, predicted protein structure and biophysical analysis rather than from culturing the viruses.
Limits and unknowns
The evolutionary interpretation remains an inference from sequence and structural evidence, not a direct observation of viruses becoming encapsulins or the reverse. The report notes that many of the viruses represented in sequence databases cannot be cultured and have no identified host. Protein-language models and AlphaFold can help identify structural relationships, but predicted similarities do not by themselves demonstrate the proposed functions of the shells or their historical direction of evolution. Laboratory characterization of the candidate viruses and their particles would be needed to test those questions.
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Small viruses point to two-way evolution between viral shells and cellular compartments
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Highlights
- Previously unknown small viruses
- Billions of sequences searched
- Small genomes, shared shell traits
- New candidates for testing
Transcript
Researchers have found previously unknown small viruses that may connect viral shells and cellular compartments.
University of Miami researchers searched billions of DNA sequences, then compared predicted protein structures.
They have smaller genomes than other known HK97-fold viruses, plus shells with encapsulin-like features.
The findings give evolutionary biologists candidates for testing whether viral-like shells enclose biochemical reactions.
But two-way evolution remains an inference; lab tests must check the particles and their functions.