Viral remnants produced by Streptomyces davawensis control host bacterial organization and reproduction — The University of Tsukuba and Nihon University clarify bacterial survival strategy

A research group led by Assistant Professor Toshiki Nagakubo and Associate Professor Masanori Toyofuku of the Faculty of Life and Environmental Sciences at the University of Tsukuba, in collaboration with Lecturer Tatsuya Nishiyama of the College of Bioresource Sciences at Nihon University, has announced that they discovered viral remnants (virus-like particles) produced by Streptomyces davawensis, a soil bacterium, and revealed the abilities of these particles to promote organization and reproduction of the host bacterium. The mystery of the role played by virus-like particles highly conserved in the genome of S. davawensis is now solved. The research group revealed that the bacterium incorporated what was once a virus and used it as a survival strategy to smoothly carry out its life cycle. The results were published in the May 24 issue of the international journal Nature Communications.

Viruses are nanoparticles comprising genetic materials and proteins and infect a variety of host organisms, from humans to bacteria. It is thought that the number of viral particles on Earth is as high as 10³¹. This number is twice as many as the total number of bacterial cells. The research group has been studying the function and significance of virus-like particles produced by S. davawensis isolated from a Philippine rainforest soil sample. S. davawensis virus-like particles were known to be genetically distant from typical actinomycetal virus-like particles and be particles of an uncommon clade. When they examined a mutant producing virtually no viral particles, the mutant colonies were observed to have markedly decreased extracellular DNA, which serves as a scaffold for the formation of the proper structure of the cell population, and abnormal aggregates trapping the cells.

To shed light on the cause of these differences, they isolated virus-like particles, comprehensively analyzed the proteins. They found that a unique enzyme protein that partially degrades genomic DNA (Tme: effector) was contained in the virus-like particles and that this is the function of those particles in question. Tme-deficient mutant bacteria showed properties similar to those of the mutant bacteria that produces virtually no viral particles.

Virus-like particles are likely once viruses (phages) that infect bacteria, and effectors injected into the host cell membrane by the virus-like particles degrade the genomic DNA partly into fragments. This mechanism, similar to the viral infection process, was hypothesized to move the DNA fragments into the extracellular milieu, thereby providing the host cell population with scaffolds and nutrients suitable for reproduction. Moving forward, the research group is considering using artificial intelligence (AI) and other methods to modify Tme as a protein delivery tool with a favorable side effect profile.

Nagakubo said, "Virus-like particles are not infectious and can be freely redesigned using AI. They are attracting worldwide attention as 'nano-sized injectors' that can deliver desired proteins to specific cells in various applications. It is widely known that genome editing technology, which is commonly used today, originated from research on microorganisms. Given their high diversity, there are still enormous untapped innovation possibilities in microorganisms."

Journal Information
Publication: Nature Communications
Title: Contractile injection systems facilitate sporogenic differentiation of Streptomyces davawensis through the action of a phage tapemeasure protein-related effector
DOI: 10.1038/s41467-024-48834-9