Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies thi...

The Department of Organismal Biology teaches and explores the evolution, development and function on the organismal level. For more information see Department of Organismal Biology - Uppsala Universit

Kubota et al. show that bacteria can use their filamentous phage to outcompete other bacteria, but increased phage production enables the evolution of cheater miniphages with truncated genomes. Miniph...

Bacteria acquire new genes by horizontal gene transfer, typically mediated by mobile genetic elements (MGEs). While plasmids, bacteriophages, and c...

Postdoctoral researcher in molecular ecology, Department of Ecology and Genetics, Uppsala University

An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...

Thioredoxins are ubiquitous redox proteins that are found in all domains of life. These conserved proteins are also found in many phages, including marine cyanophages that infect the ecologically important marine cyanobacteria. However, their role in phage infection is not known. Cyanophages also carry many small genes lacking homology to known functional domains. Whether these have a functional role or not remains unknown. Here, we explore the distribution and role of a cyanophage thioredoxin (trxA), and that of a small gene directly downstream of it (g26), in phage infection. For this we used the T7-like cyanophage, Syn5, which infects an open-ocean marine Synechococcus strain, WH8109. We found that thioredoxin genes are common in phage genomes, including in cyanophages. The g26 gene, however, is restricted in it distribution to the cyanophages. The cyanophage thioredoxin is catalytically active and it increases phage DNA replication, progeny production and competitive fitness. It also negatively impacts host growth. The g26 gene product is translationally coupled to, and thus dependent on, translation of the thioredoxin gene. This gene itself significantly increases phage virulence and fitness, yet reduces burst size. Our findings demonstrate that cyanophage thioredoxins impact phage fitness and infection physiology and that small viral genes with no homology to known genes can play an important role in the infection process. These findings provide insights into the importance of unusual genes in phage genomes and show that they are likely to play an important role in the interactions between abundant cyanobacteria and cyanophages in ocean ecosystems. ### Competing Interest Statement The authors have declared no competing interest.

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

A species of bacteria grows when both ferrihydrite and sulfide are present, but not when either is absent.

Jobb

Abstract. Lateral gene transfer is a major evolutionary process in Bacteria and Archaea. Despite its importance, lateral gene transfer quantification in na