by Merry Youle
In bacteria, the ribosome-associated peptide deformylase (PDF) removes the formyl group of the N-terminal formyl methionine of nascent proteins. This process is a prerequisite for the proteolytic removal of the unmasked methionine by methionine aminopeptidase (MAP). The enlargement shows PDF (cyan ribbon) bound to ribosomal protein L22 (magenta) next to the ribosomal tunnel exit (white star). The second interaction site of PDF on the ribosome, protein L32, is not visible in this view of the ribosome, which is sliced along the tunnel. The path of the nascent chain is indicated by yellow spheres. Source.
When a phage invades a host’s premises, it delivers only its genome and perhaps a few specialized proteins needed immediately upon arrival. Its plan is simply to supervise production. The host is relied on to provide not only the raw materials and energy, but also the production equipment needed to synthesize phage proteins and nucleic acids. This includes the machinery for further processing each protein as it leaves the ribosome. Sometimes, as in the case of the cyanophages, the host’s equipment isn’t quite enough.
Uniquely, proteins made on bacterial ribosomes, including those encoded by phage, start with an N-formylmethionine residue donated by a special initiator fMet-tRNA. As the N-terminus of the new peptide chain emerges from the ribosome exit tunnel, the formyl group is removed by the enzyme peptide deformylase (PDF); frequently the remaining N-methionine itself is also removed by a separate enzyme. Many proteins as they exit fold into their functional form with the help of a chaperone, the trigger factor (TF), stationed at the portal. Correct folding is essential for protein function, and the formyl group must be removed for proteins to fold correctly. Deletion of the PDF gene in E. coli is lethal. Likewise, actinonin, a naturally-occurring antibiotic that inhibits PDFs, also inhibits bacterial growth and disrupts photosynthesis in the chloroplasts of plants and green algae.
For most phages, a functionally adequate host PDF is something to be taken for granted. However, there is the danger that intense protein synthesis during phage infection can overwhelm the host’s supply of PDF, the upshot being improperly processed, non-functional proteins. This is more likely a problem for cyanophages. While all phages require the synthesis of various proteins used directly for their replication, cyanophages also depend on active synthesis of other proteins needed to maintain the host’s photosynthesis apparatus. This extra burden further taxes the host’s co-translational processing enzymes. Specifically, the high-turnover D1 protein of photosystem II must be replenished—the subject of an earlier post. For this problem, the cyanophages have a solution.
This story began when Sharon and colleagues searched the publicly-available marine metagenomes generated by the Global Ocean Survey (GOS), making use of their novel method to identify bacterial genes encoded in viral, not bacterial, genomes. Their yield was abundant; they found virally-encoded metabolic genes from 34 gene families. Of these 34, the most numerous were the PDFs, yielding 70 genes—all of which were from cyanophage genomes. Mapping of their data by Frank et al. located these phage PDFs throughout the oceans. Finding homologs of bacterial PDF genes in phage is one thing; demonstrating that these genes encode functional enzymes and are expressed during cyanophage infection is another. As a big step in that direction, Frank and colleagues demonstrated that cyanophage S-SSM7, a phage infecting the cyanobacterium Synechococcus WH8109, encodes a functional PDF with some phage-specific quirks.