When a Good Peptide Deformylase Gets Better
by Merry Youle
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.
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
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.
(A) Crystal structure of Synechococcus phage S‑SSM7 peptide deformylase (PDF). (B) Overlay of phage S‑SSM7 PDF (green), Synechococcus elongatus PCC 6301 PDF (cyan), and A. thaliana chloroplast PDF1B (magenta) shows striking similarity of protein folds, as well as the position of the zinc ion in the active site. The bracket indicates the C‑terminal α‑helical domain present in the bacterial and chloroplast PDFs, but absent from the cyanophage PDF. Source
The amino acid sequence of this phage PDF places it within the type 1B PDFs, the type found in cyanobacteria, chloroplasts, and other cyanophage. Its closest homolog is the PDF of Arabidopsis thaliana chloroplasts. The researchers also solved its structure to 1.95 Ǻ by X‑ray crystallography, then compared it against the structure of the PDF from a cyanobacterium (Synechococcus elongatus) as well as the one from Arabidopsis chloroplasts. The folds of all three are strikingly similar. The PDF active site is formed by the juxtaposition of three separate regions of the folded polypeptide chain. The amino acids in those essential regions are conserved in all the PDFs found in cyanobacteria and in bacteria-derived organelles (chloroplasts, mitochondria, apicoplasts). That they are also conserved in this cyanophage PDF suggests a similar catalytic activity for the phage protein.
However, the C‑terminus of the cyanophage PDF differs markedly. The canonical type 1B PDF, including the ones made by cyanobacteria and by E. coli, has an α‑helical C‑terminal domain that is important for function. Truncating that helical domain reduced the growth rate for E. coli at least tenfold. Structural studies suggested that this domain positions the enzyme at the ribosome exit tunnel where it can act on the emerging peptide chain before folding obstructs access to the N‑terminus. The PDF of cyanophage S‑SSM7 lacks that helical domain, as do at least 50 of the 70 cyanophage PDFs identified by Sharon et al. in the GOS metagenomes. This leads one to wonder if these truncated phage PDFs are catalytically active.
Kinetic assays comparing the activity of the Synechococcus phage S‑SSM7 PDF (blue) with that from S. elongatus PCC 6301 (red) on three different N‑terminal tetrapeptide substrates derived from phage or bacterial D1 proteins. Square = phage D1 (fMLIS); Solid circle = bacterial D1 (fMTSI); Open circle = bacterial D1, fMTTA. Source
Frank and colleagues investigated this directly using a deformylation assay to compare the activity of the truncated cyanophage PDF with that of the cyanobacterial PDF from S. elongatus. Not only was the phage PDF active, but it had higher in vitro catalytic activity than its cyanobacterial counterpart. The researchers were aware that synthesis of abundant D1 protein is a cyanophage priority, and also that the PDF of Arabidopsis chloroplasts is more efficient at processing D1 protein than other cellular proteins. They wondered if the cyanophage enzyme might also be most active on D1. Since the assay substrates are tetrapeptides containing N‑formylmethionine, they compared enzyme activity on N‑terminal tetrapeptides from D1 proteins versus those from the highly-expressed ribosomal proteins. Specifically, as a proxy for ribosomal proteins they used the four most common N‑terminal tetrapeptide sequences encoded in the ribosomal genes of various Synechococcus species. For D1, they used the N‑terminal tetrapeptides from the cyanophage's own D1 protein and from three D1 proteins from S. elongatus. The phage PDF showed consistently greater activity on the D1-derived tetrapeptides. We are left to wonder how this can be, how phage PDFs, lacking that C‑terminal helix, not only do their job but do it better than the ancestral cyanobacterial form of the enzyme.
Metabolic genes found in phage genomes, such as this PDF, have been casually referred to as "host" genes, often with the implication that the phage have no respect for intellectual property and simply steal whatever they find useful. But these cyanophage PDFs, although clearly related to the bacterial enzymes, now differ from them in both structure and function. The cyanophage have modified them to better suit their specialized purposes, in this case for greater activity on the high-turnover D1 protein needed to maintain host photosynthesis during infection. But the story doesn't have to end with this unidirectional transfer of genes from bacterium to phage. Other researchers earlier provided evidence that core genes of photosystem II, genes that had also been acquired by cyanophage from their hosts, have made that move multiple times; they have also moved from cyanophage back to host. Phage and bacterial gene pools overlap. We can think of the rapidly-evolving phage as providing foster homes for bacterial genes. While the genes are in their care, they can diversify more rapidly and under different selection pressures, and then sometimes return home with new capabilities.
References
Frank J, Lorimer D, Youle M, Witte P, Craig T, Abendroth J, Rohwer F, Edwards R, Segall A, Burgin A (2013). Structure and function of a cyanophage-encoded peptide deformylase The ISME Journal. DOI 10.1038/ismej.2013.4
Sharon I, Battchikova N, Aro EM, Giglione C, Meinnel T, Glaser F, Pinter RY, Breitbart M, Rohwer F, Béjà O (2011). Comparative metagenomics of microbial traits within oceanic viral communities. The ISME journal, 5 (7), 1178−1190. PMID 21307954
It's great to read Merrie's uniquely engaging authorial voice again.
Didn't we see, earlier, Bacillus anthracis discarding genes it had needed to live in humus as it grows in vivo, and re-loading them, when it returns to the soil, from phages it finds there?
I really enjoy reading this post on bacteria-phage coevolutionary dynamics: Thanks Merrie!
...Phage and bacterial gene pools overlap. Oh yes!
Another inspiring example comes from DNA replication: in E. coli, the replicative helicase DnaB enters the unwound replication origin oriC complexed with DnaC, the classical "helicase loader" of authoritative textbooks. A closer look reveals that DnaC is in fact part of the initiator/helicase loader gene pair of numerous lambdoid phages (the other variant being the lambda O/P proteins). DnaCs are present only in a small subset of the Enterobacteriaceae, but just as E. coli 'borrowed' the helicase loader from a phage, a number of Firmicutes — including B. subtilis — obtained their DnaB/DnaI helicase loaders from phages with initiator/helicase loader gene pairs (don't get mixed up: in B. subtilis, the replicative helicase is called DnaC, the helicase loaders DnaB, DnaI and DnaD).
Thanks Merry for the cyanophage story!
Merry replies:
Christoph, you say don't get mixed up, and then dish out a serving of alphabet soup! Ha! Confusing names notwithstanding, this sounds like a story worth pursuing, another story documenting the evolutionary roles played by the phages.
You made my day !! this was the fantastic post to read !!! great work and content !! thank you !!
Elio asked for a reference to anthrax treating the phagosphere as a gene library. We live to serve:
http://phenomena.nationalgeographic.com/2009/08/12/anthrax-bacteria-get-help-from-viruses-and-worms-to-survive/
Merry chimes in: Thanks for the reference to that blog post. It is an interesting story, like so many phage-related stories. 🙂
What is going on with B. anthracis involves a different mechanism, one in which the phage and its host rely on each other. A large group of the phages, the siphophages, often have a "temperate" lifestyle; instead of lysing their hosts soon after infection, they integrate their chromosome into the bacterial chromosome where it is referred to as a "prophage." Their host replicates the prophage DNA along with its own. Life-threatening stress to the host can prompt the prophage to bale out like a rat deserting a sinking ship, i.e., excise itself from the chromosome, replicate, and lyse the bacterium, as usual.
While a prophage, a few of the phage genes are usually expressed, including some that benefit the host. Prophages are notorious for encoding toxins and virulence genes that convert well-mannered bacteria into pathogens (e.g., cholera). They are also known to encode specialization genes that enable their host to live in particular environments, which takes us back to your story. Those active prophage genes benefit B. anthracis in the soil environment. Yes, a catch-22 for the bacterium. They need the prophage in order to thrive in the soil, but that prophage can turn on them and kill them.
Interesting story! I didn't know much about the peptide deformylase activity, but it brings up an idle curiosity — when I teach immunology we discuss the role of fMLP (formyl-methionine leucine proline) as a neutrophil chemotaxis factor, and the reason we always supply is that the formyl-met is only made by bacteria. But here you say the formate is removed, and must be removed for proper folding. Is that only true of some proteins? Or is the formate removed from all proteins, in which case I'm wondering why this is a chemotaxis factor? Or am I missing a subtle (or possibly not subtle) point here?
Merry replies:
Paul, I can answer part of your question: the N‑formyl methionine is removed from at least 98% of bacterial proteins. That leaves us maybe 2% for our purposes.
To answer the rest of the question, I tried to find information about the pathway for bacterial synthesis of fMLP or its function. Googling yields a deluge of information from the point of view of the immune system, and virtually zip from the bacterial point of view. fMLP is found associated with the cell membrane of enteric bacteria, but what is it doing there? How did it get routed there? Perhaps it is a short N‑terminal signal sequence directing the protein to the cell membrane where the terminal tripeptide is cleaved and released. This requires a mechanism that selectively prevents removal of the formyl group from specific proteins, which is certainly possible. The production of fMLP by a non-ribosomal peptide synthetase seems less likely. If you find any more info, please let me know.
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