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Monday, June 17, 2013

An Example of Antisense Proteogenesis?

The question of how organisms develop entirely new genes is one of the most important open questions in biology. One possibility is that new genes often develop through accidental translation of antisense strands of DNA.

An example of this can be seen with the S1 protein of the 30S bacterial ribosome. If you take the amino-acid sequence for an S1 gene and use it as the query sequence in a blast-p (protein blast), you'll mostly get back hits on other S1 proteins, but you'll also get minor (low-fidelity) hits on polynucleotide phosphorylase. Why? When you do a blast search, the search engine, by default, looks at both DNA strands of target genes (sense and antisense strands) to see if there's a potential sequence match with the query. If there's a match on the antisense strand, it will be reported along with "sense" matches. In the case of the S1 protein, blast-p searches often report weak antisense hits on polynucleotide phosphorylase in addition to strong sense hits on ribosomal S1.

Ribosomal proteins are, of course, among the most highly conserved proteins in nature. It turns out that polynucleotide phosphorylase (PNPase) is very highly conserved as well. It's an enzyme that occurs in every life form (bacteria, fungi, plants, animals), absent only in a scant handful of microbial endosymbionts that have lost the majority of their genes through deletions. While the chemical function of PNPase is well understood (it catalyzes the interconversion of nucleoside diphosphates to RNA), its physiologic purpose is not well understood, although recent research shows that PNPase-knockout mutants of E. coli exhibit lower mutation rates. (Hence, PNPase may actually be involved in generating mutations.)

The bacterium Rothia mucilaginosa, strain DY18, has a (putative) PNPase gene at a genome offset of 1277514. When this gene is used as the query for a blast-p search, the hits that come back include many strong matches for the S1 ribosomal proteins of various organisms. By "strong match," I mean better than 80% sequence identity coupled with an E-value (expectation value) of zero. (Recall that the E-value represents the approximate odds of the match in question happening due to random chance.

If we use the Genome Viewer at genomevolution.org to look at the PNPase gene of Rothia mucilaginosa, we see something extraordinarily peculiar (look carefully at the graphic below). Click to enlarge the following image, or better yet, to see this genome view for yourself, go to this link.

Notice the presence of overlapping sense and antisense open reading frames on a portion of DNA from Rothia mucilaginosa. The top reading frame contains the gene for polynucleotide phosphorylase. The lower (-1 strand) reading frame contains ribosomal S1. To see this in your own browser, go to this link.

Notice that there are overlapping genes. On the top strand is the gene for PNPase; on the bottom strand, in the same location, is a gene for ribosomal S1. These are bidirectionally overlapping open reading frames, something occasionally encountered in virus nucleic acids but rarely seen in bacterial or other genomes.

How do we explain this anomaly? It could be just that: an anomaly, two open reading frames that happen to overlap (but that aren't necessarily translated in vivo). Or it could be that at some point, many millions of years ago, the ribosomal S1 gene of a Rothia ancestor was erroneously translated via the antisense strand, producing a protein with PNPase characteristics. We don't know why PNPase confers survival value (its physiologic purpose is not fully understood), but we do know, with a fair degree of certainty, that PNPase does, in fact, confer survival value—because every organism, at every level of the tree of life, has at least one copy of PNPase. Once Rothia's ancestor, through whatever process, opened up a reading frame on the antisense strand of ribosomal S1, the reading frame stayed open, because it conferred survival value. In this way, the first Rothia PNPase was born. (Arguably.)

At some point in its history, Rothia duplicated its PNPase gene and placed a new copy at genome offset 1650959. Over time, this second copy diverged from the original copy, becoming more like E. coli PNPase (which is also to say, less S1-like). Rothia's second PNPase shows a blast-p similarity of 45% (in terms of AA identities) to E. coli PNPase, with E-value 4.0e-147. It shows a blast-p similarity of 26% (AA identities) with E. coli ribosomal S1 (E-value: 4.0e-17). Neither E. coli PNPase nor Rothia PNPase-2 overlaps an S1 gene. However, both are colocated with the ribosomal S15 protein gene. And you'll find (if you look at lots of bacterial genomes) that PNPase is almost always located immediately next to an S15 ribosomal gene.

Rothia PNPase is an example of an enzyme that may very well have started out as an antisense copy of another protein (the S1 ribosomal protein). Of course, the mere presence of bidirectionally overlapping open reading frames doesn't prove that both frames are actually transcribed and translated in vivo. But the fact that blast-p searches using PNPase as the query almost always turn up faint S1 echoes (in a wide variety of organisms) is highly suggestive of an ancestral relationship between the two proteins.

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