And The Winner Is…

by Elio

The transposases! The contest, in case you wonder, was for the most abundant set of genes in the known universe, or at least in the genomic data banks available on Earth. Aziz, Breitbart, and Edwards examined some 10 million genes from 2137 sequenced genomes (47 archaeal, 725 bacterial, 29 eukaryotic and 1336 viral) plus 187 metagenomes, in search of the gene set that is both most abundant and most ubiquitous. (Ubiquitous refers to genes that carry essential functions and are thus needed by every genome. A gene that is highly abundant in some ecosystems but not ubiquitous is likely to play an important habitat-specific role.) The winners, by far, were the genes for transposases. One could squawk that the genomes selected for sequencing to date reflect a bias towards “germs” and other microbes of human interest, and that so far the source environments for metagenomes represent only a small sample of what’s out there. But given the off-scale preponderance of the transposase genes, there is little to make one question their dominance.

Abundance of different functional roles in 2137 genomes plotted against the ubiquity of these
functional roles (defined as the number of genomes in which the functional role is represented
at least once). Source.

Not everybody seems to have transposases; only 1/3 of the viruses in this study have them. But those organisms that do tend to possess multiple copies—close to 40 on average. If you take a set of 2000 randomly sampled genes (the number found in a typical bacterial genome), 22 will encode transposases. They are also more common in free-living bacteria than in obligate pathogens or endosymbionts. The champion transposase-carrier? Possibly the marine cyanobacterium Crocosphaera watsonii, which has more than 400 copies.

So, why transposases? The authors point to their general usefulness to both viruses and cellular organisms in promoting the spread of mobile elements, thus leading to diversification. “Selfish genes” indeed! As the authors write, By securing their own replication and dissemination, transposases guarantee to thrive so long as nucleic acid-based life forms exist. This rather implies that they might imagine non-nucleic acid based life forms exist somewhere. Who says that bioinformaticists are just computational nerds?

Aziz RK, Breitbart M, & Edwards RA (2010). Transposases are the most abundant, most ubiquitous genes in nature. Nucleic acids research PMID: 20215432

Comments

[barry]

So next question: is there a PARTICULAR mobile genetic element that has travelled across the most species? or the most disparate species?

[Manuel Sanchez]

Transposon's rules!

This history reminds me the "descolada" from "Speaker for the Dead" the second book of Ender's Saga written by Orson Scott Card. A kind of anticipation of this result.

By the way. Curious that the sulphur-metabolic genes are on the extreme right-side. A souvenir from the past?

Regards

[Mark O. Martin]

So...selfish DNA or useful organismal strategy? Or a little bit of both? Kind of reminds me of the old Warner Brothers cartoon, when Bugs Bunny grabs an octopus, and exclaims "Gotcha!" The octopus wraps several arms around Bugs, and replies "On the contrary; I've got you!"

I remember hearing years ago that some halophiles had so much mobile DNA shuffling around that you could detect it with random probes and Southern blots! Yet that cannot be wholly true or genomic analysis would be...challenging.

This is a lovely bit to introduce to my microbiology students. I have already taught them the two most important enzymes on Earth (rubisco and nitrogenase). Now I have a "most abundant gene" idea to proselytize!

I particularly like your reasoning about "abundant but not ubiquitous"---a rule of thumb to teach my students about how to predict habitat-specific genes?

Which makes me think, for the umpteenth time: bacteriophage Mu. Is Mu a phage that was colonized by a transposon, or a transposon that metaphorically grew legs?

Even without non-DNA based life forms, it is a complicated, complicated microbial world within and around us. All hail the Small Masters, again!