Moselio Schaechter


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October 11, 2012

Talmudic Question #91

Why don't eukaryotes (with few exceptions) have operons in their genomes?

Comments

I think one of the challenges during eukariogenesis was to control the traffic of mobile elements from endosimbyonts to nucleus. So the interference methods developed to confront this collateral effect of eukariogenesis, ended with horizontal gene tranfers and also extinguished the activities of operons...

Eukaryotic proteins are frequently huge and corresponding mRNAs are long. Delivery from nucleus to cytoplasm takes time. Assuming that RNA is slightly fragile, making it even longer is not efficient.
Actually, instead of operons that are RNA fusion, Eukaryotes use protein fusions (as multi-domain) solving the problems compartmentalization, co-expression and increased stability.

Does the presence of relict operon-like features in some mitochondrial DNA (but not in the host nucleus) support the idea that certain eukaryotic traits of the host lineage predate acquisition of the ancestral mitochondrial endosymbiont?

"I suppose it kind of depends on what you mean by "operon". It was very recent that they found out that there is actually not much of "junk" DNA in our cells."

Unfortunately, this "finding" was itself junk. They "80% functional" number was promoted for the hype value, but to get that number they had to count any marginal detectable biochemical activity as functional. But transcription and many other cellular processes are just noisy, and you could throw some random DNA or RNA in a cell and it would have some binding just by chance. The data indicating that most of the human genome isn't doing much has been known for decades, and it hasn't gone away. Vertebrates can have genomes 10 times smaller than humans, or 10 times bigger than humans, and they all have about the same number of genes and developmental complexity. The difference in genome size is due mostly to repetitive elements, which are easily explained as mostly parasitic, mostly junk. For much, much more, see: http://www.genomicron.evolverzone.com/

I agree that there are some wonderful evocative comments here. But I would add this. In the Epulopiscium story, Elio has written previously about the issue of nucleoids needing to "service" a volume of cytoplasm (to follow the whole separation of powers metaphor). Large cytoplasmic volumes necessitate large numbers of nucleoids, because of the sheer viscosity of the nuclear material and---the ugly little secret in molecular biology---how the areas of regulatory "need" are selectively made available for Central Dogma machinery, while keeping other portions of the genome compact. This makes sense for "giant" microbes like Epulopiscium, hence the myriad nucleoids present (again, Elio presented that very effectively here at STC a while back).

My feeling is that even in the simplest of organisms, this is a deep issue. And in eukaryotes, it is even more relevant.

So I agree that negative regulation is a critical level in prokaryotes, perhaps due to the immediacy of environmental impacts on the cell (but is that not also true in single celled eukaryotes?). But I am always amazed at the interlocking patterns of related regulons, even in bacteria under a colicentric microscope.

Still, I like to think that eukaryotes have the regulatory system they do because different cell types need to regulate genes in many different ways---not like a switch, but like a dial. But again---what about the single celled eukaryotes?

I fear I suffer from multicellularcentrism, ironically. A wonderful Talmudic Question, indeed.

Elio replies: I am reminded of a Gilbert and Sullivan quote: "Things are seldom what they seem,
Skim milk masquerades as cream; ..." I wonder who's doing the masquerading here and appreciate how you extended the argument. Nice comment.

Perhaps operons are a more “primitive” state. As genomes have evolved, the benefits of smaller redeployable chunks, even on different chromosomes, have done away with localized clusters of genes.

Eukaryotes, typically have the luxury of time and the separation of powers... aka the nucleus and the uncoupling of transcription and translation. Like governments they can work out when and if they need something done, in this case the expression of a particular gene, and like the Congress of the US, the genetic program of eukaryotes can prescribe an omnibus spending bill covering all aspects of their immediate needs through the cleaver transcription of a universal transcription factor. For the prokaryotes, because of the absence of the separation of powers, the linkage of transcription & translation and because time is often of the essence they require compact genomes that can get the total job done with the assent of one promoter. No time to caucus, no time for debate, they need the job done and achieve results quickly. Eukaryotes control the majority of their transcription via positive control, while the prokaryotic world controls 75% of its expression via negative control. So this is long way of saying eukaryotes have the ability to sweat the details while the prokaryotes just have time to sweat. The net consequence as the first commenter suggested, is that the genome of eukaryotes is a mega-operon, like a federal government... all things to all?

Elio replies: How timely! And how clever! You have a way with similes (or is it analogies?), as you elegantly display from time to time in our podcast This Week in Microbiology (TWiM). Thanks for sharing this insight.

I suppose it kind of depends on what you mean by "operon". It was very recent that they found out that there is actually not much of "junk" DNA in our cells. If all or most of it is really needed, than our genome is as one big functional mega-gene. It all needs to work and cooperate in one way or another. It is all one big operon. It includes the genes, the methylated thingies (epigenetics) and the different signals that tells who should light up next. The eukaryotic genome is the operon cluster, the thingies are the promoter (located in multiple locations in, hopefully, good harmony) and the signals are the substrate.
I don’t know why it was needed at all to develop this "new" system without the standard operons. If it works, it works – right? Well, I guess not. Perhaps it was needed to ditch this standard operon business in order to become a better person. A higher being; A YOU-kryote; An I-kryote. We, the eukaryotes, wanted to evolve and indeed it yielded some kind of… well, something evolved. For what it's worth, prokaryotes are all over and we are not. Some of us kept or went back to employ operons and seem to do just fine (e.g. nematodes). Those bastards are everywhere… Maybe that’s the next big thing in medical genetics and/or biotechnology – producing operons in eukaryotes.

Elio replied: You know how to make it fun as well as enlightening. Many thanks.

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