None dare call it junk

There has been a huge amount of controversy about whether all the DNA we carry about has some purpose to carry out — or not. Could some of it be ‘junk’?.

At most 2% of our DNA actually codes for the amino acids comprising our proteins. Some (particularly the ENCODE consortium) have used the criterion of transcription of the DNA into RNA (a process which takes energy) as a sign that well over 50% of our genome is NOT junk. Others regard this transcription as the unused turnings from a lathe.

All agree however, that bacteria use a good deal of their small genomes to code for protein. The following paper http://www.pnas.org/content/112/14/4251.full quotes a figure of 84 – 89%.

Consider the humble leprosy organism.It’s a mycobacterium (like the organism causing TB), but because it essentially is confined to man, and lives inside humans for most of its existence, it has jettisoned large parts of its genome, first by throwing about 1/3 of it out (the genome is 1/3 smaller than TB from which it is thought to have diverged 66 million years ago), and second by mutation of many of its genes so protein can no longer be made from them. Why throw out all that DNA? The short answer is that it is metabolically expensive to produce and maintain DNA that you’re not using

If you want a few numbers here they are:
Genome of M. TB 4,441,529 nucleotides
Genome of M. Leprae 3,268,203 nucleotides
1,604 genes coding for protein
1,116 pseudoGenes (e.g. genes that look like they could code for proteins, but no longer can because of premature termination codons.

This brings us to the organism described in the paper — Trichodesmium erythraeum — a photosynthetic bacterium living in the ocean. When conditions are right it multiplies rapidly causing a red algal bloom (even though it isn’t an algae which are cellular). It’s probably how the Red Sea got its name.

The organism only uses 64% of its genome to code for its protein. The most interesting point is that 86% of the nonCoding (for protein anyway) DNA is transcribed into RNA.

The authors wrestle with the question of what the nonCoding DNA is doing.

“Because it is thought that many bacteria are deletion-biased (47, 77), stable maintenance of these elements from laboratory isolates to the natural samples suggest that they may be required in some fashion for growth both in culture and in situ.”

Translation: The nonCoding DNA probably isn’t junk.

They give it another shot.

“Others have hypothesized that the conserved repeat structures observed in some bacteria could function as recombination-dependent “promoter banks” for adaptation to new conditions, thereby allowing relatively quick “rewiring” of metabolism in subpopulations”

Plausible, but why waste the energy transcribing the DNA into RNA if it isn’t doing anything for the organism doing the transcribing?

Never assume that what you can’t measure or don’t understand is unimportant.

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