Re: [DIYbio] Clustered essential genes, any ideas?

Hey Koeng,

assuming that there is substantial overlap between the categories
"essential genes" and "highly expressed genes", the following may be
part of the answer:

"When the time required to replicate the chromosome exceeds the
duplication time, the dosage of genes near the origin in the cell
increases exponentially with the number of simultaneous replication
rounds. Fast-growing bacteria, such as E. coli or B. subtilis, with
multiple simultaneous replication rounds selectively accumulate highly
expressed genes near the replication origin because of this effect."

as well as

"The directionality of chromosome replication leads to a chronological
asymmetry along the replichore. Since about 1 h separates the beginning
from the end of replication, the favourable conditions leading to
replication start may no longer prevail at the end of the process and
this may result in different mutation rates and compositional biases."

Quoted from "The replication-related organization of bacterial genomes",
http://mic.sgmjournals.org/content/150/6/1609.full.

On 22.03.2014 21:15, Koeng wrote:
> Hey
>
> I have been annotating a Bacillus genome to only have essential genes
> showing (I'd like to make a minimal Bacillus cell, so far I have
> selection systems, planned out cloning steps, vectors do to this with,
> equipment and bacteria needed, ect). Its taken me quite a while but I
> finally finished. I took the 253 CDSs from
> subtiwiki http://subtiwiki.uni-goettingen.de/wiki/index.php/Essential_genes
> (manually, btw. It took forever... but I haven't learned to program yet
> so it was the only way) Something weird happened though...
>
> Out of the 374 essential proteins and RNAs (give or take 1 or 2, I
> haven't looked all the way into the RNA part) 109 of the 374 essentials
> are in a 202kb region.
>
> That's 29% of all the essential genes in a region 5% of the entire
> genome... They are also all clustered around dnaA (I read somewhere that
> dnaA is near to the origin, don't quote me I haven't looked for a while)
>
> My idea (note I have only thought about this for a very short while) of
> why this is is because during the evolution of this cell messing up
> essential genes with duplications/ recombination would cause those cells
> to be less fit for their environment, so the recombination and
> duplication/mutation occured in other parts of the genome.
>
> Do you guys have any idea of why this occurred? I am thinking of trying
> to annotate the genomes of Mycoplasma genitalium and E coli to see if
> they are similar (any programmers out there :) ). Perhaps if I do that
> and find similar results I'll publish in like F1000 or peerj.... That is
> if this hasn't already been discovered, which I will surprised if I am
> the first to find this
>
> -Koeng
>
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