Archive for the ‘Genetics’ Category

LacY permease

Friday, June 12th, 2009

I found a paper about lacY being toxic (just like tetA) when overexpressed.
http://www.jbc.org/cgi/reprint/258/9/5666.pdf

-- Emiko Sano

On John’s award

Wednesday, March 11th, 2009

It just came out in Genetics, click here to get the pdf file.

Sophie Maisnier-Patin

Why is natural selection hard to beat and when do you need to beat it?

Monday, March 9th, 2009

[This is a stub entry I'm making for John under his name. He should re-edit it with his own words. -- Eric]

Here’s a brief review I just wrote with Dan.

Why is natural selection hard to beat and when do you need to beat it?
John R. Roth and Dan I. Andersson

Bacterial genetics defeats natural selection — it uses positive selection to detect large-phenotype mutants without influencing their frequency.  Metazoans maintain organism integrity by defeating natural selection on somatic cell growth.  Bacterial genetics relies on selection strong enough to prevent growth of both the parent and common slightly-improved mutants.  When selective stringency is reduced, frequent small-effect mutations allow growth and initiate a cascade of successive improvements.  This rapid response rests on the unexpectedly high formation rate of small-effect mutations (particularly duplications and amplifications). Duplications form at a rate 104 times that of null mutations.  The high frequency of small-effect mutations reflects features of replication, repair and coding that minimize the costs of mutation.
The striking effect of small-effect mutations is seen in a system designed by John Cairns to test the effect of growth limitation on mutation rate.  A leaky E. coli mutant (lac) is plated on lactose medium.  Revertant (Lac+) colonies appear over 6 days above a lawn of (108) non-growing parent cells. These colonies have been attributed to stress-induced mutagenesis of the non-growing parent. This conclusion ignores natural selection, assuming that only large-effect mutants appear– as is true for lab genetic selections.  However, selection is not stringent in the Cairns system — small increases in lac enzymes allow growth.  Common cells with a lac duplication (and 2x the mutant enzyme level) initiate slow-growing colonies, in which selection drives a multi-step adaptation process – higher amplification, reversion to lac+ and loss of mutant lac alleles.  The high yield of revertant colonies under selection does not reflect mutagenesis, but rather the high spontaneous rate of gene duplication (10-5), amplification (10-2/step) and the selective addition of mutation targets (more cells with more mutant lac copies/cell).
Metazoan somatic cells may escape natural selection by the same mechanism.  Metazoans reduce the basal level of unexpressed genes 1000-fold (compared to bacteria) by their epi-genetic modification of DNA and histones – making it impossible for small-effect mutations to provide growth.

-- John Roth

The origin of mutants under selection: Interactions of mutation, growth and selection

Monday, March 9th, 2009

[This is a stub entry I'm making for John under his name. He should re-edit it with his own words. -- Eric]

Here’s the abstract to a new article.

The origin of mutants under selection: Interactions of mutation, growth and selection

Dan I Andersson, Diarmaid Hughes and John R Roth

In microbial genetics, positive selection detects rare cells with an altered growth phenotype (mutants or recombinants).  The frequency of mutants signals the rate of mutant formation – an increased frequency suggests a higher mutation rate.  Increases in mutant frequency are never attributed to growth under selection.  The converse is true in natural populations, where changes in phenotype frequency reflect selection, genetic drift or founder effects, but never changes in mutation rate.   The apparent conflict is resolved because restrictive rules allow laboratory selection to detect mutants without influencing their frequency.  With these rules, mutant frequency can reliably reflect mutation rates. When the rules are not followed, selection rather that mutation rate dictates mutant frequency – as in natural populations.  In several laboratory genetic systems, non-growing stressed populations show an increase in mutant frequency that has been attributed to stress-induced mutagenesis (adaptive mutation).  Since the mutant frequency is used to infer mutation rate (standard lab practice), the rules must be obeyed.  A breakdown of the rules in these systems may have allowed selection to cause frequency increases that were attributed to mutagenesis.  These systems have sparked interest in interactions between mutation and selection. This has led to a better understanding of how mutants arise, and how very frequent, small-effect mutations, such as duplications and amplifications, can contribute to mutant appearance by increasing gene dosage and mutational target size.

-- John Roth