Sunday, January 9, 2011
You pay in ribosomes for proteins
Everything costs. When cell grows, it needs energy and in needs materials. By the end of the day it comes down to accounting: if you need to make N proteins, you will need X ATPs molecules, Y aminoacids and Z ribosomes to do the job. And of all these ribosomes are the most expensive to make: they are huge, made of RNA and if you want to make proteins fast, you need lots of ribosomes!
So research team led by famous systems biologist Uri Alon decided to quantify the cost of making a protein. In order to do so, they forced E. coli producing Green Fluorescent Protein (GFP) which is inert and easy to quantify. They figured out that early in the exponential phase the cost of GFP (that is decrease in growth rate associated with production of a given amount of GFP) is high, but later on it markedly recreases!
This observation makes immediate sense: first you need to produce the tools for producing GFP (ribosomes, energy in the form of ATP etc.) and if instead of this you make GFP this GFP comes at a high prise. Corroborating with this logic, they figured out that if you transfer bacteria from energy-reach media to energy-poor, the price for GFP is low: well, you accumulated all these ribosomes during the good times, so now you can make some GFP cheap.
There could be an interesting connection here with another resent paper where in yeast it was shown that the cost of GFP is dramatically different for stable and denaturation-prone variants (for brilliant discussion of this paper see this post in It Takes 30). Is GFP equally stable in E. coli during the early and late exponential phase? Could it be that the effects observed here are reflecting mere change in GFP stability? Intracellular conditions do change in E. coli under different conditions, so it is possible that GFP is not always equally stable, and this may affect its physiological cost. Surprisingly, another report claims that in E. coli aggregated and soluble LacZ have very similar cost, which to some extent dispels my worries about GFP stability and cost.
The read-out for GFP quantification could be affected by cellular milieu as well: judging from my experience, GFP is definitely not always equally bright, and this could affect estimates of GFP concentration and thus the estimates of its physiological cost.
Discovering differences in the GFP cost in early and late exponential phase prompted the authors to try figuring out what cellular system is behind it. And they had a very good initial guess. In bacteria adaptation to changes in availability of food are regulated by the stringent response mechanisms, with RelA and SpoT proteins doing the job (see my previous posts on that subject, see 1 and 2). RelA produces ppGpp molecule that compels the cell to stop producing ribosomes and concentrate on aminoacid production, and SpoT mostly degrades ppGpp: too much of it would lead to complete inhibition of ribosomal production and eventually - death.
Therefore it is only logical that in the paper in question different knock-out strains missing RelA and SpoT were tested, and indeed, stringent response machinery turned out to the the key to radical changes of the protein cost during different stages of bacterial growth.
And here is the catch.
One of the strains they used was SpoT(-) RelA(+) strain, that is one having NO SpoT and allegedly INTACT RelA. As we discussed above this bug should be very much dead, and as yet no one managed to produce this strain. So what's about the strain presented in the paper then?
Well, there are many options. When you want, really want to knock out a gene, you finally succeed. However, bacteria want to live, and you select the ones with mutations that compensate for the knock-out of the gene you have. For instance, you can mutate main target of ppGpp, the RNA polymerase and make it insensitive to regulation. Aslo, you can mutate RelA and make it inactive. And there are several other possible compensatory mutations... In order to notice these changes in the strain you made you really need to run a lot of tests, and the authors did not.
So here is another example how bacteria are cleverly trying to fool systems biology approach (another example is here).
Update: the SpoT knock-out strain used in the original paper indeed was iffy, it had compensatory mutations in RelA and an erratum was published, which I discuss here.
Shachrai I, Zaslaver A, Alon U, & Dekel E (2010). Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. Molecular cell, 38 (5), 758-67 PMID: 20434381
Potrykus K, & Cashel M (2008). (p)ppGpp: still magical? Annual review of microbiology, 62, 35-51 PMID: 18454629
Geiler-Samerotte KA, Dion MF, Budnik BA, Wang SM, Hartl DL, & Drummond DA (2010). Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proceedings of the National Academy of Sciences of the United States of America PMID: 21187411
Plata G, Gottesman ME, & Vitkup D (2010). The rate of the molecular clock and the cost of gratuitous protein synthesis. Genome biology, 11 (9) PMID: 20920270
Mendeley group on stringent response