tag:blogger.com,1999:blog-36768584.post1945588234847412821..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Codon Optimization is Not Bunk?Keith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-36768584.post-81063143873334673732010-05-06T08:22:25.421-04:002010-05-06T08:22:25.421-04:00Given the amount of work that has been put into co...Given the amount of work that has been put into codon optimization in the past - and the many factors that have been found to have an influence on expression levels - it would highly surprise me if in the end the "solution" would turn out to be this simple; and indeed, I fear that there are some technical issues with this study. In particular: can one really deduce such "hard" generalizations about an enormously vast sequence space by testing a mere 40 genes? The use of partial least squares as a dimension reduction method (which I think is what the authors did) and verification by means of a test set should reduce the problem of overtraining somewhat, but I would be very cautious in the interpretation of these results regardless. Possibly even more so because this paper appears to be sponsored by people with a direct financial interest in a spectacular outcome.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-80788802652773923052009-12-15T06:40:42.386-05:002009-12-15T06:40:42.386-05:00http://postgenomic.com/index.phphttp://postgenomic.com/index.phptürkiye ve hayata dair herşeyhttps://www.blogger.com/profile/08028621290757062388noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-5475438318527979322009-10-24T21:14:25.517-04:002009-10-24T21:14:25.517-04:00I doubt you'd actually want to use minimal med...I doubt you'd actually want to use minimal medium -- protein production requires a lot of resources & you don't want the cell to have a hard time getting them.<br /><br />What the result does suggest is that high level protein production does induce, at least in part, severe stresses for some nutrients. Further supplementation with those nutrients might work, but it may be that the import systems for these can't work any harder. <br /><br />A very crude idea that now occurs is to take one of the poor expressing coding schemes and use it as a reporter system to evolve better strains -- with targeted mutation aimed at the production & transport of some of the amino acids which seem to be most sensitive in the analysis.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-80744428132831993962009-10-24T10:51:01.572-04:002009-10-24T10:51:01.572-04:00Does it mean that if E.coli is grown in minimal m...Does it mean that if E.coli is grown in minimal media (mimic starvation condition)protein expression would be better?thanks.<br />sam.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-9737479768327761612009-09-16T17:57:07.273-04:002009-09-16T17:57:07.273-04:00Try this linkTry <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007002" rel="nofollow">this link</a>Guyhttps://www.blogger.com/profile/02968872267548865219noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-88008803608219635552009-09-15T19:35:24.821-04:002009-09-15T19:35:24.821-04:00thanks for the concurrence on having trouble with ...thanks for the concurrence on having trouble with the link -- strangely it works for me on two different computers running two different browsers, which underscores how<br /><br />I've tried another form of the link that doesn't have any escaped characters; with luck that will work.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-10159888227715319962009-09-15T16:30:43.464-04:002009-09-15T16:30:43.464-04:00Thanks for the pointer, Keith. The link to the ar...Thanks for the pointer, Keith. The link to the article doesn't work for me either -- it looks like the Blogger software thinks it's an internal link. The URL is in the title property, which may be relevant.Victor Stevkonoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-45626762944025054522009-09-15T10:48:42.216-04:002009-09-15T10:48:42.216-04:00Well, it all depends on your tolerance for inconsi...Well, it all depends on your tolerance for inconsistent expression, particularly when dealing with a lot of proteins. Two logs is quite a spread, wouldn't you agree? It will be important for producing individual proteins, but I would see an even greater utility when screening lots of proteins for some interesting enzymatic activity, particularly when trying to assemble a whole pathway of activities. <br /><br />If you are already having the genes synthesized, in general the combinatorial space is so huge you can layer on quite a few constraints or optimizations and not run out of choices, or at a minimum use all those to rank choices. <br /><br />Optimizing against secondary structure will, as shown by the GFP example, depend on the protein being encoded. However, it isn't hard to optimize this in silico. A high probability of forming secondary structure (due to inverted repeats) is also potentially troublesome for synthesis, so most companies will be knocking it out anyway.<br /><br />Curious about the PLoS link -- it works for me. Perhaps it was something transient.<br /><br />The Mark et al work suggests a path for predicting which tRNAs are the most critical, but as you point out it still may not be the whole story. I may write some more on that tonight.Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-16278825843937357182009-09-15T07:50:29.162-04:002009-09-15T07:50:29.162-04:00While it is an interesting summary of previous fin...While it is an interesting summary of previous findings, I am not sure what the pragmatic implications of codon usage are for molecular biologists who clone and sequence genes as bread and butter work. <br />There is usually an attempt to optimize codon usage when using a construct for protein expression or transient transfection. However, most often optimizing for secondary structure is not trivial, and detecting which amino acid is being depleted requires combinatorial experiments. In the end , its not so much about optimizing expression, as getting the protein in hand. One can always simply use more runs of purification, more cells for a blot, or stronger excitation for imagaing, and achieve the same results as a high expression. <br />I can understand of course, that this kind of work might be useful to those who produce protein-based products commercially. <br /><br />PS : Your link to the PloSOne article is non-functional.Nashhttps://www.blogger.com/profile/02952597975578075192noreply@blogger.com