Has anyone encountered a case in which a construct with the native sequence
expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding
construct with a codon-optimized sequence expressed well? (The gene in question
is from cerevesiae)
Thanks,
Pat
On Fri, 2011-09-30 at 10:49 -0400, Patrick Loll wrote:
Has anyone encountered a case in which a construct with the native
sequence expressed poorly (or not at all?) in Rosetta(DE3), but the
corresponding construct with a codon-optimized sequence expressed
well? (The gene in question is from
Rosetta strains carry a plasmid that supplies several tRNAs that match codons
that are rare in E. coli. This is quite different than being explicitly
optimized to express mammalian proteins. We (the Center for Eukaryotic
Structural Genomics, a PSI-1 and PSI-2 center) used strains with the
of Patrick Loll
Sent: Fri 30.09.2011 16:49
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] is codon optimization worth it?
Has anyone encountered a case in which a construct with the native sequence
expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding
construct with a codon
In theory, if the rare codons are all covered by Rosetta's extra
tRNAs, codon optimization should not make any difference.
In practice it does because frequently it's not codon optimization per se
but changing local mRNA structure.
- Dima
bulletin board on behalf of Patrick Loll
Sent: Fri 30.09.2011 16:49
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] is codon optimization worth it?
Has anyone encountered a case in which a construct with the native sequence
expressed poorly (or not at all?) in Rosetta(DE3), but the corresponding
.
Brent
From: Anastassis Perrakis [mailto:abba...@gmail.com] On Behalf Of Anastassis
Perrakis
Sent: Friday, September 30, 2011 10:08 AM
To: Segelke, Brent W.
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] is codon optimization worth it?
Well, codon optimization is not really trouble, it's money
@JISCMAIL.AC.UK] On Behalf Of Tim Keys
Sent: Friday, September 30, 2011 8:29 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] is codon optimization worth it?
We codon optimised a poorly expressed gene from neisseria meningitides based
on a codon usage table derived from the Welch (etal
We recently published something really old-related about it:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021035
My two cents. Best, Alfredo.
Alfredo Torres-Larios, PhD
Assistant Professor
Instituto de Fisiologia Celular, UNAM
Mexico
, Brent W.
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] is codon optimization worth it?
Well, codon optimization is not really trouble, it's money. The money are
worth it usually anyway, since the optimized genes are easy to clone if you
make many constructs out of one gene, as you better
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