[BBF Standards] BB promoter standard?

[Jason Kelly]

hi standardphiles,

Wanted to revisit a discussion from a year or so ago about how to
standardize the transcriptional start site for BioBrick promoters.
(previous discussion buried in here:
http://openwetware.org/wiki/Talk:Synthetic_Biology:BioBricks/Standardization)

The reason to standardize the start site is to ensure that all BB
promoters add the same 5'UTR to mRNA.  Then if you put different
promoters upstream of the same gene the relative expression levels of
the gene would be correlated to the promoter strength (e.g. mRNA
produced / time) rather than to some secondary effect like mRNA
stability (since in theory the mRNA produced by all BB promoters
expressing the same gene would be the same).  This means you might
have more reason to believe that promoter strengths characterized with
one gene (say GFP), would have the same relative strengths when
expressing your particular gene of interest.

Also, If different promoters are adding different 5'UTRs it opens up
more opportunity for unpredictable composition effects.  For instance,
the 5'UTR of the mRNA from one promoter might fold up with the RBS of
the downstream gene preventing expression, while the 5'UTR from
another promoter would be fine.  If we adopt a standard transcription
start site you could still get folding effects that block the RBS, but
at least it would be consistent across all promoters and you could
debug it more predictably.

OK, if this sounds interesting, please take a look at 2 options for
proposed standards I posted.
http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/E.coli_promoter_standard

comment on the wiki or by email to the list:

thanks!
jason