Any Gram positive bug gurus out there?

USENET News System news at massey.ac.nz
Wed Nov 25 23:42:34 EST 1992


In article <1etkf1INN73v at menudo.uh.edu> Michael Benedik,
bchs1b at Elroy.UH.EDU writes:
>What does a Gram + ribosome binding site look like? Similar to E.coli
>or not? 
>	What about signal peptides for secreted proteins? I seem to
>remember that they are often longer. Any other different features?
>What about promoter consensus sequences? Any help you can offer will
>be greatly appreciated.
 In general, there is not a huge difference in the actual G+ RBS and
E.coli. Having said that, the actual number of G+  RBS sequenced from any
particular bug species is a lot less than from E. coli.  However, look up
any book on B. subtilis, and you will find lots of comparisons of G+
promoter and RBS sequences.
 Be careful when looking for consensus DNA or AA sequences for signal
peptides, as there do not appear to be any. What you need to look for is
groups of AA's which will at the 5' end form a hydrophilic domain
(usually about 5-7 AA) followed by a hydrophobic domain (22-35, or more
or less!!), and then the reasonably conserved Ala-X-Ala motif, (although
not always).  Generally speaking the G+ signal peptides are longer (in
the hydrophobic domian), perhaps because of the location of the signal
peptidase active site on the extra-cytoplasmic face of the plasma
membrane (where the environment will be different than in the G-'s).  A
defintive test for signal peptide activity is to fuse it to phoA or
B-lactamase, assay for activity, and look for cleavage of the signal
peptide.
      Good Luck.
                       Eamonn Gormley, E.P. Gormley at massey.ac.nz



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