The answer to the genetic code of Chlamydomas

John Francis Peden JFPEDEN at vax1.tcd.ie
Wed Jul 14 13:26:00 EST 1993

in the message <1993Jul14.013825.18332 at gserv1.dl.ac.uk> I asked

<stuff deleted> 

> today I came across a paper by W. Steven Adair and K. E. Apt, titled
> Cell wall regeneration in Chlamydomas: Accumulation of mRNA's encoding
> cell wall hydroxyproline rich glycoproteins. 
> published in
> PNAS 87: 7355-7359 (1990)
> In this paper they report two open reading frames which they 
> translate into AA and that code for Hydroxyproline rich glycoprotein,
> but they use the genetic code TAG=Y, I hadn't heard of this particular
> code before. 
> Is it universal for all C.reinhardtii genes.
> thanks in anticipation 

I recieved two replies one from Elizabeth Harris (chlamy at acpub.duke.edu)
who kindly offered to check out that paper and one from Jeff Woessener
(woessner at biolgy.wustl.edu). Who has an explanation for my query. He 
asked me to post his reply to the group.


Dear Dr. Peden,
    I have inherited Dr. Adair's clones and projects as he has unfortunately 
passed away.  This paper of his, to which you refer was a long time in the 
review process for some very valid reasons--namely the lack of conclusive 
proof that these cDNAs truly encoded the glycoproteins that he claimed they
should.  He wanted to get some DNA sequence to add to the paper as the final
bit of evidence that he was on the right track, and impetuously pushed this 
through.  I helped him to analyze his sequences and know that these errors
were not in the data that I ran through our computer.  I do remember that I 
was frustrated by the lack of any indication of where the 3' end of his clones
was, he had no RNA hybridization data and such which might have identified the
coding strand.  To make a long story short, I noted these errors in translation
soon after I received a copy of the published paper, which came out after his 
death.  TAG does not code for tyrosine in Chlamy, this is simply an error in 
interpreting the sequence.  Since I am interested in characterizing as many
of the structural wall genes in Chlamy as I can isolate, I have begun to 
reanalyze and resequence the GP1 and GP2 clones that Adair and Apt (1990)
isolated.  I firmly believe that the cDNAs do indeed encode for these HRGPs
just as Adair claimed, however my work on GP1 where I have isolated more 
cDNAs from my own libraries (wherein the clones have retained their poly A
tails) shows that the sequence that is presented in the Adair and Apt (1990)
paper is from the wrong strand and backwards!  I haven't begun to work on the
GP2 but I suspect there will be similar problems with this sequence.  I didn't
know any easy way to point out these errors until I had the proper sequence 
in hand.

Jeff Woessner

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