Dear Colleague,
As part of a recent NSF Plant Genome Research Program Award
(DBI-0211935), we are developing a maize 'plastid chip' microarray.
This chip will contain sequences representing 60 chloroplast-encoded
genes, approximately 75 mitochondrial genes (kindly provided by Dr.
Kathy Newton) and up to 800 nuclear gene sequences that are predicted
or known to encode plastid-localized proteins, or in a few cases,
mitochondrial proteins. These chips will be printed at the Boyce
Thompson Institute Center for Gene Expression Profiling and made
available to the academic community at cost, which we estimate at
$25/slide.
To identify maize genes encoding putative plastid-localized products,
we first performed BLAST searches of all UnigeneI sequences against
the predicted proteomes of rice and Arabidopsis to identify putative
homologues based on matching domain length and sequence identity. We
then analyzed both the predicted proteomes of rice and Arabidopsis
using TargetP to define a set of genes with predicted chloroplast
targeting peptides (cTP). Finally, we then compared datasets to
identify maize UnigeneI ESTs that are likely to encode homologs of
rice and/or Arabidopsis proteins with a predicted cTP. We have now
amplified and confirmed the identity of approximately 655 maize EST
sequences that are likely to encode plastid proteins based on these
criteria. Amplified PCR products will be spotted on this array
together with the chloroplast and mitochondrial sequences.
Because the functions of many of the genes in Unigene I are currently
unknown, and because the collection is enriched for highly expressed
sequences, we are seeking additional clones representing plastid
proteins (both non-green plastids and chloroplasts), as well as
mitochondrial proteins. To do so, we are soliciting members of the
maize community who may have well-characterized genomic or cDNA
clones that are not represented in Unigene I. For instance, Dr.
Eleanor Wurtzel has recently provided a collection of EST and genomic
clones encoding the structural enzymes of the carotenoid biosynthetic
pathway. Dr. Alice Barkan has also provided a number of clones
corresponding to nuclear-encoded proteins necessary for plastid RNA
processing and thylakoid protein import. The richer our collection
of clones, the more powerful the array becomes in understanding
plastid function and plastid-nuclear interactions.
As many of you are aware, an oligo-based microarray is currently
under development at the University of Arizona
https://www.fastlane.nsf.gov/servlet/showaward?award=0321663. This
oligo-based chip will contain over 30,000 maize gene sequences and
provide a powerful resource to examine global patterns of gene
expression. The goal of our plastid chip is to provide a low-cost
array to survey a subset of nuclear, plastid and mitochondrial gene
expression patterns under a range of experimental conditions. The
effectiveness of the array can be significantly bolstered through the
support of the maize community.
We will be printing our first arrays by March 2004. If you would be
willing to contribute your favorite (or other relevant) genes to this
chip, we ask that you please contact Tom Brutnell (tpb8 at cornell.edu)
or David Stern (ds28 at cornell.edu). We will forward to you a
spreadsheet for entering clone data and ask that you please send DNA
to Beth Takacs (emt32 at cornell.edu), Boyce Thompson Institute for
Plant Research, Cornell University, Tower Road, Ithaca, NY 14853 by
Feb 1, 2004. Beth is organizing and annotating the clone collection,
and coordinating our printing efforts with CGEP. We look forward to
disseminating this resource, and anticipate that it will be of broad
value to the maize community.
Sincerely,
Tom Brutnell, Boyce Thompson Institute
David Stern, Boyce Thompson Institute
Klaas van Wijk, Cornell University
Tom Clemente, University of Nebraska
--
Tom Brutnell
Boyce Thompson Institute for Plant Research
Rm 129
Tower Road
Ithaca, NY 14853
USA
http://bti.cornell.edu/Brutnell_lab2/BMGG_home.html
phone: 607-254-8656
fax: 607-254-1242
