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Maize Plastid Microarray

Tom Brutnell tpb8 at cornell.edu
Mon Dec 22 12:29:31 EST 2003

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 

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.


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
phone: 607-254-8656
fax:   607-254-1242

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