Plant Physiology 132:1825-1839 (2003)
© 2003 American Society of Plant Biologists
GENETICS, GENOMICS, AND MOLECULAR EVOLUTION
Microarray Analysis of the Genome-Wide Response to Iron Deficiency and Iron Reconstitution in the Cyanobacterium Synechocystis sp. PCC 68031,[w]
Abhay K. Singh,
Lauren M. McIntyre and
Louis A. Sherman*
Department of Biological Sciences (A.K.S., L.A.S.) and Computational
Genomics and Department of Agronomy (L.M.M.), Purdue University, West
Lafayette, Indiana 47907
A full-genome microarray of the (oxy)photosynthetic cyanobacterium
Synechocystis sp. PCC 6803 was used to identify genes that were
transcriptionally regulated by growth in iron (Fe)-deficient versus
Fe-sufficient media. Transcript accumulation for 3,165 genes in the genome was
analyzed using an analysis of variance model that accounted for slide and
replicate (random) effects and dye (a fixed) effect in testing for differences
in the four time periods. We determined that 85 genes showed statistically
significant changes in the level of transcription (P  0.05/3,165
= 0.0000158) across the four time points examined, whereas 781 genes were
characterized as interesting (P 0.05 but greater than 0.0000158;
731 of these had a fold change >1.25x). The genes identified included
those known previously to be Fe regulated, such as isiA that encodes
a novel chlorophyll-binding protein responsible for the pigment
characteristics of low-Fe (LoFe) cells. ATP synthetase and phycobilisome genes
were down-regulated in LoFe, and there were interesting changes in the
transcription of genes involved in chlorophyll biosynthesis, in photosystem I
and II assembly, and in energy metabolism. Hierarchical clustering
demonstrated that photosynthesis genes, as a class, were repressed in LoFe and
induced upon the re-addition of Fe. Specific regulatory genes were
transcriptionally active in LoFe, including two genes that show homology to
plant phytochromes (cph1 and cph2). These observations
established the existence of a complex network of regulatory interactions and
coordination in response to Fe availability.
Article, publication date, and citation information can be found at
www.plantphysiol.org/cgi/doi/10.1104/pp.103.024018.
1 This work was supported by the National Science Foundation (grant no.
MCB–0084457 to Robert Burnap and L.A.S. for the construction of the
microarray), by the Department of Energy (grant no.
DE–FG92–99ER20342 to L.A.S.), and by the U.S. Department of
Agriculture-Initiative for Future Agriculture and Food Systems (grant no.
NOO14–94-1–0318 to L.M.M.).
[w] The online version of this article contains Web-only data. The supplemental
material is available at
http://www.plantphysiol.org.
*
Corresponding author; e-mail
lsherman{at}bilbo.bio.purdue.edu;
fax 765–496–1496.
Received March 21, 2003;
returned for revision April 21, 2003;
accepted May 12, 2003.
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