Implementation of microarrays for Methylobacterium extorquens AM1.
Microarrays are an important tool for understanding global gene expression changes, and the resulting data sets can be used to direct physiologic and metabolic studies. To take advantage of this technology, 60-mer oligonucleotide microarrays were designed for Methylobacterium extorquens AM1 to study gene expression changes that occur under differing physiological conditions. The carbon utilization pathways for methanol and succinate have been well characterized, and growth with these substrates was chosen as the condition used to validate the microarray data. The data were analyzed using two different methods and compared to previously obtained experimental data. The array data processed using the Significance Analysis of Microarrays followed by p-value assessment, correlated best to the experimental data. In addition to validating the microarrays, these studies uncovered possible connections between methylotrophy, iron, and sulfur homeostasis, bacteriochlorophyll production and polyketide synthesis, and will likely aid in uncovering further metabolic networks and genes required for methylotrophy.
Okubo
Yoko
Y
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA.
Skovran
Elizabeth
E
Guo
Xiaofeng
X
Sivam
Dhileep
D
Lidstrom
Mary E
ME
D001431:Bacteriological Techniques; D002244:Carbon / Q000378:metabolism; D020869:Gene Expression Profiling; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D000432:Methanol / Q000378:metabolism; D020601:Methylobacterium extorquens / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D015203:Reproducibility of Results; D019802:Succinic Acid / Q000378:metabolism
D002244:Carbon; D019802:Succinic Acid; D000432:Methanol