Implementation of microarrays for Methylobacterium extorquens AM1

Yoko Okubo, Elizabeth Skovran, Xiaofeng Guo, Dhileep Sivam, Mary E. Lidstrom

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)325-340
Number of pages16
JournalOMICS A Journal of Integrative Biology
Volume11
Issue number4
DOIs
StatePublished - Dec 1 2007

Fingerprint

Methylobacterium extorquens
Microarrays
Bacteriochlorophylls
Polyketides
Gene Expression
Succinic Acid
Microarray Analysis
Metabolic Networks and Pathways
Oligonucleotide Array Sequence Analysis
Sulfur
Methanol
Homeostasis
Carbon
Iron
Gene expression
Technology
Growth
Genes
Oligonucleotides
Substrates

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Implementation of microarrays for Methylobacterium extorquens AM1. / Okubo, Yoko; Skovran, Elizabeth; Guo, Xiaofeng; Sivam, Dhileep; Lidstrom, Mary E.

In: OMICS A Journal of Integrative Biology, Vol. 11, No. 4, 01.12.2007, p. 325-340.

Research output: Contribution to journalArticle

Okubo, Y, Skovran, E, Guo, X, Sivam, D & Lidstrom, ME 2007, 'Implementation of microarrays for Methylobacterium extorquens AM1', OMICS A Journal of Integrative Biology, vol. 11, no. 4, pp. 325-340. https://doi.org/10.1089/omi.2007.0027
Okubo, Yoko ; Skovran, Elizabeth ; Guo, Xiaofeng ; Sivam, Dhileep ; Lidstrom, Mary E. / Implementation of microarrays for Methylobacterium extorquens AM1. In: OMICS A Journal of Integrative Biology. 2007 ; Vol. 11, No. 4. pp. 325-340.
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