Genomic Interspecies Microarray Hybridization: Rapid Discovery of Three Thousand Genes in the Maize Endophyte, Klebsiella pneumoniae 342, by Microarray Hybridization with Escherichia coli K-12 Open Reading Frames

Yuemei Dong, Jeremy D. Glasner, Frederick R. Blattner, Eric W. Triplett

Research output: Contribution to journalArticle

Abstract

In an effort to efficiently discover genes in the diazotrophic endophyte of maize, Klebsiella pneumoniae 342, DNA from strain 342 was hybridized to a microarray containing 96% (n = 4,098) of the annotated open reading frames from Escherichia coli K-12. Using a criterion of 55% identity or greater, 3,000 (70%) of the E. coli K-12 open reading frames were also found to be present in strain 342. Approximately 24% (n = 1,030) of the E. coli K-12 open reading frames are absent in strain 342. For 1.6% (n = 68) of the open reading frames, the signal was too low to make a determination regarding the presence or absence of the gene. Genes with high identity between the two organisms are those involved in energy metabolism, amino acid metabolism, fatty acid metabolism, cofactor synthesis, cell division, DNA replication, transcription, translation, transport, and regulatory proteins. Functions that were less highly conserved included carbon compound metabolism, membrane proteins, structural proteins, putative transport proteins, cell processes such as adaptation and protection, and central intermediary metabolism. Open reading frames of E. coli K-12 with little or no identity in strain 342 included putative regulatory proteins, putative chaperones, surface structure proteins, mobility proteins, putative enzymes, hypothetical proteins, and proteins of unknown function, as well as genes presumed to have been acquired by lateral transfer from sources such as phage, plasmids, or transposons. The results were in agreement with the physiological properties of the two strains. Whole genome comparisons by genomic interspecies microarray hybridization are shown to rapidly identify thousands of genes in a previously uncharacterized bacterial genome provided that the genome of a close relative has been fully sequenced. This approach will become increasingly more useful as more full genome sequences become available.

Original languageEnglish (US)
Pages (from-to)1911-1921
Number of pages11
JournalApplied and Environmental Microbiology
Volume67
Issue number4
DOIs
StatePublished - Apr 2001

Fingerprint

Escherichia coli K12
Endophytes
microarray technology
pneumonia
endophyte
Klebsiella pneumoniae
endophytes
Open Reading Frames
Zea mays
open reading frames
genomics
maize
Escherichia coli
protein
corn
gene
genome
Genes
regulatory proteins
transport proteins

ASJC Scopus subject areas

  • Biotechnology
  • Environmental Science(all)
  • Microbiology

Cite this

Genomic Interspecies Microarray Hybridization : Rapid Discovery of Three Thousand Genes in the Maize Endophyte, Klebsiella pneumoniae 342, by Microarray Hybridization with Escherichia coli K-12 Open Reading Frames. / Dong, Yuemei; Glasner, Jeremy D.; Blattner, Frederick R.; Triplett, Eric W.

In: Applied and Environmental Microbiology, Vol. 67, No. 4, 04.2001, p. 1911-1921.

Research output: Contribution to journalArticle

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