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

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. coil K-12 open reading frames were also found to be pr esent 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 rea ding frames, the signal was too low to make a determination regarding the p resence or absence of the gene. Genes with high identity between the two or ganisms are those involved in energy metabolism, amino acid metabolism, fat ty acid metabolism, cofactor synthesis, cell division, DNA replication, tra nscription, translation, transport, and regulatory proteins. Functions that were less highly conserved included carbon compound metabolism, membrane p roteins, structural proteins, putative transport proteins, cell processes s uch as adaptation and protection, and central intermediary metabolism. Open reading frames of E. coli K-12 with little or no identity in strain 342 in cluded 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 acquir ed by lateral transfer from sources such as phage, plasmids, or transposons . The results were in agreement with the physiological properties of the tw o strains. Whole genome comparisons by genomic interspecies microarray hybr idization are shown to rapidly identify thousands of genes in a previously uncharacterized bacterial genome provided that the genome of a close relati ve has been fully sequenced. This approach will become increasingly more us eful as more full genome sequences become available.