DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes
DNA microarrays constructed with full length ORFs from Shewanella oneidensis, MR-1, were hybridized with genomic DNA from nine other Shewanella species and Escherichia coli K-12. This approach enabled visualization of relationships between organisms by comparing individual ORF hybridizations to 164 genes and is further amenable to high-density high-throughput analyses of complete microbial genomes. Conserved genes (arcA and ATP synthase) were identified among all species investigated. The mtr operon, which is involved in iron reduction, was poorly conserved among other known metal-reducing Shewanella species. Results were most informative for closely related organisms with small subunit rRNA sequence similarities greater than 93% and gyrB sequence similarities greater than 80%. At this level of relatedness, the similarity between hybridization profiles was strongly correlated with sequence divergence in the gyrB gene. Results revealed that two strains of S. oneidensis (MR-1 and DLM7) were nearly identical, with only 3% of the ORFs hybridizing poorly, in contrast to hybridizations with Shewanella putrefaciens, formerly considered to be the same species as MR-1, in which 63% of the ORFs hybridized poorly (log ratios below −0.75). Genomic hybridizations showed that genes in operons had consistent levels of hybridization across an operon in comparison to a randomly sampled data set, suggesting that similar applications will be informative for identification of horizontally acquired genes. The full value of microbial genomic hybridizations lies in providing the ability to understand and display specific differences between closely related organisms providing a window into understanding microheterogeneity, bacterial speciation, and taxonomic relationships.
Additional Information© 2001 National Academy of Sciences. Edited by Rita R. Colwell, National Science Foundation, Arlington, VA, and approved June 12, 2001 (received for review April 9, 2001). We acknowledge the efforts of the research team at the Institute for Genome Research, led by Claire Fraiser, John Heidelberg, and Jonathon Eisen, for sequencing the S. oneidensis, MR-1 genome, and for assistance in genome comparisons between E. coli and MR-1. We also thank Michigan State University's Arabidopsis Functional Genomics Consortium, led by Ellen Wisman, where the majority of microarray printing and scanning was conducted, for stimulating discussion regarding microarray technology and data analysis. John Urbance is also acknowledged for assistance with phylogenetic analyses. This work was supported by Department of Energy Grants KP11020100 and WPERK802 (to J.Z.). Oak Ridge National Laboratory is managed by the University of Tennessee–Battelle Limited Liability Company for the Department of Energy under contract DE-AC05-00OR22725.
Published - PNAS-2001-Murray-9853-8.pdf