The data listed on this page is supplementary
to the original genome annotations associated with
the first Pseudomonas aeruginosa genome publication
by Stover et al. (
Nature 406:959-964. 2000). For the most up to
date annotations, please see the continually
Correction to Stover et al.
Nature 406:959-964 (2000).
of the genome. The 5570 genes, color-coded
of genomic DNA. The assembled DNA sequence
differs from the published physical map of PAO1
in that over one-quarter of the genome is inverted.
Restriction analysis was consistent with the interpretation
that this inversion was the result of recombination
the rrnA and rrnB ribosomal RNA
of atypical G+C content. The PAO1 genome
has an overall G+C content of 66.6%. However,
we noted isolated regions with lower G+C content.
These regions often had atypical codon usage and
may be the result of recent horizontal transfer.
Comparisons of the sequences of P.
aeruginosa ORFs with ORFs of other organisms
The PAO1 genome is more than a third larger than
that of E. coli K12. Several analyses suggested
that P. aeruginosa 's large genome is the result
of greater genetic complexity rather than differences
in genome organization or extensive gene duplication.
Identification of genes belonging
to known families
motifs in the P. aeruginosa genome and
four comparative genomes. Over five-hundred
genes contain motifs characteristic of transcriptional
regulators or of environmental sensors; an additional
13 genes have been demonstrated to encode transcriptional
regulators, but lack well-characterized motifs.
When homologous families of transcriptional regulators
(determined by motif searching) were compared
with other bacterial systems, the most striking
over-representations in P. aeruginosa
were observed in the LysR, AraC, sigma-ECF, LuxR
and two-component regulator families. There is
an extraordinary number of putative two-component
regulators, with 55 sensor proteins, 89 response
regulators and 14 sensor/response regulator hybrids,
more than twice the number found in E. coli
and B. subtilis.
of the OprM superfamily outer membrane proteins.
PAO1 contains approximately 150 genes for outer
membrane proteins, substantially more than other
sequenced genomes. 18 of these belong to the OprM
family and are thought to be involved in efflux
or secretion. Additional information on P.
aeruginosa outer membrane proteins.
specificity of predicted transporters.
P. aeruginosa has nearly 300 cytoplasmic
membrane transport systems. The predicted substrate
specificities of these transporters are compared
to those of E. coli, B. subtilis,
and M. tuberculosis. Additional information
comparisons of membrane transport systems.
Genetic loci that encode novel pathways
About 30% of PAO1 ORFS could be assigned a probable
function based on similarity to established sequence
motifs, but could not be assigned a definite name.
During annotation we noted that some of these genes
were in clusters for which a collective function could
be proposedfor example, the finding of adjacent
genes encoding an RND-type transport protein, a probable
RND membrane fusion protein, and an OprM-family outer
membrane protein suggests that these gene products
work together to export some undetermined substrate.