Summary auto-generated
This study examines genome organization in Pseudomonas stutzeri by analyzing 20 strains representing seven genomovars using restriction enzyme analysis and pulsed-field gel electrophoresis. Researchers found that P. stutzeri possesses a single circular chromosome ranging from 3.75 to 4.64 megabases. Using rare-cutting enzymes (I-CeuI, PacI, and SwaI), they constructed physical maps and located various genes including four rRNA operons, the origin of replication, and genes involved in denitrification and metabolism. While XbaI and SpeI fingerprints revealed unique restriction patterns for each strain, genomovar reference strains exhibited distinct rRNA gene arrangements. In most genomovars, rRNA genes were distributed around the chromosome rather than clustered near the origin of replication. Large chromosomal rearrangements appeared responsible for genomovar differences. Notably, strain JM300 displayed a unique genome organization that did not correspond to any existing genomovar, suggesting it represents a distinct lineage. The findings indicate that DNA rearrangements played a significant role in P. stutzeri diversification and evolution.
Key findings
- P. stutzeri has a single circular chromosome ranging from 3.75 to 4.64 Mb with high intraspecies variation
- Genomovars exhibit distinct rRNA operon arrangements; most distribute rrn genes equally around the chromosome rather than clustering near the origin of replication
- Large chromosomal rearrangements distinguish genomovars and drove P. stutzeri diversification and niche colonization
- Strain JM300 possesses a unique genome organization that does not correspond to any of the seven described genomovars
- XbaI and SpeI fingerprints revealed clonal variants within genomovars based on unique restriction patterns
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Abstract
In order to determine the genome variability within Pseudomonas stutzeri, 20 strains representing the seven described genomovars and strain JM300 were analyzed by using various resolution levels of rare cutting enzymes. XbaI and SpeI fingerprints revealed a high degree of heterogeneity of restriction patterns that did not correlate with the division into genomovars. However, a fragment pattern comparison led to the establishment of several groups of clonal variants within genomovars. One circular chromosome ranging in size from 3.75 to 4.64 Mb constitutes the genome of P. stutzeri strains. The I-CeuI, PacI, and SwaI low-resolution map of P. stutzeri type strain CCUG 11256 shows the locations of 12 genes, including rrn operons and the origin of replication. I-CeuI digests of the 20 strains studied plus the positions of six genes allowed a comparison of the rrn backbone organization within genomovars; the four rrn operons seemed to be at similar locations with respect to the origin of replication, as did the rest of the genes. However, a comparison of I-CeuI cleavage maps of the genomovar reference strains revealed a diverse genome organization in the genomovars relative to rrn operons and gene locations. In most genomovars, rrn operons are not arranged around the origin of replication but are equally distributed on the chromosome. Strain JM300 does not belong to any described genomovar, as determined from the organization of its genome. Large chromosomal rearrangements seem to be responsible for the differences in superordinate genome structure and must have played an important role in P. stutzeri diversification and niche colonization. An ancestral chromosome is suggested, and some plausible pathways for the generation of the various genome structures are proposed.