Physical map of the genome of Planctomyces limnophilus, a representative of the phylogenetically distinct planctomycete lineage

Abstract

A physical map of the chromosome of Planctomyces limnophilus DSM 3776T was constructed by pulsed-field gel electrophoresis techniques. A total of 32 cleavage sites for the rare-cutting restriction endonucleases PacI, PmeI, and SwaI were located on the chromosome, which was shown to be circular and approximately 5.2 Mbp in size. An extrachromosomal element was detected but was found not to be cleaved by any of the enzymes used in the analysis of the chromosome. The order of the fragments on the chromosome was determined by hybridization of excised, labelled restriction fragments to Southern blots of pulsed-field gel electrophoresis-separated restriction digests. Seven genetic markers, rrs, rrl, atpD, tuf, gyrB, rpoD, and dnaK, on the chromosome were located by hybridization. Probes for all genetic markers were obtained by PCR. For five of these markers, probes were constructed by PCR with degenerate primers targeting conserved sequences. The arrangement of the genetic markers was compared with that found in other bacteria.Planctomyces limnophilus is a member of the order Planctomycetales, a group of budding microorganisms lacking peptidoglycan and representing a phylogenetically distinct lineage within the domain Bacteria, as defined by rRNA sequence analysis (3,23,31). The ecology, phylogeny, and cell biology of the planctomycetes have been recently reviewed (11). Members of the order Planctomycetales have been observed in and isolated from aquatic habitats. The inability to recover some species, including the type species of the genus Planctomyces, P. bekefii, as pure and viable cultures led to the belief that the organisms are rare and relatively limited in distribution. However, recent studies using new cultivation methods (30), molecular identification of new isolates (36), and 16S rRNA gene (rDNA)-based molecular ecology studies (7, 21) have shown that planctomycetes are much more ubiquitous than previously thought and suggest that they may be essential contributors to nutrient cycling processes.The planctomycetes share a number of morphological features, having spherical or ovoid cells which bear crateriform structures and, in some cases, nonprosthecate appendages. The presence of a membrane-bounded nuclear body, previously unknown in bacteria, has been demonstrated in the planctomycete Gemmata obscuriglobus (12). A number of unusual molecular features have been observed, including unlinked rrn operon organization in some species (20, 24) and a short 5S rRNA molecule consisting of 109 to 111 nucleotides (3).Despite their unique properties, the planctomycetes are not well characterized genetically, and no information on the general genomic organization of planctomycete chromosomes has been reported. Physical genome maps have been constructed for representatives of most other bacterial phyla, and a conserved ''backbone'' structure of certain key housekeeping genes, to which most bacterial genomes conform, has been proposed (6). In this work, we present a physical map of the genome of P. limnophilus and show ...

The Ribosomal Intergenic Spacer and Domain I of the 23S rRNA Gene Are Phylogenetic Markers for Chlamydia spp.

“…are 40% different (91). Planctomycetes are freeliving organisms, and at least one has a genome that is five times larger than the chlamydial genome (89).…”

Phylogenetic diversity, polyamine pattern and DNA base composition of members of the order Planctomycetales

“…Members of this order differ in several characteristics from other bacterial taxa: (i) they multiply by forming buds directly from the spherical, ovoid or pear-shaped mother cell; (ii) the cell wall is stabilized by a proteinaceous layer rather than a peptidoglycan layer (Konig et al, 1984;Liesack et al, 1986); (iii) the cell surface is scattered with ' crateriform structures ' Staley et al, 1992) which, outside the planctomycetes proper, has only been reported for Porphyrobacter neustonensis (Fuerst et al, 1993); (iv) the 5s rRNA contains only 109-1 11 bases (Bomar et al, 1988); and (v) certain idiosyncrasies have been detected at the genome level (Liesack & Stackebrandt, 1989;Ward-Rainey et al, 1996).…”

Characterization of Planctomyces limnophilus and Development of Genetic Tools for Its Manipulation Establish It as a Model Species for the Phylum Planctomycetes

“…After analyzing several species (see Table S1 in the supplemental material), we chose Planctomyces limnophilus to develop methods for gene transfer and mutagenesis. The key criteria for selecting this species were (i) it displays one of the fastest growth rates among the cultured Planctomycetes (6 to 14 days to detect a colony), (ii) plasmids and bacteriophage have been described (5,16,15), and (iii) the genome sequence is available. However, the unusual cell biology is a key hallmark of Planctomycetes, and little was known about P. limnophilus in this regard (4,6).…”