Complete genome sequence of the marine planctomycete Pirellula sp. strain 1

Abstract

Pirellula sp. strain 1 (''Rhodopirellula baltica'') is a marine representative of the globally distributed and environmentally important bacterial order Planctomycetales. Here we report the complete genome sequence of a member of this independent phylum. With 7.145 megabases, Pirellula sp. strain 1 has the largest circular bacterial genome sequenced so far. The presence of all genes required for heterolactic acid fermentation, key genes for the interconversion of C1 compounds, and 110 sulfatases were unexpected for this aerobic heterotrophic isolate. Although Pirellula sp. strain 1 has a proteinaceous cell wall, remnants of genes for peptidoglycan synthesis were found. Genes for lipid A biosynthesis and homologues to the flagellar L-and P-ring protein indicate a former Gram-negative type of cell wall. Phylogenetic analysis of all relevant markers clearly affiliates the Planctomycetales to the domain Bacteria as a distinct phylum, but a deepest branching is not supported by our analyses. P irellula sp. strain 1, which is in the process of being validly described as ''Rhodopirellula baltica,'' is a marine, aerobic, heterotrophic representative of the globally distributed and environmentally important bacterial order Planctomycetales. Molecular microbial ecology studies repeatedly provided evidence that planctomycetes are abundant in terrestrial and marine habitats (1-5). For example, they inhabit phytodetrital macroaggregates in marine environments (6) and include one of the organisms known to derive energy from the anaerobic oxidation of ammonia (7). They catalyze important transformations in global carbon and nitrogen cycles. By their mineralization of marine snow particles planctomycetes have a profound impact on global biogeochemistry and climate by affecting exchange processes between the geosphere and atmosphere (8). From a phylogenetic perspective the order Planctomycetales forms an independent, monophyletic phylum of the domain Bacteria (9). It has recently been suggested to be the deepest branching bacterial phylum (10). Planctomycetes are unique in many other respects. Their cell walls do not contain peptidoglycan, the main structural polymer of most members of the domain Bacteria. They show a unique cell compartmentalization in which a single membrane separates a peripheral ribosome-free paryphoplasm from the inner riboplasm (pirellulosome). Within the riboplasm, all planctomycetes contain a condensed fibrillar nucleoid, which in Gemmata spp. is surrounded by a additional double membrane (11). These structures, together with an unusual fatty acid composition of the phospholipids, resemble eukaryotes rather than a representative of the bacterial domain (12).Characteristic for Planctomycetales are the polar cell organization and a life cycle with a polar, yeast-like cell division. Cells attach to surfaces at their vegetative poles by means of an excreted holdfast substance or stalks (13). Further unusual features are the crateriform structures on the cell surface of all planctomycetes (14). They appear as...

Proteomic analysis of carbohydrate catabolism and regulation in the marine bacteriumRhodopirellula baltica

“…Expression level prediction based on codon usage optimization was calculated for each gene in the R. baltica genome according to the method described by Karlin et al [43]. Highly expressed reference genes including ribosomal proteins, translation factors and chaperonins were extracted from the published annotation of R. baltica [26].…”

“…The category "metabolism" was further divided into eight sub-categories ( Table 2). The sub-category "sulfatases" was used, since the presence of 110 sulfatase-encoding genes was one of the major unexpected findings from the annotation of the R. baltica genome [26], 10 of which were identified on the gel. The pattern of identified proteins displayed in Fig.…”

“…Manual removal of presumably overpredicted ORFs resulted in the published set of 7325 ORF (BX119912) [26]. Thus, the possibility exists that ORFs were initially not predicted or were erroneously removed during manual refinement.…”

Evolution of the mannose-binding lectin gene in primates

“…11 MBL2 polymorphisms have been shown to be associated with increased risk of infection 12,13 and to alter the phenotypic expression of autoimmune diseases. 14,15 MBLs are proved to be common in the entire evolutionary scale, from bacteria, 16 to plants, to humans, while structural homologs of MBL2 have been found in several mammals (including humans, cow, 17 pig, 18 rabbit, 19 mouse 20 and rat 21 ), in chickens 22 and also in fishes. 23 A possible homolog has even been found in the tunicate, Styela plicata, 24 but MBL2, structurally speaking, is a typical vertebrate protein.…”

Proteomics of marine bacteria

“…The analysis of the genome sequences of the different P. marinus strains led to the identification of genes, which play a role in determining the relative fitness of the ecotypes in response to key environmental variables [11]. Glöckner et al [13] reported the complete genome sequence of Pirellula sp. strain 1 ('Rhodopirellula baltica SH1'), a marine representative of the globally distributed and environmentally important bacterial order Planctomycetales.…”