| complete genome sequence of the marine planctomycete pirellula sp. strain 1. | 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 w ... | 2003 | 12835416 |
| evaluation of the phylogenetic position of the planctomycete 'rhodopirellula baltica' sh 1 by means of concatenated ribosomal protein sequences, dna-directed rna polymerase subunit sequences and whole genome trees. | in recent years, the planctomycetes have been recognized as a phylum of environmentally important bacteria with habitats ranging from soil and freshwater to marine ecosystems. the planctomycetes form an independent phylum within the bacterial domain, whose exact phylogenetic position remains controversial. with the completion of sequencing of the genome of 'rhodopirellula baltica' sh 1, it is now possible to re-evaluate the phylogeny of the planctomycetes based on multiple genes and genome trees ... | 2004 | 15143026 |
| novel protein domains and motifs in the marine planctomycete rhodopirellula baltica. | the planctomycetes are a phylum of bacteria that have a unique cell compartmentalisation and yeast-like budding cell division and peptidoglycan-less proteinaceous cell walls. we wished to further our understanding of these unique organisms at the molecular level by searching for conserved amino acid sequence motifs and domains in the proteins encoded by rhodopirellula baltica. using blast and single-linkage clustering, we have discovered several new protein domains and sequence motifs in this pl ... | 2004 | 15251216 |
| taxonomic heterogeneity within the planctomycetales as derived by dna-dna hybridization, description of rhodopirellula baltica gen. nov., sp. nov., transfer of pirellula marina to the genus blastopirellula gen. nov. as blastopirellula marina comb. nov. and emended description of the genus pirellula. | ninety-seven strains of budding bacteria originating from various aquatic habitats and morphologically resembling planctomycetes were investigated taxonomically. taxonomic differentiation was based on dna-dna hybridization, physiological properties and chemotaxonomic tests. nineteen hybridization groups, containing 79 of the tested strains, were established. eighteen strains, however, did not fit into any of these groups. rhodopirellula baltica gen. nov., sp. nov. is described, with strain sh 1t ... | 2004 | 15388712 |
| the transcriptional regulator pool of the marine bacterium rhodopirellula baltica sh 1t as revealed by whole genome comparisons. | rhodopirellula baltica (strain sh 1t) is a free-living marine representative of the phylogenetically independent and environmentally relevant phylum planctomycetes. little is known about the regulatory strategies of free-living bacteria with large (7.15 mb) genomes. therefore, a consistent, quantitative and qualitative description was produced by comparing r. baltica's transcriptional regulator pool with that of 123 publicly available bacterial genomes. the overall results are congruous with ear ... | 2005 | 15621430 |
| archaea-like genes for c1-transfer enzymes in planctomycetes: phylogenetic implications of their unexpected presence in this phylum. | the unexpected presence of archaea-like genes for tetrahydromethanopterin (h4mpt)-dependent enzymes in the completely sequence geiome of the aerobic marine planctomycete pirellula sp. strain 1 ("rhodopirellula baltica") and in the currently sequenced genome of the aerobic freshwater planctomycete gemmata obscuriglobus strain uqm2246 revives the discussion on the origin of these genes in the bacterial domain. we compared the genomic arrangement of these genes in planctomyetes and methylotrophic p ... | 2004 | 15693614 |
| growth phase dependent regulation of protein composition in rhodopirellula baltica. | growth phase dependent changes of protein composition in the marine bacterium rhodopirellula baltica were quantitatively monitored by applying the two-dimensional difference gel electrophoresis (2d dige) technology. the number of regulated proteins (fold changes in protein abundance > absolute value(2)) increased from early (10) to late stationary growth phase (179), with fold changes reaching maximal values of 40. about 110 of these regulated protein spots were analysed by maldi-tof-ms and iden ... | 2005 | 16011746 |
| proteomic analysis of carbohydrate catabolism and regulation in the marine bacterium rhodopirellula baltica. | the marine bacterium rhodopirellula baltica is a model organism for aerobic carbohydrate degradation in marine systems, where polysaccharides represent the dominant components of biomass. on the basis of the genome sequence and a 2-d map of soluble proteins, the central catabolic routes of r. baltica were reconstructed. almost all enzymes of glycolysis and tca cycle were identified. in addition, almost all enzymes of the oxidative branch of the pentose phosphate cycle were detected. this proteom ... | 2005 | 16127727 |
| towards the proteome of the marine bacterium rhodopirellula baltica: mapping the soluble proteins. | the marine bacterium rhodopirellula baltica, a member of the phylum planctomycetes, has distinct morphological properties and contributes to remineralization of biomass in the natural environment. on the basis of its recently determined complete genome we investigated its proteome by 2-de and established a reference 2-de gel for the soluble protein fraction. approximately 1000 protein spots were excised from a colloidal coomassie-stained gel (ph 4-7), analyzed by maldi-ms and identified by pmf. ... | 2005 | 16127728 |
| highly enantioselective sec-alkyl sulfatase activity of the marine planctomycete rhodopirellula baltica shows retention of configuration. | | 2005 | 16161167 |
| biocatalytic approaches for the quantitative production of single stereoisomers from racemates. | strategies for the chemoenzymatic transformation of a racemate into a single stereoisomeric product in quantitative yield have been developed. a range of industrially relevant alpha-hydroxycarboxylic acids was deracemized in a stepwise fashion via lipase-catalysed enantioselective o-acylation, followed by mandelate racemase-catalysed racemization of the remaining non-reacted substrate enantiomer. alternatively, aliphatic alpha-hydroxycarboxylic acids were enzymatically isomerized using whole res ... | 2006 | 16545098 |
| analysis of the first genome fragment from the marine sponge-associated, novel candidate phylum poribacteria by environmental genomics. | the novel candidate phylum poribacteria is specifically associated with several marine demosponge genera. because no representatives of poribacteria have been cultivated, an environmental genomic approach was used to gain insights into genomic properties and possibly physiological/functional features of this elusive candidate division. in a large-insert library harbouring an estimated 1.1 gb of microbial community dna from aplysina aerophoba, a poribacteria-positive 16s rrna gene locus was ident ... | 2006 | 16584473 |
| whole-genome reciprocal blast analysis reveals that planctomycetes do not share an unusually large number of genes with eukarya and archaea. | the genome sequences of rhodopirellula baltica, formerly pirellula sp. strain 1, blastopirellula marina, gemmata obscuriglobus, and kuenenia stuttgartiensis were used in a series of pairwise reciprocal best-hit analyses to evaluate the contested evolutionary position of planctomycetes. contrary to previous reports which suggested that r. baltica had a high percentage of genes with closest matches to archaea and eukarya, we show here that these planctomycetes do not share an unusually large numbe ... | 2006 | 17021241 |
| phylogenetic and metabolic diversity of planctomycetes from anaerobic, sulfide- and sulfur-rich zodletone spring, oklahoma. | we investigated the phylogenetic diversity and metabolic capabilities of members of the phylum planctomycetes in the anaerobic, sulfide-saturated sediments of a mesophilic spring (zodletone spring) in southwestern oklahoma. culture-independent analyses of 16s rrna gene sequences generated using planctomycetes-biased primer pairs suggested that an extremely diverse community of planctomycetes is present at the spring. although sequences that are phylogenetically affiliated with cultured heterotro ... | 2007 | 17545322 |
| a novel anticoagulant protein with high affinity to blood coagulation factor va from tegillarca granosa. | a novel inhibitory protein against blood coagulation factor va (fva) was purified from muscle protein of granulated ark (tegillarca granosa, order arcoida, marine bivalvia) by consecutive fplc method using anion exchange and gel permeation chromatography. in the results of esiqtof tandem mass analysis and database research, it was revealed that the purified t. granosa anticoagulant protein (tgap) has 7.7 kda of molecular mass and its partial sequence, hthlqraphpnalgyhgk, has a high identity (64% ... | 2007 | 17927919 |
| expression, purification, crystallization and preliminary x-ray analysis of the polysaccharide lyase rb5312 from the marine planctomycete rhodopirellula baltica. | polysaccharide lyases belonging to family pl1 act on pectins. these anionic polymers are usually produced by terrestrial plants and therefore pectinolytic enzymes are not frequently observed in marine microorganisms. the protein rb5312 from the marine bacterium rhodopirellula baltica is distantly related to family pl1 pectate lyases, but its exact function is unclear. in this study, the expression and purification of a recombinant form of rb5312 are described. this protein was crystallized using ... | 2008 | 18323615 |
| detailed proteome analysis of growing cells of the planctomycete rhodopirellula baltica sh1t. | rhodopirellula baltica sh1(t), which was isolated from the water column of the kieler bight, a bay in the southwestern baltic sea, is a marine aerobic, heterotrophic representative of the ubiquitous bacterial phylum planctomycetes. we analyzed the r. baltica proteome by applying different preanalytical protein as well as peptide separation techniques (1-d and 2-de, hplc separation) prior to ms. that way, we could identify a total of 1115 nonredundant proteins from the intracellular proteome and ... | 2008 | 18340632 |
| different planctomycetes diversity patterns in latitudinal surface seawater of the open sea and in sediment. | the 16s rrna gene approach was applied to investigate the diversity of planctomycetes in latitudinal surface seawater of the western pacific ocean. the results revealed that the pirellula-rhodopirellula-blastopirellula clade dominated the planctomycetes community at all surface seawater sites while the minority genera gemmata and planctomyces were only found at sites h5 and h2 respectively. although the clone frequency of the prb clade seemed stable (between 83.3% and 94.1%) for all surface seaw ... | 2008 | 18545964 |
| an improved isolation method for attached-living planctomycetes of the genus rhodopirellula. | rhodopirellula baltica, an attached-living marine bacterium, was so far isolated as aerobic, heterotrophic bacterium forming pink-to-red colonies on ampicillin-containing plates. but many bacteria grow in the presence of ampicillin: marine samples from european seas contained on average 10,365 colony forming bacteria per ml water sample or sediment. therefore we developed an improved enrichment protocol to isolate rhodopirellula strains. to include attached-living bacteria, particles, plankton c ... | 2009 | 19303037 |
| biochemical characterization of haloalkane dehalogenases drba and dmbc, representatives of a novel subfamily. | this study focuses on two representatives of experimentally uncharacterized haloalkane dehalogenases from the subfamily hld-iii. we report biochemical characterization of the expression products of haloalkane dehalogenase genes drba from rhodopirellula baltica sh1 and dmbc from mycobacterium bovis 5033/66. the drba and dmbc enzymes show highly oligomeric structures and very low activities with typical substrates of haloalkane dehalogenases. | 2009 | 19502442 |
| detection and widespread distribution of the nrfa gene encoding nitrite reduction to ammonia, a short circuit in the biological nitrogen cycle that competes with denitrification. | degenerate primers to detect nrfa were designed by aligning six nrfa sequences including escherichia coli k-12, sulfurospirillum deleyianum and wolinella succinogenes. these primers amplified a 490 bp fragment of nrfa. the ability of these primers to detect nrfa was tested with chromosomal dna isolated from a variety of bacteria: they could distinguish between bacteria in which the gene is known to be present or absent. the positive reference organisms spanned the various classes of proteobacter ... | 2004 | 19712292 |
| transcriptional response of the model planctomycete rhodopirellula baltica sh1(t) to changing environmental conditions. | the marine model organism rhodopirellula baltica sh1(t) was the first planctomycete to have its genome completely sequenced. the genome analysis predicted a complex lifestyle and a variety of genetic opportunities to adapt to the marine environment. its adaptation to environmental stressors was studied by transcriptional profiling using a whole genome microarray. | 2009 | 19725962 |
| jane: efficient mapping of prokaryotic ests and variable length sequence reads on related template genomes. | ests or variable sequence reads can be available in prokaryotic studies well before a complete genome is known. use cases include (i) transcriptome studies or (ii) single cell sequencing of bacteria. without suitable software their further analysis and mapping would have to await finalization of the corresponding genome. | 2009 | 19943962 |
| determination of the diversity of rhodopirellula isolates from european seas by multilocus sequence analysis. | in the biogeography of microorganisms, the habitat size of an attached-living bacterium has never been investigated. we approached this theme with a multilocus sequence analysis (mlsa) study of new strains of rhodopirellula sp., an attached-living planctomycete. the development of an mlsa for rhodopirellula baltica enabled the characterization of the genetic diversity at the species level, beyond the resolution of the 16s rrna gene. the alleles of the nine housekeeping genes acsa, guaa, trpe, pu ... | 2010 | 19948850 |
| broad-spectrum antibiotic resistance of planctomycetes organisms determined by etest. | the in vitro susceptibility of planctomycetes organisms to antibiotics has seldom been studied and when it has, a variety of methods have been used. the objective of the study was to expand the knowledge of planctomycetes antibiotic susceptibility patterns. | 2010 | 20699245 |
| planctomycetes dominate biofilms on surfaces of the kelp laminaria hyperborea. | bacteria belonging to planctomycetes display several unique morphological and genetic features and are found in a wide variety of habitats on earth. their ecological roles in these habitats are still poorly understood. planctomycetes have previously been detected throughout the year on surfaces of the kelp laminaria hyperborea from southwestern norway. we aimed to make a detailed investigation of the abundance and phylogenetic diversity of planctomycetes inhabiting these kelp surfaces. | 2010 | 20950420 |
| life cycle analysis of the model organism rhodopirellula baltica sh 1(t) by transcriptome studies. | the marine organism rhodopirellula baltica is a representative of the globally distributed phylum planctomycetes whose members exhibit an intriguing lifestyle and cell morphology. the analysis of r. baltica's genome has revealed many biotechnologically promising features including a set of unique sulfatases and c1-metabolism genes. salt resistance and the potential for adhesion in the adult phase of the cell cycle were observed during cultivation. to promote the understanding of this model organ ... | 2010 | 21255355 |
| ammonium and attachment of rhodopirellula baltica. | a dimorphic life cycle has been described for the planctomycete rhodopirellula baltica sh1(t), with juvenile motile, free-swimming cells and adult sessile, attached-living cells. however, attachment as a response to environmental factors was not investigated. we studied the response of r. baltica to nitrogen limitation. in batch cultures, ammonium limitation coincided with a dominance of free-swimming cells and a low number of aggregates. flow cytometry revealed a quantitative shift with increas ... | 2011 | 21340506 |
| Planctomycetes diversity associated with macroalgae. | Planctomycetes associated with 12 macroalgae from the north coast of Portugal were isolated, using an improved method. A total of 138 isolates were found to comprise 10 operational taxonomic units (OTUs), with 65% of the strains being closely related to the species Rhodopirellula baltica. The other strains are probably new species or genera related to Rhodopirellula, Blastopirellula and Planctomyces. Some of the OTUs isolated are unique and have never been found before in previous studies. Catal ... | 2011 | 21726244 |