| evidence for unlinked rrn operons in the planctomycete pirellula marina. | southern hybridization of rrnas to chromosomal bamhi-digested dna of the eubacterium pirellula marina revealed the presence of two sets of 16s and 23s rrna genes. the two copies of the 23s rrna genes, located on 11- and about 13-kilobase (kb) inserts, were isolated from a lambda bacteriophage charon 35 library. the 11-kb fragment was cloned directly into pbr322, while a 5.4-kb bamhi-psti rdna subfragment of the approximately 13-kb insert was cloned into puc18. both recombinant plasmids, ppi1100 ... | 1989 | 2768196 |
| complete nucleotide sequence of a 23s ribosomal rna gene from pirellula marina. | | 1988 | 3387225 |
| screening of a fosmid library of marine environmental genomic dna fragments reveals four clones related to members of the order planctomycetales. | a fosmid library with inserts containing approximately 40 kb of marine bacterial dna (j. l. stein, t. l. marsh, k. y. wu, h. shizuya, and e. f. delong, j. bacteriol. 178:591-599, 1996) yielded four clones with 16s rrna genes from the order planctomycetales. three of the clones belong to the pirellula group and one clone belongs to the planctomyces group, based on phylogenetic and signature nucleotide analyses of full-length 16s rrna genes. sequence analysis of the ends of the genes revealed a co ... | 1998 | 9687477 |
| direct analysis of genes encoding 16s rrna from complex communities reveals many novel molecular species within the human gut. | the human intestinal tract harbors a complex microbial ecosystem which plays a key role in nutrition and health. although this microbiota has been studied in great detail by culture techniques, microscopic counts on human feces suggest that 60 to 80% of the observable bacteria cannot be cultivated. using comparative analysis of cloned 16s rrna gene (rdna) sequences, we have investigated the bacterial diversity (both cultivated and noncultivated bacteria) within an adult-male fecal sample. the 28 ... | 1999 | 10543789 |
| quantitative molecular analysis of the microbial community in marine arctic sediments (svalbard). | fluorescence in situ hybridization (fish) and rrna slot blot hybridization with 16s rrna-targeted oligonucleotide probes were used to investigate the phylogenetic composition of a marine arctic sediment (svalbard). fish resulted in the detection of a large fraction of microbes living in the top 5 cm of the sediment. up to 65.4% +/- 7.5% of total dapi (4',6'-diamidino-2-phenylindole) cell counts hybridized to the bacterial probe eub338, and up to 4.9% +/- 1.5% hybridized to the archaeal probe arc ... | 2001 | 11133470 |
| novel bacterial lineages at the (sub)division level as detected by signature nucleotide-targeted recovery of 16s rrna genes from bulk soil and rice roots of flooded rice microcosms. | using a newly developed 16s rrna gene (rdna)-targeted pcr assay with proposed group specificity for planctomycetes, we examined anoxic bulk soil of flooded rice microcosms for the presence of novel planctomycete-like diversity. for comparison, oxic rice roots were included as an additional sample in this investigation. the bacterial diversity detectable by this pcr assay was assessed by using a combined approach that included terminal restriction fragment length polymorphism (t-rflp) analysis an ... | 2001 | 11157225 |
| bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16s ribosomal dna sequencing. | we investigated the bacterial community structure in an aerated plug-flow lagoon treating pulp and paper mill effluent. for this investigation, we developed a composite method based on analyses of pcr amplicons containing the ribosomal intergenic spacer (ris) and its flanking partial 16s rrna gene. community percent similarity was determined on the basis of ris length polymorphism. a community succession was evident in the lagoon, indicated by a progressive community transition through seven sam ... | 2001 | 11282606 |
| new degenerate cytophaga-flexibacter-bacteroides-specific 16s ribosomal dna-targeted oligonucleotide probes reveal high bacterial diversity in river taff epilithon. | river microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. in this study the bacterial diversity of river taff epilithon in south wales was investigated. a 16s ribosomal dna (rdna) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. the epilithon was found to be very diverse, with an estimated 59.6% of the bacteri ... | 2002 | 11772628 |
| culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. | the phylogenetic diversity of the intestinal bacterial community in pigs was studied by comparative 16s ribosomal dna (rdna) sequence analysis. samples were collected from a total of 24 pigs representing a variety of diets, ages, and herd health status. a library comprising 4,270 cloned 16s rdna sequences obtained directly by pcr from 52 samples of either the ileum, the cecum, or the colon was constructed. in total, 375 phylotypes were identified using a 97% similarity criterion. three hundred n ... | 2002 | 11823207 |
| gene discovery within the planctomycete division of the domain bacteria using sequence tags from genomic dna libraries. | the planctomycetes comprise a distinct group of the domain bacteria, forming a separate division by phylogenetic analysis. the organization of their cells into membrane-defined compartments including membrane-bounded nucleoids, their budding reproduction and complete absence of peptidoglycan distinguish them from most other bacteria. a random sequencing approach was applied to the genomes of two planctomycete species, gemmata obscuriglobus and pirellula marina, to discover genes relevant to thei ... | 2002 | 12093378 |
| 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 |
| products transcribed from rearranged rrn genes of escherichia coli can assemble to form functional ribosomes. | to examine the flexibility of rrna operons with respect to fundamental organization, transcription, processing, and assembly of ribosomes, operon variations were introduced by a plasmid into an escherichia coli strain that has deletions of all chromosomal copies of rrna genes. in the reconstructed operons, a salmonella intervening sequence (ivs) from 23s helix 45 was introduced into the e. coli 23s gene at the same position. three different constructs of the e. coli 16s gene were then placed who ... | 2003 | 14617656 |
| molecular evidence for novel planctomycete diversity in a municipal wastewater treatment plant. | we examined anoxic and aerobic basins and an anaerobic digestor of a municipal wastewater treatment plant for the presence of novel planctomycete-like diversity. three 16s rrna gene libraries were constructed by using a 16s rrna-targeted universal reverse primer and a forward pcr primer specific for planctomyces: phylogenetic analysis of 234 16s rrna gene sequences defined 110 operational taxonomic units. the majority of these sequences clustered with the four known genera, pirellula (32%), plan ... | 2003 | 14660385 |
| discovery of the novel candidate phylum "poribacteria" in marine sponges. | marine sponges (porifera) harbor large amounts of commensal microbial communities within the sponge mesohyl. we employed 16s rrna gene library construction using specific pcr primers to provide insights into the phylogenetic identity of an abundant sponge-associated bacterium that is morphologically characterized by the presence of a membrane-bound nucleoid. in this study, we report the presence of a previously unrecognized evolutionary lineage branching deeply in the domain bacteria that is mod ... | 2004 | 15184179 |
| specific detection, isolation, and characterization of selected, previously uncultured members of the freshwater bacterioplankton community. | high-throughput cultivation was combined with rapid and group-specific phylogenetic fingerprinting in order to recover representatives of three freshwater bacterioplankton communities. a total of 570 bacterial cultures were obtained by employing the most probable number and microdrop techniques. the majority of the cultured bacteria were closely related to previously uncultured bacteria and grouped with the alpha-proteobacteria, beta-proteobacteria, actinobacteria, firmicutes, or flavobacteria-c ... | 2005 | 16204504 |
| 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 |
| metagenomics of the deep mediterranean, a warm bathypelagic habitat. | metagenomics is emerging as a powerful method to study the function and physiology of the unexplored microbial biosphere, and is causing us to re-evaluate basic precepts of microbial ecology and evolution. most marine metagenomic analyses have been nearly exclusively devoted to photic waters. | 2007 | 17878949 |
| evolution and functional characterization of the rh50 gene from the ammonia-oxidizing bacterium nitrosomonas europaea. | the family of ammonia and ammonium channel proteins comprises the amt proteins, which are present in all three domains of life with the notable exception of vertebrates, and the homologous rh proteins (rh50 and rh30) that have been described thus far only in eukaryotes. the existence of an rh50 gene in bacteria was first revealed by the genome sequencing of the ammonia-oxidizing bacterium nitrosomonas europaea. here we have used a phylogenetic approach to study the evolution of the n. europaea r ... | 2007 | 17921289 |
| genome evolution and the emergence of fruiting body development in myxococcus xanthus. | lateral gene transfer (lgt) is thought to promote speciation in bacteria, though well-defined examples have not been put forward. | 2007 | 18159227 |
| characterization and evolution of cell division and cell wall synthesis genes in the bacterial phyla verrucomicrobia, lentisphaerae, chlamydiae, and planctomycetes and phylogenetic comparison with rrna genes. | in the past, studies on the relationships of the bacterial phyla planctomycetes, chlamydiae, lentisphaerae, and verrucomicrobia using different phylogenetic markers have been controversial. investigations based on 16s rrna sequence analyses suggested a relationship of the four phyla, showing the branching order planctomycetes, chlamydiae, verrucomicrobia/lentisphaerae. phylogenetic analyses of 23s rrna genes in this study also support a monophyletic grouping and their branching order--this group ... | 2008 | 18310338 |
| phylum verrucomicrobia representatives share a compartmentalized cell plan with members of bacterial phylum planctomycetes. | the phylum verrucomicrobia is a divergent phylum within domain bacteria including members of the microbial communities of soil and fresh and marine waters; recently extremely acidophilic members from hot springs have been found to oxidize methane. at least one genus, prosthecobacter, includes species with genes homologous to those encoding eukaryotic tubulins. a significant superphylum relationship of verrucomicrobia with members of phylum planctomycetes possessing a unique compartmentalized cel ... | 2009 | 19133117 |
| high abundance of virulence gene homologues in marine bacteria. | marine bacteria can cause harm to single-celled and multicellular eukaryotes. however, relatively little is known about the underlying genetic basis for marine bacterial interactions with higher organisms. we examined whole-genome sequences from a large number of marine bacteria for the prevalence of homologues to virulence genes and pathogenicity islands known from bacteria that are pathogenic to terrestrial animals and plants. as many as 60 out of 119 genomes of marine bacteria, with no known ... | 2009 | 19207573 |
| the nana neuraminidase of streptococcus pneumoniae is involved in biofilm formation. | streptococcus pneumoniae remains a major cause of bacteremia, pneumonia, and otitis media despite vaccines and effective antibiotics. the neuraminidase of s. pneumoniae, which catalyzes the release of terminal sialic acid residues from glycoconjugates, is involved in host colonization in animal models of infection and may provide a novel target for preventing pneumococcal infection. we demonstrate that the s. pneumoniae neuraminidase (nana) cleaves sialic acid and show that it is involved in bio ... | 2009 | 19564377 |
| 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 |
| cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. | aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ... | 2009 | 19946135 |
| 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 |
| 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 |
| discovery and characterization of cadherin domains in saccharophagus degradans 2-40. | saccharophagus degradans strain 2-40 is a prominent member of newly discovered group of marine and estuarine bacteria that recycle complex polysaccharides. the s. degradans 2-40 genome codes for 15 extraordinary long polypeptides, ranging from 274 to 1,600 kda. five of these contain at least 52 cadherin (ca) and cadherin-like (cadg) domains, the types of which were reported to bind calcium ions and mediate protein/protein interactions in metazoan systems. in order to evaluate adhesive features o ... | 2010 | 20023015 |
| discovery and characterization of cadherin domains in saccharophagus degradans 2-40. | saccharophagus degradans strain 2-40 is a prominent member of newly discovered group of marine and estuarine bacteria that recycle complex polysaccharides. the s. degradans 2-40 genome codes for 15 extraordinary long polypeptides, ranging from 274 to 1,600 kda. five of these contain at least 52 cadherin (ca) and cadherin-like (cadg) domains, the types of which were reported to bind calcium ions and mediate protein/protein interactions in metazoan systems. in order to evaluate adhesive features o ... | 2010 | 20023015 |
| the compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins. | the development of the endomembrane system was a major step in eukaryotic evolution. membrane coats, which exhibit a unique arrangement of beta-propeller and alpha-helical repeat domains, play key roles in shaping eukaryotic membranes. such proteins are likely to have been present in the ancestral eukaryote but cannot be detected in prokaryotes using sequence-only searches. we have used a structure-based detection protocol to search all proteomes for proteins with this domain architecture. apart ... | 2010 | 20087413 |
| origin of the allyl group in fk506 biosynthesis. | fk506 (tacrolimus) is a secondary metabolite with a potent immunosuppressive activity, currently registered for use as immunosuppressant after organ transplantation. fk506 and fk520 are biogenetically related natural products that are synthesized by combined polyketide synthase/nonribosomal peptide synthetase systems. the entire gene cluster for biosynthesis of fk520 from streptomyces hygroscopicus var. ascomyceticus has been cloned and sequenced. on the other hand, the fk506 gene cluster from s ... | 2010 | 20194504 |
| cell biology of prokaryotic organelles. | mounting evidence in recent years has challenged the dogma that prokaryotes are simple and undefined cells devoid of an organized subcellular architecture. in fact, proteins once thought to be the purely eukaryotic inventions, including relatives of actin and tubulin control prokaryotic cell shape, dna segregation, and cytokinesis. similarly, compartmentalization, commonly noted as a distinguishing feature of eukaryotic cells, is also prevalent in the prokaryotic world in the form of protein-bou ... | 2010 | 20739411 |
| evolution and multiplicity of arginine decarboxylases in polyamine biosynthesis and essential role in bacillus subtilis biofilm formation. | arginine decarboxylases (adcs; ec 4.1.1.19) from four different protein fold families are important for polyamine biosynthesis in bacteria, archaea, and plants. biosynthetic alanine racemase fold (ar-fold) adc is widespread in bacteria and plants. we report the discovery and characterization of an ancestral form of the ar-fold adc in the bacterial chloroflexi and bacteroidetes phyla. the ancestral ar-fold adc lacks a large insertion found in escherichia coli and plant ar-fold adc and is more sim ... | 2010 | 20876533 |
| 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 |
| genome-wide influence of indel substitutions on evolution of bacteria of the pvc superphylum, revealed using a novel computational method. | whole-genome scans for positive darwinian selection are widely used to detect evolution of genome novelty. most approaches are based on evaluation of nonsynonymous to synonymous substitution rate ratio across evolutionary lineages. these methods are sensitive to saturation of synonymous sites and thus cannot be used to study evolution of distantly related organisms. in contrast, indels occur less frequently than amino acid replacements, accumulate more slowly, and can be employed to characterize ... | 2010 | 21048002 |
| complete genome sequence of pirellula staleyi type strain (atcc 27377). | pirellula staleyi schlesner and hirsch 1987 is the type species of the genus pirellula of the family planctomycetaceae. members of this pear- or teardrop-shaped bacterium show a clearly visible pointed attachment pole and can be distinguished from other planctomycetes by a lack of true stalks. strains closely related to the species have been isolated from fresh and brackish water, as well as from hypersaline lakes. here we describe the features of this organism, together with the complete genome ... | 2009 | 21304671 |
| a novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and dna viral systems. | the use of nucleases as toxins for defense, offense or addiction of selfish elements is widely encountered across all life forms. using sensitive sequence profile analysis methods, we characterize a novel superfamily (the sukh superfamily) that unites a diverse group of proteins including smi1/knr4, pgs2, fbxo3, skip16, syd, herpesviral us22, irs1 and trs1, and their bacterial homologs. using contextual analysis we present evidence that the bacterial members of this superfamily are potential imm ... | 2011 | 21306995 |
| temporal variability of coastal planctomycetes clades at station kabeltonne, north sea. | members of the bacterial phylum planctomycetes are reported in marine water samples worldwide but quantitative information is scarce. here we investigated the phylogenetic diversity, abundance and distribution of planctomycetes in surface waters off the german north sea island helgoland during different seasons by 16s ribosomal rna (rrna) gene analysis and catalyzed reporter deposition fluorescence in situ hybridization (card-fish). generally planctomycetes are more abundant in summer and autumn ... | 2011 | 21642408 |
| the atypical two-component sensor kinase lpl0330 from legionella pneumophila controls the bifunctional diguanylate cyclase-phosphodiesterase lpl0329 to modulate c-di-gmp synthesis. | a significant part of bacterial two-component system response regulators contain effector domains predicted to be involved in metabolism of c-di-gmp, a second messenger which plays a key role in many physiological processes. intracellular level of c-di-gmp is controlled by diguanylate cyclases (dgcs) and phosphodiesterases (pdes) activities associated with ggdef and eal domains, respectively. the legionella pneumophila lens genome displays 22 ggdef/eal domain-encoding genes. one of them, lpl0329 ... | 2011 | 21757706 |
| Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria. | Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2?m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this clus ... | 2011 | 22189493 |
| Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria. | Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2?m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this clus ... | 2011 | 22189493 |
| structure and molecular evolution of cdgsh iron-sulfur domains. | the recently discovered cdgsh iron-sulfur domains (cisds) are classified into seven major types with a wide distribution throughout the three domains of life. the type 1 protein mitoneet has been shown to fold into a dimer with the signature cdgsh motif binding to a [2fe-2s] cluster. however, the structures of all other types of cisds were unknown. here we report the crystal structures of type 3, 4, and 6 cisds determined at 1.5 å, 1.8 å and 1.15 å resolution, respectively. the type 3 and 4 cisd ... | 2011 | 21949752 |
| an exceptional horizontal gene transfer in plastids: gene replacement by a distant bacterial paralog and evidence that haptophyte and cryptophyte plastids are sisters. | horizontal gene transfer (hgt) to the plant mitochondrial genome has recently been shown to occur at a surprisingly high rate; however, little evidence has been found for hgt to the plastid genome, despite extensive sequencing. in this study, we analyzed all genes from sequenced plastid genomes to unearth any neglected cases of hgt and to obtain a measure of the overall extent of hgt to the plastid. | 2006 | 16956407 |
| composition and dynamics of bacterial communities of a drinking water supply system as assessed by rna- and dna-based 16s rrna gene fingerprinting. | bacterial community dynamics of a whole drinking water supply system (dwss) were studied from source to tap. raw water for this dwss is provided by two reservoirs with different water characteristics in the harz mountains of northern germany. samples were taken after different steps of treatment of raw water (i.e., flocculation, sand filtration, and chlorination) and at different points along the supply system to the tap. rna and dna were extracted from the sampled water. the 16s rrna or its gen ... | 2006 | 16517632 |
| metagenomic analysis of a southern maritime antarctic soil. | our current understanding of antarctic soils is derived from direct culture on selective media, biodiversity studies based on clone library construction and analysis, quantitative pcr amplification of specific gene sequences and the application of generic microarrays for microbial community analysis. here, we investigated the biodiversity and functional potential of a soil community at mars oasis on alexander island in the southern maritime antarctic, by applying 454 pyrosequencing technology to ... | 2012 | 23227023 |
| analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. | the planctomycetes, verrucomicrobia, chlamydiae (pvc) super-phylum contains bacteria with either complex cellular organization or simple cell structure; it also includes organisms of different lifestyles (pathogens, mutualists, commensal, and free-living). genome content evolution of this group has not been studied in a systematic fashion, which would reveal genes underlying the emergence of pvc-specific phenotypes. here, we analyzed the evolutionary dynamics of 26 pvc genomes and several outgro ... | 2012 | 23221607 |
| development of genetic tools for the manipulation of the planctomycetes. | bacteria belonging to the planctomycetes, verrucomicrobia, chlamydiae (pvc) superphylum are of interest for biotechnology, evolutionary cell biology, ecology, and human health. some pvc species lack a number of typical bacterial features while others possess characteristics that are usually more associated to eukaryotes or archaea. for example, the planctomycetes phylum is atypical for the absence of the ftsz protein and for the presence of a developed endomembrane system. studies of the cellula ... | 2016 | 27379046 |
| phylogeny of rieske/cytb complexes with a special focus on the haloarchaeal enzymes. | rieske/cytochrome b (rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and archaea. the phylogeny of their subunits follows closely the 16s-rrna phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of archaea and bacteria. haloarchaea are the only organisms found so far that acquired rieske/cytb complexes via interdomain lateral gene transfer. they encode two rieske/cytb complexes in their genomes; on ... | 2012 | 22798450 |
| noncellulosomal cohesin- and dockerin-like modules in the three domains of life. | the high-affinity cohesin-dockerin interaction was originally discovered as modular components, which mediate the assembly of the various subunits of the multienzyme cellulosome complex that characterizes some cellulolytic bacteria. until recently, the presence of cohesins and dockerins within a bacterial proteome was considered a definitive signature of a cellulosome-producing bacterium. widespread genome sequencing has since revealed a wealth of putative cohesin- and dockerin-containing protei ... | 2009 | 19025568 |
| noncellulosomal cohesin- and dockerin-like modules in the three domains of life. | the high-affinity cohesin-dockerin interaction was originally discovered as modular components, which mediate the assembly of the various subunits of the multienzyme cellulosome complex that characterizes some cellulolytic bacteria. until recently, the presence of cohesins and dockerins within a bacterial proteome was considered a definitive signature of a cellulosome-producing bacterium. widespread genome sequencing has since revealed a wealth of putative cohesin- and dockerin-containing protei ... | 2009 | 19025568 |
| the aspergillus fumigatus dihydroxyacid dehydratase ilv3a/ilvc is required for full virulence. | dihydroxyacid dehydratase (dhad) is a key enzyme in the branched-chain amino acid biosynthetic pathway that exists in a variety of organisms, including fungi, plants and bacteria, but not humans. in this study we identified four putative dhad genes from the filamentous fungus aspergillus fumigatus by homology to saccharomyces cerevisiae ilv3. two of these genes, afua_2g14210 and afua_1g03550, initially designated afilv3a and afilv3b for this study, clustered in the same group as s. cerevisiae il ... | 2012 | 23028460 |
| related giant viruses in distant locations and different habitats: acanthamoeba polyphaga moumouvirus represents a third lineage of the mimiviridae that is close to the megavirus lineage. | the 1,021,348 base pair genome sequence of the acanthamoeba polyphaga moumouvirus, a new member of the mimiviridae family infecting acanthamoeba polyphaga, is reported. the moumouvirus represents a third lineage beside mimivirus and megavirus. thereby, it is a new member of the recently proposed megavirales order. this giant virus was isolated from a cooling tower water in southeastern france but is most closely related to megavirus chiliensis, which was isolated from ocean water off the coast o ... | 2012 | 23221609 |
| structure, fluctuation and magnitude of a natural grassland soil metagenome. | the soil ecosystem is critical for human health, affecting aspects of the environment from key agricultural and edaphic parameters to critical influence on climate change. soil has more unknown biodiversity than any other ecosystem. we have applied diverse dna extraction methods coupled with high throughput pyrosequencing to explore 4.88 × 10(9) bp of metagenomic sequence data from the longest continually studied soil environment (park grass experiment at rothamsted research in the uk). results ... | 2012 | 22297556 |
| type i pyridoxal 5'-phosphate dependent enzymatic domains embedded within multimodular nonribosomal peptide synthetase and polyketide synthase assembly lines. | pyridoxal 5'-phosphate (plp)-dependent enzymes of fold type i, the most studied structural class of the plp-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. these enzymes have been found also embedded in multimodular and multidomain assembly lines involved in the biosynthesis of polyketides (pks) and nonribosomal peptides (nrps). the aim of this work is to provide a proteome-wide view of the distribution and characteristics of type i domains covalently ... | 2013 | 24148833 |
| beating the acetyl coenzyme a-pathway to the origin of life. | attempts to draft plausible scenarios for the origin of life have in the past mainly built upon palaeogeochemical boundary conditions while, as detailed in a companion article in this issue, frequently neglecting to comply with fundamental thermodynamic laws. even if demands from both palaeogeochemistry and thermodynamics are respected, then a plethora of strongly differing models are still conceivable. although we have no guarantee that life at its origin necessarily resembled biology in extant ... | 2013 | 23754811 |
| the gain and loss of chromosomal integron systems in the treponema species. | integron systems are now recognized as important agents of bacterial evolution and are prevalent in most environments. one of the human pathogens known to harbor chromosomal integrons, the treponema spirochetes are the only clade among spirochete species found to carry integrons. with the recent release of many new treponema genomes, we were able to study the distribution of chromosomal integrons in this genus. | 2013 | 23339550 |
| identification of a mammalian-type phosphatidylglycerophosphate phosphatase in the eubacterium rhodopirellula baltica. | cardiolipin is a glycerophospholipid found predominantly in the mitochondrial membranes of eukaryotes and in bacterial membranes. cardiolipin interacts with protein complexes and plays pivotal roles in cellular energy metabolism, membrane dynamics, and stress responses. we recently identified the mitochondrial phosphatase, ptpmt1, as the enzyme that converts phosphatidylglycerolphosphate (pgp) to phosphatidylglycerol, a critical step in the de novo biosynthesis of cardiolipin. upon examination o ... | 2013 | 23293031 |
| molecular detection of bacteria in plant tissues, using universal 16s ribosomal dna degenerated primers. | highly specific, sensitive and rapid tests are required for the detection and identification of covert bacterial contaminations in plant tissue cultures. current methods available for this purpose are tedious, time consuming, highly error prone, expensive, require advanced technical expertise and are sometimes ineffective. we report here the development of a sensitive polymerase chain reaction (pcr) based method for the rapid detection and identification of bacteria occurring in plant tissue cul ... | 2014 | 26019546 |
| the molecular evolution of the qo motif. | quinol oxidation in the catalytic quinol oxidation site (q(o) site) of cytochrome (cyt) bc(1) complexes is the key step of the q cycle mechanism, which laid the ground for mitchell's chemiosmotic theory of energy conversion. bifurcated electron transfer upon quinol oxidation enables proton uptake and release on opposite membrane sides, thus generating a proton gradient that fuels atp synthesis in cellular respiration and photosynthesis. the q(o) site architecture formed by cyt b and rieske iron- ... | 2014 | 25115012 |
| genome-based taxonomic classification of bacteroidetes. | the bacterial phylum bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16s rrna gene sequence. here we use a large collection of type-strain genomes from bacteroidetes and closely related ... | 2016 | 28066339 |
| novel transglutaminase-like peptidase and c2 domains elucidate the structure, biogenesis and evolution of the ciliary compartment. | in addition to their role in motility, eukaryotic cilia serve as a distinct compartment for signal transduction and regulatory sequestration of biomolecules. recent genetic and biochemical studies have revealed an extraordinary diversity of protein complexes involved in the biogenesis of cilia during each cell cycle. mutations in components of these complexes are at the heart of human ciliopathies such as nephronophthisis (nphp), meckel-gruber syndrome (mks), bardet-biedl syndrome (bbs) and joub ... | 2012 | 22983010 |
| two new families of the ftsz-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea. | several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the ftsz-tubulin superfamily. one of these families is limited in its spread to proteobacteria whereas the other is represented in ... | 2010 | 20459678 |
| natural history of the e1-like superfamily: implication for adenylation, sulfur transfer, and ubiquitin conjugation. | the e1-like superfamily is central to ubiquitin (ub) conjugation, biosynthesis of cysteine, thiamine, and moco, and several secondary metabolites. yet, its functional diversity and evolutionary history is not well understood. we develop a natural classification of this superfamily and use it to decipher the major adaptive trends occurring in the evolution of the e1-like superfamily. within the rossmann fold, e1-like proteins are closest to nad(p)/fad-dependent dehydrogenases and s-adomet-depende ... | 2009 | 19089947 |
| transcriptional regulation of nad metabolism in bacteria: nrtr family of nudix-related regulators. | a novel family of transcription factors responsible for regulation of various aspects of nad synthesis in a broad range of bacteria was identified by comparative genomics approach. regulators of this family (here termed nrtr for nudix-related transcriptional regulators), currently annotated as adp-ribose pyrophosphatases from the nudix family, are composed of an n-terminal nudix-like effector domain and a c-terminal dna-binding hth-like domain. nrtr regulons were reconstructed in diverse bacteri ... | 2008 | 18276643 |
| a novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands. | domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. | 2007 | 17250770 |
| searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis. | there are numerous examples of convergent evolution in nature. major ecological adaptations such as flight, loss of limbs in vertebrates, pesticide resistance, adaptation to a parasitic way of life, etc., have all evolved more than once, as seen by their analogous functions in separate taxa. but what about protein evolution? does the environment have a strong enough influence on intracellular processes that enzymes and other functional proteins play, to evolve similar functional roles separately ... | 2014 | 25071412 |
| complete genome sequence of planctomyces brasiliensis type strain (dsm 5305(t)), phylogenomic analysis and reclassification of planctomycetes including the descriptions of gimesia gen. nov., planctopirus gen. nov. and rubinisphaera gen. nov. and emended descriptions of the order planctomycetales and the family planctomycetaceae. | planctomyces brasiliensis schlesner 1990 belongs to the order planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall consisting of a proteinaceous layer rather than a peptidoglycan layer. the first strains of p. brasiliensis, including the type strain ifam 1448(t), were isolated from a water sample of lagoa ver ... | 2014 | 25780503 |
| bringing planctomycetes into pure culture. | planctomycetes have been known since the description of planctomyces bekefii by gimesi at the beginning of the twentieth century (1924), although the first axenic cultures were only obtained in the 1970s. since then, 11 genera with 14 species have been validly named and five candidatus genera belonging to the anaerobic ammonium oxidation, anammox bacteria have also been discovered. however, planctomycetes diversity is much broader than these numbers indicate, as shown by environmental molecular ... | 2012 | 23335915 |
| genome analysis of planctomycetes inhabiting blades of the red alga porphyra umbilicalis. | porphyra is a macrophytic red alga of the bangiales that is important ecologically and economically. we describe the genomes of three bacteria in the phylum planctomycetes (designated p1, p2 and p3) that were isolated from blades of porphyra umbilicalis (p.um.1). these three operational taxonomic units (otus) belong to distinct genera; p2 belongs to the genus rhodopirellula, while p1 and p3 represent undescribed genera within the planctomycetes. comparative analyses of the p1, p2 and p3 genomes ... | 2016 | 27015628 |
| genomic evolution of 11 type strains within family planctomycetaceae. | the species in family planctomycetaceae are ideal groups for investigating the origin of eukaryotes. their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. however, their genomic structures, potential abilities, and evolutionary status are still unknown. in this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family planctomycetaceae. then, we constructed phyl ... | 2014 | 24489782 |
| massive expansion of ubiquitination-related gene families within the chlamydiae. | gene loss, gain, and transfer play an important role in shaping the genomes of all organisms; however, the interplay of these processes in isolated populations, such as in obligate intracellular bacteria, is less understood. despite a general trend towards genome reduction in these microbes, our phylogenomic analysis of the phylum chlamydiae revealed that within the family parachlamydiaceae, gene family expansions have had pronounced effects on gene content. we discovered that the largest gene f ... | 2014 | 25069652 |
| biogeography of anaerobic ammonia-oxidizing (anammox) bacteria. | anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce n2 gas. after being discovered in a wastewater treatment plant (wwtp), anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. although anammox bacteria play an important role in removing fixed n from both engineered and natural ecosystems, broad scale anammox bacterial distributions have not yet been summarize ... | 2014 | 25147546 |
| bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, rhodopirellula baltica. | rhodopirellula baltica (r. baltica) is a planctomycete, known to have intracellular membranes. because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. the complete proteome of r. baltica was screened against the transporter classification database (tcdb) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into severa ... | 2013 | 23969110 |
| bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, rhodopirellula baltica. | rhodopirellula baltica (r. baltica) is a planctomycete, known to have intracellular membranes. because of its unusual cell structure and ecological significance, we have conducted comprehensive analyses of its transmembrane transport proteins. the complete proteome of r. baltica was screened against the transporter classification database (tcdb) to identify recognizable integral membrane transport proteins. 342 proteins were identified with a high degree of confidence, and these fell into severa ... | 2013 | 23969110 |
| genomic analysis indicates the presence of an asymmetric bilayer outer membrane in planctomycetes and verrucomicrobia. | bacteria of the phylum planctomycetes are of special interest for the study of compartmental cellular organization. members of this phylum share a very unusual prokaryotic cell plan, featuring several membrane-bound compartments. recently, it was shown that this cellular organization might extend to certain members of the phylum verrucomicrobia. the planctomycete cell plan has been defined as featuring a proteinaceous cell wall, a cytoplasmic membrane surrounding the paryphoplasm, and an intracy ... | 2012 | 22934092 |
| electron tomography of the nucleoid of gemmata obscuriglobus reveals complex liquid crystalline cholesteric structure. | the nucleoid of the planctomycete gemmata obscuriglobus is unique within the bacteria in being both highly condensed and enclosed by a double-membrane nuclear envelope, seemingly analogous to the nucleus of eukaryotes. here we have applied electron tomography to study high-pressure frozen, cryosubstituted cells of g. obscuriglobus and found multiple nested orders of dna organization within the condensed nucleoid structure. detailed examination of the nucleoid revealed a series of nested arcs cha ... | 2012 | 22993511 |
| molecular signatures for the pvc clade (planctomycetes, verrucomicrobia, chlamydiae, and lentisphaerae) of bacteria provide insights into their evolutionary relationships. | the pvc superphylum is an amalgamation of species from the phyla planctomycetes, verrucomicrobia, and chlamydiae, along with the lentisphaerae, poribacteria, and two other candidate divisions. the diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. recently, genome sequences for 37 species covering all of the main pvc groups of bacteria have become available. we have used these sequences to construct a phylogenetic tree based upon concate ... | 2012 | 23060863 |
| identification of proteins likely to be involved in morphogenesis, cell division, and signal transduction in planctomycetes by comparative genomics. | members of the planctomycetes clade share many unusual features for bacteria. their cytoplasm contains membrane-bound compartments, they lack peptidoglycan and ftsz, they divide by polar budding, and they are capable of endocytosis. planctomycete genomes have remained enigmatic, generally being quite large (up to 9 mb), and on average, 55% of their predicted proteins are of unknown function. importantly, proteins related to the unusual traits of planctomycetes remain largely unknown. thus, we em ... | 2012 | 23002222 |
| the structure of a novel thermophilic esterase from the planctomycetes species, thermogutta terrifontis reveals an open active site due to a minimal 'cap' domain. | a carboxyl esterase (ttest2) has been identified in a novel thermophilic bacterium, thermogutta terrifontis from the phylum planctomycetes and has been cloned and over-expressed in escherichia coli. the enzyme has been characterized biochemically and shown to have activity toward small p-nitrophenyl (pnp) carboxylic esters with optimal activity for pnp-acetate. the enzyme shows moderate thermostability retaining 75% activity after incubation for 30 min at 70°c. the crystal structures have been d ... | 2015 | 26635762 |
| functional and genomic analyses of alpha-solenoid proteins. | alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (armadillo and heat repeats among others). while homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. we previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. here we improved the det ... | 2013 | 24278209 |
| fuerstia marisgermanicae gen. nov., sp. nov., an unusual member of the phylum planctomycetes from the german wadden sea. | members of the phylum planctomycetes are ubiquitous bacteria that dwell in aquatic and terrestrial habitats. while planctomycetal species are important players in the global carbon and nitrogen cycle, this phylum is still undersampled and only few genome sequences are available. here we describe strain nh11(t), a novel planctomycete obtained from a crustacean shell (wadden sea, germany). the phylogenetically closest related cultivated species is gimesia maris, sharing only 87% 16s rrna sequence ... | 2016 | 28066393 |
| biochemical characterization of a family 15 carbohydrate esterase from a bacterial marine arctic metagenome. | the glucuronoyl esterase enzymes of wood-degrading fungi (carbohydrate esterase family 15; ce15) form part of the hemicellulolytic and cellulolytic enzyme systems that break down plant biomass, and have possible applications in biotechnology. homologous enzymes are predicted in the genomes of several bacteria, however these have been much less studied than their fungal counterparts. here we describe the recombinant production and biochemical characterization of a bacterial ce15 enzyme denoted mz ... | 2016 | 27433797 |