| physical map of the genome of planctomyces limnophilus, a representative of the phylogenetically distinct planctomycete lineage. | 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 c ... | 1996 | 8606164 |
| 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 |
| 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 |
| 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 |
| emerging roles for the ro 60-kda autoantigen in noncoding rna metabolism. | all cells contain an enormous variety of ribonucleoprotein (rnp) complexes that function in diverse processes. although the mechanisms by which many of these rnps contribute to cell metabolism are well understood, the roles of others are only now beginning to be revealed. a member of this latter category, the ro 60-kda protein and its associated noncoding y rnas, was discovered because the protein component is a frequent target of the autoimmune response in patients with the rheumatic diseases s ... | 2011 | 21823229 |
| cluster k mycobacteriophages: insights into the evolutionary origins of mycobacteriophage tm4. | five newly isolated mycobacteriophages--angelica, crimd, adephagia, anaya, and pixie--have similar genomic architectures to mycobacteriophage tm4, a previously characterized phage that is widely used in mycobacterial genetics. the nucleotide sequence similarities warrant grouping these into cluster k, with subdivision into three subclusters: k1, k2, and k3. although the overall genome architectures of these phages are similar, tm4 appears to have lost at least two segments of its genome, a centr ... | 2011 | 22053209 |
| characterization of planctomyces limnophilus and development of genetic tools for its manipulation establish it as a model species for the phylum planctomycetes. | planctomycetes represent a remarkable clade in the domain bacteria because they play crucial roles in global carbon and nitrogen cycles and display cellular structures that closely parallel those of eukaryotic cells. studies on planctomycetes have been hampered by the lack of genetic tools, which we developed for planctomyces limnophilus. | 2011 | 21724885 |
| widespread occurrence of secondary lipid biosynthesis potential in microbial lineages. | bacterial production of long-chain omega-3 polyunsaturated fatty acids (pufas), such as eicosapentaenoic acid (epa, 20:5n-3) and docosahexaenoic acid (dha, 22:6n-3), is constrained to a narrow subset of marine γ-proteobacteria. the genes responsible for de novo bacterial pufa biosynthesis, designated pfaeabcd, encode large, multi-domain protein complexes akin to type i iterative fatty acid and polyketide synthases, herein referred to as "pfa synthases". in addition to the archetypal pfa synthase ... | 2011 | 21629834 |
| complete genome sequence of planctomyces limnophilus type strain (mü 290). | planctomyces limnophilus hirsch and müller 1986 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 which is stabilized by a proteinaceous layer rather than a peptidoglycan layer. besides pirellula staleyi, this is the second completed genome sequence of the family planctomycetaceae. p. ... | 2010 | 21304691 |
| marine integrons containing novel integrase genes, attachment sites, atti, and associated gene cassettes in polluted sediments from suez and tokyo bays. | in order to understand the structure and biological significance of integrons and associated gene cassettes in marine polluted sediments, metagenomic dnas were extracted from sites at suez and tokyo bays. pcr amplicons containing new integrase genes, inti, linked with novel gene cassettes, were recovered and had sizes from 1.8 to 2.5 kb. this approach uncovered, for the first time, the structure and diversity of both marine integron attachment site, atti, and the first gene cassette, the most ef ... | 2011 | 21248857 |
| comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. | the nuclear pore complex (npc) facilitates molecular trafficking between nucleus and cytoplasm and is an integral feature of the eukaryote cell. it exhibits eight-fold rotational symmetry and is comprised of approximately 30 nucleoporins (nups) in different stoichiometries. nups are broadly conserved between yeast, vertebrates and plants, but few have been identified among other major eukaryotic groups. | 2010 | 20949036 |
| molecular detection of anaerobic ammonium-oxidizing (anammox) bacteria in high-temperature petroleum reservoirs. | anaerobic ammonium-oxidizing (anammox) process plays an important role in the nitrogen cycle of the worldwide anoxic and mesophilic habitats. recently, the existence and activity of anammox bacteria have been detected in some thermophilic environments, but their existence in the geothermal subterranean oil reservoirs is still not reported. this study investigated the abundance, distribution and functional diversity of anammox bacteria in nine out of 17 high-temperature oil reservoirs by molecula ... | 2010 | 20740282 |
| predicting the pathway involved in post-translational modification of elongation factor p in a subset of bacterial species. | background: the bacterial elongation factor p (ef-p) is strictly conserved in bacteria and essential for protein synthesis. it is homologous to the eukaryotic translation initiation factor 5a (eif5a). a highly conserved eif5a lysine is modified into an unusual amino acid derived from spermidine, hypusine. hypusine is absolutely required for eif5a's role in translation in saccharomyces cerevisiae. the homologous lysine of ef-p is also modified to a spermidine derivative in escherichia coli. howev ... | 2010 | 20070887 |
| 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 |
| detection and cultivation of soil verrucomicrobia. | only one isolate each of the class "spartobacteria" (subdivision 2 of the phylum verrucomicrobia) and of subdivision 3 of verrucomicrobia have previously been reported to grow in laboratory culture. using media that had been used successfully in other studies to isolate members of diverse groups of soil bacteria, we generated a collection of over 1,200 isolates from soil from a pasture. an oligonucleotide probe that targets the 16s rrna genes of verrucomicrobia was used to screen this collection ... | 2005 | 16332828 |
| 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 |
| use of dna and peptide nucleic acid molecular beacons for detection and quantification of rrna in solution and in whole cells. | dna and peptide nucleic acid (pna) molecular beacons were successfully used to detect rrna in solution. in addition, pna molecular beacon hybridizations were found to be useful for the quantification of rrna: hybridization signals increased in a linear fashion with the 16s rrna concentrations used in this experiment (between 0.39 and 25 nm) in the presence of 50 nm pna mb. dna and pna molecular beacons were successfully used to detect whole cells in fluorescence in situ hybridization (fish) expe ... | 2003 | 12957960 |
| 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 |
| conservation of sigma-core rna polymerase proximity relationships between the enhancer-independent and enhancer-dependent sigma classes. | two distinct classes of rna polymerase sigma factors (sigma) exist in bacteria and are largely unrelated in primary amino acid sequence and their modes of transcription activation. using tethered iron chelate (fe-babe) derivatives of the enhancer-dependent sigma(54), we mapped several sites of proximity to the beta and beta' subunits of the core rna polymerase. remarkably, most sites localized to those previously identified as close to the enhancer-independent sigma(70) and sigma(38). this indic ... | 2000 | 10856247 |
| functionality of purified sigma(n) (sigma(54)) and a nifa-like protein from the hyperthermophile aquifex aeolicus. | the genome sequence of the extremely thermophilic bacterium aquifex aeolicus encodes alternative sigma factor sigma(n) (sigma(54), rpon) and five potential sigma(n)-dependent transcriptional activators. although a. aeolicus possesses no recognizable nitrogenase genes, two of the activators have a high degree of sequence similarity to nifa proteins from nitrogen-fixing proteobacteria. we identified five putative sigma(n)-dependent promoters upstream of operons implicated in functions including su ... | 2000 | 10692367 |
| evolutionary cell biology of division mode in the bacterial planctomycetes-verrucomicrobia- chlamydiae superphylum. | bacteria from the planctomycetes, verrucomicrobia, and chlamydiae (pvc) superphylum are exceptions to the otherwise dominant mode of division by binary fission, which is based on the interaction between the ftsz protein and the peptidoglycan (pg) biosynthesis machinery. some pvc bacteria are deprived of the ftsz protein and were also thought to lack pg. how these bacteria divide is still one of the major mysteries of microbiology. the presence of pg has recently been revealed in planctomycetes a ... | 2016 | 28018303 |
| phylogenetic analysis of particle-attached and free-living bacterial communities in the columbia river, its estuary, and the adjacent coastal ocean. | the columbia river estuary is a dynamic system in which estuarine turbidity maxima trap and extend the residence time of particles and particle-attached bacteria over those of the water and free-living bacteria. particle-attached bacteria dominate bacterial activity in the estuary and are an important part of the estuarine food web. pcr-amplified 16s rrna genes from particle-attached and free-living bacteria in the columbia river, its estuary, and the adjacent coastal ocean were cloned, and 239 ... | 1999 | 10388721 |
| the presence of a dnak (hsp70) multigene family in members of the orders planctomycetales and verrucomicrobiales. | sequences of the dnak gene, coding for the 70-kda heat shock protein (hsp70), were determined for six members of the order planctomycetales, including representatives of three genera, and for the only cultivated member of the order verrucomicrobiales, verrucomicrobium spinosum. a fragment of the dnak gene was amplified from these strains by pcr with oligonucleotide primers targeting regions of the dnak gene that are conserved at the amino acid level, and the resulting pcr products were cloned in ... | 1997 | 9335284 |
| 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 |
| 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 |
| presence of a classical rrm-fold palm domain in thg1-type 3'- 5'nucleic acid polymerases and the origin of the ggdef and crispr polymerase domains. | almost all known nucleic acid polymerases catalyze 5'-3' polymerization by mediating the attack on an incoming nucleotide 5' triphosphate by the 3'oh from the growing polynucleotide chain in a template dependent or independent manner. the only known exception to this rule is the thg1 rna polymerase that catalyzes 3'-5' polymerization in vitro and also in vivo as a part of the maturation process of histidinyl trna. while the initial reaction catalyzed by thg1 has been compared to adenylation cata ... | 2010 | 20591188 |
| evolution of dna ligases of nucleo-cytoplasmic large dna viruses of eukaryotes: a case of hidden complexity. | eukaryotic nucleo-cytoplasmic large dna viruses (ncldv) encode most if not all of the enzymes involved in their dna replication. it has been inferred that genes for these enzymes were already present in the last common ancestor of the ncldv. however, the details of the evolution of these genes that bear on the complexity of the putative ancestral ncldv and on the evolutionary relationships between viruses and their hosts are not well understood. | 2009 | 20021668 |
| 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 |
| the genealogic tree of mycobacteria reveals a long-standing sympatric life into free-living protozoa. | free-living protozoa allow horizontal gene transfer with and between the microorganisms that they host. they host mycobacteria for which the sources of transferred genes remain unknown. using blastp, we searched within the genomes of 15 mycobacteria for homologous genes with 34 amoeba-resistant bacteria and the free-living protozoa dictyostelium discoideum. subsequent phylogenetic analysis of these sequences revealed that eight mycobacterial open-reading frames (orfs) were probably acquired via ... | 2012 | 22511965 |
| phylogenetic analysis and in situ identification of bacteria community composition in an acidic sphagnum peat bog. | the bacteria community composition in an acidic sphagnum peat bog (ph 3.9 to 4.5) was characterized by a combination of 16s rrna gene clone library analysis, rrna-targeted fluorescence in situ hybridization (fish), and cultivation. among 84 environmental 16s rrna gene clones, a set of only 16 cloned sequences was closely related (>or=95% similarity) to taxonomically described organisms. main groups of clones were affiliated with the acidobacteria (24 clones), alphaproteobacteria (20), verrucomic ... | 2006 | 16517660 |
| comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. | comparative analysis of bacterial diversity in freshwater sediment collected from a shallow eutrophic lake was performed by using 16s rrna gene clone library and improved cultivation-based techniques. our study demonstrated that the use of gellan gum as a gelling reagent instead of agar was more effective at increasing culturability, cultivating a diverse array of novel microbes, and reducing the gaps of the results between molecular and cultivation-based analyses. | 2005 | 15812052 |
| structure/function analysis of a type iii polyketide synthase in the brown alga ectocarpus siliculosus reveals a biochemical pathway in phlorotannin monomer biosynthesis. | brown algal phlorotannins are structural analogs of condensed tannins in terrestrial plants and, like plant phenols, they have numerous biological functions. despite their importance in brown algae, phlorotannin biosynthetic pathways have been poorly characterized at the molecular level. we found that a predicted type iii polyketide synthase in the genome of the brown alga ectocarpus siliculosus, pks1, catalyzes a major step in the biosynthetic pathway of phlorotannins (i.e., the synthesis of ph ... | 2013 | 23983220 |
| sequence, structure and functional diversity of pd-(d/e)xk phosphodiesterase superfamily. | proteins belonging to pd-(d/e)xk phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, dna repair and trna-intron splicing. their malfunction in humans triggers severe diseases, such as fanconi anemia and xeroderma pigmentosum. to date there have been several attempts to identify and classify new pd-(d/e)kk phosphodiesterases using remote homology detection methods. such efforts are complicated, because the superfamily exhibit ... | 2012 | 22638584 |
| calpain chronicle--an enzyme family under multidisciplinary characterization. | calpain is an intracellular ca2+-dependent cysteine protease (ec 3.4.22.17; clan ca, family c02) discovered in 1964. it was also called canp (ca2+-activated neutral protease) as well as casf, cdp, kaf, etc. until 1990. calpains are found in almost all eukaryotes and a few bacteria, but not in archaebacteria. calpains have a limited proteolytic activity, and function to transform or modulate their substrates' structures and activities; they are therefore called, "modulator proteases." in the huma ... | 2011 | 21670566 |
| keys to eukaryality: planctomycetes and ancestral evolution of cellular complexity. | planctomycetes are known to display compartmentalization via internal membranes, thus resembling eukaryotes. significantly, the planctomycete gemmata obscuriglobus has not only a nuclear region surrounded by a double-membrane, but is also capable of protein uptake via endocytosis. in order to clearly analyze implications for homology of their characters with eukaryotes, a correct understanding of planctomycete structure is an essential starting point. here we outline the major features of such s ... | 2012 | 22586422 |
| influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. | metagenomic data sets were generated from samples collected along a coastal to open ocean transect between southern california bight and california current waters during a seasonal upwelling event, providing an opportunity to examine the impact of episodic pulses of cold nutrient-rich water into surface ocean microbial communities. the data set consists of ~5.8 million predicted proteins across seven sites, from three different size classes: 0.1-0.8, 0.8-3.0 and 3.0-200.0 μm. taxonomic and metab ... | 2012 | 22278668 |
| characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides. | bacterial microcompartments (bmcs) are organelles that encapsulate functionally linked enzymes within a proteinaceous shell. the prototypical example is the carboxysome, which functions in carbon fixation in cyanobacteria and some chemoautotrophs. it is increasingly apparent that diverse heterotrophic bacteria contain bmcs that are involved in catabolic reactions, and many of the bmcs are predicted to have novel functions. however, most of these putative organelles have not been experimentally c ... | 2014 | 24487526 |
| 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 |
| planctomycetes do possess a peptidoglycan cell wall. | most bacteria contain a peptidoglycan (pg) cell wall, which is critical for maintenance of shape and important for cell division. in contrast, planctomycetes have been proposed to produce a proteinaceous cell wall devoid of pg. the apparent absence of pg has been used as an argument for the putative planctomycetal ancestry of all bacterial lineages. here we show, employing multiple bioinformatic methods, that planctomycetal genomes encode proteins required for pg synthesis. furthermore, we bioch ... | 2015 | 25964217 |
| 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 |
| ether- and ester-bound iso-diabolic acid and other lipids in members of acidobacteria subdivision 4. | recently, iso-diabolic acid (13,16-dimethyl octacosanedioic acid) has been identified as a major membrane-spanning lipid of subdivisions 1 and 3 of the acidobacteria, a highly diverse phylum within the bacteria. this finding pointed to the acidobacteria as a potential source for the bacterial glycerol dialkyl glycerol tetraethers that occur ubiquitously in peat, soil, lakes, and hot springs. here, we examined the lipid composition of seven phylogenetically divergent strains of subdivision 4 of t ... | 2014 | 24928878 |
| domain architectures of sigma54-dependent transcriptional activators. | | 2003 | 12618438 |
| incorporating genomics and bioinformatics across the life sciences curriculum. | | 2010 | 20711478 |
| community transcriptomics reveals universal patterns of protein sequence conservation in natural microbial communities. | combined metagenomic and metatranscriptomic datasets make it possible to study the molecular evolution of diverse microbial species recovered from their native habitats. the link between gene expression level and sequence conservation was examined using shotgun pyrosequencing of microbial community dna and rna from diverse marine environments, and from forest soil. | 2011 | 21426537 |
| transposon mutagenesis of planctomyces limnophilus and analysis of a pcka mutant. | a planctomyces limnophilus mutant generated using the ez-tn5 transposome was found to possess an insertion within pcka, encoding phosphoenolpyruvate carboxykinase. disruption of pcka expression and elimination of enzymatic activity resulted in poor growth in glucose-free medium, demonstrating a gluconeogenic role for pcka in p. limnophilus. | 2012 | 22798371 |
| 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 |
| 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 |
| global and targeted lipid analysis of gemmata obscuriglobus reveals the presence of lipopolysaccharide, a signature of the classical gram-negative outer membrane. | planctomycete bacteria possess many unusual cellular properties, contributing to a cell plan long considered to be unique among the bacteria. however, data from recent studies are more consistent with a modified gram-negative cell plan. a key feature of the gram-negative plan is the presence of an outer membrane (om), for which lipopolysaccharide (lps) is a signature molecule. despite genomic evidence for an om in planctomycetes, no biochemical verification has been reported. we attempted to det ... | 2016 | 26483522 |
| global and targeted lipid analysis of gemmata obscuriglobus reveals the presence of lipopolysaccharide, a signature of the classical gram-negative outer membrane. | planctomycete bacteria possess many unusual cellular properties, contributing to a cell plan long considered to be unique among the bacteria. however, data from recent studies are more consistent with a modified gram-negative cell plan. a key feature of the gram-negative plan is the presence of an outer membrane (om), for which lipopolysaccharide (lps) is a signature molecule. despite genomic evidence for an om in planctomycetes, no biochemical verification has been reported. we attempted to det ... | 2016 | 26483522 |
| genomic and biochemical analysis of the diaminopimelate and lysine biosynthesis pathway in verrucomicrobium spinosum: identification and partial characterization of l,l-diaminopimelate aminotransferase and udp-n-acetylmuramoylalanyl-d-glutamyl-2,6-meso-diaminopimelate ligase. | the gram-negative bacterium verrucomicrobium spinosum has attracted interest in recent years following the sequencing and annotation of its genome. comparative genomic analysis of v. spinosum using diaminopimelate/lysine metabolic genes from chlamydia trachomatis suggests that v. spinosum employs the l,l-diaminopimelate aminotransferase (dapl) pathway for diaminopimelate/lysine biosynthesis. the open reading frame corresponding to the putative dapl ortholog was cloned and the recombinant enzyme ... | 2012 | 22783236 |
| discovery strategies of bioactive compounds synthesized by nonribosomal peptide synthetases and type-i polyketide synthases derived from marine microbiomes. | considering that 70% of our planet's surface is covered by oceans, it is likely that undiscovered biodiversity is still enormous. a large portion of marine biodiversity consists of microbiomes. they are very attractive targets of bioprospecting because they are able to produce a vast repertoire of secondary metabolites in order to adapt in diverse environments. in many cases secondary metabolites of pharmaceutical and biotechnological interest such as nonribosomal peptides (nrps) and polyketides ... | 2016 | 27092515 |
| detection of verrucomicrobia in a pasture soil by pcr-mediated amplification of 16s rrna genes. | oligonucleotide primers were designed and used to amplify, by pcr, partial 16s rrna genes of members of the bacterial division verrucomicrobia in dna extracted from a pasture soil. by applying most-probable-number theory to the assay, verrucomicrobia appeared to contribute some 0.2% of the soil dna. amplified ribosomal dna restriction analysis of 53 cloned pcr-amplified partial 16s rrna gene fragments and comparative sequence analysis of 21 nonchimeric partial 16s rrna genes showed that these pr ... | 1999 | 10473454 |
| biodiversity, community structural shifts, and biogeography of prokaryotes within antarctic continental shelf sediment. | 16s ribosomal dna (rdna) clone library analysis was conducted to assess prokaryotic diversity and community structural changes within a surficial sediment core obtained from an antarctic continental shelf area (depth, 761 m) within the mertz glacier polynya (mgp) region. libraries were created from three separate horizons of the core (0- to 0.4-cm, 1.5- to 2.5-cm, and 20- to 21-cm depth positions). the results indicated that at the oxic sediment surface (depth, 0 to 0.4 cm) the microbial communi ... | 2003 | 12732511 |
| bioinformatic characterization of glycyl radical enzyme-associated bacterial microcompartments. | bacterial microcompartments (bmcs) are proteinaceous organelles encapsulating enzymes that catalyze sequential reactions of metabolic pathways. bmcs are phylogenetically widespread; however, only a few bmcs have been experimentally characterized. among them are the carboxysomes and the propanediol- and ethanolamine-utilizing microcompartments, which play diverse metabolic and ecological roles. the substrate of a bmc is defined by its signature enzyme. in catabolic bmcs, this enzyme typically gen ... | 2015 | 26407889 |
| determination of rna polymerase binding surfaces of transcription factors by nmr spectroscopy. | in bacteria, rna polymerase (rnap), the central enzyme of transcription, is regulated by n-utilization substance (nus) transcription factors. several of these factors interact directly, and only transiently, with rnap to modulate its function. as details of these interactions are largely unknown, we probed the rnap binding surfaces of escherichia coli (e. coli) nus factors by nuclear magnetic resonance (nmr) spectroscopy. perdeuterated factors with [(1)h,(13)c]-labeled methyl groups of val, leu, ... | 2015 | 26560741 |
| metagenome and metatranscriptome revealed a highly active and intensive sulfur cycle in an oil-immersed hydrothermal chimney in guaymas basin. | the hydrothermal vent system is a typical chemosynthetic ecosystem in which microorganisms play essential roles in the geobiochemical cycling. although it has been well-recognized that the inorganic sulfur compounds are abundant and actively converted through chemosynthetic pathways, the sulfur budget in a hydrothermal vent is poorly characterized due to the complexity of microbial sulfur cycling resulting from the numerous parties involved in the processes. in this study, we performed an integr ... | 2015 | 26617579 |
| salmon gill poxvirus, the deepest representative of the chordopoxvirinae. | poxviruses are large dna viruses of vertebrates and insects causing disease in many animal species, including reptiles, birds, and mammals. although poxvirus-like particles were detected in diseased farmed koi carp, ayu, and atlantic salmon, their genetic relationships to poxviruses were not established. here, we provide the first genome sequence of a fish poxvirus, which was isolated from farmed atlantic salmon. in the present study, we used quantitative pcr and immunohistochemistry to determin ... | 2015 | 26136578 |
| elucidating essential role of conserved carboxysomal protein ccmn reveals common feature of bacterial microcompartment assembly. | bacterial microcompartments are organelles composed of a protein shell that surrounds functionally related proteins. bioinformatic analysis of sequenced genomes indicates that homologs to shell protein genes are widespread among bacteria and suggests that the shell proteins are capable of encapsulating diverse enzymes. the carboxysome is a bacterial microcompartment that enhances co(2) fixation in cyanobacteria and some chemoautotrophs by sequestering ribulose-1,5-bisphosphate carboxylase/oxygen ... | 2012 | 22461622 |
| chorismate pyruvate-lyase and 4-hydroxy-3-solanesylbenzoate decarboxylase are required for plastoquinone biosynthesis in the cyanobacterium synechocystis sp. pcc6803. | plastoquinone is a redox active lipid that serves as electron transporter in the bifunctional photosynthetic-respiratory transport chain of cyanobacteria. to examine the role of genes potentially involved in cyanobacterial plastoquinone biosynthesis, we have focused on three synechocystis sp. pcc 6803 genes likely encoding a chorismate pyruvate-lyase (sll1797) and two 4-hydroxy-3-solanesylbenzoate decarboxylases (slr1099 and sll0936). the functions of the encoded proteins were investigated by co ... | 2013 | 24337576 |
| chorismate pyruvate-lyase and 4-hydroxy-3-solanesylbenzoate decarboxylase are required for plastoquinone biosynthesis in the cyanobacterium synechocystis sp. pcc6803. | plastoquinone is a redox active lipid that serves as electron transporter in the bifunctional photosynthetic-respiratory transport chain of cyanobacteria. to examine the role of genes potentially involved in cyanobacterial plastoquinone biosynthesis, we have focused on three synechocystis sp. pcc 6803 genes likely encoding a chorismate pyruvate-lyase (sll1797) and two 4-hydroxy-3-solanesylbenzoate decarboxylases (slr1099 and sll0936). the functions of the encoded proteins were investigated by co ... | 2013 | 24337576 |
| the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation. | full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ... | 2013 | 24084083 |
| the active site of tthpolx is adapted to prevent 8-oxo-dgtp misincorporation. | full genome sequencing of bacterial genomes has revealed the presence of numerous genes encoding family x dna polymerases. these enzymes play a variety of biological roles and, accordingly, display often striking functional differences. here we report that the polx from the heat-stable organism thermus thermophilus (tthpolx) inserts the four dntps with strong asymmetry. we demonstrate that this behaviour is related to the presence of a single divergent residue in the active site of tthpolx. muta ... | 2013 | 24084083 |
| developing techniques for the utilization of planctomycetes as producers of bioactive molecules. | planctomycetes are conspicuous, ubiquitous, environmentally important bacteria. they can attach to various surfaces in aquatic habitats and form biofilms. their unique ftsz-independent budding cell division mechanism is associated with slow growth and doubling times from 6 h up to 1 month. despite this putative disadvantage in the struggle to colonize surfaces, planctomycetes are frequently associated with aquatic phototrophic organisms such as diatoms, cyanobacteria or kelp, whereby planctomyce ... | 2016 | 27594849 |
| new lic vectors for production of proteins from genes containing rare codons. | in the effort to produce proteins coded by diverse genomes, structural genomics projects often must express genes containing codons that are rare in the production strain. to address this problem, genes expressing trnas corresponding to those codons are typically coexpressed from a second plasmid in the host strain, or from genes incorporated into production plasmids. here we describe the modification of a series of lic pmcsg vectors currently used in the high-throughput (htp) production of prot ... | 2013 | 24057978 |
| relevance of gc content to the conservation of dna polymerase iii/mismatch repair system in gram-positive bacteria. | the mechanism of dna replication is one of the driving forces of genome evolution. bacterial dna polymerase iii, the primary complex of dna replication, consists of polc and dnae. polc is conserved in gram-positive bacteria, especially in the firmicutes with low gc content, whereas dnae is widely conserved in most gram-negative and gram-positive bacteria. polc contains two domains, the 3'-5'exonuclease domain and the polymerase domain, while dnae only possesses the polymerase domain. accordingly ... | 2013 | 24062730 |
| the metagenome of the marine anammox bacterium 'candidatus scalindua profunda' illustrates the versatility of this globally important nitrogen cycle bacterium. | anaerobic ammonium-oxidizing (anammox) bacteria are responsible for a significant portion of the loss of fixed nitrogen from the oceans, making them important players in the global nitrogen cycle. to date, marine anammox bacteria found in marine water columns and sediments worldwide belong almost exclusively to the 'candidatus scalindua' species, but the molecular basis of their metabolism and competitive fitness is presently unknown. we applied community sequencing of a marine anammox enrichmen ... | 2013 | 22568606 |
| synthesis of fluorescent d-amino acids and their use for probing peptidoglycan synthesis and bacterial growth in situ. | fluorescent d-amino acids (fdaas) are efficiently incorporated into the peptidoglycans (pgs) of diverse bacterial species at the sites of pg biosynthesis, allowing specific and covalent probing of bacterial growth with minimal perturbation. here we provide a protocol for the synthesis of four fdaas emitting light in blue (hcc-amino-d-alanine, hada), green (nbd-amino-d-alanine, nada, and fluorescein-d-lysine, fdl) or red (tamra-d-lysine, tdl) and for their use in pg labeling of live bacteria. our ... | 2014 | 25474031 |
| synthesis of fluorescent d-amino acids and their use for probing peptidoglycan synthesis and bacterial growth in situ. | fluorescent d-amino acids (fdaas) are efficiently incorporated into the peptidoglycans (pgs) of diverse bacterial species at the sites of pg biosynthesis, allowing specific and covalent probing of bacterial growth with minimal perturbation. here we provide a protocol for the synthesis of four fdaas emitting light in blue (hcc-amino-d-alanine, hada), green (nbd-amino-d-alanine, nada, and fluorescein-d-lysine, fdl) or red (tamra-d-lysine, tdl) and for their use in pg labeling of live bacteria. our ... | 2014 | 25474031 |
| ftsz-less prokaryotic cell division as well as ftsz- and dynamin-less chloroplast and non-photosynthetic plastid division. | the chloroplast division machinery is a mixture of a stromal ftsz-based complex descended from a cyanobacterial ancestor of chloroplasts and a cytosolic dynamin-related protein (drp) 5b-based complex derived from the eukaryotic host. molecular genetic studies have shown that each component of the division machinery is normally essential for normal chloroplast division. however, several exceptions have been found. in the absence of the ftsz ring, non-photosynthetic plastids are able to proliferat ... | 2014 | 25309558 |
| characterization of the first cultured representative of verrucomicrobia subdivision 5 indicates the proposal of a novel phylum. | the recently isolated strain l21-fru-ab(t) represents moderately halophilic, obligately anaerobic and saccharolytic bacteria that thrive in the suboxic transition zones of hypersaline microbial mats. phylogenetic analyses based on 16s rrna genes, rpob proteins and gene content indicated that strain l21-fru-ab(t) represents a novel species and genus affiliated with a distinct phylum-level lineage originally designated verrucomicrobia subdivision 5. a survey of environmental 16s rrna gene sequence ... | 2016 | 27300277 |
| the structural basis of coenzyme a recycling in a bacterial organelle. | bacterial microcompartments (bmcs) are proteinaceous organelles that encapsulate critical segments of autotrophic and heterotrophic metabolic pathways; they are functionally diverse and are found across 23 different phyla. the majority of catabolic bmcs (metabolosomes) compartmentalize a common core of enzymes to metabolize compounds via a toxic and/or volatile aldehyde intermediate. the core enzyme phosphotransacylase (ptac) recycles coenzyme a and generates an acyl phosphate that can serve as ... | 2016 | 26959993 |
| diverse bacterial microcompartment organelles. | bacterial microcompartments (mcps) are sophisticated protein-based organelles used to optimize metabolic pathways. they consist of metabolic enzymes encapsulated within a protein shell, which creates an ideal environment for catalysis and facilitates the channeling of toxic/volatile intermediates to downstream enzymes. the metabolic processes that require mcps are diverse and widely distributed and play important roles in global carbon fixation and bacterial pathogenesis. the protein shells of m ... | 2014 | 25184561 |
| viruses in a 14th-century coprolite. | coprolites are fossilized fecal material that can reveal information about ancient intestinal and environmental microbiota. viral metagenomics has allowed systematic characterization of viral diversity in environmental and human-associated specimens, but little is known about the viral diversity in fossil remains. here, we analyzed the viral community of a 14th-century coprolite from a closed barrel in a middle ages site in belgium using electron microscopy and metagenomics. viruses that infect ... | 2014 | 24509925 |
| the bacterial enhancer-dependent sigma(54) (sigma(n)) transcription factor. | | 2000 | 10894718 |
| veillonella, firmicutes: microbes disguised as gram negatives. | the firmicutes represent a major component of the intestinal microflora. the intestinal firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. although most firmicutes are gram positive, members of the class negativicutes, including the genus veillonella, stain gram negative. veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerob ... | 2013 | 24976898 |
| diversity of planctomycetes in soil in relation to soil history and environmental heterogeneity. | members of the planctomycetes, which were once thought to occur primarily in aquatic environments, have been discovered in soils on five continents, revealing that these bacteria are a widespread and numerically abundant component of microbial communities in soil. we examined the diversity of planctomycetes in soil samples obtained from experimental plots at an agricultural site in order to assess the extent of planctomycetes diversity in soil, to determine whether management effects such as pas ... | 2006 | 16820439 |
| a microbial oasis in the hypersaline atacama subsurface discovered by a life detector chip: implications for the search for life on mars. | the atacama desert has long been considered a good mars analogue for testing instrumentation for planetary exploration, but very few data (if any) have been reported about the geomicrobiology of its salt-rich subsurface. we performed a mars analogue drilling campaign next to the salar grande (atacama, chile) in july 2009, and several cores and powder samples from up to 5 m deep were analyzed in situ with ldchip300 (a life detector chip containing 300 antibodies). here, we show the discovery of a ... | 2011 | 22149750 |