| molecular paleontology and complexity in the last eukaryotic common ancestor. | eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. this event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. while some well-validated examples of fossil microbial eukaryotes for this time frame have been described, these can provide only basic morphology and the molecular machinery present in these organisms has remained unknown. complete and partial ge ... | 2013 | 23895660 |
| polyketide genes in the marine sponge plakortis simplex: a new group of mono-modular type i polyketide synthases from sponge symbionts. | sponge symbionts are a largely unexplored source of new and unusual metabolic pathways. insights into the distribution and function of metabolic genes of sponge symbionts are crucial to dissect and exploit their biotechnological potential. screening of the metagenome of the marine sponge plakortis simplex led to the discovery of the swf family, a new group of mono-modular type i polyketide synthase/fatty acid synthase (pks/fas) specifically associated with sponge symbionts. two different example ... | 2013 | 24249289 |
| pyrosequencing-based assessment of the bacteria diversity in surface and subsurface peat layers of a northern wetland, with focus on poorly studied phyla and candidate divisions. | northern peatlands play a key role in the global carbon and water budget, but the bacterial diversity in these ecosystems remains poorly described. here, we compared the bacterial community composition in the surface (0-5 cm depth) and subsurface (45-50 cm) peat layers of an acidic (ph 4.0) sphagnum-dominated wetland, using pyrosequencing of 16s rrna genes. the denoised sequences (37,229 reads, average length ∼430 bp) were affiliated with 27 bacterial phyla and corresponded to 1,269 operational ... | 2013 | 23700443 |
| three-dimensional reconstruction of bacteria with a complex endomembrane system. | the division of cellular space into functionally distinct membrane-defined compartments has been one of the major transitions in the history of life. such compartmentalization has been claimed to occur in members of the planctomycetes, verrucomicrobiae, and chlamydiae bacterial superphylum. here we have investigated the three-dimensional organization of the complex endomembrane system in the planctomycete bacteria gemmata obscuriglobus. we reveal that the g. obscuriglobus cells are neither compa ... | 2013 | 23700385 |
| phylogeny-driven target selection for large-scale genome-sequencing (and other) projects. | despite the steadily decreasing costs of genome sequencing, prioritizing organisms for sequencing remains important in large-scale projects. phylogeny-based selection is of interest to identify those organisms whose genomes can be expected to differ most from those that have already been sequenced. here, we describe a method that infers a phylogenetic scoring independent of which set of organisms has previously been targeted, which is computationally simple and easy to apply in practice. the sco ... | 2013 | 23991265 |
| tiny cells meet big questions: a closer look at bacterial cell biology. | while studying actin assembly as a graduate student with matt welch at the university of california at berkeley, my interest was piqued by reports of surprising observations in bacteria: the identification of numerous cytoskeletal proteins, actin homologues fulfilling spindle-like functions, and even the presence of membrane-bound organelles. curiosity about these phenomena drew me to lucy shapiro's lab at stanford university for my postdoctoral research. in the shapiro lab, and now in my lab at ... | 2013 | 23580191 |
| evolutionary acquisition and loss of saxitoxin biosynthesis in dinoflagellates: the second "core" gene, sxtg. | saxitoxin and its derivatives are potent neurotoxins produced by several cyanobacteria and dinoflagellate species. sxta is the initial enzyme in the biosynthesis of saxitoxin. the dinoflagellate full mrna and partial genomic sequences have previously been characterized, and it appears that sxta originated in dinoflagellates through a horizontal gene transfer from a bacterium. so far, little is known about the remaining genes involved in this pathway in dinoflagellates. here we characterize sxtg, ... | 2013 | 23335767 |
| microbial cytochromes p450: biodiversity and biotechnology. where do cytochromes p450 come from, what do they do and what can they do for us? | the first eukaryote genome revealed three yeast cytochromes p450 (cyps), hence the subsequent realization that some microbial fungal genomes encode these proteins in 1 per cent or more of all genes (greater than 100) has been surprising. they are unique biocatalysts undertaking a wide array of stereo- and regio-specific reactions and so hold promise in many applications. based on ancestral activities that included 14α-demethylation during sterol biosynthesis, it is now seen that cyps are part of ... | 2013 | 23297358 |
| the 2-methylcitrate cycle is implicated in the detoxification of propionate in toxoplasma gondii. | toxoplasma gondii belongs to the coccidian subgroup of the apicomplexa phylum. the coccidia are obligate intracellular pathogens that establish infection in their mammalian host via the enteric route. these parasites lack a mitochondrial pyruvate dehydrogenase complex but have preserved the degradation of branched-chain amino acids (bcaa) as a possible pathway to generate acetyl-coa. importantly, degradation of leucine, isoleucine and valine could lead to concomitant accumulation of propionyl-co ... | 2013 | 23279335 |
| drug strategies targeting cyp51 in neglected tropical diseases. | | 2014 | 25337991 |
| planctomycetes dna in febrile aplastic patients with leukemia, rash, diarrhea, and micronodular pneumonia. | we found planctomycetes dna in 2 out of 100 blood samples from patients suffering from leukemia with neutropenia induced by chemotherapy, as well as fever, rash, pneumonia, and diarrhea. antibiotic-resisting planctomycetes may be pathogenic in these patients. | 2014 | 24920769 |
| chemosensory regulation of a heat-repeat protein couples aggregation and sporulation in myxococcus xanthus. | chemosensory systems are complex, highly modified two-component systems (tcs) used by bacteria to control various biological functions ranging from motility to sporulation. chemosensory systems and tcs both modulate phosphorelays comprised of histidine kinases and response regulators, some of which are single-domain response regulators (sd-rrs) such as chey. in this study, we have identified and characterized the che7 chemosensory system of myxococcus xanthus, a common soil bacterium which displ ... | 2014 | 24957622 |
| comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease. | polymicrobial diseases are caused by combinations of multiple bacteria, which can lead to not only mild but also life-threatening illnesses. periodontitis represents a polymicrobial disease; porphyromonas gingivalis, treponema denticola and tannerella forsythia, called 'the red complex', have been recognized as the causative agents of periodontitis. although molecular interactions among the three species could be responsible for progression of periodontitis, the relevant genetic mechanisms are u ... | 2014 | 25171331 |
| comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease. | polymicrobial diseases are caused by combinations of multiple bacteria, which can lead to not only mild but also life-threatening illnesses. periodontitis represents a polymicrobial disease; porphyromonas gingivalis, treponema denticola and tannerella forsythia, called 'the red complex', have been recognized as the causative agents of periodontitis. although molecular interactions among the three species could be responsible for progression of periodontitis, the relevant genetic mechanisms are u ... | 2014 | 25171331 |
| comparative analysis of functional metagenomic annotation and the mappability of short reads. | to assess the functional capacities of microbial communities, including those inhabiting the human body, shotgun metagenomic reads are often aligned to a database of known genes. such homology-based annotation practices critically rely on the assumption that short reads can map to orthologous genes of similar function. this assumption, however, and the various factors that impact short read annotation, have not been systematically evaluated. to address this challenge, we generated an extremely l ... | 2014 | 25148512 |
| 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 |
| 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 |
| spatially segregated transcription and translation in cells of the endomembrane-containing bacterium gemmata obscuriglobus. | the dogma of coupled transcription and translation in bacteria has been challenged by recent reports of spatial segregation of these processes within the relatively simple cellular organization of the model organisms escherichia coli and bacillus subtilis. the bacterial species gemmata obscuriglobus possesses an extensive endomembrane system. the membranes generate a very convoluted intracellular architecture in which some of the cell's ribosomes appear to have less direct access to the cell's n ... | 2014 | 25024214 |
| bacterial set domain proteins and their role in eukaryotic chromatin modification. | it has been shown by many researchers that set-domain containing proteins modify chromatin structure and, as expected, genes coding for set-domain containing proteins have been found in all eukaryotic genomes sequenced to date. however, during the last years, a great number of bacterial genomes have been sequenced and an important number of putative genes involved in histone post-translational modifications (histone ptms) have been identified in many bacterial genomes. here, i aim at presenting ... | 2014 | 24765100 |
| 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 |
| structural studies of planctomycete gemmata obscuriglobus support cell compartmentalisation in a bacterium. | members of phylum planctomycetes have been proposed to possess atypical cell organisation for the bacteria, having a structure of sectioned cells consistent with internal compartments surrounded by membranes. here via electron tomography we confirm the presence of compartments in the planctomycete gemmata obscuriglobus cells. resulting 3-d models for the most prominent structures, nuclear body and riboplasm, demonstrate their entirely membrane - enclosed nature. immunogold localization of the ft ... | 2014 | 24632833 |
| biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. | the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ... | 2014 | 24688489 |
| biotechnology of polyketides: new breath of life for the novel antibiotic genetic pathways discovery through metagenomics. | the discovery of secondary metabolites produced by microorganisms (e.g., penicillin in 1928) and the beginning of their industrial application (1940) opened new doors to what has been the main medication source for the treatment of infectious diseases and tumors. in fact, approximately 80 years after the discovery of the first antibiotic compound, and despite all of the warnings about the failure of the "goose that laid the golden egg," the potential of this wealth is still inexorable: simply ad ... | 2014 | 24688489 |
| crystallization around solid-like nanosized docks can explain the specificity, diversity, and stability of membrane microdomains. | to date, it is widely accepted that microdomains do form in the biological membranes of all eukaryotic cells, and quite possibly also in prokaryotes. those sub-micrometric domains play crucial roles in signaling, in intracellular transport, and even in inter-cellular communications. despite their ubiquitous distribution, and the broad and lasting interest invested in those microdomains, their actual nature and composition, and even the physical rules that regiment their assembly still remain elu ... | 2014 | 24634670 |
| the dynamic nature of genomes across the tree of life. | genomes are dynamic in lineages across the tree of life. among bacteria and archaea, for example, dna content varies throughout life cycles, and nonbinary cell division in diverse lineages indicates the need for coordination of the inheritance of genomes. these observations contrast with the textbook view that bacterial and archaeal genomes are monoploid (i.e., single copied) and fixed both within species and throughout an individual's lifetime. here, we synthesize information on three aspects o ... | 2014 | 24500971 |
| the candidate phylum poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features. | the candidate phylum poribacteria is one of the most dominant and widespread members of the microbial communities residing within marine sponges. cell compartmentalization had been postulated along with their discovery about a decade ago and their phylogenetic association to the planctomycetes, verrucomicrobia, chlamydiae superphylum was proposed soon thereafter. in the present study we revised these features based on genomic data obtained from six poribacterial single cells. we propose that por ... | 2014 | 24498082 |
| 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 |
| draft genome of gemmata massiliana sp. nov, a water-borne planctomycetes species exhibiting two variants. | gemmata massiliana is a new planctomycetes bacterium isolated from a hospital water network in france, using a new culture medium. it is an aerobic microorganism with optimal growth at ph 8, at 30 °c and salinity ≤ 1.25 % nacl. g. massiliana is resistant to β-lactam antibiotics, due to lack of peptidoglycan in its cell wall.g. massiliana shares a 97 % 16s rrna gene sequence similarity with the nearest species, gemmata obscuriglobus; and 99 % similarity with unnamed soil isolates. its 9,249,437-b ... | 2015 | 26649148 |
| the 29(th) annual symposium of the protein society, barcelona, spain, july 22-25, 2015. | | 2015 | 26452528 |
| genome of the facultative scuticociliatosis pathogen pseudocohnilembus persalinus provides insight into its virulence through horizontal gene transfer. | certain ciliates of the subclass scuticociliatia (scuticociliates) are facultative parasites of fishes in which they cause a suite of diseases collectively termed scuticociliatosis. hitherto, comparatively little was known about genetics and genomics of scuticociliates or the mechanism of scuticociliatosis. in this study, a laboratory culture of the facultatively pathogenic scuticociliate pseudocohnilembus persalinus was established and its genome sequenced, giving the first genome of a marine c ... | 2015 | 26486372 |
| open questions on the origin of eukaryotes. | despite recent progress, the origin of the eukaryotic cell remains enigmatic. it is now known that the last eukaryotic common ancestor was complex and that endosymbiosis played a crucial role in eukaryogenesis at least via the acquisition of the alphaproteobacterial ancestor of mitochondria. however, the nature of the mitochondrial host is controversial, although the recent discovery of an archaeal lineage phylogenetically close to eukaryotes reinforces models proposing archaea-derived hosts. we ... | 2015 | 26455774 |
| endosymbiotic theories for eukaryote origin. | for over 100 years, endosymbiotic theories have figured in thoughts about the differences between prokaryotic and eukaryotic cells. more than 20 different versions of endosymbiotic theory have been presented in the literature to explain the origin of eukaryotes and their mitochondria. very few of those models account for eukaryotic anaerobes. the role of energy and the energetic constraints that prokaryotic cell organization placed on evolutionary innovation in cell history has recently come to ... | 2015 | 26323761 |
| cell walls and the convergent evolution of the viral envelope. | why some viruses are enveloped while others lack an outer lipid bilayer is a major question in viral evolution but one that has received relatively little attention. the viral envelope serves several functions, including protecting the rna or dna molecule(s), evading recognition by the immune system, and facilitating virus entry. despite these commonalities, viral envelopes come in a wide variety of shapes and configurations. the evolution of the viral envelope is made more puzzling by the fact ... | 2015 | 26378223 |
| the initial state of the human gut microbiome determines its reshaping by antibiotics. | microbiome studies have demonstrated the high inter-individual diversity of the gut microbiota. however, how the initial composition of the microbiome affects the impact of antibiotics on microbial communities is relatively unexplored. to specifically address this question, we administered a second-generation cephalosporin, cefprozil, to healthy volunteers. stool samples gathered before antibiotic exposure, at the end of the treatment and 3 months later were analysed using shotgun metagenomic se ... | 2015 | 26359913 |
| the initial state of the human gut microbiome determines its reshaping by antibiotics. | microbiome studies have demonstrated the high inter-individual diversity of the gut microbiota. however, how the initial composition of the microbiome affects the impact of antibiotics on microbial communities is relatively unexplored. to specifically address this question, we administered a second-generation cephalosporin, cefprozil, to healthy volunteers. stool samples gathered before antibiotic exposure, at the end of the treatment and 3 months later were analysed using shotgun metagenomic se ... | 2015 | 26359913 |
| bacterial sigma factors and anti-sigma factors: structure, function and distribution. | sigma factors are multi-domain subunits of bacterial rna polymerase (rnap) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in rna synthesis. this review focuses on the structure and function of the major sigma-70 class that includes the housekeeping sigma factor (group 1) that directs the bulk of transcription during active growth, and structurally-related alternative sigma factors (groups 2-4) that control a w ... | 2015 | 26131973 |
| 18 ghz electromagnetic field induces permeability of gram-positive cocci. | the effect of electromagnetic field (emf) exposures at the microwave (mw) frequency of 18 ghz, on four cocci, planococcus maritimus kmm 3738, staphylococcus aureus cip 65.8(t), s. aureus atcc 25923 and s. epidermidis atcc 14990(t), was investigated. we demonstrate that exposing the bacteria to an emf induced permeability in the bacterial membranes of all strains studied, as confirmed directly by transmission electron microscopy (tem), and indirectly via the propidium iodide assay and the uptake ... | 2015 | 26077933 |
| 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 |
| olsg (sinac_1600) is an ornithine lipid n-methyltransferase from the planctomycete singulisphaera acidiphila. | ornithine lipids (ols) are phosphorus-free membrane lipids widespread in bacteria but absent from archaea and eukaryotes. in addition to the unmodified ols, a variety of ol derivatives hydroxylated in different structural positions has been reported. recently, methylated derivatives of ols were described in several planctomycetes isolated from a peat bog in northern russia, although the gene/enzyme responsible for the n-methylation of ol remained obscure. here we identify and characterize the ol ... | 2015 | 25925947 |
| a multi-functional tubulovesicular network as the ancestral eukaryotic endomembrane system. | the origin of the eukaryotic endomembrane system is still the subject of much speculation. we argue that the combination of two recent hypotheses addressing the eukaryotic endomembrane's early evolution supports the possibility that the ancestral membranes were organised as a multi-functional tubulovesicular network. one of the potential selective advantages provided by this organisation was the capacity to perform endocytosis. this possibility is illustrated by membrane organisations observed i ... | 2015 | 25811639 |
| the oxidosqualene cyclase from the oomycete saprolegnia parasitica synthesizes lanosterol as a single product. | the first committed step of sterol biosynthesis is the cyclisation of 2,3-oxidosqualene to form either lanosterol (la) or cycloartenol (ca). this is catalyzed by an oxidosqualene cyclase (osc). la and ca are subsequently converted into various sterols by a series of enzyme reactions. the specificity of the osc therefore determines the final composition of the end sterols of an organism. despite the functional importance of oscs, the determinants of their specificity are not well understood. in s ... | 2016 | 27881978 |
| microorganisms in confined habitats: microbial monitoring and control of intensive care units, operating rooms, cleanrooms and the international space station. | indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. most indoor environments are connected to the natural environment by high ventilation, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (iss) are extraordinary living and working areas for humans, with a limited exchange with the environment. the purposes for confinement are different: a p ... | 2016 | 27790191 |
| human contamination in public genome assemblies. | contamination in genome assembly can lead to wrong or confusing results when using such genome as reference in sequence comparison. although bacterial contamination is well known, the problem of human-originated contamination received little attention. in this study we surveyed 45,735 available genome assemblies for evidence of human contamination. we used lineage specificity to distinguish between contamination and conservation. we found that 154 genome assemblies contain fragments that with hi ... | 2016 | 27611326 |
| compartmentalization in pvc super-phylum: evolution and impact. | the pvc super-phylum gathers bacteria from seven phyla (planctomycetes, verrucomicrobiae, chlamydiae, lentisphaera, poribacteria, op3, wwe2) presenting different lifestyles, cell plans and environments. planctomyces and several verrucomicrobiae exhibit a complex cell plan, with an intracytoplasmic membrane inducing the compartmentalization of the cytoplasm into two regions (pirellulosome and paryphoplasm). the evolution and function of this cell plan is still subject to debate. in this work, we ... | 2016 | 27507008 |
| sterol synthesis in diverse bacteria. | sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. however, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. phylogenomic studies have identified g ... | 2016 | 27446030 |
| 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 |
| network-assisted investigation of virulence and antibiotic-resistance systems in pseudomonas aeruginosa. | pseudomonas aeruginosa is a gram-negative bacterium of clinical significance. although the genome of pao1, a prototype strain of p. aeruginosa, has been extensively studied, approximately one-third of the functional genome remains unknown. with the emergence of antibiotic-resistant strains of p. aeruginosa, there is an urgent need to develop novel antibiotic and anti-virulence strategies, which may be facilitated by an approach that explores p. aeruginosa gene function in systems-level models. h ... | 2016 | 27194047 |
| cytotoxicity of nanoparticles contained in food on intestinal cells and the gut microbiota. | toxicity of nanoparticles (nps) upon oral exposure has been studied in animals using physiological changes, behavior, histology, and blood analysis for evaluation. the effects recorded include the combination of the action on cells of the exposed animal and the reaction of the microorganisms that populate the external and internal surfaces of the body. the importance of these microorganisms, collectively termed as microbiota, for the health of the host has been widely recognized. they may also i ... | 2016 | 27058534 |
| 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 |
| 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 |
| 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 |
| comparative sequence analysis of is50/tn5 transposase. | comparative sequence analysis of is50 transposase-related protein sequences in conjunction with known structural, biochemical, and genetic data was used to determine domains and residues that play key roles in is50 transposase function. blast and clustalw analyses have been used to find and analyze six complete protein sequences that are related to the is50 transposase. the protein sequence identity of these six homologs ranged from 25 to 55% in comparison to the is50 transposase. homologous mot ... | 2004 | 15576772 |
| highly divergent genes for methanopterin-linked c1 transfer reactions in lake washington, assessed via metagenomic analysis and mrna detection. | the origins and the evolutionary history of tetrahydromethanopterin-linked c1 transfer reactions that are part of two environmentally important biotransformations, methylotrophy and methanogenesis, are still not well understood. in previous studies, we have expanded the known phylogenetic diversity of these reactions by identifying genes highly diverging from the ones associated with cultivated proteobacteria, planctomycetes, or archaea (m. g. kalyuzhnaya, m. e. lidstrom, and l. chistoserdova, m ... | 2005 | 16332881 |
| the origin of modern terrestrial life. | the study of the origin of life covers many areas of expertise and requires the input of various scientific communities. in recent years, this research field has often been viewed as part of a broader agenda under the name of "exobiology" or "astrobiology." in this review, we have somewhat narrowed this agenda, focusing on the origin of modern terrestrial life. the adjective "modern" here means that we did not speculate on different forms of life that could have possibly appeared on our planet, ... | 2007 | 19404443 |
| functional metagenomics reveals previously unrecognized diversity of antibiotic resistance genes in gulls. | wildlife may facilitate the spread of antibiotic resistance (ar) between human-dominated habitats and the surrounding environment. here, we use functional metagenomics to survey the diversity and genomic context of ar genes in gulls. using this approach, we found a variety of ar genes not previously detected in gulls and wildlife, including class a and c β-lactamases as well as six tetracycline resistance gene types. an analysis of the flanking sequences indicates that most of these genes are pr ... | 2011 | 22347872 |
| structural and functional insights from the metagenome of an acidic hot spring microbial planktonic community in the colombian andes. | a taxonomic and annotated functional description of microbial life was deduced from 53 mb of metagenomic sequence retrieved from a planktonic fraction of the neotropical high andean (3,973 meters above sea level) acidic hot spring el coquito (ec). a classification of unassembled metagenomic reads using different databases showed a high proportion of gammaproteobacteria and alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16s rrna gene fragments we observed th ... | 2012 | 23251687 |