Publications

membrane-bounded nucleoid in the eubacterium gemmatata obscuriglobus.	the freshwater budding eubacterium gemmata obscuriglobus possesses a dna-containing nuclear region that is bounded by two nuclear membranes. the membrane-bounded nature of the nucleoid in this bacterium was shown by thin sectioning of chemically fixed cells, thin sectioning of freeze-substituted cells, and freeze-fracture/freeze-etch. the fibrillar nucleoid was surrounded by electron-dense granules that were in turn enveloped by two nuclear membranes separated by an electron-transparent space. i ...	1991	11607213
unraveling the extent of diversity within the order planctomycetales.	the phylogenetic positions of 22 isolates that morphologically resemble members of the family planctomycetaceae were determined by sequence analysis of genes coding for 16s rrna. while nine and eight isolates could be assigned to the genera planctomyces and pirellula, respectively, three strains grouped near isosphaera pallida and one strain was closely related to gemmata obscuriglobus. no isolate was found to be related to a previously described species of any of the four genera at the species ...	1995	7793948
isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, penaeus monodon.	bacteria phenotypically resembling members of the phylogenetically distinct planctomycete group of the domain bacteria were isolated from postlarvae of the giant tiger prawn, penaeus monodon. a selective medium designed in the light of planctomycete antibiotic resistance characteristics was used for this isolation. planctomycetes were isolated from both healthy and monodon baculovirus-infected prawn postlarvae. the predominant colony type recovered from postlarvae regardless of viral infection s ...	1997	8979353
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
the chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists.	we present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. a chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. the archaebacterium, a thermoacidophil resembling extant thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to spirochaeta or hollandina that oxidized sulfide to sulfur. selection pressure for speed swimming and oxygen avoi ...	2000	10860956
comparative 16s rrna analysis of lake bacterioplankton reveals globally distributed phylogenetic clusters including an abundant group of actinobacteria.	in a search for cosmopolitan phylogenetic clusters of freshwater bacteria, we recovered a total of 190 full and partial 16s ribosomal dna (rdna) sequences from three different lakes (lake gossenköllesee, austria; lake fuchskuhle, germany; and lake baikal, russia). the phylogenetic comparison with the currently available rdna data set showed that our sequences fall into 16 clusters, which otherwise include bacterial rdna sequences of primarily freshwater and soil, but not marine, origin. six of t ...	2000	11055963
isolation of gemmata-like and isosphaera-like planctomycete bacteria from soil and freshwater.	new cultured strains of the planctomycete division (order planctomycetales) of the domain bacteria related to species in the genera gemmata and isosphaera were isolated from soil, freshwater, and a laboratory ampicillin solution. phylogenetic analysis of the 16s rrna gene from eight representative isolates showed that all the isolates were members of the planctomycete division. six isolates clustered with gemmata obscuriglobus and related strains, while two isolates clustered with isosphaera pal ...	2002	11772655
spatial distribution of total, ammonia-oxidizing, and denitrifying bacteria in biological wastewater treatment reactors for bioregenerative life support.	bioregenerative life support systems may be necessary for long-term space missions due to the high cost of lifting supplies and equipment into orbit. in this study, we investigated two biological wastewater treatment reactors designed to recover potable water for a spacefaring crew being tested at johnson space center. the experiment (lunar-mars life support test project-phase iii) consisted of four crew members confined in a test chamber for 91 days. in order to recycle all water during the exp ...	2002	11976099
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
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
phylogenetic and biochemical evidence for sterol synthesis in the bacterium gemmata obscuriglobus.	sterol biosynthesis is viewed primarily as a eukaryotic process, and the frequency of its occurrence in bacteria has long been a subject of controversy. two enzymes, squalene monooxygenase and oxidosqualene cyclase, are the minimum necessary for initial biosynthesis of sterols from squalene. in this work, 19 protein gene sequences for eukaryotic squalene monooxygenase and 12 protein gene sequences for eukaryotic oxidosqualene cyclase were compared with all available complete and partial prokaryo ...	2003	14660793
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
integron diversity in heavy-metal-contaminated mine tailings and inferences about integron evolution.	integrons are horizontal gene transfer (hgt) systems containing elements necessary for site-specific recombination and expression of foreign dna. the overall phylogenetic distribution of integrons and range of genes that can be transferred by integrons are unknown. this report contains an exploration of integrons in an environmental microbial community and an investigation of integron evolution. first, using culture-independent techniques, we explored the diversity of integrons and integron-tran ...	2004	14766601
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
biomarkers for in situ detection of anaerobic ammonium-oxidizing (anammox) bacteria.		2005	15811989
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
a census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial iq, extroverts and introverts.	analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction.	2005	15955239
analysis of gene islands involved in methanopterin-linked c1 transfer reactions reveals new functions and provides evolutionary insights.	in this study, the occurrence and chromosomal clustering of genes encoding c(1) transfer reactions linked to tetrahydromethanopterin (h(4)mpt) were analyzed in a variety of proteobacteria and in representatives of the planctomycetes via genomic analysis or via partial sequencing by cosmid walking. although a tendency for clustering was found common for the genes of interest, significant variations in gene order and the degree of clustering were uncovered both between and within different groups ...	2005	15968072
some assembly required: yeast septins provide the instruction manual.	septins are a family of conserved proteins that form hetero-oligomeric complexes that assemble into filaments. the filaments can be organized into linear arrays, coils, rings and gauzes. they serve as membrane-associated scaffolds and as barriers to demarcate local compartments, especially for the establishment of the septation site for cytokinesis. studies in budding and fission yeast have revealed many of the protein-protein interactions that govern the formation of multi-septin complexes. gtp ...	2005	16009555
mtdc, a novel class of methylene tetrahydromethanopterin dehydrogenases.	novel methylene tetrahydromethanopterin (h4mpt) dehydrogenase enzymes, named mtdc, were purified after expressing in escherichia coli genes from, respectively, gemmata sp. strain wa1-1 and environmental dna originating from unidentified microbial species. the mtdc enzymes were shown to possess high affinities for methylene-h4mpt and nadp but low affinities for methylene tetrahydrofolate or nad. the substrate range and the kinetic properties revealed by mtdc enzymes distinguish them from the prev ...	2005	16109948
identification of bacteria in biofilm and bulk water samples from a nonchlorinated model drinking water distribution system: detection of a large nitrite-oxidizing population associated with nitrospira spp.	in a model drinking water distribution system characterized by a low assimilable organic carbon content (<10 microg/liter) and no disinfection, the bacterial community was identified by a phylogenetic analysis of rrna genes amplified from directly extracted dna and colonies formed on r2a plates. biofilms of defined periods of age (14 days to 3 years) and bulk water samples were investigated. culturable bacteria were associated with proteobacteria and bacteriodetes, whereas independently of culti ...	2005	16332854
steroids, triterpenoids and molecular oxygen.	there is a close connection between modern-day biosynthesis of particular triterpenoid biomarkers and presence of molecular oxygen in the environment. thus, the detection of steroid and triterpenoid hydrocarbons far back in earth history has been used to infer the antiquity of oxygenic photosynthesis. this prompts the question: were these compounds produced similarly in the past? in this paper, we address this question with a review of the current state of knowledge surrounding the oxygen requir ...	2006	16754609
cell evolution and earth history: stasis and revolution.	this synthesis has three main parts. the first discusses the overall tree of life and nature of the last common ancestor (cenancestor). i emphasize key steps in cellular evolution important for ordering and timing the major evolutionary innovations in the history of the biosphere, explaining especially the origins of the eukaryote cell and of bacterial flagella and cell envelope novelties. second, i map the tree onto the fossil record and discuss dates of key events and their biogeochemical impa ...	2006	16754610
the last eukaryotic common ancestor (leca): acquisition of cytoskeletal motility from aerotolerant spirochetes in the proterozoic eon.	we develop a symbiogenetic concept of the origin of eukaryotic intracellular motility systems from anaerobic but aerotolerant spirochetes in sulfide-rich environments. the last eukaryotic common ancestors (lecas) have extant archaeprotist descendants: motile nucleated cells with embden-meyerhof glycolysis and substrate-level phosphorylation that lack the alpha-proteobacterial symbiont that became the mitochondrion. swimming and regulated o(2)-tolerance via sulfide oxidation already had been acqu ...	2006	16938841
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
identification of important regions for ethylene binding and signaling in the transmembrane domain of the etr1 ethylene receptor of arabidopsis.	the ethylene binding domain (ebd) of the arabidopsis thaliana etr1 receptor is modeled as three membrane-spanning helices. we surveyed ethylene binding activity in different kingdoms and performed a bioinformatic analysis of the ebd. ethylene binding is confined to land plants, chara, and a group of cyanobacteria but is largely absent in other organisms, consistent with our finding that ebd-like sequences are overrepresented among plant and cyanobacterial species. we made amino acid substitution ...	2006	17189345
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
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
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
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
palaeoproterozoic ice houses and the evolution of oxygen-mediating enzymes: the case for a late origin of photosystem ii.	two major geological problems regarding the origin of oxygenic photosynthesis are (i) identifying a source of oxygen pre-dating the biological oxygen production and capable of driving the evolution of oxygen tolerance, and (ii) determining when oxygenic photosynthesis evolved. one solution to the first problem is the accumulation of photochemically produced h(2)o(2) at the surface of the glaciers and its subsequent incorporation into ice. melting at the glacier base would release h(2)o(2), which ...	2008	18487128
profilegrids as a new visual representation of large multiple sequence alignments: a case study of the reca protein family.	multiple sequence alignments are a fundamental tool for the comparative analysis of proteins and nucleic acids. however, large data sets are no longer manageable for visualization and investigation using the traditional stacked sequence alignment representation.	2008	19102758
a new family of polymerases related to superfamily a dna polymerases and t7-like dna-dependent rna polymerases.	using sequence profile methods and structural comparisons we characterize a previously unknown family of nucleic acid polymerases in a group of mobile elements from genomes of diverse bacteria, an algal plastid and certain dna viruses, including the recently reported sputnik virus. using contextual information from domain architectures and gene-neighborhoods we present evidence that they are likely to possess both primase and dna polymerase activity, comparable to the previously reported prim-po ...	2008	18834537
genomics of biological wastewater treatment.		2008	21261852
the last universal common ancestor: emergence, constitution and genetic legacy of an elusive forerunner.	since the reclassification of all life forms in three domains (archaea, bacteria, eukarya), the identity of their alleged forerunner (last universal common ancestor or luca) has been the subject of extensive controversies: progenote or already complex organism, prokaryote or protoeukaryote, thermophile or mesophile, product of a protracted progression from simple replicators to complex cells or born in the cradle of "catalytically closed" entities? we present a critical survey of the topic and s ...	2008	18613974
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
horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein s4.	the universal ribosomal protein s4 is essential for the initiation of small subunit ribosomal assembly and translational accuracy. being part of the information processing machinery of the cell, the gene for s4 is generally thought of as being inherited vertically and has been used in concatenated gene phylogenies. here we report the evolution of ribosomal protein s4 in relation to a broad sharing of zinc/non-zinc forms of the gene and study the scope of horizontal gene transfer (hgt) of s4 duri ...	2009	19640295
electron cryotomography: a new view into microbial ultrastructure.	electron cryotomography (ect) is an emerging technology that allows thin samples such as small bacterial cells to be imaged in 3d in a nearly native state to 'molecular' (approximately 4nm) resolution. as such, ect is beginning to deliver long-awaited insight into the positions and structures of cytoskeletal filaments, cell wall elements, motility machines, chemoreceptor arrays, internal compartments, and other ultrastructures. here we briefly explain ect, review its recent contributions to micr ...	2009	19427259
phylogenomics of dna topoisomerases: their origin and putative roles in the emergence of modern organisms.	topoisomerases are essential enzymes that solve topological problems arising from the double-helical structure of dna. as a consequence, one should have naively expected to find homologous topoisomerases in all cellular organisms, dating back to their last common ancestor. however, as observed for other enzymes working with dna, this is not the case. phylogenomics analyses indicate that different sets of topoisomerases were present in the most recent common ancestors of each of the three cellula ...	2009	19208647
new superfamilies of eukaryotic dna transposons and their internal divisions.	despite their enormous diversity and abundance, all currently known eukaryotic dna transposons belong to only 15 superfamilies. here, we report two new superfamilies of dna transposons, named sola and zator. sola transposons encode ddd-transposases (transposase, tpase) and are flanked by 4-bp target site duplications (tsd). elements from the sola superfamily are distributed in a variety of species including bacteria, protists, plants, and metazoans. they can be divided into three distinct groups ...	2009	19174482
the cell cycle of the planctomycete gemmata obscuriglobus with respect to cell compartmentalization.	gemmata obscuriglobus is a distinctive member of the divergent phylum planctomycetes, all known members of which are peptidoglycan-less bacteria with a shared compartmentalized cell structure and divide by a budding process. g. obscuriglobus in addition shares the unique feature that its nucleoid dna is surrounded by an envelope consisting of two membranes forming an analogous structure to the membrane-bounded nucleoid of eukaryotes and therefore g. obscuriglobus forms a special model for cell b ...	2009	19144151
formation of multilayered photosynthetic biofilms in an alkaline thermal spring in yellowstone national park, wyoming.	in this study, glass rods suspended at the air-water interface in the runoff channel of fairy geyser, yellowstone national park, wy, were used as a substratum to promote the development of biofilms that resembled multilayered mat communities in the splash zone at the geyser's source. this approach enabled the establishment of the temporal relationship between the appearance of cyanobacteria, which ultimately formed the outer green layer, and the development of a red underlayer containing roseifl ...	2009	19218404
insights into the evolution of sialic acid catabolism among bacteria.	sialic acids comprise a family of nine-carbon amino sugars that are prevalent in mucus rich environments. sialic acids from the human host are used by a number of pathogens as an energy source. here we explore the evolution of the genes involved in the catabolism of sialic acid.	2009	19470179
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
prokaryotic homologs of argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.	in eukaryotes, rna interference (rnai) is a major mechanism of defense against viruses and transposable elements as well of regulating translation of endogenous mrnas. the rnai systems recognize the target rna molecules via small guide rnas that are completely or partially complementary to a region of the target. key components of the rnai systems are proteins of the argonaute-piwi family some of which function as slicers, the nucleases that cleave the target rna that is base-paired to a guide r ...	2009	19706170
bioinformatics and functional analysis define four distinct groups of alkb dna-dioxygenases in bacteria.	the iron(ii)- and 2-oxoglutarate (2og)-dependent dioxygenase alkb from escherichia coli (ecalkb) repairs alkylation damage in dna by direct reversal. ecalkb substrates include methylated bases, such as 1-methyladenine (m(1)a) and 3-methylcytosine (m(3)c), as well as certain bulkier lesions, for example the exocyclic adduct 1,n(6)-ethenoadenine (epsilona). ecalkb is the only bacterial alkb protein characterized to date, and we here present an extensive bioinformatics and functional analysis of ba ...	2009	19786499
unusual thermal disassembly of the spfh domain oligomer from pyrococcus horikoshii.	stomatin, prohibitin, flotillin, and hflk/c (spfh) domain proteins are membrane proteins that are widely conserved from bacteria to mammals. the molecular functions of these proteins have not been established. in mammals, the domain is often found in raft-associated proteins such as flotillin and podocin. we determined the structure of the spfh domain of ph0470 derived from pyrococcus horikoshii using nmr. the structure closely resembles that of the spfh domain of the paralog ph1511, except for ...	2009	19804735
phylogenomics of sterol synthesis: insights into the origin, evolution, and diversity of a key eukaryotic feature.	the availability of complete genomes from a wide sampling of eukaryotic diversity has allowed the application of phylogenomics approaches to study the origin and evolution of unique eukaryotic cellular structures, but these are still poorly applied to study unique eukaryotic metabolic pathways. sterols are a good example because they are an essential feature of eukaryotic membranes. the sterol pathway has been well dissected in vertebrates, fungi, and land plants. however, although different typ ...	2009	20333205
chromatin organization and radio resistance in the bacterium gemmata obscuriglobus.	the organization of chromatin has a major impact on cellular activities, such as gene expression. for bacteria, it was suggested that the spatial organization of the genetic material correlates with transcriptional levels, implying a specific architecture of the chromosome within the cytoplasm. accordingly, recent technological advances have emphasized the organization of the genetic material within nucleoid structures. gemmata obscuriglobus, a member of the phylum planctomycetes, exhibits a dis ...	2009	19074379
chromatin organization and radio resistance in the bacterium gemmata obscuriglobus.	the organization of chromatin has a major impact on cellular activities, such as gene expression. for bacteria, it was suggested that the spatial organization of the genetic material correlates with transcriptional levels, implying a specific architecture of the chromosome within the cytoplasm. accordingly, recent technological advances have emphasized the organization of the genetic material within nucleoid structures. gemmata obscuriglobus, a member of the phylum planctomycetes, exhibits a dis ...	2009	19074379
gene cloning and characterization of a novel esterase from activated sludge metagenome.	a metagenomic library was prepared using pcc2fos vector containing about 3.0 gbp of community dna from the microbial assemblage of activated sludge. screening of a part of the un-amplified library resulted in the finding of 1 unique lipolytic clone capable of hydrolyzing tributyrin, in which an esterase gene was identified. this esterase/lipase gene consists of 834 bp and encodes a polypeptide (designated estas) of 277 amino acid residuals with a molecular mass of 31 kda. sequence analysis indic ...	2009	20028524
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
protein uptake by bacteria: an endocytosis-like process in the planctomycete gemmata obscuriglobus.	endocytosis is a fundamental process of membrane-trafficking in eukaryotes, but has not been known to occur in bacteria or archaea. the origin of endocytosis is central to the understanding of evolution of the first eukaryotes and their endomembrane systems. in a recent study we have established that an endocytosis-like process for uptake of proteins into cells occurs in a bacterium, gemmata obscuriglobus, a member of the distinctive phylum planctomycetes of peptidoglycan-less budding bacteria. ...	2010	21331243
endocytosis-like protein uptake in the bacterium gemmata obscuriglobus.	endocytosis is a process by which extracellular material such as macromolecules can be incorporated into cells via a membrane-trafficking system. although universal among eukaryotes, endocytosis has not been identified in bacteria or archaea. however, intracellular membranes are known to compartmentalize cells of bacteria in the phylum planctomycetes, suggesting the potential for endocytosis and membrane trafficking in members of this phylum. here we show that cells of the planctomycete gemmata ...	2010	20566852
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
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
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
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
uniting sex and eukaryote origins in an emerging oxygenic world.	theories about eukaryote origins (eukaryogenesis) need to provide unified explanations for the emergence of diverse complex features that define this lineage. models that propose a prokaryote-to-eukaryote transition are gridlocked between the opposing "phagocytosis first" and "mitochondria as seed" paradigms, neither of which fully explain the origins of eukaryote cell complexity. sex (outcrossing with meiosis) is an example of an elaborate trait not yet satisfactorily addressed in theories abou ...	2010	20731852
bacteria with a eukaryotic touch: a glimpse of ancient evolution?		2010	20624972
single-cell genomics reveals the lifestyle of poribacteria, a candidate phylum symbiotically associated with marine sponges.	in this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum poribacteria, members of which are nearly exclusively found in marine sponges. the microbial consortia of the mediterranean sponge aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated 'whole-genome amplification'. pyrosequencing of a single amplified genome (sag) derived from a memb ...	2010	20613790
single-cell genomics reveals the lifestyle of poribacteria, a candidate phylum symbiotically associated with marine sponges.	in this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum poribacteria, members of which are nearly exclusively found in marine sponges. the microbial consortia of the mediterranean sponge aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated 'whole-genome amplification'. pyrosequencing of a single amplified genome (sag) derived from a memb ...	2010	20613790
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
the influence of rickettsiologists on post-modern microbiology.	many of the definitions in microbiology are currently false. we have reviewed the great denominations of microbiology and attempted to free microorganisms from the theories of the twentieth century. the presence of compartmentation and a nucleoid in planctomycetes clearly calls into question the accuracy of the definitions of eukaryotes and prokaryotes. archaea are viewed as prokaryotes resembling bacteria. however, the name archaea, suggesting an archaic origin of lifestyle, is inconsistent wit ...	2011	22919574
transitional forms between the three domains of life and evolutionary implications.	the question as to the origin and relationship between the three domains of life is lodged in a phylogenetic impasse. the dominant paradigm is to see the three domains as separated. however, the recently characterized bacterial species have suggested continuity between the three domains. here, we review the evidence in support of this hypothesis and evaluate the implications for and against the models of the origin of the three domains of life. the existence of intermediate steps between the thr ...	2011	21920985
evolution: on a bender--bars, escrts, cops, and finally getting your coat.	tremendous variety in form and function is displayed among the intracellular membrane systems of different eukaryotes. until recently, few clues existed as to how these internal membrane systems had originated and diversified. however, proteomic, structural, and comparative genomics studies together have revealed extensive similarities among many of the protein complexes used in controlling the morphology and trafficking of intracellular membranes. these new insights have had a profound impact o ...	2011	21670211
distribution and functions of sterols and sphingolipids.	sterols and sphingolipids are considered mainly eukaryotic lipids even though both are present in some prokaryotes, with sphingolipids being more widespread than sterols. both sterols and sphingolipids differ in their structural features in vertebrates, plants, and fungi. interestingly, some invertebrates cannot synthesize sterols de novo and seem to have a reduced dependence on sterols. sphingolipids and sterols are found in the plasma membrane, but we do not have a clear picture of their preci ...	2011	21454248
a novel sterol desaturase-like protein promoting dealkylation of phytosterols in tetrahymena thermophila.	the gene ttherm_00438800 (des24) from the ciliate tetrahymena thermophila encodes a protein with three conserved histidine clusters, typical of the fatty acid hydroxylase superfamily. despite its high similarity to sterol desaturase-like enzymes, the phylogenetic analysis groups des24p in a separate cluster more related to bacterial than to eukaryotic proteins, suggesting a possible horizontal gene transfer event. a somatic knockout of des24 revealed that the gene encodes a protein, des24p, whic ...	2011	21257793
harnessing the power of microbial genomics for exploring exceptions and shifting perceptions.		2011	21687802
harnessing the power of microbial genomics for exploring exceptions and shifting perceptions.		2011	21687802
comprehensive analysis of host gene expression in autographa californica nucleopolyhedrovirus-infected spodoptera frugiperda cells.	autographa californica multicapsid nucleopolyhedrovirus (acmnpv) is the best-studied baculovirus and most commonly used virus vector for baculovirus expression vector systems. the effect of acmnpv infection on host cells is incompletely understood. a microarray based on spodoptera frugiperda ests was used to investigate the impact of acmnpv on host gene expression in cultured s. frugiperda, sf21 cells. most host genes were down-regulated over the time course of infection, although a small number ...	2011	21276998
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
squalene-hopene cyclases.	hopanoids and sterols are members of a large group of cyclic triterpenoic compounds that have important functions in many prokaryotic and eukaryotic organisms. they are biochemically synthesized from linear precursors (squalene, 2,3-oxidosqualene) in only one enzymatic step that is catalyzed by squalene-hopene cyclase (shc) or oxidosqualene cyclase (osc). shcs and oscs are related in amino acid sequences and probably are derived from a common ancestor. the shc reaction requires the formation of ...	2011	21531832
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
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
the n-terminal amphipathic helix of the topological specificity factor mine is associated with shaping membrane curvature.	pole-to-pole oscillations of the min proteins in escherichia coli are required for the proper placement of the division septum. direct interaction of mine with the cell membrane is critical for the dynamic behavior of the min system. in vitro, this mine-membrane interaction led to membrane deformation; however, the underlying mechanism remained unclear. here we report that mine-induced membrane deformation involves the formation of an amphipathic helix of mine(2-9), which, together with the adja ...	2011	21738659
conservation of the human integrin-type beta-propeller domain in bacteria.	integrins are heterodimeric cell-surface receptors with key functions in cell-cell and cell-matrix adhesion. integrin α and β subunits are present throughout the metazoans, but it is unclear whether the subunits predate the origin of multicellular organisms. several component domains have been detected in bacteria, one of which, a specific 7-bladed β-propeller domain, is a unique feature of the integrin α subunits. here, we describe a structure-derived motif, which incorporates key features of e ...	2011	22022374
Planctomycetes and eukaryotes: a case of analogy not homology.	Planctomycetes, Verrucomicrobia and Chlamydia are prokaryotic phyla, sometimes grouped together as the PVC superphylum of eubacteria. Some PVC species possess interesting attributes, in particular, internal membranes that superficially resemble eukaryotic endomembranes. Some biologists now claim that PVC bacteria are nucleus-bearing prokaryotes and are considered evolutionary intermediates in the transition from prokaryote to eukaryote. PVC prokaryotes do not possess a nucleus and are not interm ...	2011	21858844
Cholesterol catabolism as a therapeutic target in Mycobacterium tuberculosis.	Mycobacterium tuberculosis (Mtb) is an intracellular pathogen that infects 10 million people worldwide and kills 2 million people every year. The uptake and utilization of nutrients by Mtb within the host cell is still poorly understood, although lipids play an important role in Mtb persistence. The recent identification of a large regulon of cholesterol catabolic genes suggests that Mtb can use host sterol for infection and persistence. In this review, we report on recent progress in elucidatio ...	2011	21924910
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
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
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
evaluating the evolutionary origins of unexpected character distributions within the bacterial planctomycetes-verrucomicrobia-chlamydiae superphylum.	recently, several characters that are absent from most bacteria, but which are found in many eukaryotes or archaea, have been identified within the bacterial planctomycetes-verrucomicrobia-chlamydiae (pvc) superphylum. hypotheses of the evolutionary history of such characters are commonly based on the inference of phylogenies of gene or protein families associated with the traits, estimated from multiple sequence alignments (msas). so far, studies of this kind have focused on the distribution of ...	2012	23189077
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
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
anaerobic ammonium-oxidizing bacteria: unique microorganisms with exceptional properties.	anaerobic ammonium-oxidizing (anammox) bacteria defy many microbiological concepts and share numerous properties with both eukaryotes and archaea. among their most intriguing characteristics are their compartmentalized cell plan and archaeon-like cell wall. here we review our current knowledge about anammox cell biology. the anammox cell is divided into three separate compartments by bilayer membranes. the anammox cell consists of (from outside to inside) the cell wall, paryphoplasm, riboplasm, ...	2012	22933561
dynamic viral populations in hypersaline systems as revealed by metagenomic assembly.	viruses of the bacteria and archaea play important roles in microbial evolution and ecology, and yet viral dynamics in natural systems remain poorly understood. here, we created de novo assemblies from 6.4 gbp of metagenomic sequence from eight community viral concentrate samples, collected from 12 h to 3 years apart from hypersaline lake tyrrell (lt), victoria, australia. through extensive manual assembly curation, we reconstructed 7 complete and 28 partial novel genomes of viruses and virus-li ...	2012	22773627
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
enrichment of microbial electrolysis cell biocathodes from sediment microbial fuel cell bioanodes.	electron-accepting (electrotrophic) biocathodes were produced by first enriching graphite fiber brush electrodes as the anodes in sediment-type microbial fuel cells (smfcs) using two different marine sediments and then electrically inverting the anodes to function as cathodes in two-chamber bioelectrochemical systems (bess). electron consumption occurred at set potentials of -439 mv and -539 mv (versus the potential of a standard hydrogen electrode) but not at -339 mv in minimal media lacking or ...	2012	22610438
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
telmatocola sphagniphila gen. nov., sp. nov., a novel dendriform planctomycete from northern wetlands.	members of the phylum planctomycetes are common inhabitants of northern wetlands. we used barcoded pyrosequencing to survey bacterial diversity in an acidic (ph 4.0) sphagnum peat sampled from the peat bog obukhovskoye, european north russia. a total of 21189 bacterial 16s rrna gene sequences were obtained, of which 1081 reads (5.1%) belonged to the planctomycetes. two-thirds of these sequences affiliated with planctomycete groups for which characterized representatives have not yet been availab ...	2012	22529844
practical considerations for conducting ecotoxicity test methods with manufactured nanomaterials: what have we learnt so far?	this review paper reports the consensus of a technical workshop hosted by the european network, nanoimpactnet (nin). the workshop aimed to review the collective experience of working at the bench with manufactured nanomaterials (mnms), and to recommend modifications to existing experimental methods and oecd protocols. current procedures for cleaning glassware are appropriate for most mnms, although interference with electrodes may occur. maintaining exposure is more difficult with mnms compared ...	2012	22422174
lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen.	sterols are key components of eukaryotic cellular membranes that are synthesized by multi-enzyme pathways that require molecular oxygen. because prokaryotes fundamentally lack sterols, it is unclear how the vast diversity of bacterivorous eukaryotes that inhabit hypoxic environments obtain, or synthesize, sterols. here we show that tetrahymanol, a triterpenoid that does not require molecular oxygen for its biosynthesis, likely functions as a surrogate of sterol in eukaryotes inhabiting oxygen-po ...	2012	22296756
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
why are bacteria different from eukaryotes?		2013	24330667
architecture and host interface of environmental chlamydiae revealed by electron cryotomography.	chlamydiae comprise important pathogenic and symbiotic bacteria that alternate between morphologically and physiologically different life stages during their developmental cycle. using electron cryotomography, we characterize the ultrastructure of the developmental stages of three environmental chlamydiae: parachlamydia acanthamoebae, protochlamydia amoebophila and simkania negevensis. we show that chemical fixation and dehydration alter the cell shape of parachlamydia and that the crescent body ...	2013	24118768