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Kletzin A, Heimerl T, Flechsler J, van Niftrik L, Rachel R, Klingl A. Cytochromes c in Archaea: distribution, maturation, cell architecture, and the special case of Ignicoccus hospitalis. Front Microbiol 2015; 6:439. [PMID: 26029183 PMCID: PMC4429474 DOI: 10.3389/fmicb.2015.00439] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/23/2015] [Indexed: 01/25/2023] Open
Abstract
Cytochromes c (Cytc) are widespread electron transfer proteins and important enzymes in the global nitrogen and sulfur cycles. The distribution of Cytc in more than 300 archaeal proteomes deduced from sequence was analyzed with computational methods including pattern and similarity searches, secondary and tertiary structure prediction. Two hundred and fifty-eight predicted Cytc (with single, double, or multiple heme c attachment sites) were found in some but not all species of the Desulfurococcales, Thermoproteales, Archaeoglobales, Methanosarcinales, Halobacteriales, and in two single-cell genome sequences of the Thermoplasmatales, all of them Cren- or Euryarchaeota. Other archaeal phyla including the Thaumarchaeota are so far free of these proteins. The archaeal Cytc sequences were bundled into 54 clusters of mutual similarity, some of which were specific for Archaea while others had homologs in the Bacteria. The cytochrome c maturation system I (CCM) was the only one found. The highest number and variability of Cytc were present in those species with known or predicted metal oxidation and/or reduction capabilities. Paradoxical findings were made in the haloarchaea: several Cytc had been purified biochemically but corresponding proteins were not found in the proteomes. The results are discussed with emphasis on cell morphologies and envelopes and especially for double-membraned Archaea-like Ignicoccus hospitalis. A comparison is made with compartmentalized bacteria such as the Planctomycetes of the Anammox group with a focus on the putative localization and roles of the Cytc and other electron transport proteins.
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Affiliation(s)
- Arnulf Kletzin
- Department of Biology, Sulfur Biochemistry and Microbial Bioenergetics, Technische Universität Darmstadt Darmstadt, Germany
| | - Thomas Heimerl
- Fakultät für Biologie und Vorklinische Medizin, Zentrum für Elektronenmikroskopie, Universität Regensburg Regensburg, Germany
| | - Jennifer Flechsler
- Fakultät für Biologie und Vorklinische Medizin, Zentrum für Elektronenmikroskopie, Universität Regensburg Regensburg, Germany
| | - Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University Nijmegen Nijmegen, Netherlands
| | - Reinhard Rachel
- Fakultät für Biologie und Vorklinische Medizin, Zentrum für Elektronenmikroskopie, Universität Regensburg Regensburg, Germany
| | - Andreas Klingl
- Department of Biology I, Plant Development, Biocenter LMU Munich Planegg-Martinsried, Germany
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Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem. ISME JOURNAL 2015; 9:2697-711. [PMID: 25918833 DOI: 10.1038/ismej.2015.66] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 02/05/2015] [Accepted: 03/18/2015] [Indexed: 11/08/2022]
Abstract
Marine microbial communities experience daily fluctuations in light and temperature that can have important ramifications for carbon and nutrient cycling. Elucidation of such short time scale community-wide dynamics is hindered by system complexity. Hypersaline aquatic environments have lower species richness than marine environments and can be well-defined spatially, hence they provide a model system for diel cycle analysis. We conducted a 3-day time series experiment in a well-defined pool in hypersaline Lake Tyrrell, Australia. Microbial communities were tracked by combining cultivation-independent lipidomic, metagenomic and microscopy methods. The ratio of total bacterial to archaeal core lipids in the planktonic community increased by up to 58% during daylight hours and decreased by up to 32% overnight. However, total organism abundances remained relatively consistent over 3 days. Metagenomic analysis of the planktonic community composition, resolved at the genome level, showed dominance by Haloquadratum species and six uncultured members of the Halobacteriaceae. The post 0.8 μm filtrate contained six different nanohaloarchaeal types, three of which have not been identified previously, and cryo-transmission electron microscopy imaging confirmed the presence of small cells. Notably, these nano-sized archaea showed a strong diel cycle, with a pronounced increase in relative abundance over the night periods. We detected no eukaryotic algae or other photosynthetic primary producers, suggesting that carbon resources may derive from patchily distributed microbial mats at the sediment-water interface or from surrounding land. Results show the operation of a strong community-level diel cycle, probably driven by interconnected temperature, light abundance, dissolved oxygen concentration and nutrient flux effects.
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Unravelling the Role of the F55 Regulator in the Transition from Lysogeny to UV Induction of Sulfolobus Spindle-Shaped Virus 1. J Virol 2015; 89:6453-61. [PMID: 25878101 DOI: 10.1128/jvi.00363-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/03/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Sulfolobus spindle-shaped virus 1 represents a model for studying virus-host interaction in harsh environments, and it is so far the only member of the family Fuselloviridae that shows a UV-inducible life cycle. Although the virus has been extensively studied, mechanisms underpinning the maintenance of lysogeny as well as those regulating the UV induction have received little attention. Recently, a novel SSV1 transcription factor, F55, was identified. This factor was able to bind in vitro to several sequences derived from the early and UV-inducible promoters of the SSV1 genome. The location of these binding sites together with the differential affinity of F55 for these sequences led to the hypothesis that this protein might be involved in the maintenance of the SSV1 lysogeny. Here, we report an in vivo survey of the molecular events occurring at the UV-inducible region of the SSV1 genome, with a focus on the binding profile of F55 before and after the UV irradiation. The binding of F55 to the target promoters correlates with transcription repression, whereas its dissociation is paralleled by transcription activation. Therefore, we propose that F55 acts as a molecular switch for the transcriptional regulation of the early viral genes. IMPORTANCE Functional genomic studies of SSV1 proteins have been hindered by the lack of similarity with other characterized proteins. As a result, few insights into their in vivo roles have been gained throughout the last 3 decades. Here, we report the first in vivo investigation of an SSV1 transcription regulator, F55, that plays a key role in the transition from the lysogenic to the induced state of SSV1. We show that F55 regulates the expression of the UV-inducible as well as the early genes. Moreover, the differential affinity of this transcription factor for these targets allows a fine-tuned and temporal coordinated regulation of transcription of viral genes.
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54
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Aliaga Goltsman DS, Comolli LR, Thomas BC, Banfield JF. Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities. THE ISME JOURNAL 2015; 9:1014-23. [PMID: 25361394 PMCID: PMC4817702 DOI: 10.1038/ismej.2014.200] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/08/2014] [Accepted: 09/16/2014] [Indexed: 12/21/2022]
Abstract
A fundamental question in microbial ecology relates to community structure, and how this varies across environment types. It is widely believed that some environments, such as those at very low pH, host simple communities based on the low number of taxa, possibly due to the extreme environmental conditions. However, most analyses of species richness have relied on methods that provide relatively low ribosomal RNA (rRNA) sampling depth. Here we used community transcriptomics to analyze the microbial diversity of natural acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. Our analyses target deep pools of rRNA gene transcripts recovered from both natural and laboratory-grown biofilms across varying developmental stages. In all, 91.8% of the ∼ 254 million Illumina reads mapped to rRNA genes represented in the SILVA database. Up to 159 different taxa, including Bacteria, Archaea and Eukaryotes, were identified. Diversity measures, ordination and hierarchical clustering separate environmental from laboratory-grown biofilms. In part, this is due to the much larger number of rare members in the environmental biofilms. Although Leptospirillum bacteria generally dominate biofilms, we detect a wide variety of other Nitrospira organisms present at very low abundance. Bacteria from the Chloroflexi phylum were also detected. The results indicate that the primary characteristic that has enabled prior extensive cultivation-independent 'omic' analyses is not simplicity but rather the high dominance by a few taxa. We conclude that a much larger variety of organisms than previously thought have adapted to this extreme environment, although only few are selected for at any one time.
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Affiliation(s)
| | - Luis R Comolli
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brian C Thomas
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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55
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Luef B, Frischkorn KR, Wrighton KC, Holman HYN, Birarda G, Thomas BC, Singh A, Williams KH, Siegerist CE, Tringe SG, Downing KH, Comolli LR, Banfield JF. Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun 2015; 6:6372. [DOI: 10.1038/ncomms7372] [Citation(s) in RCA: 266] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/23/2015] [Indexed: 02/04/2023] Open
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Lang K, Schuldes J, Klingl A, Poehlein A, Daniel R, Brune A. New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. Appl Environ Microbiol 2015; 81:1338-52. [PMID: 25501486 PMCID: PMC4309702 DOI: 10.1128/aem.03389-14] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/08/2014] [Indexed: 11/20/2022] Open
Abstract
The recently discovered seventh order of methanogens, the Methanomassiliicoccales (previously referred to as “Methanoplasmatales”), so far consists exclusively of obligately hydrogen-dependent methylotrophs. We sequenced the complete genome of “Candidatus Methanoplasma termitum” from a highly enriched culture obtained from the intestinal tract of termites and compared it with the previously published genomes of three other strains from the human gut, including the first isolate of the order. Like all other strains, “Ca. Methanoplasma termitum” lacks the entire pathway for CO2 reduction to methyl coenzyme Mand produces methane by hydrogen-dependent reduction of methanol or methylamines, which is consistent with additional physiological data. However, the shared absence of cytochromes and an energy-converting hydrogenase for the reoxidation of the ferredoxin produced by the soluble heterodisulfide reductase indicates that Methanomassiliicoccales employ a new mode of energy metabolism, which differs from that proposed for the obligately methylotrophic Methanosphaera stadtmanae. Instead, all strains possess a novel complex that is related to the F420:methanophenazine oxidoreductase (Fpo) of Methanosarcinales butlacks an F420-oxidizing module, resembling the apparently ferredoxin-dependent Fpo-like homolog in Methanosaeta thermophila. Since all Methanomassiliicoccales also lack the subunit E of the membrane-bound heterodisulfide reductase (HdrDE), wepropose that the Fpo-like complex interacts directly with subunit D, forming an energy-converting ferredoxin: heterodisulfideoxidoreductase. The dual function of heterodisulfide in Methanomassiliicoccales, which serves both in electron bifurcation and as terminal acceptor in a membrane-associated redox process, may be a unique characteristic of the novel order.
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Affiliation(s)
- Kristina Lang
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörg Schuldes
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Andreas Klingl
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Anja Poehlein
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Andreas Brune
- Department of Biogeochemistry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
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57
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Lovley DR, Malvankar NS. Seeing is believing: novel imaging techniques help clarify microbial nanowire structure and function. Environ Microbiol 2015; 17:2209-15. [PMID: 25384844 DOI: 10.1111/1462-2920.12708] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 10/26/2014] [Accepted: 11/06/2014] [Indexed: 11/30/2022]
Abstract
Novel imaging approaches have recently helped to clarify the properties of 'microbial nanowires'. Geobacter sulfurreducens pili are actual wires. They possess metallic-like conductivity, which can be attributed to overlapping pi-pi orbitals of key aromatic amino acids. Electrostatic force microscopy recently confirmed charge propagation along the pili, in a manner similar to carbon nanotubes. The pili are essential for long-range electron transport to insoluble electron acceptors and interspecies electron transfer. Previous claims that Shewanella oneidensis also produce conductive pili have recently been recanted, based on novel live-imaging studies. The putative pili are, in fact, long extensions of the cytochrome-rich outer membrane and periplasm that, when dried, collapse to form filaments with dimensions similar to pili. It has yet to be demonstrated whether the cytochrome-to-cytochrome electron hopping documented in the dried membrane extensions takes place in intact hydrated membrane extensions or whether the membrane extensions enhance electron transport to insoluble electron acceptors such as Fe(III) oxides or electrodes. These findings demonstrate that G. sulfurreducens conductive pili and the outer membrane extensions of S. oneidensis are fundamentally different in composition, mechanism of electron transport and physiological role. New methods for evaluating filament conductivity will facilitate screening the microbial world for nanowires and elucidating their function.
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Affiliation(s)
- Derek R Lovley
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA
| | - Nikhil S Malvankar
- Department of Microbiology, University of Massachusetts, Amherst, MA, USA.,Department of Physics, University of Massachusetts, Amherst, MA, USA
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58
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Brine assemblages of ultrasmall microbial cells within the ice cover of Lake Vida, Antarctica. Appl Environ Microbiol 2015; 80:3687-98. [PMID: 24727273 DOI: 10.1128/aem.00276-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The anoxic and freezing brine that permeates Lake Vida's perennial ice below 16 m contains an abundance of very small (≤0.2-μm) particles mixed with a less abundant population of microbial cells ranging from >0.2 to 1.5 μm in length. Fluorescent DNA staining, electron microscopy (EM) observations, elemental analysis, and extraction of high-molecular-weight genomic DNA indicated that a significant portion of these ultrasmall particles are cells. A continuous electron-dense layer surrounding a less electron-dense region was observed by EM, indicating the presence of a biological membrane surrounding a cytoplasm. The ultrasmall cells are 0.192 ± 0.065 μm, with morphology characteristic of coccoid and diplococcic bacterial cells, often surrounded by iron-rich capsular structures. EM observations also detected the presence of smaller unidentified nanoparticles of 0.020 to 0.140 μm among the brine cells. A 16S rRNA gene clone library from the brine 0.1- to 0.2-μm-size fraction revealed a relatively low-diversity assemblage of Bacteria sequences distinct from the previously reported >0.2-μm-cell-size Lake Vida brine assemblage. The brine 0.1- to 0.2-μm-size fraction was dominated by the Proteobacteria-affiliated genera Herbaspirillum, Pseudoalteromonas, and Marinobacter. Cultivation efforts of the 0.1- to 0.2-μm-size fraction led to the isolation of Actinobacteria-affiliated genera Microbacterium and Kocuria. Based on phylogenetic relatedness and microscopic observations, we hypothesize that the ultrasmall cells in Lake Vida brine are ultramicrocells that are likely in a reduced size state as a result of environmental stress or life cycle-related conditions.
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59
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Delgado L, Martínez G, López-Iglesias C, Mercadé E. Cryo-electron tomography of plunge-frozen whole bacteria and vitreous sections to analyze the recently described bacterial cytoplasmic structure, the Stack. J Struct Biol 2015; 189:220-9. [PMID: 25617813 DOI: 10.1016/j.jsb.2015.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/13/2015] [Indexed: 11/25/2022]
Abstract
Cryo-electron tomography (CET) of plunge-frozen whole bacteria and vitreous sections (CETOVIS) were used to revise and expand the structural knowledge of the "Stack", a recently described cytoplasmic structure in the Antarctic bacterium Pseudomonas deceptionensis M1(T). The advantages of both techniques can be complementarily combined to obtain more reliable insights into cells and their components with three-dimensional imaging at different resolutions. Cryo-electron microscopy (Cryo-EM) and CET of frozen-hydrated P. deceptionensis M1(T) cells confirmed that Stacks are found at different locations within the cell cytoplasm, in variable number, separately or grouped together, very close to the plasma membrane (PM) and oriented at different angles (from 35° to 90°) to the PM, thus establishing that they were not artifacts of the previous sample preparation methods. CET of plunge-frozen whole bacteria and vitreous sections verified that each Stack consisted of a pile of oval disc-like subunits, each disc being surrounded by a lipid bilayer membrane and separated from each other by a constant distance with a mean value of 5.2±1.3nm. FM4-64 staining and confocal microscopy corroborated the lipid nature of the membrane of the Stacked discs. Stacks did not appear to be invaginations of the PM because no continuity between both membranes was visible when whole bacteria were analyzed. We are still far from deciphering the function of these new structures, but a first experimental attempt links the Stacks with a given phase of the cell replication process.
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Affiliation(s)
- Lidia Delgado
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain; Department of Microbiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Gema Martínez
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain
| | - Carmen López-Iglesias
- Cryo-Electron Microscopy, Scientific and Technological Centers, University of Barcelona, Barcelona, Spain.
| | - Elena Mercadé
- Department of Microbiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain.
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60
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Biology of a widespread uncultivated archaeon that contributes to carbon fixation in the subsurface. Nat Commun 2014; 5:5497. [PMID: 25425419 DOI: 10.1038/ncomms6497] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/07/2014] [Indexed: 02/03/2023] Open
Abstract
Subsurface microbial life contributes significantly to biogeochemical cycling, yet it remains largely uncharacterized, especially its archaeal members. This 'microbial dark matter' has been explored by recent studies that were, however, mostly based on DNA sequence information only. Here, we use diverse techniques including ultrastuctural analyses to link genomics to biology for the SM1 Euryarchaeon lineage, an uncultivated group of subsurface archaea. Phylogenomic analyses reveal this lineage to belong to a widespread group of archaea that we propose to classify as a new euryarchaeal order ('Candidatus Altiarchaeales'). The representative, double-membraned species 'Candidatus Altiarchaeum hamiconexum' has an autotrophic metabolism that uses a not-yet-reported Factor420-free reductive acetyl-CoA pathway, confirmed by stable carbon isotopic measurements of archaeal lipids. Our results indicate that this lineage has evolved specific metabolic and structural features like nano-grappling hooks empowering this widely distributed archaeon to predominate anaerobic groundwater, where it may represent an important carbon dioxide sink.
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61
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Klingl A. S-layer and cytoplasmic membrane - exceptions from the typical archaeal cell wall with a focus on double membranes. Front Microbiol 2014; 5:624. [PMID: 25505452 PMCID: PMC4243693 DOI: 10.3389/fmicb.2014.00624] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 10/31/2014] [Indexed: 11/13/2022] Open
Abstract
The common idea of typical cell wall architecture in archaea consists of a pseudo-crystalline proteinaceous surface layer (S-layer), situated upon the cytoplasmic membrane. This is true for the majority of described archaea, hitherto. Within the crenarchaea, the S-layer often represents the only cell wall component, but there are various exceptions from this wall architecture. Beside (glycosylated) S-layers in (hyper)thermophilic cren- and euryarchaea as well as halophilic archaea, one can find a great variety of other cell wall structures like proteoglycan-like S-layers (Halobacteria), glutaminylglycan (Natronococci), methanochondroitin (Methanosarcina) or double layered cell walls with pseudomurein (Methanothermus and Methanopyrus). The presence of an outermost cellular membrane in the crenarchaeal species Ignicoccus hospitalis already gave indications for an outer membrane similar to Gram-negative bacteria. Although there is just limited data concerning their biochemistry and ultrastructure, recent studies on the euryarchaeal methanogen Methanomassiliicoccus luminyensis, cells of the ARMAN group, and the SM1 euryarchaeon delivered further examples for this exceptional cell envelope type consisting of two membranes.
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Affiliation(s)
- Andreas Klingl
- Plant Development, Department of Biology, Biocenter LMU Munich - Botany, Ludwig Maximilian University Munich Munich, Germany
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62
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Perras AK, Wanner G, Klingl A, Mora M, Auerbach AK, Heinz V, Probst AJ, Huber H, Rachel R, Meck S, Moissl-Eichinger C. Grappling archaea: ultrastructural analyses of an uncultivated, cold-loving archaeon, and its biofilm. Front Microbiol 2014; 5:397. [PMID: 25140167 PMCID: PMC4122167 DOI: 10.3389/fmicb.2014.00397] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 07/14/2014] [Indexed: 11/13/2022] Open
Abstract
Similarly to Bacteria, Archaea are microorganisms that interact with their surrounding environment in a versatile manner. To date, interactions based on cellular structure and surface appendages have mainly been documented using model systems of cultivable archaea under laboratory conditions. Here, we report on the microbial interactions and ultrastructural features of the uncultivated SM1 Euryarchaeon, which is highly dominant in its biotope. Therefore, biofilm samples taken from the Sippenauer Moor, Germany, were investigated via transmission electron microscopy (TEM; negative staining, thin-sectioning) and scanning electron microscopy (SEM) in order to elucidate the fine structures of the microbial cells and the biofilm itself. The biofilm consisted of small archaeal cocci (0.6 μm diameter), arranged in a regular pattern (1.0-2.0 μm distance from cell to cell), whereas each archaeon was connected to 6 other archaea on average. Extracellular polymeric substances (EPS) were limited to the close vicinity of the archaeal cells, and specific cell surface appendages (hami, Moissl et al., 2005) protruded beyond the EPS matrix enabling microbial interaction by cell-cell contacts among the archaea and between archaea and bacteria. All analyzed hami revealed their previously described architecture of nano-grappling hooks and barb-wire basal structures. Considering the archaeal cell walls, the SM1 Euryarchaea exhibited a double-membrane, which has rarely been reported for members of this phylogenetic domain. Based on these findings, the current generalized picture on archaeal cell walls needs to be revisited, as archaeal cell structures are more complex and sophisticated than previously assumed, particularly when looking into the uncultivated majority.
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Affiliation(s)
- Alexandra K Perras
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Gerhard Wanner
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich Planegg-Martinsried, Germany
| | - Andreas Klingl
- Department of Biology I, Biozentrum Ludwig Maximilian University of Munich Planegg-Martinsried, Germany ; Zellbiologie, Philipps-Universität Marburg Marburg, Germany ; LOEWE Research Centre for Synthetic Microbiology (Synmikro) Marbug, Germany
| | - Maximilian Mora
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Anna K Auerbach
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Veronika Heinz
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Alexander J Probst
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Harald Huber
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Reinhard Rachel
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
| | - Sandra Meck
- Department of Microbiology and Archaea Center, University of Regensburg Regensburg, Germany
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63
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Comolli LR, Banfield JF. Inter-species interconnections in acid mine drainage microbial communities. Front Microbiol 2014; 5:367. [PMID: 25120533 PMCID: PMC4110969 DOI: 10.3389/fmicb.2014.00367] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 07/01/2014] [Indexed: 02/04/2023] Open
Abstract
Metagenomic studies are revolutionizing our understanding of microbes in the biosphere. They have uncovered numerous proteins of unknown function in tens of essentially unstudied lineages that lack cultivated representatives. Notably, few of these microorganisms have been visualized, and even fewer have been described ultra-structurally in their essentially intact, physiologically relevant states. Here, we present cryogenic transmission electron microscope (cryo-TEM) 2D images and 3D tomographic datasets for archaeal species from natural acid mine drainage (AMD) microbial communities. Ultrastructural findings indicate the importance of microbial interconnectedness via a range of mechanisms, including direct cytoplasmic bridges and pervasive pili. The data also suggest a variety of biological structures associated with cell-cell interfaces that lack explanation. Some may play roles in inter-species interactions. Interdependences amongst the archaea may have confounded prior isolation efforts. Overall, the findings underline knowledge gaps related to archaeal cell components and highlight the likely importance of co-evolution in shaping microbial lineages.
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Affiliation(s)
- Luis R Comolli
- Structural Biology and Imaging Department, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jill F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley Berkeley, CA, USA
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Abstract
Cell division, intuitively, is often dependent upon increases in cellular mass and volume. Less obvious is the reciprocal regulation of growth by the cell division cycle. In budding yeast, this link is mediated by the cell-cycle-dependent polarization of actin.
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65
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Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage. ISME JOURNAL 2014; 8:1259-74. [PMID: 24430486 PMCID: PMC4030236 DOI: 10.1038/ismej.2013.242] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 11/27/2013] [Accepted: 12/04/2013] [Indexed: 01/07/2023]
Abstract
Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including ‘ARMAN' (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O2 concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO2, CH4, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called ‘ARMAN'-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H2, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H2 in acidic suboxic macroscopic growths.
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67
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Abstract
Viruses with spindle-shaped virions are abundant in diverse environments. Over the years, such viruses have been isolated from a wide range of archaeal hosts. Evolutionary relationships between them remained enigmatic, however. Here, using structural proteins as markers, we define familial ties among these "dark horses" of the virosphere and segregate all spindle-shaped viruses into two distinct evolutionary lineages, corresponding to Bicaudaviridae and Fuselloviridae. Our results illuminate the utility of structure-based virus classification and bring additional order to the virosphere.
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68
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Yamada H, Chikamatsu K, Aono A, Mitarai S. Pre-fixation of virulent Mycobacterium tuberculosis with glutaraldehyde preserves exquisite ultrastructure on transmission electron microscopy through cryofixation and freeze-substitution with osmium-acetone at ultralow temperature. J Microbiol Methods 2013; 96:50-5. [PMID: 24200708 DOI: 10.1016/j.mimet.2013.10.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 10/22/2013] [Accepted: 10/24/2013] [Indexed: 10/26/2022]
Abstract
Sample preparations for transmission electron microscopy of virulent Mycobacterium tuberculosis are usually performed with chemical fixation using glutaraldehyde (GA) in a biosafety area followed by post-fixation with aqueous osmium tetroxide (OT) in a conventional laboratory outside the biosafety area. Freeze-substitution with osmium-acetone (OA) at ultralow temperature (-85°C) has been shown to provide high quality final images and preserves cellular structures intact. However, some preparation procedures for freeze-substitution often require large fixed devices for freezing in a special laboratory. We have reported a novel freeze-substitution preparation method that can be performed using a portable device in a biosafety cabinet at biosafety level (BSL) 3 areas. Here, as a next step, we examined whether images obtained from rapid freeze-substitution (RFS) after fixation with glutaraldehyde (GA>RFS) are of comparable quality to those obtained using standard RFS. GA>RFS provided excellent preservation of mycobacterial cell ultrastructure, including visualization of cytoplasmic ribosomes, DNA fibers, and the outer membrane. The average number of ribosomes per cubic micrometer counted on RFS and GA>RFS was not significantly different (6987.8±2181.0 and 6888.9±1799.3, respectively). These values were higher, but not significantly so, than those obtained using conventional chemical fixation (5018.7±2511.3). This procedure may be useful for RFS preparation of unculturable mycobacteria strains or virulent strains isolated in laboratories that cannot perform RFS.
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Affiliation(s)
- Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan.
| | - Kinuyo Chikamatsu
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Akio Aono
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
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69
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Abstract
Biofilms are currently viewed as the most common form in which microorganisms exist in nature. Bacterial biofilms play important roles in disease and industrial applications, and they have been studied in great detail. Although it is well accepted that archaea are not only the extremists they were thought to be as they occupy nearly every habitat where also bacteria are found, it is surprising how little molecular details are known about archaeal biofilm formation. Therefore, we aim to highlight the available information and indicate open questions in this field.
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Affiliation(s)
- Alvaro Orell
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany;
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70
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Luef B, Fakra SC, Csencsits R, Wrighton KC, Williams KH, Wilkins MJ, Downing KH, Long PE, Comolli LR, Banfield JF. Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth. THE ISME JOURNAL 2013; 7:338-50. [PMID: 23038172 PMCID: PMC3554402 DOI: 10.1038/ismej.2012.103] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/30/2012] [Accepted: 07/30/2012] [Indexed: 11/09/2022]
Abstract
Iron-reducing bacteria (FeRB) play key roles in anaerobic metal and carbon cycling and carry out biogeochemical transformations that can be harnessed for environmental bioremediation. A subset of FeRB require direct contact with Fe(III)-bearing minerals for dissimilatory growth, yet these bacteria must move between mineral particles. Furthermore, they proliferate in planktonic consortia during biostimulation experiments. Thus, a key question is how such organisms can sustain growth under these conditions. Here we characterized planktonic microbial communities sampled from an aquifer in Rifle, Colorado, USA, close to the peak of iron reduction following in situ acetate amendment. Samples were cryo-plunged on site and subsequently examined using correlated two- and three-dimensional cryogenic transmission electron microscopy (cryo-TEM) and scanning transmission X-ray microscopy (STXM). The outer membranes of most cells were decorated with aggregates up to 150 nm in diameter composed of ∼3 nm wide amorphous, Fe-rich nanoparticles. Fluorescent in situ hybridization of lineage-specific probes applied to rRNA of cells subsequently imaged via cryo-TEM identified Geobacter spp., a well-studied group of FeRB. STXM results at the Fe L(2,3) absorption edges indicate that nanoparticle aggregates contain a variable mixture of Fe(II)-Fe(III), and are generally enriched in Fe(III). Geobacter bemidjiensis cultivated anaerobically in the laboratory on acetate and hydrous ferric oxyhydroxides also accumulated mixed-valence nanoparticle aggregates. In field-collected samples, FeRB with a wide variety of morphologies were associated with nano-aggregates, indicating that cell surface Fe(III) accumulation may be a general mechanism by which FeRB can grow while in planktonic suspension.
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Affiliation(s)
- Birgit Luef
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA
| | - Sirine C Fakra
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Advanced Light Source, Berkeley, CA, USA
| | - Roseann Csencsits
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA
| | - Kelly C Wrighton
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - Kenneth H Williams
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Berkeley, CA, USA
| | - Michael J Wilkins
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, USA
| | - Kenneth H Downing
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA
| | - Philip E Long
- Lawrence Berkeley National Laboratory, Earth Sciences Division, Berkeley, CA, USA
| | - Luis R Comolli
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
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71
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Justice NB, Pan C, Mueller R, Spaulding SE, Shah V, Sun CL, Yelton AP, Miller CS, Thomas BC, Shah M, VerBerkmoes N, Hettich R, Banfield JF. Heterotrophic archaea contribute to carbon cycling in low-pH, suboxic biofilm communities. Appl Environ Microbiol 2012; 78:8321-30. [PMID: 23001646 PMCID: PMC3497393 DOI: 10.1128/aem.01938-12] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 09/13/2012] [Indexed: 11/20/2022] Open
Abstract
Archaea are widely distributed and yet are most often not the most abundant members of microbial communities. Here, we document a transition from Bacteria- to Archaea-dominated communities in microbial biofilms sampled from the Richmond Mine acid mine drainage (AMD) system (∼pH 1.0, ∼38°C) and in laboratory-cultivated biofilms. This transition occurs when chemoautotrophic microbial communities that develop at the air-solution interface sink to the sediment-solution interface and degrade under microaerobic and anaerobic conditions. The archaea identified in these sunken biofilms are from the class Thermoplasmata, and in some cases, the highly divergent ARMAN nanoarchaeal lineage. In several of the sunken biofilms, nanoarchaea comprise 10 to 25% of the community, based on fluorescent in situ hybridization and metagenomic analyses. Comparative community proteomic analyses show a persistence of bacterial proteins in sunken biofilms, but there is clear evidence for amino acid modifications due to acid hydrolysis. Given the low representation of bacterial cells in sunken biofilms based on microscopy, we infer that hydrolysis reflects proteins derived from lysed cells. For archaea, we detected ∼2,400 distinct proteins, including a subset involved in proteolysis and peptide uptake. Laboratory cultivation experiments using complex carbon substrates demonstrated anaerobic enrichment of Ferroplasma and Aplasma coupled to the reduction of ferric iron. These findings indicate dominance of acidophilic archaea in degrading biofilms and suggest that they play roles in anaerobic nutrient cycling at low pH.
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Affiliation(s)
| | - Chongle Pan
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Ryan Mueller
- University of California–Berkeley, Berkeley, California, USA
| | | | - Vega Shah
- University of California–Berkeley, Berkeley, California, USA
| | | | | | | | - Brian C. Thomas
- University of California–Berkeley, Berkeley, California, USA
| | - Manesh Shah
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Robert Hettich
- Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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72
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Moraru C, Amann R. Crystal ball: Fluorescence in situ hybridization in the age of super-resolution microscopy. Syst Appl Microbiol 2012; 35:549-52. [DOI: 10.1016/j.syapm.2012.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 10/03/2012] [Accepted: 10/05/2012] [Indexed: 11/26/2022]
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73
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Roberts E, Stone JE, Luthey-Schulten Z. Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation. J Comput Chem 2012; 34:245-55. [PMID: 23007888 DOI: 10.1002/jcc.23130] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/13/2012] [Accepted: 08/31/2012] [Indexed: 11/09/2022]
Abstract
Spatial stochastic simulation is a valuable technique for studying reactions in biological systems. With the availability of high-performance computing (HPC), the method is poised to allow integration of data from structural, single-molecule and biochemical studies into coherent computational models of cells. Here, we introduce the Lattice Microbes software package for simulating such cell models on HPC systems. The software performs either well-stirred or spatially resolved stochastic simulations with approximated cytoplasmic crowding in a fast and efficient manner. Our new algorithm efficiently samples the reaction-diffusion master equation using NVIDIA graphics processing units and is shown to be two orders of magnitude faster than exact sampling for large systems while maintaining an accuracy of !0.1%. Display of cell models and animation of reaction trajectories involving millions of molecules is facilitated using a plug-in to the popular VMD visualization platform. The Lattice Microbes software is open source and available for download at http://www.scs.illinois.edu/schulten/lm
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Affiliation(s)
- Elijah Roberts
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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74
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Comolli LR, Duarte R, Baum D, Luef B, Downing KH, Larson DM, Csencsits R, Banfield JF. A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments. Microsc Res Tech 2012; 75:829-36. [PMID: 22213355 PMCID: PMC4677670 DOI: 10.1002/jemt.22001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 11/11/2011] [Indexed: 11/05/2022]
Abstract
We present a modern, light portable device specifically designed for environmental samples for cryogenic transmission-electron microscopy (cryo-TEM) by on-site cryo-plunging. The power of cryo-TEM comes from preparation of artifact-free samples. However, in many studies, the samples must be collected at remote field locations, and the time involved in transporting samples back to the laboratory for cryogenic preservation can lead to severe degradation artifacts. Thus, going back to the basics, we developed a simple mechanical device that is light and easy to transport on foot yet effective. With the system design presented here we are able to obtain cryo-samples of microbes and microbial communities not possible to culture, in their near-intact environmental conditions as well as in routine laboratory work, and in real time. This methodology thus enables us to bring the power of cryo-TEM to microbial ecology.
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Affiliation(s)
- Luis R Comolli
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
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75
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Lederer C, Heider D, van den Boom J, Hoffmann D, Mueller JW, Bayer P. Single-domain parvulins constitute a specific marker for recently proposed deep-branching archaeal subgroups. Evol Bioinform Online 2011; 7:135-48. [PMID: 22065628 PMCID: PMC3204937 DOI: 10.4137/ebo.s7683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Peptidyl-prolyl cis/trans isomerases (PPIases) are enzymes assisting protein folding and protein quality control in organisms of all kingdoms of life. In contrast to the other sub-classes of PPIases, the cyclophilins and the FK-506 binding proteins, little was formerly known about the parvulin type of PPIase in Archaea. Recently, the first solution structure of an archaeal parvulin, the PinA protein from Cenarchaeum symbiosum, was reported. Investigation of occurrence and frequency of PPIase sequences in numerous archaeal genomes now revealed a strong tendency for thermophilic microorganisms to reduce the number of PPIases. Single-domain parvulins were mostly found in the genomes of recently proposed deep-branching archaeal subgroups, the Thaumarchaeota and the ARMANs (archaeal Richmond Mine acidophilic nanoorganisms). Hence, we used the parvulin sequence to reclassify available archaeal metagenomic contigs, thereby, adding new members to these subgroups. A combination of genomic background analysis and phylogenetic approaches of parvulin sequences suggested that the assigned sequences belong to at least two distinct groups of Thaumarchaeota. Finally, machine learning approaches were applied to identify amino acid residues that separate archaeal and bacterial parvulin proteins from each other. When mapped onto the recent PinA solution structure, most of these positions form a cluster at one site of the protein possibly indicating a different functionality of the two groups of parvulin proteins.
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76
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Comolli LR, Luef B, Chan CS. High-resolution 2D and 3D cryo-TEM reveals structural adaptations of two stalk-forming bacteria to an Fe-oxidizing lifestyle. Environ Microbiol 2011; 13:2915-29. [PMID: 21895918 DOI: 10.1111/j.1462-2920.2011.02567.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aerobic neutrophilic Fe-oxidizing bacteria (FeOB) thrive where oxic and iron-rich anoxic waters meet. Here, iron microbial mats are commonly developed by stalk-forming Fe-oxidizers adapted to these iron-rich gradient environments, somehow avoiding iron encrustation. Few details are known about FeOB physiology; thus, the bases of these adaptations, notably the mechanisms of interactions with iron, are poorly understood. We examined two stalked FeOB: the marine Zetaproteobacterium Mariprofundus ferrooxydans and a terrestrial Betaproteobacterium Gallionella-like organism. We used cryo-transmission electron microscopy and cryo-electron tomography to provide unprecedented ultrastructural data on intact cell-mineral systems. Both FeOB localize iron mineral formation at stalk extrusion sites, while avoiding surface and periplasmic mineralization. The M. ferrooxydans cell surface is densely covered in fibrils while the terrestrial FeOB surface is smooth, suggesting a difference in surface chemistry. Only the terrestrial FeOB exhibited a putative chemotaxis apparatus, which may be due to differences in chemotaxis mechanisms. Both FeOB have a single flagellum, which alone is insufficient to account for cell motion during iron oxidation, suggesting that stalk extrusion is a mechanism for motility. Our results delineate the physical framework of iron transformations and characterize possible structural adaptations to the iron-oxidizing lifestyle. This study shows ultrastructural similarities and differences between two distinct FeOB, setting the stage for further (e.g. genomic) comparisons that will help us understand functional differences and evolutionary history.
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Affiliation(s)
- Luis R Comolli
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, CA 94720, USA.
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77
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Environmental, biogeographic, and biochemical patterns of archaea of the family Ferroplasmaceae. Appl Environ Microbiol 2011; 77:5071-8. [PMID: 21685165 DOI: 10.1128/aem.00726-11] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
About 10 years ago, a new family of cell wall-deficient, iron-oxidizing archaea, Ferroplasmaceae, within the large archaeal phylum Euryarchaeota, was described. In this minireview, I summarize the research progress achieved since then and report on the current status of taxonomy, biogeography, physiological diversity, biochemistry, and other research areas involving this exciting group of acidophilic archaea.
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78
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Liberton M, Austin JR, Berg RH, Pakrasi HB. Unique thylakoid membrane architecture of a unicellular N2-fixing cyanobacterium revealed by electron tomography. PLANT PHYSIOLOGY 2011; 155:1656-66. [PMID: 21173021 PMCID: PMC3091100 DOI: 10.1104/pp.110.165332] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cyanobacteria, descendants of the endosymbiont that gave rise to modern-day chloroplasts, are vital contributors to global biological energy conversion processes. A thorough understanding of the physiology of cyanobacteria requires detailed knowledge of these organisms at the level of cellular architecture and organization. In these prokaryotes, the large membrane protein complexes of the photosynthetic and respiratory electron transport chains function in the intracellular thylakoid membranes. Like plants, the architecture of the thylakoid membranes in cyanobacteria has direct impact on cellular bioenergetics, protein transport, and molecular trafficking. However, whole-cell thylakoid organization in cyanobacteria is not well understood. Here we present, by using electron tomography, an in-depth analysis of the architecture of the thylakoid membranes in a unicellular cyanobacterium, Cyanothece sp. ATCC 51142. Based on the results of three-dimensional tomographic reconstructions of near-entire cells, we determined that the thylakoids in Cyanothece 51142 form a dense and complex network that extends throughout the entire cell. This thylakoid membrane network is formed from the branching and splitting of membranes and encloses a single lumenal space. The entire thylakoid network spirals as a peripheral ring of membranes around the cell, an organization that has not previously been described in a cyanobacterium. Within the thylakoid membrane network are areas of quasi-helical arrangement with similarities to the thylakoid membrane system in chloroplasts. This cyanobacterial thylakoid arrangement is an efficient means of packing a large volume of membranes in the cell while optimizing intracellular transport and trafficking.
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79
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Roberts E, Magis A, Ortiz JO, Baumeister W, Luthey-Schulten Z. Noise contributions in an inducible genetic switch: a whole-cell simulation study. PLoS Comput Biol 2011; 7:e1002010. [PMID: 21423716 PMCID: PMC3053318 DOI: 10.1371/journal.pcbi.1002010] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 01/03/2011] [Indexed: 11/18/2022] Open
Abstract
Stochastic expression of genes produces heterogeneity in clonal populations of bacteria under identical conditions. We analyze and compare the behavior of the inducible lac genetic switch using well-stirred and spatially resolved simulations for Escherichia coli cells modeled under fast and slow-growth conditions. Our new kinetic model describing the switching of the lac operon from one phenotype to the other incorporates parameters obtained from recently published in vivo single-molecule fluorescence experiments along with in vitro rate constants. For the well-stirred system, investigation of the intrinsic noise in the circuit as a function of the inducer concentration and in the presence/absence of the feedback mechanism reveals that the noise peaks near the switching threshold. Applying maximum likelihood estimation, we show that the analytic two-state model of gene expression can be used to extract stochastic rates from the simulation data. The simulations also provide mRNA–protein probability landscapes, which demonstrate that switching is the result of crossing both mRNA and protein thresholds. Using cryoelectron tomography of an E. coli cell and data from proteomics studies, we construct spatial in vivo models of cells and quantify the noise contributions and effects on repressor rebinding due to cell structure and crowding in the cytoplasm. Compared to systems without spatial heterogeneity, the model for the fast-growth cells predicts a slight decrease in the overall noise and an increase in the repressors rebinding rate due to anomalous subdiffusion. The tomograms for E. coli grown under slow-growth conditions identify the positions of the ribosomes and the condensed nucleoid. The smaller slow-growth cells have increased mRNA localization and a larger internal inducer concentration, leading to a significant decrease in the lifetime of the repressor–operator complex and an increase in the frequency of transcriptional bursts. Expressing genes in a bacterial cell is noisy and random. A colony of bacteria grown from a single cell can show remarkable differences in the copy number per cell of a given protein after only a few generations. In this work we use computer simulations to study the variation in how individual cells in a population express a set of genes in response to an environmental signal. The modeled system is the lac genetic switch that Escherichia coli uses to find, collect, and process lactose sugar from the environment. The noise inherent in the genetic circuit controlling the cell's response determines how similar the cells are to each other and we study how the different components of the circuit affect this noise. Furthermore, an estimated 30–50% of the cell volume is taken up by a wide variety of large biomolecules. To study the response of the circuit caused by crowding, we simulate the circuit inside a three-dimensional model of an E. coli cell built using data from cryoelectron tomography reconstructions of a single cell and proteomics data. Correctly including random effects of molecular crowding will be critical to developing fully dynamic models of living cells.
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Affiliation(s)
- Elijah Roberts
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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80
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Jarrell KF, Walters AD, Bochiwal C, Borgia JM, Dickinson T, Chong JPJ. Major players on the microbial stage: why archaea are important. MICROBIOLOGY-SGM 2011; 157:919-936. [PMID: 21330437 DOI: 10.1099/mic.0.047837-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As microbiology undergoes a renaissance, fuelled in part by developments in new sequencing technologies, the massive diversity and abundance of microbes becomes yet more obvious. The Archaea have traditionally been perceived as a minor group of organisms forced to evolve into environmental niches not occupied by their more 'successful' and 'vigorous' counterparts, the bacteria. Here we outline some of the evidence gathered by an increasingly large and productive group of scientists that demonstrates not only that the Archaea contribute significantly to global nutrient cycling, but also that they compete successfully in 'mainstream' environments. Recent data suggest that the Archaea provide the major routes for ammonia oxidation in the environment. Archaea also have huge economic potential that to date has only been fully realized in the production of thermostable polymerases. Archaea have furnished us with key paradigms for understanding fundamentally conserved processes across all domains of life. In addition, they have provided numerous exemplars of novel biological mechanisms that provide us with a much broader view of the forms that life can take and the way in which micro-organisms can interact with other species. That this information has been garnered in a relatively short period of time, and appears to represent only a small proportion of what the Archaea have to offer, should provide further incentives to microbiologists to investigate the underlying biology of this fascinating domain.
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Affiliation(s)
- Ken F Jarrell
- Department of Microbiology and Immunology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Alison D Walters
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Chitvan Bochiwal
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Juliet M Borgia
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Thomas Dickinson
- Sheffield Hallam University, City Campus, Howard Street, Sheffield S1 1WB, UK
| | - James P J Chong
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
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81
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Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, VerBerkmoes NC, Hettich RL, Banfield JF. Enigmatic, ultrasmall, uncultivated Archaea. Proc Natl Acad Sci U S A 2010; 107:8806-11. [PMID: 20421484 PMCID: PMC2889320 DOI: 10.1073/pnas.0914470107] [Citation(s) in RCA: 204] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete approximately 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher coding density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISME J 3:159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged.
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Affiliation(s)
| | - Luis R. Comolli
- Lawrence Berkeley National Laboratories, Berkeley, CA 94720; and
| | | | | | | | - Brian D. Dill
- Chemical Sciences Divisions, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | | | | | - Robert L. Hettich
- Chemical Sciences Divisions, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Jillian F. Banfield
- Department of Earth and Planetary Science and
- Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720
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82
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3D segmentation of cell boundaries from whole cell cryogenic electron tomography volumes. J Struct Biol 2010; 170:134-45. [DOI: 10.1016/j.jsb.2009.12.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Revised: 12/14/2009] [Accepted: 12/16/2009] [Indexed: 11/20/2022]
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83
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AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature. ISME JOURNAL 2010; 4:599-610. [PMID: 20164865 DOI: 10.1038/ismej.2009.158] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Similar to virtually all components of natural environments, microbial systems are inherently complex and dynamic. Advances in cultivation-independent molecular methods have provided a route to study microbial consortia in their natural surroundings and to begin resolving the community structure, dominant metabolic processes and inter-organism interactions. However, the utility of these methods generally scales inversely with community complexity. By applying genomics-enabled methods to the study of natural microbial communities with reduced levels of species richness, a relatively comprehensive understanding of the metabolic networks and evolutionary processes within these communities can be attained. In such well-defined model systems, it is also possible to link emergent ecological patterns to their molecular and evolutionary underpinnings, facilitating construction of predictive ecosystem models. In this study, we review over a decade of research on one such system-acid mine drainage biofilm communities. We discuss the value and limitations of tractable model microbial communities in developing molecular methods for microbial ecology and in uncovering principles that may explain behavior in more complex systems.
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84
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Bowman GR, Comolli LR, Gaietta GM, Fero M, Hong SH, Jones Y, Lee JH, Downing KH, Ellisman MH, McAdams HH, Shapiro L. Caulobacter PopZ forms a polar subdomain dictating sequential changes in pole composition and function. Mol Microbiol 2010; 76:173-89. [PMID: 20149103 DOI: 10.1111/j.1365-2958.2010.07088.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The bacterium Caulobacter crescentus has morphologically and functionally distinct cell poles that undergo sequential changes during the cell cycle. We show that the PopZ oligomeric network forms polar ribosome exclusion zones that change function during cell cycle progression. The parS/ParB chromosomal centromere is tethered to PopZ at one pole prior to the initiation of DNA replication. During polar maturation, the PopZ-centromere tether is broken, and the PopZ zone at that pole then switches function to act as a recruitment factor for the ordered addition of multiple proteins that promote the transformation of the flagellated pole into a stalked pole. Stalked pole assembly, in turn, triggers the initiation of chromosome replication, which signals the formation of a new PopZ zone at the opposite cell pole, where it functions to anchor the newly duplicated centromere that has traversed the long axis of the cell. We propose that pole-specific control of PopZ function co-ordinates polar development and cell cycle progression by enabling independent assembly and tethering activities at the two cell poles.
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Affiliation(s)
- Grant R Bowman
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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85
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Milne JLS, Subramaniam S. Cryo-electron tomography of bacteria: progress, challenges and future prospects. Nat Rev Microbiol 2009; 7:666-75. [PMID: 19668224 DOI: 10.1038/nrmicro2183] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent advances in three-dimensional electron microscopy provide remarkable tools to image the interior of bacterial cells. Glimpses of cells at resolutions that are 1-2 orders of magnitude higher than those currently attained with light microscopy can now be obtained with cryo-electron tomography, especially when used in combination with new tools for image averaging. This Review highlights recent advances in this area and provides an assessment of the general applicability, current limitations and type of structural information that can be obtained about the organization of intact cells using tomography. Possible future directions for whole cell imaging are also discussed.
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Affiliation(s)
- Jacqueline L S Milne
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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86
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Cryo-electron tomography in biology and medicine. Ann Anat 2009; 191:427-45. [PMID: 19559584 DOI: 10.1016/j.aanat.2009.04.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 04/23/2009] [Indexed: 12/16/2022]
Abstract
During the last six decades electron microscopy (EM) has been essential to ultra-structural studies of the cell to understand the fundamentals of cellular morphology and processes underlying diseases. More recently, electron tomography (ET) has emerged as a novel approach able to provide three-dimensional (3D) information on cells and tissues at molecular level. Electron tomography is comparable to medical tomographic techniques like CAT, PET and MRI in the sense that it provides a 3D view of an object, yet it does so at a cellular scale and with nanometer resolution. Electron tomography has the unique ability to visualize molecular assemblies, cytoskeletal elements and organelles within cells. The three-dimensional perspective it provides has revised our understanding of cellular organization and its relation with morphological changes in normal development and disease. Cryo-electron tomography of vitrified samples at cryogenic temperatures combines excellent structural preservation with direct high-resolution imaging. The use of cryo-preparation and imaging techniques eliminates artifacts induced by plastic embedding and staining of the samples is circumvented. This review describes the technique of cryo-electron tomography, its basic principles, cryo-specimen preparation, tomographic data acquisition and image processing. A number of illustrative examples ranging from whole cells, cytoskeletal filaments, viruses and organelles are presented along with a comprehensive list of research articles employing cryo-electron tomography as the key ultrastuctural technique.
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87
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Li Z, Jensen GJ. Electron cryotomography: a new view into microbial ultrastructure. Curr Opin Microbiol 2009; 12:333-40. [PMID: 19427259 PMCID: PMC2747746 DOI: 10.1016/j.mib.2009.03.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 03/20/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
Abstract
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 microbiology, and conclude with a discussion of future prospects.
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Affiliation(s)
- Zhuo Li
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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