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Aliaga Goltsman DS, Comolli LR, Thomas BC, Banfield JF. Community transcriptomics reveals unexpected high microbial diversity in acidophilic biofilm communities. ISME J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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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] [What about the content of this article? (0)] [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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3
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Holmes DE, Giloteaux L, Chaurasia AK, Williams KH, Luef B, Wilkins MJ, Wrighton KC, Thompson CA, Comolli LR, Lovley DR. Evidence of Geobacter-associated phage in a uranium-contaminated aquifer. ISME J 2015; 9:333-46. [PMID: 25083935 PMCID: PMC4303627 DOI: 10.1038/ismej.2014.128] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 05/27/2014] [Accepted: 06/14/2014] [Indexed: 11/08/2022]
Abstract
Geobacter species may be important agents in the bioremediation of organic and metal contaminants in the subsurface, but as yet unknown factors limit the in situ growth of subsurface Geobacter well below rates predicted by analysis of gene expression or in silico metabolic modeling. Analysis of the genomes of five different Geobacter species recovered from contaminated subsurface sites indicated that each of the isolates had been infected with phage. Geobacter-associated phage sequences were also detected by metagenomic and proteomic analysis of samples from a uranium-contaminated aquifer undergoing in situ bioremediation, and phage particles were detected by microscopic analysis in groundwater collected from sediment enrichment cultures. Transcript abundance for genes from the Geobacter-associated phage structural proteins, tail tube Gp19 and baseplate J, increased in the groundwater in response to the growth of Geobacter species when acetate was added, and then declined as the number of Geobacter decreased. Western blot analysis of a Geobacter-associated tail tube protein Gp19 in the groundwater demonstrated that its abundance tracked with the abundance of Geobacter species. These results suggest that the enhanced growth of Geobacter species in the subsurface associated with in situ uranium bioremediation increased the abundance and activity of Geobacter-associated phage and show that future studies should focus on how these phages might be influencing the ecology of this site.
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Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
- Western New England University, Springfield, MA, USA
| | - Ludovic Giloteaux
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Akhilesh K Chaurasia
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Birgit Luef
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | | | - Kelly C Wrighton
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Courtney A Thompson
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Luis R Comolli
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Derek R Lovley
- Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, USA
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4
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Allen FI, Comolli LR, Kusoglu A, Modestino MA, Minor AM, Weber AZ. Morphology of Hydrated As-Cast Nafion Revealed through Cryo Electron Tomography. ACS Macro Lett 2015; 4:1-5. [PMID: 35596390 DOI: 10.1021/mz500606h] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nafion is an ion-containing random copolymer used as a solid electrolyte in many electrochemical applications thanks to its remarkable ionic conductivity and mechanical stability. Understanding the mechanism of ion transport in Nafion, which depends strongly on hydration, therefore requires a complete picture of its morphology in dry and hydrated form. Here we report on a nanoscale study of dry versus hydrated as-cast 100 nm Nafion membranes using analytical transmission electron microscopy (TEM) and cryogenic TEM tomography, respectively. For the dry membrane, spherical clusters ∼3.5 nm in diameter corresponding to the hydrophilic sulfonic-acid-containing phase are identified. In contrast, cryo TEM tomography of the hydrated membrane reveals an interconnected channel-type network, with a domain spacing of ∼5 nm, and presents the first nanoscale 3D views of the internal structure of hydrated Nafion obtained by a direct-imaging approach.
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Affiliation(s)
- Frances I. Allen
- Department of Materials Science and Engineering and ⊥Department of Chemical
and Biomolecular
Engineering, University of California, Berkeley, California 94720, United States
- National Center for Electron Microscopy, Molecular
Foundry, §Life
Sciences Division, and ∥Environmental
Energy Technologies Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Luis R. Comolli
- Department of Materials Science and Engineering and ⊥Department of Chemical
and Biomolecular
Engineering, University of California, Berkeley, California 94720, United States
- National Center for Electron Microscopy, Molecular
Foundry, §Life
Sciences Division, and ∥Environmental
Energy Technologies Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ahmet Kusoglu
- Department of Materials Science and Engineering and ⊥Department of Chemical
and Biomolecular
Engineering, University of California, Berkeley, California 94720, United States
- National Center for Electron Microscopy, Molecular
Foundry, §Life
Sciences Division, and ∥Environmental
Energy Technologies Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Miguel A. Modestino
- Department of Materials Science and Engineering and ⊥Department of Chemical
and Biomolecular
Engineering, University of California, Berkeley, California 94720, United States
- National Center for Electron Microscopy, Molecular
Foundry, §Life
Sciences Division, and ∥Environmental
Energy Technologies Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrew M. Minor
- Department of Materials Science and Engineering and ⊥Department of Chemical
and Biomolecular
Engineering, University of California, Berkeley, California 94720, United States
- National Center for Electron Microscopy, Molecular
Foundry, §Life
Sciences Division, and ∥Environmental
Energy Technologies Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Adam Z. Weber
- Department of Materials Science and Engineering and ⊥Department of Chemical
and Biomolecular
Engineering, University of California, Berkeley, California 94720, United States
- National Center for Electron Microscopy, Molecular
Foundry, §Life
Sciences Division, and ∥Environmental
Energy Technologies Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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5
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Kim K, Geng J, Tunuguntla R, Comolli LR, Grigoropoulos CP, Ajo-Franklin CM, Noy A. Osmotically-driven transport in carbon nanotube porins. Nano Lett 2014; 14:7051-7056. [PMID: 25372973 DOI: 10.1021/nl5034446] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report the measurements of transport of ions and uncharged species through carbon nanotube (CNT) porins--short segments of CNTs inserted into a lipid bilayer membrane. Rejection characteristics of the CNT porins are governed by size exclusion for the uncharged species. In contrast, rejection of ionic species is governed by the electrostatic repulsion and Donnan membrane equilibrium. Permeability of monovalent cations follows the general trend in the hydrated ion size, except in the case of Cs(+) ions.
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Affiliation(s)
- Kyunghoon Kim
- Biology and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory , Livermore, California 94550, United States
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6
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Legg BA, Zhu M, Comolli LR, Gilbert B, Banfield JF. Impacts of ionic strength on three-dimensional nanoparticle aggregate structure and consequences for environmental transport and deposition. Environ Sci Technol 2014; 48:13703-13710. [PMID: 25380400 DOI: 10.1021/es502654q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The transport of nanoparticles through aqueous systems is a complex process with important environmental policy ramifications. Ferrihydrite nanoparticles commonly form aggregates, with structures that depend upon solution chemistry. The impact of aggregation state on transport and deposition is not fully understood. In this study, small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM) were used to directly observe the aggregate structure of ferrihydrite nanoparticles and show how the aggregate structure responds to changing ionic strength. These results were correlated with complementary studies on ferrihydrite transport through saturated quartz sand columns. Within deionized water, nanoparticles form stable suspensions of low-density fractal aggregates that are resistant to collapse. The particles subsequently show limited deposition on sand grain surfaces. Within sodium nitrate solutions the aggregates collapse into denser clusters, and nanoparticle deposition increases dramatically by forming thick, localized, and mechanically unstable deposits. Such deposits limit nanoparticle transport and make transport less predictable. The action of ionic strength is distinct from simpler models of colloidal stability and transport, in that salt not only drives aggregation or attachment but also alters the behavior of preexisting aggregates by triggering their collapse.
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Affiliation(s)
- Benjamin A Legg
- Department of Earth and Planetary Science, University of California , Berkeley, California 94720, United States
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7
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Affiliation(s)
- Luis R Comolli
- Beamline 4.2.2, Advanced Light Source, ALS-Molecular Biology Consortium Berkeley, CA, USA
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8
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Legg BA, Zhu M, Comolli LR, Gilbert B, Banfield JF. Determination of the three-dimensional structure of ferrihydrite nanoparticle aggregates. Langmuir 2014; 30:9931-9940. [PMID: 25079430 DOI: 10.1021/la502128d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Aggregation impacts the reactivity, colloidal stability, and transport behavior of nanomaterials, yet methods to characterize basic structural features of aggregates are limited. Here, cryo-transmission electron microscope (cryo-TEM) based tomography is utilized as a method for directly imaging fragile aggregates of nanoparticles in aqueous suspension and an approach for extracting quantitative fractal dimensions from the resulting three-dimensional structural models is introduced. The structural quantification approach is based upon the mass autocorrelation function, and is directly comparable with small-angle X-ray scattering (SAXS) models. This enables accurate characterization of aggregate structure, even in suspensions where the aggregate cluster size is highly polydisperse and traditional SAXS modeling is not reliable. This technique is applied to study real suspensions of ferrihydrite nanoparticles. By comparing tomographic measurements with SAXS-based measurements, we infer that certain suspensions contain polydisperse aggregate size distributions. In other suspensions, fractal-type structures are identified with low intrinsic fractal dimensions. The fractal dimensions are lower than would be predicted by simple models of particle aggregation, and this low dimensionality enables large, low-density aggregates to exist in stable colloidal suspension.
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Affiliation(s)
- Benjamin A Legg
- Earth and Planetary Science, University of California-Berkeley , Berkeley, California 94720, United States
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9
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Madeo D, Comolli LR, Mocenni C. Emergence of microbial networks as response to hostile environments. Front Microbiol 2014; 5:407. [PMID: 25191306 PMCID: PMC4137228 DOI: 10.3389/fmicb.2014.00407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/18/2014] [Indexed: 11/13/2022] Open
Abstract
The majority of microorganisms live in complex communities under varying conditions. One pivotal question in evolutionary biology is the emergence of cooperative traits and their sustainment in altered environments or in the presence of free-riders. Co-occurrence patterns in the spatial distribution of biofilms can help define species' identities, and systems biology tools are revealing networks of interacting microorganisms. However, networks of inter-dependencies involving micro-organisms in the planktonic phase may be just as important, with the added complexity that they are not bounded in space. An integrated approach linking imaging, "Omics" and modeling has the potential to enable new hypothesis and working models. In order to understand how cooperation can emerge and be maintained without abilities like memory or recognition we use evolutionary game theory as the natural framework to model cell-cell interactions arising from evolutive decisions. We consider a finite population distributed in a spatial domain (biofilm), and divided into two interacting classes with different traits. This interaction can be weighted by distance, and produces physical connections between two elements allowing them to exchange finite amounts of energy and matter. Available strategies to each individual of one class in the population are the propensities or "willingness" to connect any individual of the other class. Following evolutionary game theory, we propose a mathematical model which explains the patterns of connections which emerge when individuals are able to find connection strategies that asymptotically optimize their fitness. The process explains the formation of a network for efficiently exchanging energy and matter among individuals and thus ensuring their survival in hostile environments.
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Affiliation(s)
- Dario Madeo
- Department of Information Engineering and Mathematics, University of Siena Siena, Italy
| | - Luis R Comolli
- Structural Biology and Imaging Department, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Chiara Mocenni
- Department of Information Engineering and Mathematics, University of Siena Siena, Italy
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10
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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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11
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Frandsen C, Legg BA, Comolli LR, Zhang H, Gilbert B, Johnson E, Banfield JF. Aggregation-induced growth and transformation of β-FeOOH nanorods to micron-sized α-Fe2O3spindles. CrystEngComm 2014. [DOI: 10.1039/c3ce40983j] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Bowman GR, Perez AM, Ptacin JL, Ighodaro E, Folta-Stogniew E, Comolli LR, Shapiro L. Oligomerization and higher-order assembly contribute to sub-cellular localization of a bacterial scaffold. Mol Microbiol 2013; 90:776-95. [PMID: 24102805 DOI: 10.1111/mmi.12398] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2013] [Indexed: 02/02/2023]
Abstract
In Caulobacter crescentus, the PopZ polar scaffold protein supports asymmetric cell division by recruiting distinct sets of binding partners to opposite cell poles. To understand how polar organizing centres are established by PopZ, we investigated a set of mutated PopZ proteins for defects in sub-cellular localization and recruitment activity. We identified a domain within the C-terminal 76 amino acids that is necessary and sufficient for accumulation as a single subcellular focus, a domain within the N-terminal 23 amino acids that is necessary for bipolar targeting, and a linker domain between these localization determinants that tolerates large variation. Mutations that inhibited dynamic PopZ localization inhibited the recruitment of other factors to cell poles. Mutations in the C-terminal domain also blocked discrete steps in the assembly of higher-order structures. Biophysical analysis of purified wild type and assembly defective mutant proteins indicates that PopZ self-associates into an elongated trimer, which readily forms a dimer of trimers through lateral contact. The final six amino acids of PopZ are necessary for connecting the hexamers into filaments, and these structures are important for sub-cellular localization. Thus, PopZ undergoes multiple orders of self-assembly, and the formation of an interconnected superstructure is a key feature of polar organization in Caulobacter.
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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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13
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Yelton AP, Comolli LR, Justice NB, Castelle C, Denef VJ, Thomas BC, Banfield JF. Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea. BMC Genomics 2013; 14:485. [PMID: 23865623 PMCID: PMC3750248 DOI: 10.1186/1471-2164-14-485] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/15/2013] [Indexed: 11/10/2022] Open
Abstract
Background Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. Results We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. Conclusion The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.
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Affiliation(s)
- Alexis P Yelton
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
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14
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Shin SH, Comolli LR, Tscheliessnig R, Wang C, Nam KT, Hexemer A, Siegerist CE, De Yoreo JJ, Bertozzi CR. Self-assembly of "S-bilayers", a step toward expanding the dimensionality of S-layer assemblies. ACS Nano 2013; 7:4946-4953. [PMID: 23705800 DOI: 10.1021/nn400263j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein-based assemblies with ordered nanometer-scale features in three dimensions are of interest as functional nanomaterials but are difficult to generate. Here we report that a truncated S-layer protein assembles into stable bilayers, which we characterized using cryogenic-electron microscopy, tomography, and X-ray spectroscopy. We find that emergence of this supermolecular architecture is the outcome of hierarchical processes; the proteins condense in solution to form 2-D crystals, which then stack parallel to one another to create isotropic bilayered assemblies. Within this bilayered structure, registry between lattices in two layers was disclosed, whereas the intrinsic symmetry in each layer was altered. Comparison of these data to images of wild-type SbpA layers on intact cells gave insight into the interactions responsible for bilayer formation. These results establish a platform for engineering S-layer assemblies with 3-D architecture.
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Affiliation(s)
- Seong-Ho Shin
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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15
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Comolli LR, Siegerist CE, Shin SH, Bertozzi C, Regan W, Zettl A, De Yoreo J. Conformational Transitions at an S-Layer Growing Boundary Resolved by Cryo-TEM. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Comolli LR, Siegerist CE, Shin SH, Bertozzi C, Regan W, Zettl A, De Yoreo J. Inside Cover: Conformational Transitions at an S-Layer Growing Boundary Resolved by Cryo-TEM (Angew. Chem. Int. Ed. 18/2013). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/anie.201302596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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17
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Comolli LR, Siegerist CE, Shin SH, Bertozzi C, Regan W, Zettl A, De Yoreo J. Innentitelbild: Conformational Transitions at an S-Layer Growing Boundary Resolved by Cryo-TEM (Angew. Chem. 18/2013). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Comolli LR, Siegerist CE, Shin SH, Bertozzi C, Regan W, Zettl A, De Yoreo J. Conformational transitions at an S-layer growing boundary resolved by cryo-TEM. Angew Chem Int Ed Engl 2013; 52:4829-32. [PMID: 23564404 DOI: 10.1002/anie.201300543] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/06/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Luis R Comolli
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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19
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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. ISME J 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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Song K, Comolli LR, Horowitz M. Removing high contrast artifacts via digital inpainting in cryo-electron tomography: An application of compressed sensing. J Struct Biol 2012; 178:108-20. [DOI: 10.1016/j.jsb.2012.01.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 12/16/2011] [Accepted: 01/02/2012] [Indexed: 11/26/2022]
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22
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Knierim B, Luef B, Wilmes P, Webb RI, Auer M, Comolli LR, Banfield JF. Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities. Environ Microbiol Rep 2012; 4:36-41. [PMID: 23757227 PMCID: PMC4444221 DOI: 10.1111/j.1758-2229.2011.00275.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Transmission electron microscopy (TEM) can provide ultrastructural information for cells in microbial community samples and phylogenetic information can be recovered via molecular surveys. Here we report an approach to link these data sets by coupling fluorescence in situ hybridization (FISH) with either conventional biological or cryogenic TEM. The method could fundamentally improve our understanding of the organization and functioning of microbial communities in natural systems.
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Affiliation(s)
- Bernhard Knierim
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, California, USA
| | - Birgit Luef
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, California, USA
- Department of Earth and Planetary Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | - Paul Wilmes
- Department of Earth and Planetary Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | - Richard I. Webb
- Centre for Microscopy and Microanalysis (CMM), The University of Queensland, St. Lucia, Queensland, Australia
| | - Manfred Auer
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, California, USA
| | - Luis R. Comolli
- Lawrence Berkeley National Laboratory, Life Sciences Division, Berkeley, California, USA
- Corresponding Authors: ;
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
- Corresponding Authors: ;
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23
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Singer E, Emerson D, Webb EA, Barco RA, Kuenen JG, Nelson WC, Chan CS, Comolli LR, Ferriera S, Johnson J, Heidelberg JF, Edwards KJ. Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium. PLoS One 2011; 6:e25386. [PMID: 21966516 PMCID: PMC3179512 DOI: 10.1371/journal.pone.0025386] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 09/02/2011] [Indexed: 12/21/2022] Open
Abstract
Mariprofundus ferrooxydans PV-1 has provided the first genome of the recently discovered Zetaproteobacteria subdivision. Genome analysis reveals a complete TCA cycle, the ability to fix CO(2), carbon-storage proteins and a sugar phosphotransferase system (PTS). The latter could facilitate the transport of carbohydrates across the cell membrane and possibly aid in stalk formation, a matrix composed of exopolymers and/or exopolysaccharides, which is used to store oxidized iron minerals outside the cell. Two-component signal transduction system genes, including histidine kinases, GGDEF domain genes, and response regulators containing CheY-like receivers, are abundant and widely distributed across the genome. Most of these are located in close proximity to genes required for cell division, phosphate uptake and transport, exopolymer and heavy metal secretion, flagellar biosynthesis and pilus assembly suggesting that these functions are highly regulated. Similar to many other motile, microaerophilic bacteria, genes encoding aerotaxis as well as antioxidant functionality (e.g., superoxide dismutases and peroxidases) are predicted to sense and respond to oxygen gradients, as would be required to maintain cellular redox balance in the specialized habitat where M. ferrooxydans resides. Comparative genomics with other Fe(II) oxidizing bacteria residing in freshwater and marine environments revealed similar content, synteny, and amino acid similarity of coding sequences potentially involved in Fe(II) oxidation, signal transduction and response regulation, oxygen sensation and detoxification, and heavy metal resistance. This study has provided novel insights into the molecular nature of Zetaproteobacteria.
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Affiliation(s)
- Esther Singer
- Geomicrobiology Group, Department of Earth Sciences, University of Southern California, Los Angeles, California, United States of America
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine, United States of America
| | - Eric A. Webb
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, California, United States of America
| | - Roman A. Barco
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, California, United States of America
| | - J. Gijs Kuenen
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - William C. Nelson
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, California, United States of America
| | - Clara S. Chan
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Luis R. Comolli
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Steve Ferriera
- J. Craig Venter Institute, San Diego, California, United States of America
| | - Justin Johnson
- J. Craig Venter Institute, San Diego, California, United States of America
| | - John F. Heidelberg
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, California, United States of America
| | - Katrina J. Edwards
- Geomicrobiology Group, Department of Earth Sciences, University of Southern California, Los Angeles, California, United States of America
- Department of Biological Sciences, Marine Environmental Biology Section, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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24
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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25
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Abstract
Cell division in Gram-negative organisms requires coordinated invagination of the multilayered cell envelope such that each daughter receives an intact inner membrane, peptidoglycan (PG) layer and outer membrane (OM). Here, we identify DipM, a putative LytM endopeptidase in Caulobacter crescentus, and show that it plays a critical role in maintaining cell envelope architecture during growth and division. DipM localized to the division site in an FtsZ-dependent manner via its PG-binding LysM domains. Although not essential for viability, DeltadipM cells exhibited gross morphological defects, including cell widening and filamentation, indicating a role in cell shape maintenance and division that we show requires its LytM domain. Strikingly, cells lacking DipM also showed OM blebbing at the division site, at cell poles and along the cell body. Cryo electron tomography of sacculi isolated from cells depleted of DipM revealed marked thickening of the PG as compared to wild type, which we hypothesize leads to loss of trans-envelope contacts between components of the Tol-Pal complex. We conclude that DipM is required for normal envelope invagination during division and to maintain a sacculus of constant thickness that allows for maintenance of OM connections throughout the cell envelope.
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Affiliation(s)
- Erin D Goley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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26
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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Bowman GR, Comolli LR, Zhu J, Eckart M, Koenig M, Downing KH, Moerner WE, Earnest T, Shapiro L. A polymeric protein anchors the chromosomal origin/ParB complex at a bacterial cell pole. Cell 2008; 134:945-55. [PMID: 18805088 DOI: 10.1016/j.cell.2008.07.015] [Citation(s) in RCA: 239] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 04/15/2008] [Accepted: 07/11/2008] [Indexed: 10/21/2022]
Abstract
Bacterial replication origins move towards opposite ends of the cell during DNA segregation. We have identified a proline-rich polar protein, PopZ, required to anchor the separated Caulobacter crescentus chromosome origins at the cell poles, a function that is essential for maintaining chromosome organization and normal cell division. PopZ interacts directly with the ParB protein bound to specific DNA sequences near the replication origin. As the origin/ParB complex is being replicated and moved across the cell, PopZ accumulates at the cell pole and tethers the origin in place upon arrival. The polar accumulation of PopZ occurs by a diffusion/capture mechanism that requires the MreB cytoskeleton. High molecular weight oligomers of PopZ assemble in vitro into a filamentous network with trimer junctions, suggesting that the PopZ network and ParB-bound DNA interact in an adhesive complex, fixing the chromosome origin at the cell pole.
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Affiliation(s)
- Grant R Bowman
- Department of Developmental Biology, Stanford University School of Medicine, Beckman Center, Stanford, CA 94305, USA
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29
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Comolli LR, Spakowitz AJ, Siegerist CE, Jardine PJ, Grimes S, Anderson DL, Bustamante C, Downing KH. Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process. Virology 2007; 371:267-77. [PMID: 18001811 DOI: 10.1016/j.virol.2007.07.035] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Revised: 06/07/2007] [Accepted: 07/27/2007] [Indexed: 11/18/2022]
Abstract
The goal of the work reported here is to understand the precise molecular mechanism of the process of DNA packaging in dsDNA bacteriophages. Cryo-EM was used to directly visualize the architecture of the DNA inside the capsid and thus to measure fundamental physical parameters such as inter-strand distances, local curvatures, and the degree of order. We obtained cryo-EM images of bacteriophage that had packaged defined fragments of the genome as well as particles that had partially completed the packaging process. The resulting comparison of structures observed at intermediate and final stages shows that there is no unique, deterministic DNA packaging pathway. Monte Carlo simulations of the packaging process provide insights on the forces involved and the resultant structures.
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Affiliation(s)
- Luis R Comolli
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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30
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Amat F, Moussavi F, Comolli LR, Elidan G, Downing KH, Horowitz M. Markov random field based automatic image alignment for electron tomography. J Struct Biol 2007; 161:260-75. [PMID: 17855124 DOI: 10.1016/j.jsb.2007.07.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Revised: 06/18/2007] [Accepted: 07/10/2007] [Indexed: 11/17/2022]
Abstract
We present a method for automatic full-precision alignment of the images in a tomographic tilt series. Full-precision automatic alignment of cryo electron microscopy images has remained a difficult challenge to date, due to the limited electron dose and low image contrast. These facts lead to poor signal to noise ratio (SNR) in the images, which causes automatic feature trackers to generate errors, even with high contrast gold particles as fiducial features. To enable fully automatic alignment for full-precision reconstructions, we frame the problem probabilistically as finding the most likely particle tracks given a set of noisy images, using contextual information to make the solution more robust to the noise in each image. To solve this maximum likelihood problem, we use Markov Random Fields (MRF) to establish the correspondence of features in alignment and robust optimization for projection model estimation. The resulting algorithm, called Robust Alignment and Projection Estimation for Tomographic Reconstruction, or RAPTOR, has not needed any manual intervention for the difficult datasets we have tried, and has provided sub-pixel alignment that is as good as the manual approach by an expert user. We are able to automatically map complete and partial marker trajectories and thus obtain highly accurate image alignment. Our method has been applied to challenging cryo electron tomographic datasets with low SNR from intact bacterial cells, as well as several plastic section and X-ray datasets.
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Affiliation(s)
- Fernando Amat
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
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31
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Abstract
We illustrate the combined use of cryo-electron tomography and spectroscopic difference imaging in the study of subcellular structure and subcellular bodies in whole bacteria. We limited our goal and focus to bodies with a distinct elemental composition that was in a sufficiently high concentration to provide the necessary signal-to-noise level at the relatively large sample thicknesses of the intact cell. This combination proved very powerful, as demonstrated by the identification of a phosphorus-rich body in Caulobacter crescentus. We also confirmed the presence of a body rich in carbon, demonstrated that these two types of bodies are readily recognized and distinguished from each other, and provided, for the first time to our knowledge, structural information about them in their intact state. In addition, we also showed the presence of a similar type of phosphorus-rich body in Deinococcus grandis, a member of a completely unrelated bacteria genus. Cryo-electron microscopy and tomography allowed the study of the biogenesis and morphology of these bodies at resolutions better than 10 nm, whereas spectroscopic difference imaging provided a direct identification of their chemical composition.
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Affiliation(s)
- L R Comolli
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
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32
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Jang SB, Jeong MS, Carter RJ, Holbrook EL, Comolli LR, Holbrook SR. Novel crystal form of the ColE1 Rom protein. Acta Crystallogr D Biol Crystallogr 2006; 62:619-27. [PMID: 16699189 DOI: 10.1107/s0907444906012388] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Accepted: 04/05/2006] [Indexed: 11/10/2022]
Abstract
The RNA I modulator protein (Rom) acts as a co-regulator of ColE1 plasmid copy number by binding to RNA kissing hairpins and stabilizing their interaction. The structure of Rom has been determined in a new crystal form from X-ray diffraction data to 2.5 A resolution. In this structure, a dimer of the 57-amino-acid protein is found in the asymmetric unit. Each subunit consists almost entirely of two antiparallel alpha-helices joined by a short hairpin bend. The dimer contains a non-crystallographic twofold axis and forms a highly regular four-alpha-helical bundle. The structural packing in this novel crystal form is different from previously known Rom structures. The asymmetric unit contains one dimer, giving a crystal volume per protein weight (V(M)) of 1.83 A(3) Da(-1) and a low solvent content of 30%. Strong packing interactions and low solvation are characteristic of the structure. The Rom protein was cocrystallized with the Tar-Tar* kissing hairpin RNA. Although the electron-density maps do not show bound RNA, altered conformations in the side chains of Rom that are known to be involved in RNA binding have been identified. These results provide additional information about Rom protein conformational flexibility and suggest that the presence of a highly charged polymer such as RNA can promote tight packing of an RNA-binding protein, even when the RNA itself is not observed in the crystal.
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Affiliation(s)
- Se Bok Jang
- Korea Nanobiotechnology Center, Pusan National University, Jangjeon-dong, Keumjeong-gu, Busan 609-735, South Korea.
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33
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Rosenberg OS, Deindl S, Comolli LR, Hoelz A, Downing KH, Nairn AC, Kuriyan J. Oligomerization states of the association domain and the holoenyzme of Ca2+/CaM kinase II. FEBS J 2006; 273:682-94. [PMID: 16441656 DOI: 10.1111/j.1742-4658.2005.05088.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Ca2+/calmodulin activated protein kinase II (CaMKII) is an oligomeric protein kinase with a unique holoenyzme architecture. The subunits of CaMKII are bound together into the holoenzyme by the association domain, a C-terminal region of approximately 140 residues in the CaMKII polypeptide. Single particle analyses of electron micrographs have suggested previously that the holoenyzme forms a dodecamer that contains two stacked 6-fold symmetric rings. In contrast, a recent crystal structure of the isolated association domain of mouse CaMKIIalpha has revealed a tetradecameric assembly with two stacked 7-fold symmetric rings. In this study, we have determined the crystal structure of the Caenorhabditis elegans CaMKII association domain and it too forms a tetradecamer. We also show by electron microscopy that in its fully assembled form the CaMKII holoenzyme is a dodecamer but without the kinase domains, either from expression of the isolated association domain in bacteria or following their removal by proteolysis, the association domains form a tetradecamer. We speculate that the holoenzyme is held in its 6-fold symmetric state by the interactions of the N-terminal approximately 1-335 residues and that the removal of this region allows the association domain to convert into a more stable 7-fold symmetric form.
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Affiliation(s)
- Oren S Rosenberg
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3202, USA
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34
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Judd EM, Comolli LR, Chen JC, Downing KH, Moerner WE, McAdams HH. Distinct constrictive processes, separated in time and space, divide caulobacter inner and outer membranes. J Bacteriol 2005; 187:6874-82. [PMID: 16199556 PMCID: PMC1251605 DOI: 10.1128/jb.187.20.6874-6882.2005] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cryoelectron microscope tomography (cryoEM) and a fluorescence loss in photobleaching (FLIP) assay were used to characterize progression of the terminal stages of Caulobacter crescentus cell division. Tomographic cryoEM images of the cell division site show separate constrictive processes closing first the inner membrane (IM) and then the outer membrane (OM) in a manner distinctly different from that of septum-forming bacteria. FLIP experiments had previously shown cytoplasmic compartmentalization (when cytoplasmic proteins can no longer diffuse between the two nascent progeny cell compartments) occurring 18 min before daughter cell separation in a 135-min cell cycle so the two constrictive processes are separated in both time and space. In the very latest stages of both IM and OM constriction, short membrane tether structures are observed. The smallest observed pre-fission tethers were 60 nm in diameter for both the inner and outer membranes. Here, we also used FLIP experiments to show that both membrane-bound and periplasmic fluorescent proteins diffuse freely through the FtsZ ring during most of the constriction procession.
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Affiliation(s)
- Ellen M Judd
- Department of Applied Physics, Stanford University School of Medicine, 279 Campus Drive, Beckman Center B300, Stanford, CA 94305-5329, USA
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35
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Comolli LR, Downing KH. Dose tolerance at helium and nitrogen temperatures for whole cell electron tomography. J Struct Biol 2005; 152:149-56. [PMID: 16198601 DOI: 10.1016/j.jsb.2005.08.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2005] [Revised: 07/28/2005] [Accepted: 08/17/2005] [Indexed: 11/25/2022]
Abstract
Electron tomography is currently the only method that allows the direct three-dimensional visualization of macromolecules in an unperturbed cellular context. In principle, tomography should enable the identification and localization of the major macromolecular complexes within intact bacteria, embedded in amorphous ice. In an effort to optimize conditions for recording data that would bring us close to the theoretical limits, we present here a comparison of the dose tolerance of Caulobacter crescentus cells embedded in amorphous ice at liquid helium versus liquid nitrogen temperature. The inner and outer cell membranes, and the periodic structure of the S-layer of this Gram-negative bacterium provide ideal features to monitor changes in contrast and order as a function of dose. The loss of order in the S-layer occurs at comparable doses at helium and nitrogen temperatures. Macroscopic bubbling within the cell and the plastic support develops at both temperatures, but more slowly at helium temperature. The texture of the bubbles is finer in initial stages at helium temperature, giving an impression of contrast reversal in some parts of the specimen. Bubbles evolve differently in different organelles, presumably a consequence of their different chemical composition and mechanical properties. Finally, the amorphous ice "flows" at helium temperature, causing changes in the relative positions of markers within the specimen and distorting the cells. We conclude that for cryo-electron tomography of whole cells liquid nitrogen temperature provides better overall data quality.
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Affiliation(s)
- Luis R Comolli
- Life Science Division, Lawrence Berkeley National Laboratory, CA, USA
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36
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Abstract
Telomerase is a ribonucleoprotein (RNP) required for maintenance of telomeres. Although up-regulated telomerase activity is closely linked to the cellular immortality characteristic of late stage carcinogenesis, recently, mutations in the telomerase RNA gene in humans have been associated with dyskeratosis congenita and aplastic anemia, both typified by impaired haemopoietic function. These mutations include base changes in a highly conserved putative telomerase RNA pseudoknot. Here, by using in vitro telomerase assays, NMR, and UV absorbance melting analyses of model oligonucleotides designed to form a "trans-pseudoknot," we describe functional, structural, and energetic properties of this structure. We demonstrate that the pseudoknot domain exists in two alternative states of nearly equal stability in solution: one is the previously proposed pseudoknot formed by pairing P3 with the loop domain of P2b, and the other is a structured P2b loop alone. We show that the two-base mutation (GC1078 --> AG) present in one gene copy in a family with dyskeratosis congenita abrogates telomerase activity. This mutation hyperstabilizes the P2b intraloop structure, blocking pseudoknot formation. Conversely, when the P3 pseudoknot pairing is hyperstabilized by deleting a conserved bulge in P3, telomerase activity also decreases. We propose that the P2bP3 pseudoknot domain acts as a molecular switch, and interconversion between its two states is important for telomerase function. Phylogenetic covariation in the P2b and P3 sequences of 35 species provides a compelling set of "natural" compensatory base pairing changes supporting the existence of the crucial molecular switch.
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Affiliation(s)
- Luis R Comolli
- Departments of Pharmaceutical Chemistry and Biochemistry and Biophysics, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
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37
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Abstract
The NMR structure of the 3' stem-loop (3'SL) from human U4 snRNA was determined to gain insight into the structural basis for conservation of this stem-loop sequence from vertebrates. 3'SL sequences from human, rat, mouse and chicken U4 snRNA each consist of a 7 bp stem capped by a UACG tetraloop. No high resolution structure has previously been reported for a UACG tetraloop. The UACG tetraloop portion of the 3'SL was especially well defined by the NMR data, with a total of 92 NOE-derived restraints (about 15 per residue), including 48 inter-residue restraints (about 8 per residue) for the tetraloop and closing C-G base pair. Distance restraints were derived from NOESY spectra using MARDIGRAS with random error analysis. Refinement of the 20mer RNA hairpin structure was carried out using the programs DYANA and miniCarlo. In the UACG tetraloop, U and G formed a base pair stabilized by two hydrogen bonds, one between the 2'-hydroxyl proton of U and carbonyl oxygen of G, another between the imino proton of G and carbonyl oxygen O2 of U. In addition, the amino group of C formed a hydrogen bond with the phosphate oxygen of A. G adopted a syn orientation about the glycosidic bond, while the sugar puckers of A and C were either C2'-endo or flexible. The conformation of the UACG tetraloop was, overall, similar to that previously reported for UUCG tetraloops, another member of the UNCG class of tetraloops. The presence of an A, rather than a U, at the variable position, however, presents a distinct surface for interaction of the 3'SL tetraloop with either RNA or protein residues that may stabilize interactions important for active spliceosome formation. Such tertiary interactions may explain the conservation of the UACG tetraloop motif in 3'SL sequences from U4 snRNA in vertebrates.
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Affiliation(s)
- Luis R Comolli
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143, USA
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38
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Abstract
An RNA 'kissing' complex is formed by the association of two hairpins via base pairing of their complementary loops. This sense-antisense RNA motif is used in the regulation of many cellular processes, including Escherichia coli ColE1 plasmid copy number. The RNA one modulator protein (Rom) acts as a co-regulator of ColE1 plasmid copy number by binding to the kissing hairpins and stabilizing their interaction. We have used heteronuclear two-dimensional NMR spectroscopy to map the interface between Rom and a kissing complex formed by the loop of the trans -activation response (Tar) element of immunodeficiency virus 1 (HIV-1) and its complement. The protein binding interface was obtained from changes in amide proton signals of uniformly 15N-labeled Rom with increasing concentrations of unlabeled Tar-Tar*. Similarly, the RNA-binding interface was obtained from changes in imino proton signals of uniformly 15N-labeled Tar with increasing concentrations of unlabeled Rom. Our results are in agreement with previous mutagenesis studies and provide additional information on Rom residues involved in RNA binding. The kissing hairpin interface with Rom leads to a model in which the protein contacts the minor groove of the loop-loop helix and, to a lesser extent, the major groove of the stems.
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Affiliation(s)
- L R Comolli
- Department of Chemistry, University of California at Berkeley and Structural Biology Department, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-1460, USA
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Pelton JG, Comolli LR. Sequence specific 1HN, 15N, 1H alpha, 13C alpha, and 13C beta assignments for RNA-1 modulator protein ROM. J Biomol NMR 1998; 11:463-464. [PMID: 9691290 DOI: 10.1023/a:1008283704026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- J G Pelton
- Department of Chemistry, University of California, Berkeley 94720-1460, USA
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