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Spatially segregated transcription and translation in cells of the endomembrane-containing bacterium Gemmata obscuriglobus. Proc Natl Acad Sci U S A 2014; 111:11067-72. [PMID: 25024214 DOI: 10.1073/pnas.1409187111] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dogma of coupled transcription and translation in bacteria has been challenged by recent reports of spatial segregation of these processes within the relatively simple cellular organization of the model organisms Escherichia coli and Bacillus subtilis. The bacterial species Gemmata obscuriglobus possesses an extensive endomembrane system. The membranes generate a very convoluted intracellular architecture in which some of the cell's ribosomes appear to have less direct access to the cell's nucleoid(s) than others. This observation prompted us to test the hypothesis that a substantial proportion of G. obscuriglobus translation may be spatially segregated from transcription. Using immunofluorescence and immunoelectron microscopy, we showed that translating ribosomes are localized throughout the cell, with a quantitatively greater proportion found in regions distal to nucleoid(s). Our results extend information about the phylogenetic and morphological diversity of bacteria in which the spatial organization of transcription and translation has been studied. These findings also suggest that endomembranes may provide an obstacle to colocated transcription and translation, a role for endomembranes that has not been reported previously for a prokaryotic organism. Our studies of G. obscuriglobus may provide a useful background for consideration of the evolutionary development of eukaryotic cellular complexity and how it led to decoupled processes of gene expression in eukaryotes.
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Sagulenko E, Morgan GP, Webb RI, Yee B, Lee KC, Fuerst JA. Structural studies of planctomycete Gemmata obscuriglobus support cell compartmentalisation in a bacterium. PLoS One 2014; 9:e91344. [PMID: 24632833 PMCID: PMC3954628 DOI: 10.1371/journal.pone.0091344] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 02/11/2014] [Indexed: 12/03/2022] Open
Abstract
Members of phylum Planctomycetes have been proposed to possess atypical cell organisation for the Bacteria, having a structure of sectioned cells consistent with internal compartments surrounded by membranes. Here via electron tomography we confirm the presence of compartments in the planctomycete Gemmata obscuriglobus cells. Resulting 3-D models for the most prominent structures, nuclear body and riboplasm, demonstrate their entirely membrane - enclosed nature. Immunogold localization of the FtsK protein also supports the internal organisation of G.obscuriglobus cells and their unique mechanism of cell division. We discuss how these new data expand our knowledge on bacterial cell biology and suggest evolutionary consequences of the findings.
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Affiliation(s)
- Evgeny Sagulenko
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Garry P. Morgan
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Richard I. Webb
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin Yee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kuo-Chang Lee
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - John A. Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
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Kamke J, Rinke C, Schwientek P, Mavromatis K, Ivanova N, Sczyrba A, Woyke T, Hentschel U. The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features. PLoS One 2014; 9:e87353. [PMID: 24498082 PMCID: PMC3909097 DOI: 10.1371/journal.pone.0087353] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/19/2013] [Indexed: 01/02/2023] Open
Abstract
The candidate phylum Poribacteria is one of the most dominant and widespread members of the microbial communities residing within marine sponges. Cell compartmentalization had been postulated along with their discovery about a decade ago and their phylogenetic association to the Planctomycetes, Verrucomicrobia, Chlamydiae superphylum was proposed soon thereafter. In the present study we revised these features based on genomic data obtained from six poribacterial single cells. We propose that Poribacteria form a distinct monophyletic phylum contiguous to the PVC superphylum together with other candidate phyla. Our genomic analyses supported the possibility of cell compartmentalization in form of bacterial microcompartments. Further analyses of eukaryote-like protein domains stressed the importance of such proteins with features including tetratricopeptide repeats, leucin rich repeats as well as low density lipoproteins receptor repeats, the latter of which are reported here for the first time from a sponge symbiont. Finally, examining the most abundant protein domain family on poribacterial genomes revealed diverse phyH family proteins, some of which may be related to dissolved organic posphorus uptake.
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Affiliation(s)
- Janine Kamke
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Wuerzburg, Wuerzburg, Germany
| | - Christian Rinke
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Patrick Schwientek
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Kostas Mavromatis
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Alexander Sczyrba
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Wuerzburg, Wuerzburg, Germany
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PVC bacteria: variation of, but not exception to, the Gram-negative cell plan. Trends Microbiol 2014; 22:14-20. [DOI: 10.1016/j.tim.2013.10.008] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 10/22/2013] [Accepted: 10/25/2013] [Indexed: 11/17/2022]
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Theriot JA. Why are bacteria different from eukaryotes? BMC Biol 2013; 11:119. [PMID: 24330667 PMCID: PMC3874686 DOI: 10.1186/1741-7007-11-119] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 12/09/2013] [Indexed: 01/09/2023] Open
Affiliation(s)
- Julie A Theriot
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA.
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Abstract
We report the presence of a membranous tubulovesicular network in the planctomycete bacterium Gemmata obscuriglobus. This endomembrane system interacts with membrane coat proteins and is capable of protein internalization and degradation. Taken together, this suggests that the planctomycetal bacterium could illuminate the emergence of complex endomembrane systems.
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Affiliation(s)
- Devrim Acehan
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Fuerst JA, Sagulenko E. Towards understanding the molecular mechanism of the endocytosis-like process in the bacterium Gemmata obscuriglobus. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:1732-8. [PMID: 24144586 DOI: 10.1016/j.bbamcr.2013.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 12/22/2022]
Abstract
An endocytosis-like process of protein uptake in the planctomycete Gemmata obscuriglobus is a recently discovered process unprecedented in the bacterial world. The molecular mechanisms underlying this process are not yet characterized. A homolog of the MC (membrane-coating) proteins of eukaryotes has been proposed to be involved in the mechanism of this process, but its relationship to eukaryote proteins is controversial. However, a number of other proteins of G. obscuriglobus with domains homologous to those involved in endocytosis in eukaryotes can also be identified. Here we critically evaluate current bioinformatic knowledge, and suggest practical experimental steps to overcome the limits of bioinformatics in elucidating the molecular mechanism of endocytosis in bacteria. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- John A Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia.
| | - Evgeny Sagulenko
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
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Chen AH, Robinson-Mosher A, Savage DF, Silver PA, Polka JK. The bacterial carbon-fixing organelle is formed by shell envelopment of preassembled cargo. PLoS One 2013; 8:e76127. [PMID: 24023971 PMCID: PMC3762834 DOI: 10.1371/journal.pone.0076127] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 08/23/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Cyanobacteria play a significant role in the global carbon cycle. In Synechococcuselongatus, the carbon-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is concentrated into polyhedral, proteinaceous compartments called carboxysomes. METHODOLOGY/PRINCIPAL FINDINGS Using live cell fluorescence microscopy, we show that carboxysomes are first detected as small seeds of RuBisCO that colocalize with existing carboxysomes. These seeds contain little or no shell protein, but increase in RuBisCO content over several hours, during which time they are exposed to the solvent. The maturing seed is then enclosed by shell proteins, a rapid process that seals RuBisCO from the cytosol to establish a distinct, solvent-protected microenvironment that is oxidizing relative to the cytosol. These closure events can be spatially and temporally coincident with the appearance of a nascent daughter RuBisCO seed. CONCLUSIONS/SIGNIFICANCE Carboxysomes assemble in a stepwise fashion, inside-to-outside, revealing that cargo is the principle organizer of this compartment's biogenesis. Our observations of the spatial relationship of seeds to previously formed carboxysomes lead us to propose a model for carboxysome replication via sequential fission, polymerization, and encapsulation of their internal cargo.
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Affiliation(s)
- Anna H. Chen
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Avi Robinson-Mosher
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - David F. Savage
- Department of Molecular and Cell Biology, Department of Chemistry and Energy Biosciences Institute, University of California, Berkeley, California, United States of America
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
| | - Jessica K. Polka
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, United States of America
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From genome mining to phenotypic microarrays: Planctomycetes as source for novel bioactive molecules. Antonie van Leeuwenhoek 2013; 104:551-67. [PMID: 23982431 DOI: 10.1007/s10482-013-0007-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/14/2013] [Indexed: 01/19/2023]
Abstract
Most members of the phylum Planctomycetes share many unusual traits that are unique for bacteria, since they divide independent of FtsZ through asymmetric budding, possess a complex life cycle and comprise a compartmentalized cell plan. Besides their complex cell biological features Planctomycetes are environmentally important and play major roles in global matter fluxes. Such features have been successfully employed in biotechnological applications such as the anaerobic oxidation of ammonium in wastewater treatment plants or the utilization of enzymes for biotechnological processes. However, little is known about planctomycetal secondary metabolites. This is surprising as Planctomycetes have several key features in common with known producers of small bioactive molecules such as Streptomycetes or Myxobacteria: a complex life style and large genome sizes. Planctomycetal genomes with an average size of 6.9 MB appear as tempting targets for drug discovery approaches. To enable the hunt for bioactive molecules from Planctomycetes, we performed a comprehensive genome mining approach employing the antiSMASH secondary metabolite identification pipeline and found 102 candidate genes or clusters within the analyzed 13 genomes. However, as most genes and operons related to secondary metabolite production are exclusively expressed under certain environmental conditions, we optimized Phenotype MicroArray protocols for Rhodopirellula baltica and Planctomyces limnophilus to allow high throughput screening of putative stimulating carbon sources. Our results point towards a previously postulated relationship of Planctomycetes with algae or plants, which secrete compounds that might serve as trigger to stimulate the secondary metabolite production in Planctomycetes. Thus, this study provides the necessary starting point to explore planctomycetal small molecules for drug development.
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Fuerst JA. The PVC superphylum: exceptions to the bacterial definition? Antonie van Leeuwenhoek 2013; 104:451-66. [PMID: 23912444 DOI: 10.1007/s10482-013-9986-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/22/2013] [Indexed: 11/30/2022]
Abstract
The PVC superphylum is a grouping of distinct phyla of the domain bacteria proposed initially on the basis of 16S rRNA gene sequence analysis. It consists of a core of phyla Planctomycetes, Verrucomicrobia and Chlamydiae, but several other phyla have been considered to be members, including phylum Lentisphaerae and several other phyla consisting only of yet-to-be cultured members. The genomics-based links between Planctomycetes, Verrucomicrobia and Chlamydiae have been recently strengthened, but there appear to be other features which may confirm the relationship at least of Planctomycetes, Verrucomicrobia and Lentisphaerae. Remarkably these include the unique planctomycetal compartmentalized cell plan differing from the cell organization typical for bacteria. Such a shared cell plan suggests that the common ancestor of the PVC superphylum members may also have been compartmentalized, suggesting this is an evolutionarily homologous feature at least within the superphylum. Both the PVC endomembranes and the eukaryote-homologous membrane-coating MC proteins linked to endocytosis ability in Gemmata obscuriglobus and shared by PVC members suggest such homology may extend beyond the bacteria to the Eukarya. If so, either our definition of bacteria may have to change or PVC members admitted to be exceptions. The cases for and against considering the PVC superphylum members as exceptions to the bacteria are discussed, and arguments for them as exceptions presented. Recent critical analysis has favoured convergence and analogy for explaining eukaryote-like features in planctomycetes and other PVC organisms. The case is made for constructing hypotheses leaving the possibility of homology and evolutionary links to eukaryote features open. As the case of discovery of endocytosis-like protein uptake in planctomycetes has suggested, this may prove a strong basis for the immediate future of experimental research programs in the PVC scientific community.
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Affiliation(s)
- John A Fuerst
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia,
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61
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Santarella-Mellwig R, Pruggnaller S, Roos N, Mattaj IW, Devos DP. Three-dimensional reconstruction of bacteria with a complex endomembrane system. PLoS Biol 2013; 11:e1001565. [PMID: 23700385 PMCID: PMC3660258 DOI: 10.1371/journal.pbio.1001565] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Accepted: 04/11/2013] [Indexed: 01/08/2023] Open
Abstract
The apparently complex membrane organization of Gemmata obscuriglobus, and probably all PVC superphylum members, comprises interconnected invaginations and is topologically identical to the “classical” Gram-negative bacterial membrane system. The division of cellular space into functionally distinct membrane-defined compartments has been one of the major transitions in the history of life. Such compartmentalization has been claimed to occur in members of the Planctomycetes, Verrucomicrobiae, and Chlamydiae bacterial superphylum. Here we have investigated the three-dimensional organization of the complex endomembrane system in the planctomycete bacteria Gemmata obscuriglobus. We reveal that the G. obscuriglobus cells are neither compartmentalized nor nucleated as none of the spaces created by the membrane invaginations are closed; instead, they are all interconnected. Thus, the membrane organization of G. obscuriglobus, and most likely all PVC members, is not different from, but an extension of, the “classical” Gram-negative bacterial membrane system. Our results have implications for our definition and understanding of bacterial cell organization, the genesis of complex structure, and the origin of the eukaryotic endomembrane system. The compartmentalization of cellular space has been an important evolutionary innovation, allowing for the functional specialization of cellular space. This compartmentalization is extensively developed in eukaryotes and although not as complex and developed, compartments with specialized function are known to occur in bacteria and can be surprisingly sophisticated. Nevertheless, members of the Planctomycetes, Verrucomicrobiae, and Chlamydiae (PVC) bacterial superphylum are exceptional in displaying diverse and extensive intracellular membranous organization. We investigated the three-dimensional organization of the complex endomembrane system in the planctomycete bacterium Gemmata obscuriglobus. We reveal that the G. obscuriglobus cells are neither compartmentalized nor nucleated, contrary to previous claims, as none of the spaces created by the membrane invaginations is topologically closed; instead, they are all interconnected. The organization of cellular space is similar to that of a classical Gram-negative bacterium modified by the presence of large invaginations of the inner membrane inside the cytoplasm. Thus, the membrane organization of G. obscuriglobus, and most likely all PVC members, is not fundamentally different from, but is rather an extension of, the “classical” Gram-negative bacterial membrane system.
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Affiliation(s)
| | | | - Norbert Roos
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Iain W. Mattaj
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Damien P. Devos
- European Molecular Biology Laboratory, Heidelberg, Germany
- * E-mail:
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62
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Abstract
While studying actin assembly as a graduate student with Matt Welch at the University of California at Berkeley, my interest was piqued by reports of surprising observations in bacteria: the identification of numerous cytoskeletal proteins, actin homologues fulfilling spindle-like functions, and even the presence of membrane-bound organelles. Curiosity about these phenomena drew me to Lucy Shapiro's lab at Stanford University for my postdoctoral research. In the Shapiro lab, and now in my lab at Johns Hopkins, I have focused on investigating the mechanisms of bacterial cytokinesis. Spending time as both a eukaryotic cell biologist and a bacterial cell biologist has convinced me that bacterial cells present the same questions as eukaryotic cells: How are chromosomes organized and accurately segregated? How is force generated for cytokinesis? How is polarity established? How are signals transduced within and between cells? These problems are conceptually similar between eukaryotes and bacteria, although their solutions can differ significantly in specifics. In this Perspective, I provide a broad view of cell biological phenomena in bacteria, the technical challenges facing those of us who peer into bacterial cells, and areas of common ground as research in eukaryotic and bacterial cell biology moves forward.
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Affiliation(s)
- Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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63
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Jogler C, Waldmann J, Huang X, Jogler M, Glöckner FO, Mascher T, Kolter R. Identification of proteins likely to be involved in morphogenesis, cell division, and signal transduction in Planctomycetes by comparative genomics. J Bacteriol 2012; 194:6419-30. [PMID: 23002222 PMCID: PMC3497475 DOI: 10.1128/jb.01325-12] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 09/14/2012] [Indexed: 12/20/2022] Open
Abstract
Members of the Planctomycetes clade share many unusual features for bacteria. Their cytoplasm contains membrane-bound compartments, they lack peptidoglycan and FtsZ, they divide by polar budding, and they are capable of endocytosis. Planctomycete genomes have remained enigmatic, generally being quite large (up to 9 Mb), and on average, 55% of their predicted proteins are of unknown function. Importantly, proteins related to the unusual traits of Planctomycetes remain largely unknown. Thus, we embarked on bioinformatic analyses of these genomes in an effort to predict proteins that are likely to be involved in compartmentalization, cell division, and signal transduction. We used three complementary strategies. First, we defined the Planctomycetes core genome and subtracted genes of well-studied model organisms. Second, we analyzed the gene content and synteny of morphogenesis and cell division genes and combined both methods using a "guilt-by-association" approach. Third, we identified signal transduction systems as well as sigma factors. These analyses provide a manageable list of candidate genes for future genetic studies and provide evidence for complex signaling in the Planctomycetes akin to that observed for bacteria with complex life-styles, such as Myxococcus xanthus.
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64
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Gupta RS, Bhandari V, Naushad HS. Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships. Front Microbiol 2012; 3:327. [PMID: 23060863 PMCID: PMC3444138 DOI: 10.3389/fmicb.2012.00327] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/23/2012] [Indexed: 11/13/2022] Open
Abstract
The PVC superphylum is an amalgamation of species from the phyla Planctomycetes, Verrucomicrobia, and Chlamydiae, along with the Lentisphaerae, Poribacteria, and two other candidate divisions. The diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. Recently, genome sequences for 37 species covering all of the main PVC groups of bacteria have become available. We have used these sequences to construct a phylogenetic tree based upon concatenated sequences for 16 proteins and identify molecular signatures in protein sequences that are specific for the species from these phyla or those providing molecular links among them. Of the useful molecular markers identified in the present work, six conserved signature indels (CSIs) in the proteins Cyt c oxidase, UvrD helicase, urease, and a helicase-domain containing protein are specific for the species from the Verrucomicrobia phylum; three other CSIs in an ABC transporter protein, cobyrinic acid ac-diamide synthase, and SpoVG protein are specific for the Planctomycetes species. Additionally, a 3 aa insert in the RpoB protein is uniquely present in all sequenced Chlamydiae, Verrucomicrobia, and Lentisphaerae species, providing evidence for the shared ancestry of the species from these three phyla. Lastly, we have also identified a conserved protein of unknown function that is exclusively found in all sequenced species from the phyla Chlamydiae, Verrucomicrobia, Lentisphaerae, and Planctomycetes suggesting a specific linkage among them. The absence of this protein in Poribacteria, which branches separately from other members of the PVC clade, indicates that it is not specifically related to the PVC clade of bacteria. The molecular markers described here in addition to clarifying the evolutionary relationships among the PVC clade of bacteria also provide novel tools for their identification and for genetic and biochemical studies on these organisms.
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Affiliation(s)
- Radhey S. Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
| | - Vaibhav Bhandari
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
| | - Hafiz Sohail Naushad
- Department of Biochemistry and Biomedical Sciences, McMaster UniversityHamilton, ON, Canada
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65
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Yee B, Sagulenko E, Morgan GP, Webb RI, Fuerst JA. Electron tomography of the nucleoid of Gemmata obscuriglobus reveals complex liquid crystalline cholesteric structure. Front Microbiol 2012; 3:326. [PMID: 22993511 PMCID: PMC3440768 DOI: 10.3389/fmicb.2012.00326] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 08/23/2012] [Indexed: 11/13/2022] Open
Abstract
The nucleoid of the planctomycete Gemmata obscuriglobus is unique within the Bacteria in being both highly condensed and enclosed by a double-membrane nuclear envelope, seemingly analogous to the nucleus of eukaryotes. Here we have applied electron tomography to study high-pressure frozen, cryosubstituted cells of G. obscuriglobus and found multiple nested orders of DNA organization within the condensed nucleoid structure. Detailed examination of the nucleoid revealed a series of nested arcs characteristic of liquid crystalline cholesteric DNA structure. The finest fibers were arranged in parallel concentrically in a double-twist organization. At the highest order of nucleoid organization, several of these structures come together to form the core of the G. obscuriglobus nucleoid. The complex structure of DNA within this nucleoid may have implications for understanding the evolutionary significance of compartmentalized planctomycete cells.
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Affiliation(s)
- Benjamin Yee
- School of Chemistry and Molecular Biosciences, The University of Queensland St. Lucia, QLD, Australia
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66
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Abstract
The evolution of the nucleus, the defining feature of eukaryotic cells, was long shrouded in speculation and mystery. There is now strong evidence that nuclear pore complexes (NPCs) and nuclear membranes coevolved with the endomembrane system, and that the last eukaryotic common ancestor (LECA) had fully functional NPCs. Recent studies have identified many components of the nuclear envelope in living Opisthokonts, the eukaryotic supergroup that includes fungi and metazoan animals. These components include diverse chromatin-binding membrane proteins, and membrane proteins with adhesive lumenal domains that may have contributed to the evolution of nuclear membrane architecture. Further discoveries about the nucleoskeleton suggest that the evolution of nuclear structure was tightly coupled to genome partitioning during mitosis.
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Affiliation(s)
- Katherine L Wilson
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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67
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Reynaud EG, Devos DP. Transitional forms between the three domains of life and evolutionary implications. Proc Biol Sci 2011; 278:3321-8. [PMID: 21920985 PMCID: PMC3177640 DOI: 10.1098/rspb.2011.1581] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The question as to the origin and relationship between the three domains of life is lodged in a phylogenetic impasse. The dominant paradigm is to see the three domains as separated. However, the recently characterized bacterial species have suggested continuity between the three domains. Here, we review the evidence in support of this hypothesis and evaluate the implications for and against the models of the origin of the three domains of life. The existence of intermediate steps between the three domains discards the need for fusion to explain eukaryogenesis and suggests that the last universal common ancestor was complex. We propose a scenario in which the ancestor of the current bacterial Planctomycetes, Verrucomicrobiae and Chlamydiae superphylum was related to the last archaeal and eukaryotic common ancestor, thus providing a way out of the phylogenetic impasse.
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Affiliation(s)
- Emmanuel G Reynaud
- School of Biology and Environmental Science, UCD Science Centre, Belfield, Dublin 4, Ireland.
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68
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Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat Rev Microbiol 2011; 9:403-13. [PMID: 21572457 DOI: 10.1038/nrmicro2578] [Citation(s) in RCA: 280] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Planctomycetes form a distinct phylum of the domain Bacteria and possess unusual features such as intracellular compartmentalization and a lack of peptidoglycan in their cell walls. Remarkably, cells of the genus Gemmata even contain a membrane-bound nucleoid analogous to the eukaryotic nucleus. Moreover, the so-called 'anammox' planctomycetes have a unique anaerobic, autotrophic metabolism that includes the ability to oxidize ammonium; this process is dependent on a characteristic membrane-bound cell compartment called the anammoxosome, which might be a functional analogue of the eukaryotic mitochondrion. The compartmentalization of planctomycetes challenges our hypotheses regarding the origins of eukaryotic organelles. Furthermore, the recent discovery of both an endocytosis-like ability and proteins homologous to eukaryotic clathrin in a planctomycete marks this phylum as one to watch for future research on the origin and evolution of the eukaryotic cell.
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Characterization of Planctomyces limnophilus and development of genetic tools for its manipulation establish it as a model species for the phylum Planctomycetes. Appl Environ Microbiol 2011; 77:5826-9. [PMID: 21724885 DOI: 10.1128/aem.05132-11] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Planctomycetes represent a remarkable clade in the domain Bacteria because they play crucial roles in global carbon and nitrogen cycles and display cellular structures that closely parallel those of eukaryotic cells. Studies on Planctomycetes have been hampered by the lack of genetic tools, which we developed for Planctomyces limnophilus.
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70
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Yee B, Sagulenko E, Fuerst JA. Making heads or tails of the HU proteins in the planctomycete Gemmata obscuriglobus. MICROBIOLOGY-SGM 2011; 157:2012-2021. [PMID: 21511768 DOI: 10.1099/mic.0.047605-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Gemmata obscuriglobus has a highly condensed nucleoid which is implicated in its resistance to radiation. However, the mechanisms by which such compaction is achieved, and the proteins responsible, are still unknown. Here we have examined the genome of G. obscuriglobus for the presence of proteins homologous to those that have been associated with nucleoid condensation. We found two different proteins homologous to the bacterial nucleoid-associated protein HU, one with an N-terminal and one with a C-terminal extension relative to the amino acid sequence of the HU found in Escherichia coli. Sequence analysis revealed that one of these HU homologues represents a novel type with a high number of prolines in its C-terminal extension, whereas the other one has motifs similar to the N terminus of the HU homologue from the radio-resistant bacterium Deinococcus radiodurans. The occurrence of two such HU homologue proteins with these two different terminal extensions in one organism appears to be unique among the Bacteria.
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Affiliation(s)
- Benjamin Yee
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland 4072, Australia
| | - Evgeny Sagulenko
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland 4072, Australia
| | - John A Fuerst
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Queensland 4072, Australia
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71
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Ward NL, Klotz MG. Harnessing the power of microbial genomics for exploring exceptions and shifting perceptions. Front Microbiol 2011; 1:146. [PMID: 21687802 PMCID: PMC3109305 DOI: 10.3389/fmicb.2010.00146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 12/22/2010] [Indexed: 11/13/2022] Open
Affiliation(s)
- Naomi L Ward
- Department of Molecular Biology, University of Wyoming Laramie, WY, USA
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72
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73
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Kamneva OK, Liberles DA, Ward NL. Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method. Genome Biol Evol 2010; 2:870-86. [PMID: 21048002 PMCID: PMC3000692 DOI: 10.1093/gbe/evq071] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Whole-genome scans for positive Darwinian selection are widely used to detect evolution of genome novelty. Most approaches are based on evaluation of nonsynonymous to synonymous substitution rate ratio across evolutionary lineages. These methods are sensitive to saturation of synonymous sites and thus cannot be used to study evolution of distantly related organisms. In contrast, indels occur less frequently than amino acid replacements, accumulate more slowly, and can be employed to characterize evolution of diverged organisms. As indels are also subject to the forces of natural selection, they can generate functional changes through positive selection. Here, we present a new computational approach to detect selective constraints on indel substitutions at the whole-genome level for distantly related organisms. Our method is based on ancestral sequence reconstruction, takes into account the varying susceptibility of different types of secondary structure to indels, and according to simulation studies is conservative. We applied this newly developed framework to characterize the evolution of organisms of the Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) bacterial superphylum. The superphylum contains organisms with unique cell biology, physiology, and diverse lifestyles. It includes bacteria with simple cell organization and more complex eukaryote-like compartmentalization. Lifestyles range from free-living organisms to obligate pathogens. In this study, we conduct a whole-genome level analysis of indel substitutions specific to evolutionary lineages of the PVC superphylum and found that indels evolved under positive selection on up to 12% of gene tree branches. We also analyzed possible functional consequences for several case studies of predicted indel events.
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Affiliation(s)
| | | | - Naomi L. Ward
- Department of Molecular Biology, University of Wyoming
- Department of Botany, University of Wyoming
- Program in Ecology, University of Wyoming
- Corresponding author: E-mail:
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Fuerst JA, Sagulenko E. Protein uptake by bacteria: An endocytosis-like process in the planctomycete Gemmata obscuriglobus. Commun Integr Biol 2010; 3:572-5. [PMID: 21331243 DOI: 10.4161/cib.3.6.13061] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 07/19/2010] [Indexed: 12/29/2022] Open
Abstract
Endocytosis is a fundamental process of membrane-trafficking in eukaryotes, but has not been known to occur in bacteria or archaea. The origin of endocytosis is central to the understanding of evolution of the first eukaryotes and their endomembrane systems. In a recent study we have established that an endocytosis-like process for uptake of proteins into cells occurs in a bacterium, Gemmata obscuriglobus, a member of the distinctive phylum Planctomycetes of peptidoglycan-less budding bacteria. Members of this phylum characteristically possess cells divided into compartments separated by internal membranes and in the case of G. obscuriglobus these compartments include one where a double membrane envelope surrounds its nucleoid DNA, as well as an outer ribosome- free region of cytoplasm. Proteins can be internalized by cells from the external milieu and collected into this ribosome-free compartment, and this process is energy-dependent and appears to be receptor-mediated. As in eukaryote endocytosis, internalized proteins are associated with vesicles, and can be subjected to proteolytic degradation. The discovery of this process in a bacterium has significant implications for our understanding of the origins of endocytosis in eukaryotes.
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Affiliation(s)
- John A Fuerst
- School of Chemistry and Molecular Biosciences; The University of Queensland St. Lucia; St. Lucia, QLD Australia
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75
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Bacteria with a eukaryotic touch: a glimpse of ancient evolution? Proc Natl Acad Sci U S A 2010; 107:12739-40. [PMID: 20624972 DOI: 10.1073/pnas.1007720107] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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76
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Endocytosis-like protein uptake in the bacterium Gemmata obscuriglobus. Proc Natl Acad Sci U S A 2010; 107:12883-8. [PMID: 20566852 DOI: 10.1073/pnas.1001085107] [Citation(s) in RCA: 159] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endocytosis is a process by which extracellular material such as macromolecules can be incorporated into cells via a membrane-trafficking system. Although universal among eukaryotes, endocytosis has not been identified in Bacteria or Archaea. However, intracellular membranes are known to compartmentalize cells of bacteria in the phylum Planctomycetes, suggesting the potential for endocytosis and membrane trafficking in members of this phylum. Here we show that cells of the planctomycete Gemmata obscuriglobus have the ability to uptake proteins present in the external milieu in an energy-dependent process analogous to eukaryotic endocytosis, and that internalized proteins are associated with vesicle membranes. Occurrence of such ability in a bacterium is consistent with autogenous evolution of endocytosis and the endomembrane system in an ancestral noneukaryote cell.
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77
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Santarella-Mellwig R, Franke J, Jaedicke A, Gorjanacz M, Bauer U, Budd A, Mattaj IW, Devos DP. The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins. PLoS Biol 2010; 8:e1000281. [PMID: 20087413 PMCID: PMC2799638 DOI: 10.1371/journal.pbio.1000281] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 12/08/2009] [Indexed: 02/06/2023] Open
Abstract
Compartmentalized bacteria have proteins that are structurally related to eukaryotic membrane coats, and one of these proteins localizes at the membrane of vesicles formed inside bacterial cells. The development of the endomembrane system was a major step in eukaryotic evolution. Membrane coats, which exhibit a unique arrangement of β-propeller and α-helical repeat domains, play key roles in shaping eukaryotic membranes. Such proteins are likely to have been present in the ancestral eukaryote but cannot be detected in prokaryotes using sequence-only searches. We have used a structure-based detection protocol to search all proteomes for proteins with this domain architecture. Apart from the eukaryotes, we identified this protein architecture only in the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum, many members of which share a compartmentalized cell plan. We determined that one such protein is partly localized at the membranes of vesicles formed inside the cells in the planctomycete Gemmata obscuriglobus. Our results demonstrate similarities between bacterial and eukaryotic compartmentalization machinery, suggesting that the bacterial PVC superphylum contributed significantly to eukaryogenesis. Despite decades of research, the origin of eukaryotic cells remains an unsolved issue. The endomembrane system defines the eukaryotic cell, and its origin is linked to that of eukaryotes. A search was conducted within all known sequences for proteins that are characteristic of the eukaryotic endomembrane system, using a combination of fold types that is uniquely found in the membrane coat proteins. Outside eukaryotes, such proteins were solely found in the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum. By immuno-electron microscopy, one of these bacterial proteins was found to localize adjacent to the membranes of vesicles found within the cells of one member of the PVC superphylum. Thus, there appear to be similarities between bacterial and eukaryotic compartmentalization systems, suggesting that the bacterial PVC superphylum may have contributed significantly to eukaryogenesis.
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Affiliation(s)
| | - Josef Franke
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, United States of America
| | | | | | - Ulrike Bauer
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aidan Budd
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Iain W. Mattaj
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Damien P. Devos
- European Molecular Biology Laboratory, Heidelberg, Germany
- * E-mail:
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78
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Chromatin organization and radio resistance in the bacterium Gemmata obscuriglobus. J Bacteriol 2008; 191:1439-45. [PMID: 19074379 DOI: 10.1128/jb.01513-08] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The organization of chromatin has a major impact on cellular activities, such as gene expression. For bacteria, it was suggested that the spatial organization of the genetic material correlates with transcriptional levels, implying a specific architecture of the chromosome within the cytoplasm. Accordingly, recent technological advances have emphasized the organization of the genetic material within nucleoid structures. Gemmata obscuriglobus, a member of the phylum Planctomycetes, exhibits a distinctive nucleoid structure in which chromatin is encapsulated within a discrete membrane-bound compartment. Here, we show that this soil and freshwater bacterium tolerates high doses of UV and ionizing radiation. Cryoelectron tomography of frozen hydrated sections and electron microscopy of freeze-substituted cells have indicated a more highly ordered condensed-chromatin organization in actively dividing and stationary-phase G. obscuriglobus cells. These three-dimensional analyses revealed a complex network of double membranes that engulf the condensed DNA. Bioinformatics analysis has revealed the existence of a putative component involved in nonhomologous DNA end joining that presumably plays a role in maintaining chromatin integrity within the bacterium. Thus, our observations further support the notion that packed chromatin organization enhances radiation tolerance.
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79
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Semes for analysis of evolution: de Duve's peroxisomes and Meyer's hydrogenases in the sulphurous Proterozoic eon. Nat Rev Genet 2007; 8:nrg2071-c1. [DOI: 10.1038/nrg2071-c1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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80
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Quirino BF, Pappas GJ, Tagliaferro AC, Collevatti RG, Neto EL, da Silva MRSS, Bustamante MMC, Krüger RH. Molecular phylogenetic diversity of bacteria associated with soil of the savanna-like Cerrado vegetation. Microbiol Res 2007; 164:59-70. [PMID: 17324564 DOI: 10.1016/j.micres.2006.12.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2006] [Indexed: 11/24/2022]
Abstract
The Brazilian savanna-like vegetation of Cerrado is rapidly being converted to pasture and agricultural fields. A 16S rDNA-based approach was taken to study the bacterial community associated with the soil of a native cerrado area (sensu stricto) and an area that has been converted to pasture. The bacterial group most abundantly identified in cerrado sensu stricto soil was the alpha-Proteobacteria while in cerrado converted to pasture the Actinobacteria were the most abundant. Rarefaction curves indicate that the species richness of cerrado sensu stricto is greater than that of cerrado converted to pasture. Furthermore, lineage-through-time plots show that the expected richness of species present in cerrado sensu stricto soil is approximately 10 times greater than that of cerrado converted to pasture.
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Affiliation(s)
- Betania F Quirino
- Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN Quadra 916, Av. W5 Norte, 70790-160 Brasília, DF, Brazil
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81
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Fuchsman CA, Rocap G. Whole-genome reciprocal BLAST analysis reveals that planctomycetes do not share an unusually large number of genes with Eukarya and Archaea. Appl Environ Microbiol 2006; 72:6841-4. [PMID: 17021241 PMCID: PMC1610313 DOI: 10.1128/aem.00429-06] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequences of Rhodopirellula baltica, formerly Pirellula sp. strain 1, Blastopirellula marina, Gemmata obscuriglobus, and Kuenenia stuttgartiensis were used in a series of pairwise reciprocal best-hit analyses to evaluate the contested evolutionary position of Planctomycetes. Contrary to previous reports which suggested that R. baltica had a high percentage of genes with closest matches to Archaea and Eukarya, we show here that these Planctomycetes do not share an unusually large number of genes with the Archaea or Eukarya, compared with other Bacteria. Thus, best-hit analyses may assign phylogenetic affinities incorrectly if close relatives are absent from the sequence database.
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Affiliation(s)
- Clara A Fuchsman
- School of Oceanography, Box 357940, University of Washington, Seattle, WA 98195, USA
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82
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Margulis L, Chapman M, Guerrero R, Hall J. The last eukaryotic common ancestor (LECA): acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon. Proc Natl Acad Sci U S A 2006; 103:13080-5. [PMID: 16938841 PMCID: PMC1559756 DOI: 10.1073/pnas.0604985103] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We develop a symbiogenetic concept of the origin of eukaryotic intracellular motility systems from anaerobic but aerotolerant spirochetes in sulfide-rich environments. The last eukaryotic common ancestors (LECAs) have extant archaeprotist descendants: motile nucleated cells with Embden-Meyerhof glycolysis and substrate-level phosphorylation that lack the alpha-proteobacterial symbiont that became the mitochondrion. Swimming and regulated O(2)-tolerance via sulfide oxidation already had been acquired by sulfidogenic wall-less archaebacteria (thermoplasmas) after aerotolerant cytoplasmic-tubule-containing spirochetes (eubacteria) attached to them. Increasing stability of sulfide-oxidizing/sulfur-reducing consortia analogous to extant sulfur syntrophies (Thiodendron) led to fusion. The eubacteria-archaebacteria symbiosis became permanent as the nucleus evolved by prokaryotic recombination with membrane hypertrophy, analogous to Gemmata obscuriglobus and other delta-proteobacteria with membrane-bounded nucleoids. Histone-coated DNA, protein-synthetic RNAs, amino-acylating, and other enzymes were contributed by the sulfidogen whereas most intracellular motility derives from the spirochete. From this redox syntrophy in anoxic and microoxic Proterozoic habitats LECA evolved. The nucleus originated by recombination of eu- and archaebacterial DNA that remained attached to eubacterial motility structures and became the microtubular cytoskeleton, including the mitotic apparatus. Direct LECA descendants include free-living archaeprotists in anoxic environments: archamoebae, metamonads, parabasalids, and some mammalian symbionts with mitosomes. LECA later acquired the fully aerobic Krebs cycle-oxidative phosphorylation-mitochondrial metabolism by integration of the protomitochondrion, a third alpha-proteobacterial symbiont from which the ancestors to most protoctists, all fungi, plants, and animals evolved. Secondarily anaerobic eukaryotes descended from LECA after integration of this oxygen-respiring eubacterium. Explanatory power and experimental predictions for molecular biology of the LECA concept are stated.
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Affiliation(s)
- Lynn Margulis
- *Department of Geosciences, University of Massachusetts, Amherst, MA 01003
| | - Michael Chapman
- Department of Biology, Holy Cross College, Worcester, MA 01610
| | - Ricardo Guerrero
- Department of Microbiology, University of Barcelona, 08028 Barcelona, Spain; and
| | - John Hall
- *Department of Geosciences, University of Massachusetts, Amherst, MA 01003
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83
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Cavalier-Smith T. Cell evolution and Earth history: stasis and revolution. Philos Trans R Soc Lond B Biol Sci 2006; 361:969-1006. [PMID: 16754610 PMCID: PMC1578732 DOI: 10.1098/rstb.2006.1842] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This synthesis has three main parts. The first discusses the overall tree of life and nature of the last common ancestor (cenancestor). I emphasize key steps in cellular evolution important for ordering and timing the major evolutionary innovations in the history of the biosphere, explaining especially the origins of the eukaryote cell and of bacterial flagella and cell envelope novelties. Second, I map the tree onto the fossil record and discuss dates of key events and their biogeochemical impact. Finally, I present a broad synthesis, discussing evidence for a three-phase history of life. The first phase began perhaps ca 3.5 Gyr ago, when the origin of cells and anoxic photosynthesis generated the arguably most primitive prokaryote phylum, Chlorobacteria (= Chloroflexi), the first negibacteria with cells bounded by two acyl ester phospholipid membranes. After this 'chlorobacterial age' of benthic anaerobic evolution protected from UV radiation by mineral grains, two momentous quantum evolutionary episodes of cellular innovation and microbial radiation dramatically transformed the Earth's surface: the glycobacterial revolution initiated an oxygenic 'age of cyanobacteria' and, as the ozone layer grew, the rise of plankton; immensely later, probably as recently as ca 0.9 Gyr ago, the neomuran revolution ushered in the 'age of eukaryotes', Archaebacteria (arguably the youngest bacterial phylum), and morphological complexity. Diversification of glycobacteria ca 2.8 Gyr ago, predominantly inhabiting stratified benthic mats, I suggest caused serial depletion of 13C by ribulose 1,5-bis-phosphate caboxylase/oxygenase (Rubisco) to yield ultralight late Archaean organic carbon formerly attributed to methanogenesis plus methanotrophy. The late origin of archaebacterial methanogenesis ca 720 Myr ago perhaps triggered snowball Earth episodes by slight global warming increasing weathering and reducing CO2 levels, to yield runaway cooling; the origin of anaerobic methane oxidation ca 570 Myr ago reduced methane flux at source, stabilizing Phanerozoic climates. I argue that the major cellular innovations exhibit a pattern of quantum evolution followed by very rapid radiation and then substantial stasis, as described by Simpson. They yielded organisms that are a mosaic of extremely conservative and radically novel features, as characterized by De Beer's phrase 'mosaic evolution'. Evolution is not evenly paced and there are no real molecular clocks.
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84
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Kulichevskaya IS, Pankratov TA, Dedysh SN. Detection of representatives of the Planctomycetes in Sphagnum peat bogs by molecular and cultivation approaches. Microbiology (Reading) 2006. [DOI: 10.1134/s0026261706030155] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Abstract
One of the most important outcomes of modern biology has been the demonstration of the unity of life. All living beings are in fact descendants of a unique ancestor commonly referred to as Luca (the Last universal common ancestor). The discovery - nearly 30 years ago by Carl Woese - that present-day life on our planet can be assigned to only three domains: two of prokaryotic nature (Archaea and Bacteria), and one eukaryoyic (Eucarya), has given birth to a new field of investigation aimed at determining the nature of Luca. Today, thanks to the accumulation of genomic data, we can loop back into the past and infer a few characters of Luca by comparing what present-day organisms have in common. For example, it is now clear that Luca was a cellular organism provided with a cytoplasmic membrane, and that it harboured already a quite sophisticated translation apparatus. However, the inference of other characters of Luca from comparative genomics is less straightforward: for instance, a few key molecular mechanisms for DNA replication are non-homologous across the three domains and their distribution is often puzzling. This evidence has been embraced by proponents of the hypothesis that Luca harboured an RNA genome and that its replacement by DNA and the appearance of the corresponding molecular systems would have occurred independently in the three life domains after their divergence. However, an equally likely scenario would be that of a Luca with a DNA genome and of a subsequent replacement of its DNA-replication systems by non-homologous counterparts either in the bacterial or in the archaeal/eukaroytic branch. Nevertheless, including the viral world into the picture of the tree of life may thus provide us with precious insights into our most distant past since the invention and spread potential of viruses may have played a key role in early evolution.
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Affiliation(s)
- Patrick Forterre
- Biologie Moléculaire du gène chez les extrêmophiles (BMGE), Département de Microbiologie fondamentale et médicale, Institut Pasteur, Paris, France.
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87
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Abstract
The phylum Planctomycetes of the domain Bacteria consists of budding, peptidoglycan-less organisms important for understanding the origins of complex cell organization. Their significance for cell biology lies in their possession of intracellular membrane compartmentation. All planctomycetes share a unique cell plan, in which the cell cytoplasm is divided into compartments by one or more membranes, including a major cell compartment containing the nucleoid. Of special significance is Gemmata obscuriglobus, in which the nucleoid is enveloped in two membranes to form a nuclear body that is analogous to the structure of a eukaryotic nucleus. Planctomycete compartmentation may have functional physiological roles, as in the case of anaerobic ammonium-oxidizing anammox planctomycetes, in which the anammoxosome harbors specialized enzymes and is wrapped in an envelope possessing unique ladderane lipids. Organisms in phyla other than the phylum Planctomycetes may possess compartmentation similar to that of some planctomycetes, as in the case of members of the phylum Poribacteria from marine sponges.
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Affiliation(s)
- John A Fuerst
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
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88
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Staley JT, Bouzek H, Jenkins C. Eukaryotic signature proteins of Prosthecobacter dejongeii and Gemmata sp. Wa-1 as revealed by in silico analysis. FEMS Microbiol Lett 2005; 243:9-14. [PMID: 15667994 DOI: 10.1016/j.femsle.2004.11.034] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2004] [Revised: 08/05/2004] [Accepted: 11/16/2004] [Indexed: 11/15/2022] Open
Abstract
The genomes of representatives of three bacterial phyla have been compared with the list of 347 eukaryotic signature proteins (ESPs) derived by Hartman and Fedorov [Proc. Natl. Acad. Sci. USA 99 (2002) 1420]. The species included Prosthecobacter dejongeii of the Verrucomicrobia phylum, Gemmata sp. Wa-1 of the Planctomycetes phylum and Caulobacter crescentus of the Proteobacteria. The protist Trypanosoma brucei was used as a eukaryotic control. P. dejongeii had unique ERGO blast matches to alpha-, beta-, and gamma-tubulin, to Set2, a transcriptional factor associated with eukaryotic DNA, and to LAMMER protein kinase for a total of 10 high-scoring ESP matches altogether. Gemmata sp. Wa-1 shared four of its 17 high-scoring ESP matches with P. dejongeii, and that information coupled with other genomic data provides strong support that these two phyla are related to one another. If the ESP list is an accurate listing of unique eukaryotic proteins, then the low number of high-scoring matches between the proteins of these two bacteria with the list raises doubts about these phyla being direct ancestors of the Eucarya. However, this does not rule out the possibility that ancestral members of either the Verrucomicrobia or Planctomycetes may have played an important role in the evolution of a proto-eukaryotic organism.
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Affiliation(s)
- James T Staley
- Department of Microbiology, University of Washington, P.O. Box 98195, Seattle, WA 98195, USA.
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89
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Butler MK, Fuerst JA. Comparative analysis of ribonuclease P RNA of the planctomycetes. Int J Syst Evol Microbiol 2004; 54:1333-1344. [PMID: 15280311 DOI: 10.1099/ijs.0.03013-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The planctomycetes, order Planctomycetales, are a distinct phylum of domain Bacteria. Genes encoding the RNA portion of ribonuclease P (RNase P) of some planctomycete members were sequenced and compared with existing database planctomycete sequences. rnpB gene sequences encoding RNase P RNA were generated by a conserved primer PCR strategy for Planctomyces brasiliensis, Planctomyces limnophilus, Pirellula marina, Pirellula staleyi strain ATCC 35122, Isosphaera pallida, one other Isosphaera strain, Gemmata obscuriglobus and three other strains of the Gemmata group. These sequences were aligned against reference bacterial sequences and secondary structures of corresponding RNase P RNAs deduced by a comparative approach. P12 helices were found to be highly variable in length, as were helices P16.1 and P19, when present. RNase P RNA secondary structures of Gemmata isolates were found to have unusual features relative to other planctomycetes, including a long P9 helix and an insert in the P13 helix not found in any other member of domain Bacteria. These unique features are consistent with other unusual properties of this genus, distinguishing it from other bacteria. Phylogenetic analyses indicate that relationships between planctomycetes derived from RNase P RNA are consistent with 16S rRNA-based analyses.
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Affiliation(s)
- Margaret K Butler
- Department of Microbiology and Parasitology, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - John A Fuerst
- Department of Microbiology and Parasitology, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
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90
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Studholme DJ, Fuerst JA, Bateman A. Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09666.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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91
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Abstract
The structural elucidation of clear but distant homologs of actin and tubulin in bacteria and GFP labeling of these proteins promises to reinvigorate the field of prokaryotic cell biology. FtsZ (the tubulin homolog) and MreB/ParM (the actin homologs) are indispensable for cellular tasks that require the cell to accurately position molecules, similar to the function of the eukaryotic cytoskeleton. FtsZ is the organizing molecule of bacterial cell division and forms a filamentous ring around the middle of the cell. Many molecules, including MinCDE, SulA, ZipA, and FtsA, assist with this process directly. Recently, genes much more similar to tubulin than to FtsZ have been identified in Verrucomicrobia. MreB forms helices underneath the inner membrane and probably defines the shape of the cell by positioning transmembrane and periplasmic cell wall-synthesizing enzymes. Currently, no interacting proteins are known for MreB and its relatives that help these proteins polymerize or depolymerize at certain times and places inside the cell. It is anticipated that MreB-interacting proteins exist in analogy to the large number of actin binding proteins in eukaryotes. ParM (a plasmid-borne actin homolog) is directly involved in pushing certain single-copy plasmids to the opposite poles by ParR/parC-assisted polymerization into double-helical filaments, much like the filaments formed by actin, F-actin. Mollicutes seem to have developed special systems for cell shape determination and motility, such as the fibril protein in Spiroplasma.
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Affiliation(s)
- Jan Löwe
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom.
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92
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Pearson A, Budin M, Brocks JJ. Phylogenetic and biochemical evidence for sterol synthesis in the bacterium Gemmata obscuriglobus. Proc Natl Acad Sci U S A 2003; 100:15352-7. [PMID: 14660793 PMCID: PMC307571 DOI: 10.1073/pnas.2536559100] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2003] [Indexed: 11/18/2022] Open
Abstract
Sterol biosynthesis is viewed primarily as a eukaryotic process, and the frequency of its occurrence in bacteria has long been a subject of controversy. Two enzymes, squalene monooxygenase and oxidosqualene cyclase, are the minimum necessary for initial biosynthesis of sterols from squalene. In this work, 19 protein gene sequences for eukaryotic squalene monooxygenase and 12 protein gene sequences for eukaryotic oxidosqualene cyclase were compared with all available complete and partial prokaryotic genomes. The only unequivocal matches for a sterol biosynthetic pathway were in the proteobacterium, Methylococcus capsulatus, in which sterol biosynthesis is known, and in the planctomycete, Gemmata obscuriglobus. The latter species contains the most abbreviated sterol pathway yet identified in any organism. Analysis shows that the major sterols in Gemmata are lanosterol and its uncommon isomer, parkeol. There are no subsequent modifications of these products. In bacteria, the sterol biosynthesis genes occupy a contiguous coding region and possibly comprise a single operon. Phylogenetic trees constructed for both enzymes show that the sterol pathway in bacteria and eukaryotes has a common ancestry. It is likely that this contiguous reading frame was exchanged between bacteria and early eukaryotes via lateral gene transfer or endosymbiotic events. The primitive sterols produced by Gemmata suggest that this genus could retain the most ancient remnants of the sterol biosynthetic pathway.
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Affiliation(s)
- Ann Pearson
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA 02138, USA.
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93
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Dolan MF, Melnitsky H, Margulis L, Kolnicki R. Motility proteins and the origin of the nucleus. THE ANATOMICAL RECORD 2002; 268:290-301. [PMID: 12382325 DOI: 10.1002/ar.10161] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Hypotheses on the origin of eukaryotic cells must account for the origin of the microtubular cytoskeletal structures (including the mitotic spindle, undulipodium/cilium (so-called flagellum) and other structures underlain by the 9(2)+2 microtubular axoneme) in addition to the membrane-bounded nucleus. Whereas bacteria with membrane-bounded nucleoids have been described, no precedent for mitotic, cytoskeletal, or axonemal microtubular structures are known in prokaryotes. Molecular phylogenetic analyses indicate that the cells of the earliest-branching lineages of eukaryotes contain the karyomastigont cytoskeletal system. These protist cells divide via an extranuclear spindle and a persistent nuclear membrane. We suggest that this association between the centriole/kinetosome axoneme (undulipodium) and the nucleus existed from the earliest stage of eukaryotic cell evolution. We interpret the karyomastigont to be a legacy of the symbiosis between thermoacidophilic archaebacteria and motile eubacteria from which the first eukaryote evolved. Mutually inconsistent hypotheses for the origin of the nucleus are reviewed and sequenced proteins of cell motility are discussed because of their potential value in resolving this problem. A correlation of fossil evidence with modern cell and microbiological studies leads us to the karyomastigont theory of the origin of the nucleus.
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Affiliation(s)
- Michael F Dolan
- Department of Geosciences, University of Massachusetts, Morrill Science Center, Amherst 01003, USA.
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94
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Jenkins C, Kedar V, Fuerst JA. Gene discovery within the planctomycete division of the domain Bacteria using sequence tags from genomic DNA libraries. Genome Biol 2002; 3:RESEARCH0031. [PMID: 12093378 PMCID: PMC116728 DOI: 10.1186/gb-2002-3-6-research0031] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2002] [Revised: 04/15/2002] [Accepted: 04/17/2002] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The planctomycetes comprise a distinct group of the domain Bacteria, forming a separate division by phylogenetic analysis. The organization of their cells into membrane-defined compartments including membrane-bounded nucleoids, their budding reproduction and complete absence of peptidoglycan distinguish them from most other Bacteria. A random sequencing approach was applied to the genomes of two planctomycete species, Gemmata obscuriglobus and Pirellula marina, to discover genes relevant to their cell biology and physiology. RESULTS Genes with a wide variety of functions were identified in G. obscuriglobus and Pi. marina, including those of metabolism and biosynthesis, transport, regulation, translation and DNA replication, consistent with established phenotypic characters for these species. The genes sequenced were predominantly homologous to those in members of other divisions of the Bacteria, but there were also matches with nuclear genomic genes of the domain Eukarya, genes that may have appeared in the planctomycetes via horizontal gene transfer events. Significant among these matches are those with two genes atypical for Bacteria and with significant cell-biology implications - integrin alpha-V and inter-alpha-trypsin inhibitor protein - with homologs in G. obscuriglobus and Pi. marina respectively. CONCLUSIONS The random-sequence-tag approach applied here to G. obscuriglobus and Pi. marina is the first report of gene recovery and analysis from members of the planctomycetes using genome-based methods. Gene homologs identified were predominantly similar to genes of Bacteria, but some significant best matches to genes from Eukarya suggest that lateral gene transfer events between domains may have involved this division at some time during its evolution.
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Affiliation(s)
- Cheryl Jenkins
- Department of Microbiology and Parasitology, School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Queensland 4072, Australia.
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95
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Wang J, Jenkins C, Webb RI, Fuerst JA. Isolation of Gemmata-like and Isosphaera-like planctomycete bacteria from soil and freshwater. Appl Environ Microbiol 2002; 68:417-22. [PMID: 11772655 PMCID: PMC126576 DOI: 10.1128/aem.68.1.417-422.2002] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2001] [Accepted: 10/15/2001] [Indexed: 11/20/2022] Open
Abstract
New cultured strains of the planctomycete division (order Planctomycetales) of the domain Bacteria related to species in the genera Gemmata and Isosphaera were isolated from soil, freshwater, and a laboratory ampicillin solution. Phylogenetic analysis of the 16S rRNA gene from eight representative isolates showed that all the isolates were members of the planctomycete division. Six isolates clustered with Gemmata obscuriglobus and related strains, while two isolates clustered with Isosphaera pallida. A double-membrane-bounded nucleoid was observed in Gemmata-related isolates but not in Isosphaera-related isolates, consistent with the ultrastructures of existing species of each genus. Two isolates from this study represent the first planctomycetes successfully cultivated from soil.
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Affiliation(s)
- Jenny Wang
- Department of Microbiology and Parasitology, School of Molecular and Microbial Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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96
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Margulis L, Dolan MF, Guerrero R. The chimeric eukaryote: origin of the nucleus from the karyomastigont in amitochondriate protists. Proc Natl Acad Sci U S A 2000; 97:6954-9. [PMID: 10860956 PMCID: PMC34369 DOI: 10.1073/pnas.97.13.6954] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a testable model for the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. A chimeric cell evolved via symbiogenesis by syntrophic merger between an archaebacterium and a eubacterium. The archaebacterium, a thermoacidophil resembling extant Thermoplasma, generated hydrogen sulfide to protect the eubacterium, a heterotrophic swimmer comparable to Spirochaeta or Hollandina that oxidized sulfide to sulfur. Selection pressure for speed swimming and oxygen avoidance led to an ancient analogue of the extant cosmopolitan bacterial consortium "Thiodendron latens." By eubacterial-archaebacterial genetic integration, the chimera, an amitochondriate heterotroph, evolved. This "earliest branching protist" that formed by permanent DNA recombination generated the nucleus as a component of the karyomastigont, an intracellular complex that assured genetic continuity of the former symbionts. The karyomastigont organellar system, common in extant amitochondriate protists as well as in presumed mitochondriate ancestors, minimally consists of a single nucleus, a single kinetosome and their protein connector. As predecessor of standard mitosis, the karyomastigont preceded free (unattached) nuclei. The nucleus evolved in karyomastigont ancestors by detachment at least five times (archamoebae, calonymphids, chlorophyte green algae, ciliates, foraminifera). This specific model of syntrophic chimeric fusion can be proved by sequence comparison of functional domains of motility proteins isolated from candidate taxa.
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Affiliation(s)
- L Margulis
- Department of Geosciences, Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
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97
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Abstract
It is widely held that the profound differences in cellular architecture between prokaryotes and eukaryotes, in particular the housing of eukaryotic chromosomes within a nuclear membrane, also extends to the properties of their chromosomes. When chromosomal multiplicity, ploidy, linearity, transcriptional silencing, partitioning, and packaging are considered, no consistent association is found between any of these properties and the presence or absence of a nuclear membrane. Some of the perceived differences can be attributed to cytological limitations imposed by the small size of bacterial nucleoids and the arbitrary choice of representative organisms for comparison. We suggest that the criterion of nucleosome-based packaging of chromosomal DNA may be more useful than the prokaryote/eukaryote dichotomy for inferring the broadest phylogenetic relationships among organisms.
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Affiliation(s)
- A J Bendich
- Departments of Botany and Genetics, University of Washington, Seattle, Washington 98195-5325, USA
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98
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Thiry M. Ultrastructural methods for nucleic acid detection by immunocytology. PROGRESS IN HISTOCHEMISTRY AND CYTOCHEMISTRY 1999; 34:87-159. [PMID: 10546283 DOI: 10.1016/s0079-6336(99)80008-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In the present review are summarized recent developments in immunocytochemical detection of nucleic acids in biological materials at the ultrastructural level. Not only the approaches using antibodies to natural nucleic acids are described but also the techniques involving the use of antibodies raised against various nucleotide analogs incorporated beforehand into nucleic acids. Special emphasis is placed on each method's potential and limitations. These methods, combined or not with molecular biotechnology, are powerful tools for studying the structure and function of nucleic acids. They can be used to investigate the distribution and topological organization of DNA and RNA molecules or of specialized within these molecules in the cells.
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Affiliation(s)
- M Thiry
- Laboratory of Cell and Tissue Biology, Institute of Histology, University of Liège, Belgium.
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99
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Vellai T, Vida G. The origin of eukaryotes: the difference between prokaryotic and eukaryotic cells. Proc Biol Sci 1999; 266:1571-7. [PMID: 10467746 PMCID: PMC1690172 DOI: 10.1098/rspb.1999.0817] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Eukaryotes have long been thought to have arisen by evolving a nucleus, endomembrane, and cytoskeleton. In contrast, it was recently proposed that the first complex cells, which were actually proto-eukaryotes, arose simultaneously with the acquisition of mitochondria. This so-called symbiotic association hypothesis states that eukaryotes emerged when some ancient anaerobic archaebacteria (hosts) engulfed respiring alpha-proteobacteria (symbionts), which evolved into the first energy-producing organelles. Therefore, the intracellular compartmentalization of the energy-converting metabolism that was bound originally to the plasma membrane appears to be the key innovation towards eukaryotic genome and cellular organization. The novel energy metabolism made it possible for the nucleotide synthetic apparatus of cells to be no longer limited by subsaturation with substrates and catalytic components. As a consequence, a considerable increase has occurred in the size and complexity of eukaryotic genomes, providing the genetic basis for most of the further evolutionary changes in cellular complexity. On the other hand, the active uptake of exogenous DNA, which is general in bacteria, was no longer essential in the genome organization of eukaryotes. The mitochondrion-driven scenario for the first eukaryotes explains the chimera-like composition of eukaryotic genomes as well as the metabolic and cellular organization of eukaryotes.
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Affiliation(s)
- T Vellai
- Institute for Advanced Study, Collegium Budapest, Hungary
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100
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Strous M, Fuerst JA, Kramer EH, Logemann S, Muyzer G, van de Pas-Schoonen KT, Webb R, Kuenen JG, Jetten MS. Missing lithotroph identified as new planctomycete. Nature 1999; 400:446-9. [PMID: 10440372 DOI: 10.1038/22749] [Citation(s) in RCA: 802] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
With the increased use of chemical fertilizers in agriculture, many densely populated countries face environmental problems associated with high ammonia emissions. The process of anaerobic ammonia oxidation ('anammox') is one of the most innovative technological advances in the removal of ammonia nitrogen from waste water. This new process combines ammonia and nitrite directly into dinitrogen gas. Until now, bacteria capable of anaerobically oxidizing ammonia had never been found and were known as "lithotrophs missing from nature". Here we report the discovery of this missing lithotroph and its identification as a new, autotrophic member of the order Planctomycetales, one of the major distinct divisions of the Bacteria. The new planctomycete grows extremely slowly, dividing only once every two weeks. At present, it cannot be cultivated by conventional microbiological techniques. The identification of this bacterium as the one responsible for anaerobic oxidation of ammonia makes an important contribution to the problem of unculturability.
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MESH Headings
- Ammonia/metabolism
- Bacteria/classification
- Bacteria/isolation & purification
- Bacteria/metabolism
- Bacteria/ultrastructure
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/isolation & purification
- Bacteria, Anaerobic/metabolism
- Bacteria, Anaerobic/ultrastructure
- Biofilms/classification
- DNA, Bacterial/classification
- DNA, Bacterial/genetics
- Molecular Sequence Data
- Oxidation-Reduction
- Phylogeny
- RNA, Bacterial/classification
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/classification
- RNA, Ribosomal, 16S/genetics
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Affiliation(s)
- M Strous
- Department of Biotechnology, Delft University of Technology, The Netherlands
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