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López-García P, Moreira D. The symbiotic origin of the eukaryotic cell. C R Biol 2023; 346:55-73. [PMID: 37254790 DOI: 10.5802/crbiol.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 06/01/2023]
Abstract
Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.
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Kirsch SH, Haeckl FPJ, Müller R. Beyond the approved: target sites and inhibitors of bacterial RNA polymerase from bacteria and fungi. Nat Prod Rep 2022; 39:1226-1263. [PMID: 35507039 DOI: 10.1039/d1np00067e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: 2016 to 2022RNA polymerase (RNAP) is the central enzyme in bacterial gene expression representing an attractive and validated target for antibiotics. Two well-known and clinically approved classes of natural product RNAP inhibitors are the rifamycins and the fidaxomycins. Rifampicin (Rif), a semi-synthetic derivative of rifamycin, plays a crucial role as a first line antibiotic in the treatment of tuberculosis and a broad range of bacterial infections. However, more and more pathogens such as Mycobacterium tuberculosis develop resistance, not only against Rif and other RNAP inhibitors. To overcome this problem, novel RNAP inhibitors exhibiting different target sites are urgently needed. This review includes recent developments published between 2016 and today. Particular focus is placed on novel findings concerning already known bacterial RNAP inhibitors, the characterization and development of new compounds isolated from bacteria and fungi, and providing brief insights into promising new synthetic compounds.
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Affiliation(s)
- Susanne H Kirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany. .,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124 Braunschweig, Germany.,Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
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3
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Moody ERR, Mahendrarajah TA, Dombrowski N, Clark JW, Petitjean C, Offre P, Szöllősi GJ, Spang A, Williams TA. An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes. eLife 2022; 11:66695. [PMID: 35190025 PMCID: PMC8890751 DOI: 10.7554/elife.66695] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacterial domains. By contrast, recent analyses of a broader set of non-ribosomal genes have suggested that Archaea may be less divergent from Bacteria, and that estimates of inter-domain distance are inflated due to accelerated evolution of ribosomal proteins along the inter-domain branch. Resolving this debate is key to determining the diversity of the archaeal and bacterial domains, the shape of the tree of life, and our understanding of the early course of cellular evolution. Here, we investigate the evolutionary history of the marker genes key to the debate. We show that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set. By contrast, analysis of a broad range of manually curated marker gene datasets from an evenly sampled set of 700 Archaea and Bacteria reveals that current methods likely underestimate the AB branch length due to substitutional saturation and poor model fit; that the best-performing phylogenetic markers tend to support longer inter-domain branch lengths; and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable. Furthermore, our phylogeny inferred from the 27 highest-ranked marker genes recovers a clade of DPANN at the base of the Archaea and places the bacterial Candidate Phyla Radiation (CPR) within Bacteria as the sister group to the Chloroflexota.
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Affiliation(s)
- Edmund R R Moody
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Tara A Mahendrarajah
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Nina Dombrowski
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - James W Clark
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Celine Petitjean
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Pierre Offre
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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4
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Fouqueau T, Blombach F, Cackett G, Carty AE, Matelska DM, Ofer S, Pilotto S, Phung DK, Werner F. The cutting edge of archaeal transcription. Emerg Top Life Sci 2018; 2:517-533. [PMID: 33525828 PMCID: PMC7289017 DOI: 10.1042/etls20180014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/01/2018] [Accepted: 10/04/2018] [Indexed: 12/26/2022]
Abstract
The archaeal RNA polymerase (RNAP) is a double-psi β-barrel enzyme closely related to eukaryotic RNAPII in terms of subunit composition and architecture, promoter elements and basal transcription factors required for the initiation and elongation phase of transcription. Understanding archaeal transcription is, therefore, key to delineate the universally conserved fundamental mechanisms of transcription as well as the evolution of the archaeo-eukaryotic transcription machineries. The dynamic interplay between RNAP subunits, transcription factors and nucleic acids dictates the activity of RNAP and ultimately gene expression. This review focusses on recent progress in our understanding of (i) the structure, function and molecular mechanisms of known and less characterized factors including Elf1 (Elongation factor 1), NusA (N-utilization substance A), TFS4, RIP and Eta, and (ii) their evolution and phylogenetic distribution across the expanding tree of Archaea.
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Affiliation(s)
- Thomas Fouqueau
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Fabian Blombach
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Gwenny Cackett
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Alice E Carty
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Dorota M Matelska
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Sapir Ofer
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Simona Pilotto
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Duy Khanh Phung
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
| | - Finn Werner
- RNAP laboratory, Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, U.K
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6
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Fouqueau T, Blombach F, Werner F. Evolutionary Origins of Two-Barrel RNA Polymerases and Site-Specific Transcription Initiation. Annu Rev Microbiol 2017; 71:331-348. [PMID: 28657884 DOI: 10.1146/annurev-micro-091014-104145] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolution-related multisubunit RNA polymerases (RNAPs) carry out RNA synthesis in all domains life. Although their catalytic cores and fundamental mechanisms of transcription elongation are conserved, the initiation stage of the transcription cycle differs substantially in bacteria, archaea, and eukaryotes in terms of the requirements for accessory factors and details of the molecular mechanisms. This review focuses on recent insights into the evolution of the transcription apparatus with regard to (a) the surprisingly pervasive double-Ψ β-barrel active-site configuration among different nucleic acid polymerase families, (b) the origin and phylogenetic distribution of TBP, TFB, and TFE transcription factors, and
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Affiliation(s)
- Thomas Fouqueau
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom; ,
| | - Fabian Blombach
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom; ,
| | - Finn Werner
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom; ,
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Maier LK, Benz J, Fischer S, Alstetter M, Jaschinski K, Hilker R, Becker A, Allers T, Soppa J, Marchfelder A. Deletion of the Sm1 encoding motif in the lsm gene results in distinct changes in the transcriptome and enhanced swarming activity of Haloferax cells. Biochimie 2015; 117:129-37. [DOI: 10.1016/j.biochi.2015.02.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/26/2015] [Indexed: 01/08/2023]
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8
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Spang A, Saw JH, Jørgensen SL, Zaremba-Niedzwiedzka K, Martijn J, Lind AE, van Eijk R, Schleper C, Guy L, Ettema TJG. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 2015; 521:173-179. [PMID: 25945739 PMCID: PMC4444528 DOI: 10.1038/nature14447] [Citation(s) in RCA: 672] [Impact Index Per Article: 74.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/01/2015] [Indexed: 12/22/2022]
Abstract
The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.
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Affiliation(s)
- Anja Spang
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jimmy H Saw
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Steffen L Jørgensen
- Department of Biology, Centre for Geobiology, University of Bergen, N-5020 Bergen, Norway
| | | | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Anders E Lind
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Roel van Eijk
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
| | - Christa Schleper
- Department of Biology, Centre for Geobiology, University of Bergen, N-5020 Bergen, Norway.,Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, A-1090 Vienna, Austria
| | - Lionel Guy
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden.,Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123 Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123 Uppsala, Sweden
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10
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Wang D, Guo C, Gu L, Zhang X. Comparative study of the marR genes within the family Enterobacteriaceae. J Microbiol 2014; 52:452-9. [PMID: 24723108 DOI: 10.1007/s12275-014-3586-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/11/2013] [Accepted: 12/30/2013] [Indexed: 01/22/2023]
Abstract
marR genes are members of an ancient family originally identified in Escherichia coli. This family is widely distributed in archaea and bacteria. Homologues of this family have a conserved winged helix fold. MarR proteins are involved in non-specific resistance systems conferring resistance to multiple antibiotics. Extensive studies have shown the importance of MarR proteins in physiology and pathogenicity in Enterobacteria, but little is known about their origin or evolution. In this study, all the marR genes in 43 enterobacterial genomes representing 14 genera were identified, and the phylogenetic relationships and genetic parameters were analyzed. Several major findings were made. Three conserved marR genes originated earlier than Enterobacteriaceae and a geneloss event was found to have taken place in Yersinia pestis Antiqua. Three functional genes, rovA, hor, and slyA, were found to be clear orthologs among Enterobacteriaceae. The copy number of marR genes in Enterobacteriaceae was found to vary from 2 to 11. These marR genes exhibited a faster rate of nucleotide substitution than housekeeping genes did. Specifically, the regions of marR domain were found to be subject to strong purifying selection. The phylogenetic relationship and genetic parameter analyses were consistent with conservation and specificity of marR genes. These dual characters helped MarR to maintain a conserved binding motif and variable C-terminus, which are important to adaptive responses to a number of external stimuli in Enterobacteriaceae.
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Affiliation(s)
- Dan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093, Nanjing, P. R. China
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Abstract
The development of rigorous molecular taxonomy pioneered by Carl Woese has freed evolution science to explore numerous cellular activities that lead to genome change in evolution. These activities include symbiogenesis, inter- and intracellular horizontal DNA transfer, incorporation of DNA from infectious agents, and natural genetic engineering, especially the activity of mobile elements. This article reviews documented examples of all these processes and proposes experiments to extend our understanding of cell-mediated genome change.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology; University of Chicago; Chicago, IL USA
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12
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Close encounters of the third domain: the emerging genomic view of archaeal diversity and evolution. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:202358. [PMID: 24348093 PMCID: PMC3852633 DOI: 10.1155/2013/202358] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 09/21/2013] [Indexed: 01/06/2023]
Abstract
The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life.
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Forterre P. The common ancestor of archaea and eukarya was not an archaeon. ARCHAEA (VANCOUVER, B.C.) 2013; 2013:372396. [PMID: 24348094 PMCID: PMC3855935 DOI: 10.1155/2013/372396] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 09/24/2013] [Indexed: 02/06/2023]
Abstract
It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the "prokaryotic" phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.
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Affiliation(s)
- Patrick Forterre
- Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France
- Université Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR 8621, 91405 Orsay Cedex, France
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The legacy of Carl Woese and Wolfram Zillig: from phylogeny to landmark discoveries. Nat Rev Microbiol 2013; 11:713-9. [PMID: 24037452 DOI: 10.1038/nrmicro3124] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two pioneers of twentieth century biology passed away during the past decade, Wolfram Zillig in April 2005 and Carl Woese in December 2012. Among several other accomplishments, Woese has been celebrated for the discovery of the domain Archaea and for establishing rRNA as the 'Rosetta Stone' of evolutionary and environmental microbiology. His work inspired many scientists in various fields of biology, and among them was Wolfram Zillig, who is credited with the discovery of several unique molecular features of archaea. In this Essay, we highlight the remarkable achievements of Woese and Zillig and consider how they have shaped the archaeal research landscape.
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Wu D, Jospin G, Eisen JA. Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One 2013; 8:e77033. [PMID: 24146954 PMCID: PMC3798382 DOI: 10.1371/journal.pone.0077033] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 09/06/2013] [Indexed: 02/01/2023] Open
Abstract
With the astonishing rate that genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as “marker” genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities (e.g., construction of species trees, phylogenetic based assignment of metagenomic sequence reads to taxonomic groups, phylogeny-based assessment of alpha- and beta-diversity of microbial communities from metagenomic data). We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for “all bacteria and archaea”, 114 for “all bacteria (greatly expanding on the ∼30 commonly used), and 100 s to 1000 s for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.
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Affiliation(s)
- Dongying Wu
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America
- Department of Energy (DOE)-Joint Genome Institute, Walnut Creek, California, United States of America
- * E-mail:
| | - Guillaume Jospin
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America
| | - Jonathan A. Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America
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16
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Affiliation(s)
- Robert O J Weinzierl
- Department of Life Sciences, Division of Biomolecular Sciences, Imperial College London , Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, United Kingdom
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Nayak KC. Comparative genome sequence analysis of Sulfolobus acidocaldarius and 9 other isolates of its genus for factors influencing codon and amino acid usage. Gene 2013; 513:163-73. [DOI: 10.1016/j.gene.2012.10.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 10/08/2012] [Accepted: 10/21/2012] [Indexed: 11/17/2022]
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Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA. Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS One 2011; 6:e18011. [PMID: 21437252 PMCID: PMC3060911 DOI: 10.1371/journal.pone.0018011] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Accepted: 02/20/2011] [Indexed: 02/01/2023] Open
Abstract
Background Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early events in the evolution of gene families and of species. Methodology/Principal Findings We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) Expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences. Conclusions/Significance Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.
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Affiliation(s)
- Dongying Wu
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America
| | - Martin Wu
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America
- University of Virginia, Charlottesville, Virginia, United States of America
| | - Aaron Halpern
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
- The J. Craig Venter Institute, La Jolla, California, United States of America
| | - Douglas B. Rusch
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
- The J. Craig Venter Institute, La Jolla, California, United States of America
| | - Shibu Yooseph
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
- The J. Craig Venter Institute, La Jolla, California, United States of America
| | - Marvin Frazier
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
- The J. Craig Venter Institute, La Jolla, California, United States of America
| | - J. Craig Venter
- The J. Craig Venter Institute, Rockville, Maryland, United States of America
- The J. Craig Venter Institute, La Jolla, California, United States of America
| | - Jonathan A. Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California Davis Genome Center, University of California Davis, Davis, California, United States of America
- * E-mail:
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19
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Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proc Natl Acad Sci U S A 2010; 107:17252-5. [PMID: 20852068 DOI: 10.1073/pnas.1000265107] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The traditional tree of life shows eukaryotes as a distinct lineage of living things, but many studies have suggested that the first eukaryotic cells were chimeric, descended from both Eubacteria (through the mitochondrion) and Archaebacteria. Eukaryote nuclei thus contain genes of both eubacterial and archaebacterial origins, and these genes have different functions within eukaryotic cells. Here we report that archaebacterium-derived genes are significantly more likely to be essential to yeast viability, are more highly expressed, and are significantly more highly connected and more central in the yeast protein interaction network. These findings hold irrespective of whether the genes have an informational or operational function, so that many features of eukaryotic genes with prokaryotic homologs can be explained by their origin, rather than their function. Taken together, our results show that genes of archaebacterial origin are in some senses more important to yeast metabolism than genes of eubacterial origin. This importance reflects these genes' origin as the ancestral nuclear component of the eukaryotic genome.
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Fischer S, Benz J, Späth B, Maier LK, Straub J, Granzow M, Raabe M, Urlaub H, Hoffmann J, Brutschy B, Allers T, Soppa J, Marchfelder A. The archaeal Lsm protein binds to small RNAs. J Biol Chem 2010; 285:34429-38. [PMID: 20826804 DOI: 10.1074/jbc.m110.118950] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Proteins of the Lsm family, including eukaryotic Sm proteins and bacterial Hfq, are key players in RNA metabolism. Little is known about the archaeal homologues of these proteins. Therefore, we characterized the Lsm protein from the haloarchaeon Haloferax volcanii using in vitro and in vivo approaches. H. volcanii encodes a single Lsm protein, which belongs to the Lsm1 subfamily. The lsm gene is co-transcribed and overlaps with the gene for the ribosomal protein L37e. Northern blot analysis shows that the lsm gene is differentially transcribed. The Lsm protein forms homoheptameric complexes and has a copy number of 4000 molecules/cell. In vitro analyses using electrophoretic mobility shift assays and ultrasoft mass spectrometry (laser-induced liquid bead ion desorption) showed a complex formation of the recombinant Lsm protein with oligo(U)-RNA, tRNAs, and an small RNA. Co-immunoprecipitation with a FLAG-tagged Lsm protein produced in vivo confirmed that the protein binds to small RNAs. Furthermore, the co-immunoprecipitation revealed several protein interaction partners, suggesting its involvement in different cellular pathways. The deletion of the lsm gene is viable, resulting in a pleiotropic phenotype, indicating that the haloarchaeal Lsm is involved in many cellular processes, which is in congruence with the number of protein interaction partners.
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Spang A, Hatzenpichler R, Brochier-Armanet C, Rattei T, Tischler P, Spieck E, Streit W, Stahl DA, Wagner M, Schleper C. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol 2010; 18:331-40. [PMID: 20598889 DOI: 10.1016/j.tim.2010.06.003] [Citation(s) in RCA: 393] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 05/26/2010] [Accepted: 06/04/2010] [Indexed: 11/25/2022]
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Chattopadhyay S, Sahoo S, Kanner WA, Chakrabarti J. Pressures in archaeal protein coding genes: a comparative study. Comp Funct Genomics 2010; 4:56-65. [PMID: 18629113 PMCID: PMC2447400 DOI: 10.1002/cfg.246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2002] [Accepted: 11/25/2002] [Indexed: 11/06/2022] Open
Abstract
Our studies on the bases of codons from 11 completely sequenced archaeal genomes show that, as we move from GC-rich to AT-rich protein-coding gene-containing species, the differences between G and C and between A and T, the purine load (AG content), and also the overall persistence (i.e. the tendency of a base to be followed by the same base) within codons, all increase almost simultaneously, although the extent of increase is different over the three positions within codons. These findings suggest that the deviations from the second parity rule (through the increasing differences between complementary base contents) and the increasing purine load hinder the chance of formation of the intra-strand Watson-Crick base-paired secondary structures in mRNAs (synonymous with the protein-coding genes we dealt with), thereby increasing the translational efficiency. We hypothesize that the ATrich protein-coding gene-containing archaeal species might have better translational efficiency than their GC-rich counterparts.
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Affiliation(s)
- Sujay Chattopadhyay
- Department of Theoretical Physics, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700 032, India.
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Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW. CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res 2009; 38:D497-501. [PMID: 19884131 PMCID: PMC2808912 DOI: 10.1093/nar/gkp914] [Citation(s) in RCA: 591] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The new CORUM 2.0 release encompasses 2837 protein complexes offering the largest and most comprehensive publicly available dataset of mammalian protein complexes. The CORUM dataset is built from 3198 different genes, representing ∼16% of the protein coding genes in humans. Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. Recent developments include mapping of functional annotation to Gene Ontology terms as well as cross-references to Entrez Gene identifiers. In addition, a ‘Phylogenetic Conservation’ analysis tool was implemented that analyses the potential occurrence of orthologous protein complex subunits in mammals and other selected groups of organisms. This allows one to predict the occurrence of protein complexes in different phylogenetic groups. CORUM is freely accessible at (http://mips.helmholtz-muenchen.de/genre/proj/corum/index.html).
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Affiliation(s)
- Andreas Ruepp
- Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany.
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Lal S, Cheema S, Kalia VC. Phylogeny vs genome reshuffling: horizontal gene transfer. Indian J Microbiol 2008; 48:228-42. [PMID: 23100716 PMCID: PMC3450171 DOI: 10.1007/s12088-008-0034-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Accepted: 06/06/2008] [Indexed: 10/21/2022] Open
Abstract
The evolutionary events in organisms can be tracked to the transfer of genetic material. The inheritance of genetic material among closely related organisms is a slow evolutionary process. On the other hand, the movement of genes among distantly related species can account for rapid evolution. The later process has been quite evident in the appearance of antibiotic resistance genes among human and animal pathogens. Phylogenetic trees based on such genes and those involved in metabolic activities reflect the incongruencies in comparison to the 16S rDNA gene, generally used for taxonomic relationships. Such discrepancies in gene inheritance have been termed as horizontal gene transfer (HGT) events. In the post-genomic era, the explosion of known sequences through large-scale sequencing projects has unraveled the weakness of traditional 16S rDNA gene tree based evolutionary model. Various methods to scrutinize HGT events include atypical composition, abnormal sequence similarity, anomalous phylogenetic distribution, unusual phyletic patterns, etc. Since HGT generates greater genetic diversity, it is likely to increase resource use and ecosystem resilience.
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Affiliation(s)
- Sadhana Lal
- Microbial Biotechnology and Genomics; Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Mall Road, Delhi, 110 007 India
| | - Simrita Cheema
- Microbial Biotechnology and Genomics; Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Mall Road, Delhi, 110 007 India
| | - Vipin C. Kalia
- Microbial Biotechnology and Genomics; Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Mall Road, Delhi, 110 007 India
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Banati F, Koroknai A, Salamon D, Takacs M, Minarovits-Kormuta S, Wolf H, Niller HH, Minarovits J. CpG-methylation silences the activity of the RNA polymerase III transcribed EBER-1 promoter of Epstein-Barr virus. FEBS Lett 2008; 582:705-9. [DOI: 10.1016/j.febslet.2008.01.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Accepted: 01/25/2008] [Indexed: 11/24/2022]
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26
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Naji S, Bertero MG, Spitalny P, Cramer P, Thomm M. Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement. Nucleic Acids Res 2007; 36:676-87. [PMID: 18073196 PMCID: PMC2241882 DOI: 10.1093/nar/gkm1086] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The active center clefts of RNA polymerase (RNAP) from the archaeon Pyrococcus furiosus (Pfu) and of yeast RNAP II are nearly identical, including four protruding loops, the lid, rudder, fork 1 and fork 2. Here we present a structure–function analysis of recombinant Pfu RNAP variants lacking these cleft loops, and analyze the function of each loop at different stages of the transcription cycle. All cleft loops except fork 1 were required for promoter-directed transcription and efficient elongation. Unprimed de novo transcription required fork 2, the lid was necessary for primed initial transcription. Analysis of templates containing a pre-melted bubble showed that rewinding of upstream DNA drives RNA separation from the template. During elongation, downstream DNA strand separation required template strand binding to an invariant arginine in switch 2, and apparently interaction of an invariant arginine in fork 2 with the non-template strand.
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Affiliation(s)
- Souad Naji
- Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
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Coulson RMR, Touboul N, Ouzounis CA. Lineage-specific partitions in archaeal transcription. ARCHAEA (VANCOUVER, B.C.) 2007; 2:117-25. [PMID: 17350932 PMCID: PMC2686387 DOI: 10.1155/2006/629868] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Accepted: 10/23/2006] [Indexed: 11/18/2022]
Abstract
The phylogenetic distribution of the components comprising the transcriptional machinery in the crenarchaeal and euryarchaeal lineages of the Archaea was analyzed in a systematic manner by genome-wide profiling of transcription complements in fifteen complete archaeal genome sequences. Initially, a reference set of transcription-associated proteins (TAPs) consisting of sequences functioning in all aspects of the transcriptional process, and originating from the three domains of life, was used to query the genomes. TAP-families were detected by sequence clustering of the TAPs and their archaeal homologues, and through extensive database searching, these families were assigned a function. The phylogenetic origins of archaeal genes matching hidden Markov model profiles of protein domains associated with transcription, and those encoding the TAP-homologues, showed there is extensive lineage-specificity of proteins that function as regulators of transcription: most of these sequences are present solely in the Euryarchaeota, with nearly all of them homologous to bacterial DNA-binding proteins. Strikingly, the hidden Markov model profile searches revealed that archaeal chromatin and histone-modifying enzymes also display extensive taxon-restrictedness, both across and within the two phyla.
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Affiliation(s)
- Richard M R Coulson
- Microarray Group, The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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Luo J, Hall BD. A multistep process gave rise to RNA polymerase IV of land plants. J Mol Evol 2006; 64:101-12. [PMID: 17160640 DOI: 10.1007/s00239-006-0093-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2006] [Accepted: 10/04/2006] [Indexed: 02/07/2023]
Abstract
Since their discovery in Metazoa, the three nuclear RNA polymerases (RNAPs) have been found in fungi, plants, and diverse protists. In all eukaryotes studied to date, RNAPs I, II, and III collectively transcribe all major RNAs made in the nucleus. We have found genes for the largest subunit (RPD1/RPE1) of a new DNA-dependent RNAP, RNAP IV, in all major land plant taxa and in closely related green algae. Genes for the second-largest subunit (RPD2) of this enzyme were found in all land plants. Phylogenetic study indicates that RNAP IV genes are sister to the corresponding RNAP II genes. Our results show the genesis of RNAP IV to be a multistep process in which the largest and second-largest subunit genes evolved by independent duplication events in the ancestors of Charales and land plants. These findings provide insights into evolutionary mechanisms that can explain the origin of multiple RNAPs in the eukaryotic nucleus.
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Affiliation(s)
- Jie Luo
- Department of Biology, University of Washington, Seattle, WA 98195, USA
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Fahey RC, Sundquist AR. Evolution of glutathione metabolism. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 64:1-53. [PMID: 1675828 DOI: 10.1002/9780470123102.ch1] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- R C Fahey
- Department of Chemistry, University of California, San Diego, La Jolla
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Hartman H, Favaretto P, Smith TF. The archaeal origins of the eukaryotic translational system. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2006; 2:1-9. [PMID: 16877317 PMCID: PMC2685589 DOI: 10.1155/2006/431618] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Among the 78 eukaryotic ribosomal proteins, eleven are specific to Eukarya, 33 are common only to Archaea and Eukarya and 34 are homologous (at least in part) to those of both Bacteria and Archaea. Several other translational proteins are common only to Eukarya and Archaea (e.g., IF2a, SRP19, etc.), whereas others are shared by the three phyla (e.g., EFTu/EF1A and SRP54). Although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translational machinery, especially the ribosomal proteins, there have been numerous unique and ubiquitous additions to the eukaryotic translational system besides the 11 unique eukaryotic ribosomal proteins. These include peptide additions to most of the 67 archaeal homolog proteins, rRNA insertions, the 5.8S RNA and the Alu extension to the SRP RNA. Our comparative analysis of these and other eukaryotic features among the three different cellular phylodomains supports the idea that an archaeal translational system was most likely incorporated by means of endosymbiosis into a host cell that was neither bacterial nor archaeal in any modern sense. Phylogenetic analyses provide support for the timing of this acquisition coinciding with an ancient bottleneck in prokaryotic diversity.
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Affiliation(s)
- Hyman Hartman
- Biological Engineering Division, Building 56, Room 354, Massachusetts Institute of Technology, Cambridge MA 02139, USA
- BioMolecular Engineering Research Center, Boston University, 36 Cummington St., Boston MA 02215, USA
| | - Paola Favaretto
- BioMolecular Engineering Research Center, Boston University, 36 Cummington St., Boston MA 02215, USA
| | - Temple F. Smith
- BioMolecular Engineering Research Center, Boston University, 36 Cummington St., Boston MA 02215, USA
- Corresponding author ()
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31
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Goede B, Naji S, von Kampen O, Ilg K, Thomm M. Protein-protein interactions in the archaeal transcriptional machinery: binding studies of isolated RNA polymerase subunits and transcription factors. J Biol Chem 2006; 281:30581-92. [PMID: 16885163 DOI: 10.1074/jbc.m605209200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription in Archaea is directed by a pol II-like RNA polymerase and homologues of TBP and TFIIB (TFB) but the crystal structure of the archaeal enzyme and the subunits involved in recruitment of RNA polymerase to the promoter-TBP-TFB-complex are unknown. We described here the cloning expression and purification of 11 bacterially expressed subunits of the Pyrococcus furiosus RNAP. Protein interactions of subunits with each other and of archaeal transcription factors TFB and TFB with RNAP subunits were studied by Far-Western blotting and reconstitution of subcomplexes from single subunits in solution. In silico comparison of a consensus sequence of archaeal RNAP subunits with the sequence of yeast pol II subunits revealed a high degree of conservation of domains of the enzymes forming the cleft and catalytic center of the enzyme. Interaction studies with the large subunits were complicated by the low solubility of isolated subunits B, A', and A'', but an interaction network of the smaller subunits of the enzyme was established. Far-Western analyses identified subunit D as structurally important key polypeptide of RNAP involved in interactions with subunits B, L, N, and P and revealed also a strong interaction of subunits E' and F. Stable complexes consisting of subunits E' and F, of D and L and a BDLNP-subcomplex were reconstituted and purified. Gel shift analyses revealed an association of the BDLNP subcomplex with promoter-bound TBP-TFB. These results suggest a major role of subunit B (Rpb2) in RNAP recruitment to the TBP-TFB promoter complex.
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Affiliation(s)
- Bernd Goede
- Lehrstuhl für Allgemeine Mikrobiologie, Universität Kiel, am Botanischen Garten 1-9, 24107 Kiel, Germany
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Dewhirst FE, Shen Z, Scimeca MS, Stokes LN, Boumenna T, Chen T, Paster BJ, Fox JG. Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics. J Bacteriol 2005; 187:6106-18. [PMID: 16109952 PMCID: PMC1196133 DOI: 10.1128/jb.187.17.6106-6118.2005] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31' and 27'. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.
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Affiliation(s)
- Floyd E Dewhirst
- Department of Molecular Genetics, The Forsyth Institute, Boston, Massachusetts 02115, USA
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Chen L, Brügger K, Skovgaard M, Redder P, She Q, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk HP, Garrett RA. The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota. J Bacteriol 2005; 187:4992-9. [PMID: 15995215 PMCID: PMC1169522 DOI: 10.1128/jb.187.14.4992-4999.2005] [Citation(s) in RCA: 237] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sulfolobus acidocaldarius is an aerobic thermoacidophilic crenarchaeon which grows optimally at 80 degrees C and pH 2 in terrestrial solfataric springs. Here, we describe the genome sequence of strain DSM639, which has been used for many seminal studies on archaeal and crenarchaeal biology. The circular genome carries 2,225,959 bp (37% G+C) with 2,292 predicted protein-encoding genes. Many of the smaller genes were identified for the first time on the basis of comparison of three Sulfolobus genome sequences. Of the protein-coding genes, 305 are exclusive to S. acidocaldarius and 866 are specific to the Sulfolobus genus. Moreover, 82 genes for untranslated RNAs were identified and annotated. Owing to the probable absence of active autonomous and nonautonomous mobile elements, the genome stability and organization of S. acidocaldarius differ radically from those of Sulfolobus solfataricus and Sulfolobus tokodaii. The S. acidocaldarius genome contains an integrated, and probably encaptured, pARN-type conjugative plasmid which may facilitate intercellular chromosomal gene exchange in S. acidocaldarius. Moreover, it contains genes for a characteristic restriction modification system, a UV damage excision repair system, thermopsin, and an aromatic ring dioxygenase, all of which are absent from genomes of other Sulfolobus species. However, it lacks genes for some of their sugar transporters, consistent with it growing on a more limited range of carbon sources. These results, together with the many newly identified protein-coding genes for Sulfolobus, are incorporated into a public Sulfolobus database which can be accessed at http://dac.molbio.ku.dk/dbs/Sulfolobus.
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Affiliation(s)
- Lanming Chen
- Danish Archaea Centre, Institute of Molecular Biology, Copenhagen University
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Abstract
Many Archaea, in contrast to bacteria, produce a high proportion of leaderless transcripts, show a wide variation in their consensus Shine-Dalgarno (S-D) sequences and frequently use GUG and UUG start codons. In order to understand the basis for these differences, 18 complete archaeal genomes were examined for sequence signals that are positionally conserved upstream from genes. These functional motifs include box A promoter sequences for leaderless transcripts and S-D sequences for transcripts with leaders. Most of the box A sequences were preceded by a BRE-like motif and followed by a previously undetected A/T peak centred on position -10. Moreover, the sequence of the predominant S-D motifs in an archaeon is shown to depend on the precise number of nucleotides between the conserved anti-S-D CCUCC sequence and the 3'-terminal nucleotide of 16S RNA. Correlations with phylogenetic trees, constructed for the 18 Archaea, reveal that usage of high levels of both S-D motifs, and GUG and UUG start codons occurs exclusively in the shorter branched Archaea. High levels of leaderless transcripts are found in the longer branched Archaea.
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Affiliation(s)
- Elfar Torarinsson
- Danish Archaea Centre, Institute of Molecular Biology, Copenhagen University, Sølvgade 83H, DK-1307 Copenhagen K, Denmark
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Nickerson J, Drouin G. The sequence of the largest subunit of RNA polymerase II is a useful marker for inferring seed plant phylogeny. Mol Phylogenet Evol 2004; 31:403-15. [PMID: 15062783 DOI: 10.1016/j.ympev.2003.08.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2002] [Revised: 08/05/2003] [Indexed: 10/27/2022]
Abstract
We used RT-PCR to sequence approximately 3 kb of the gene coding for the largest subunit of RNA polymerase II (rpb1) from nine land plants. Our results show that plant rpb1 genes all have a similar GC-content and that their amino acid sequences evolve at a similar rate in most species we examined, except for the Arabidopsis thaliana and rice sequences which evolve faster. This gene also exists as a single copy in most species and contains enough phylogenetically informative sites to resolve the evolutionary relationships among seed plants. Protein maximum parsimony, as well as neighbor-joining and maximum likelihood analyses of DNA and protein sequences, all generated identical tree topologies with similar strong support values at each node. The angiosperms are a clade comprising Amborella as a sister group to all other angiosperms, followed by Nymphaea, Magnolia, Arabidopsis, and a monocot clade containing maize and rice. The gymnosperms also form a monophyletic clade with Welwitschia and pine grouped together and sister to a Cycas and Zamia clade. These findings concur with recent studies that refute the Anthophyte Hypothesis and place Amborella at the base of the angiosperm tree. These rpb1 sequences also give a more consistent picture of seed plant relationships than similar analyses performed on data sets made of 18S rDNA, atpB, and rbcL sequences from the same species. These sequences therefore show great promise to help further resolve the phylogenetic relationships of seed plants.
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Affiliation(s)
- Jennifer Nickerson
- Département de biologie, Université d'Ottawa, 30 Marie Curie, Ottawa, Ont., Canada K1N 6N5
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Brochier C, Forterre P, Gribaldo S. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol 2004; 5:R17. [PMID: 15003120 PMCID: PMC395767 DOI: 10.1186/gb-2004-5-3-r17] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2003] [Revised: 01/05/2004] [Accepted: 01/21/2004] [Indexed: 11/25/2022] Open
Abstract
This article presents a phylogenetic analysis of the Archea based on sets of transcription and translation proteins. The phylogenies shed light on the evolutionary position of Methanopyrus kandleri. Background Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consisting of 14 proteins involved in transcription and 53 ribosomal proteins (3,275 and 6,377 positions, respectively). Results Important relationships were confirmed, notably the dichotomy of the archaeal domain as represented by the Crenarchaeota and Euryarchaeota, the sister grouping of Sulfolobales and Aeropyrum pernix, and the monophyly of a large group comprising Thermoplasmatales, Archaeoglobus fulgidus, Methanosarcinales and Halobacteriales, with the latter two orders forming a robust cluster. The main difference concerned the position of Methanopyrus kandleri, which grouped with Methanococcales and Methanobacteriales in the translation tree, whereas it emerged at the base of the euryarchaeotes in the transcription tree. The incongruent placement of M. kandleri is likely to be the result of a reconstruction artifact due to the high evolutionary rates displayed by the components of its transcription apparatus. Conclusions We show that two informational systems, transcription and translation, provide a largely congruent signal for archaeal phylogeny. In particular, our analyses support the appearance of methanogenesis after the divergence of the Thermococcales and a late emergence of aerobic respiration from within methanogenic ancestors. We discuss the possible link between the evolutionary acceleration of the transcription machinery in M. kandleri and several unique features of this archaeon, in particular the absence of the elongation transcription factor TFS.
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Affiliation(s)
- Céline Brochier
- Equipe Phylogénomique, Université Aix-Marseille I, Centre Saint-Charles, 13331 Marseille Cedex 3, France.
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Rivetti C, Codeluppi S, Dieci G, Bustamante C. Visualizing RNA extrusion and DNA wrapping in transcription elongation complexes of bacterial and eukaryotic RNA polymerases. J Mol Biol 2003; 326:1413-26. [PMID: 12595254 DOI: 10.1016/s0022-2836(03)00042-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Transcription ternary complexes of Escherichia coli RNA polymerase and yeast RNA polymerase III have been analyzed by atomic force microscopy. Using the method of nucleotide omission and different DNA templates, E.coli RNAP has been stalled at position +24, +70 and +379 and RNAP III at position +377 from the starting site. Conformational analysis of E.coli RNAP elongation complexes reveals an average DNA compaction of 22nm and a DNA deformation compatible with approximately 180 degrees DNA wrapping against the enzyme. The extent of protein-DNA interaction attributed to wrapping, however, is less than that of corresponding open promoter complexes. DNA wrapping was also observed for RNAP III elongation complexes, which showed a DNA compaction of 30nm. When the RNA polymerases were stalled far from the promoter (+379 and +377), the growing RNA transcript was often visible and it was prevalently seen exiting from the enzyme on the opposite side relative to the smallest angle subtended by the upstream and downstream DNA arms. Surprisingly, we found that many complexes had a second RNAP, not involved in transcription, bound to the growing RNA of a ternary complex. DNA wrapping in the elongation complex suggests a possible mechanism by which the polymerase may overcome the physical barrier to transcription imposed by the nucleosomes.
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MESH Headings
- Bacterial Proteins/metabolism
- DNA Primers/chemistry
- DNA, Bacterial/chemistry
- DNA, Bacterial/metabolism
- DNA, Fungal/chemistry
- DNA, Fungal/metabolism
- DNA-Binding Proteins/metabolism
- DNA-Directed RNA Polymerases/metabolism
- Electrophoretic Mobility Shift Assay
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Microscopy, Atomic Force
- Nucleic Acid Conformation
- Nucleosomes/metabolism
- Peptide Chain Elongation, Translational
- Polymerase Chain Reaction
- Promoter Regions, Genetic
- Protein Binding
- RNA Polymerase III/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- Saccharomyces cerevisiae/chemistry
- Saccharomyces cerevisiae/enzymology
- Templates, Genetic
- Transcription, Genetic
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Affiliation(s)
- Claudio Rivetti
- Department of Biochemistry and Molecular Biology, University of Parma, 43100, Parma, Italy.
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38
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Taillardat-Bisch AV, Raoult D, Drancourt M. RNA polymerase beta-subunit-based phylogeny of Ehrlichia spp., Anaplasma spp., Neorickettsia spp. and Wolbachia pipientis. Int J Syst Evol Microbiol 2003; 53:455-458. [PMID: 12710612 DOI: 10.1099/ijs.0.02411-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequence analysis of rpoB, the gene encoding the beta-subunit of RNA polymerase, was used in a phylogenetic investigation of nine species from the genera Ehrlichia, Neorickettsia, Wolbachia and Anaplasma. The complete nucleotide sequences obtained for Anaplasma phagocytophilum (HGE agent), Ehrlichia chaffeensis, Neorickettsia sennetsu, Neorickettsia risticii, Anaplasma marginale and Wolbachia pipientis were amongst the longest rpoB sequences in GenBank and ranged from 4074 bp for N. sennetsu to 4311 bp for W. pipientis. Additional partial rpoB sequences were obtained for Ehrlichia canis, Ehrlichia ruminantium and Ehrlichia muris. Identical phylogenetic trees were inferred from multiple sequence alignments of the nucleotide sequences and the derived amino acid sequences using either distance, maximum-likelihood or parsimony methods. This study confirms the phylogeny previously inferred from sequence analyses of the 16S rRNA gene, groESL and gltA and allows the confirmation of four monophyletic clades. The rpoB nucleotide sequences were more variable than the 16S rRNA gene and groESL sequences at the species level.
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Affiliation(s)
- Anne-Véronique Taillardat-Bisch
- Unité des Rickettsies, CNRS UPRES-A 6020, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Didier Raoult
- Unité des Rickettsies, CNRS UPRES-A 6020, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Michel Drancourt
- Unité des Rickettsies, CNRS UPRES-A 6020, Université de la Méditerranée, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
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39
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Thore S, Mayer C, Sauter C, Weeks S, Suck D. Crystal structures of the Pyrococcus abyssi Sm core and its complex with RNA. Common features of RNA binding in archaea and eukarya. J Biol Chem 2003; 278:1239-47. [PMID: 12409299 DOI: 10.1074/jbc.m207685200] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. Their proposed function is to mediate RNA-RNA interactions. We present here the crystal structures of Pyrococcus abyssi Sm protein (PA-Sm1) and its complex with a uridine heptamer. The overall structure of the protein complex, a heptameric ring with a central cavity, is similar to that proposed for the eukaryotic Sm core complex and found for other archaeal Sm proteins. RNA molecules bind to the protein at two different sites. They interact specifically inside the ring with three highly conserved residues, defining the uridine-binding pocket. In addition, nucleotides also interact on the surface formed by the N-terminal alpha-helix as well as a conserved aromatic residue in beta-strand 2 of the PA-Sm1 protein. The mutation of this conserved aromatic residue shows the importance of this second site for the discrimination between RNA sequences. Given the high structural homology between archaeal and eukaryotic Sm proteins, the PA-Sm1.RNA complex provides a model for how the small nuclear RNA contacts the Sm proteins in the Sm core. In addition, it suggests how Sm proteins might exert their function as modulators of RNA-RNA interactions.
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Affiliation(s)
- Stéphane Thore
- Structural Biology Program, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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40
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Willis SH, Kazmierczak KM, Carter RH, Rothman-Denes LB. N4 RNA polymerase II, a heterodimeric RNA polymerase with homology to the single-subunit family of RNA polymerases. J Bacteriol 2002; 184:4952-61. [PMID: 12193610 PMCID: PMC135322 DOI: 10.1128/jb.184.18.4952-4961.2002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage N4 middle genes are transcribed by a phage-coded, heterodimeric, rifampin-resistant RNA polymerase, N4 RNA polymerase II (N4 RNAPII). Sequencing and transcriptional analysis revealed that the genes encoding the two subunits comprising N4 RNAPII are translated from a common transcript initiating at the N4 early promoter Pe3. These genes code for proteins of 269 and 404 amino acid residues with sequence similarity to the single-subunit, phage-like RNA polymerases. The genes encoding the N4 RNAPII subunits, as well as a synthetic construct encoding a fusion polypeptide, have been cloned and expressed. Both the individually expressed subunits and the fusion polypeptide reconstitute functional enzymes in vivo and in vitro.
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Affiliation(s)
- S H Willis
- Department of Molecular Genetics, The University of Chicago, Chicago, Illinois 60637, USA
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41
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Stiller JW, Hall BD. Evolution of the RNA polymerase II C-terminal domain. Proc Natl Acad Sci U S A 2002; 99:6091-6. [PMID: 11972039 PMCID: PMC122907 DOI: 10.1073/pnas.082646199] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2001] [Indexed: 11/18/2022] Open
Abstract
In recent years a great deal of biochemical and genetic research has focused on the C-terminal domain (CTD) of the largest subunit (RPB1) of DNA-dependent RNA polymerase II. This strongly conserved domain of tandemly repeated heptapeptides has been linked functionally to important steps in the initiation and processing of mRNA transcripts in both animals and fungi. Although they are absolutely required for viability in these organisms, C-terminal tandem repeats do not occur in RPB1 sequences from diverse eukaryotic taxa. Here we present phylogenetic analyses of RPB1 sequences showing that canonical CTD heptads are strongly conserved in only a subset of eukaryotic groups, all apparently descended from a single common ancestor. Moreover, eukaryotic groups in which the most complex patterns of ontogenetic development occur are descended from this CTD-containing ancestor. Consistent with the results of genetic and biochemical investigations of CTD function, these analyses suggest that the enhanced control over RNA polymerase II transcription conveyed by acquired CTD/protein interactions was an important step in the evolution of intricate patterns of gene expression that are a hallmark of large, developmentally complex eukaryotic organisms.
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Affiliation(s)
- John W Stiller
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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42
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Kwon HJ, Park KY, Kim SJ, Yoo HS. Application of nucleotide sequence of RNA polymerase beta-subunit gene (rpoB) to molecular differentiation of serovars of Salmonella enterica subsp. enterica. Vet Microbiol 2001; 82:121-9. [PMID: 11423203 DOI: 10.1016/s0378-1135(01)00384-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
To establish a molecular differentiation method for Salmonella enterica subsp. enterica, a hyper-variable region of RNA polymerase beta-subunit (rpoB) of S. enterica subsp. enterica (I), serotype Typhimurium, and Escherichia coli were investigated through comparison of nucleotide sequence of the region. The hyper-variable region was identified at 612-937 of the gene. After PCR amplification of the region in the 17 serotypes and two biotypes of serotype Gallinarum of S. enterica subsp. enterica (I), the nucleotide sequences of the region were determined and compared. All serotypes were distantly related to E. coli with 82.8-84.7% identities in nucleotide sequence while showing 96.6-100% identities with each other. According to the phylogenetic analysis based on the sequenced region with the neighbor-joining method, relatedness of biotype Gallinarum to serotype Enteritidis and biotype Pullorum was determined. Biotype Gallinarum was more closely related to serotype Enteritidis than biotype Pullorum. These results suggested that the 612-937 variable region of rpoB might be useful for molecular evolutionary analysis of serotypes of S. enterica subsp. enterica (I).
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Affiliation(s)
- H J Kwon
- Department of Avian Diseases, College of Veterinary Medicine, Seoul National University, Suwon 441-744, South Korea
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43
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She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC, Clausen IG, Curtis BA, De Moors A, Erauso G, Fletcher C, Gordon PM, Heikamp-de Jong I, Jeffries AC, Kozera CJ, Medina N, Peng X, Thi-Ngoc HP, Redder P, Schenk ME, Theriault C, Tolstrup N, Charlebois RL, Doolittle WF, Duguet M, Gaasterland T, Garrett RA, Ragan MA, Sensen CW, Van der Oost J. The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 2001; 98:7835-40. [PMID: 11427726 PMCID: PMC35428 DOI: 10.1073/pnas.141222098] [Citation(s) in RCA: 636] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2001] [Accepted: 05/04/2001] [Indexed: 12/23/2022] Open
Abstract
The genome of the crenarchaeon Sulfolobus solfataricus P2 contains 2,992,245 bp on a single chromosome and encodes 2,977 proteins and many RNAs. One-third of the encoded proteins have no detectable homologs in other sequenced genomes. Moreover, 40% appear to be archaeal-specific, and only 12% and 2.3% are shared exclusively with bacteria and eukarya, respectively. The genome shows a high level of plasticity with 200 diverse insertion sequence elements, many putative nonautonomous mobile elements, and evidence of integrase-mediated insertion events. There are also long clusters of regularly spaced tandem repeats. Different transfer systems are used for the uptake of inorganic and organic solutes, and a wealth of intracellular and extracellular proteases, sugar, and sulfur metabolizing enzymes are encoded, as well as enzymes of the central metabolic pathways and motility proteins. The major metabolic electron carrier is not NADH as in bacteria and eukarya but probably ferredoxin. The essential components required for DNA replication, DNA repair and recombination, the cell cycle, transcriptional initiation and translation, but not DNA folding, show a strong eukaryal character with many archaeal-specific features. The results illustrate major differences between crenarchaea and euryarchaea, especially for their DNA replication mechanism and cell cycle processes and their translational apparatus.
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Affiliation(s)
- Q She
- Microbial Genome Group, Institute of Molecular Biology, University of Copenhagen, Sølvgade 83H, DK-1307 Copenhagen, Denmark
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44
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Törö I, Thore S, Mayer C, Basquin J, Séraphin B, Suck D. RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex. EMBO J 2001; 20:2293-303. [PMID: 11331594 PMCID: PMC125243 DOI: 10.1093/emboj/20.9.2293] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic Sm and Sm-like proteins associate with RNA to form the core domain of ribonucleoprotein particles involved in pre-mRNA splicing and other processes. Recently, putative Sm proteins of unknown function have been identified in Archaea. We show by immunoprecipitation experiments that the two Sm proteins present in Archaeoglobus fulgidus (AF-Sm1 and AF-Sm2) associate with RNase P RNA in vivo, suggesting a role in tRNA processing. The AF-Sm1 protein also interacts specifically with oligouridylate in vitro. We have solved the crystal structures of this protein and a complex with RNA. AF-Sm1 forms a seven-membered ring, with the RNA interacting inside the central cavity on one face of the doughnut-shaped complex. The bases are bound via stacking and specific hydrogen bonding contacts in pockets lined by residues highly conserved in archaeal and eukaryotic Sm proteins, while the phosphates remain solvent accessible. A comparison with the structures of human Sm protein dimers reveals closely related monomer folds and intersubunit contacts, indicating that the architecture of the Sm core domain and RNA binding have been conserved during evolution.
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Affiliation(s)
| | | | - Claudine Mayer
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, 69012 Heidelberg, Germany and
Centre de Génétique Moleculaire, CNRS, Avenue De la Terrasse, 91198 Gif sur Yvette Cedex, France Present address: Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris, France Corresponding author e-mail:
S.Thore and C.Mayer contributed equally to this work
| | | | - Bertrand Séraphin
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, 69012 Heidelberg, Germany and
Centre de Génétique Moleculaire, CNRS, Avenue De la Terrasse, 91198 Gif sur Yvette Cedex, France Present address: Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris, France Corresponding author e-mail:
S.Thore and C.Mayer contributed equally to this work
| | - Dietrich Suck
- European Molecular Biology Laboratory, Meyerhofstrasse 1, Postfach 102209, 69012 Heidelberg, Germany and
Centre de Génétique Moleculaire, CNRS, Avenue De la Terrasse, 91198 Gif sur Yvette Cedex, France Present address: Université Pierre et Marie Curie, 4 Place Jussieu, 75252 Paris, France Corresponding author e-mail:
S.Thore and C.Mayer contributed equally to this work
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45
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Mayer C, Suck D, Poch O. The archaeal homolog of the Imp4 protein, a eukaryotic U3 snoRNP component. Trends Biochem Sci 2001; 26:143-4. [PMID: 11246005 DOI: 10.1016/s0968-0004(00)01779-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Homologs of the Imp4 protein, a component specific to the eukaryotic U3 snoRNP complex, have been found in all archaeal genomes. The archaeal and eukaryotic Imp4 proteins that are related to four other protein families, the Imp4-like, the SSF1 homologs and two sets of hypothetical proteins, are characterized by the Imp4 signature pattern. These findings, together with the presence of other snoRNPs homologs in Archaea, provide evidence for similar RNA processing and folding in Eukarya and Archaea.
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Affiliation(s)
- C Mayer
- Structural and Computational Biology Programme, EMBL, Meyerhofstr. 1, 69012 Heidelberg, Germany.
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46
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Renesto P, Gouvernet J, Drancourt M, Roux V, Raoult D. Use of rpoB gene analysis for detection and identification of Bartonella species. J Clin Microbiol 2001; 39:430-7. [PMID: 11158086 PMCID: PMC87755 DOI: 10.1128/jcm.39.2.430-437.2001] [Citation(s) in RCA: 186] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2000] [Accepted: 11/06/2000] [Indexed: 11/20/2022] Open
Abstract
Identification of Bartonella species is of increasing importance as the number of infections in which these bacteria are involved increases. To date, these gram-negative bacilli have been identified by various serological, biochemical, and genotypic methods. However, the development of alternative tools is required, principally to circumvent a major risk of contamination during sample manipulation. The aim of our study was to investigate the possible identification of various Bartonella species by comparison of RNA polymerase beta-subunit gene (rpoB) sequences. This approach has previously been shown to be useful for the identification of members of the family Enterobacteriaceae (C. M. Mollet, M. Drancourt, and D. Raoult, Mol. Microbiol. 26:1005-1011, 1997). Following PCR amplification with specific oligonucleotides, a 825-bp region of the rpoB gene was sequenced from 13 distinct Bartonella strains. Analysis of these sequences allowed selection of three restriction enzymes (ApoI, AluI, and AflIII) useful for discerning the different strains by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis. To confirm the potential value of such an approach for identification of Bartonella, the rpoB PCR was then applied to 94 clinical samples, and the results obtained were identical to those obtained by our reference PCR method. Twenty-four isolates were also adequately identified by PCR-RFLP analysis. In all cases, our results were in accordance with those of the reference method. Moreover, conserved regions of DNA were chosen as suitable primer targets for PCR amplification of a 439-bp fragment which can be easily sequenced.
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Affiliation(s)
- P Renesto
- Unité des Rickettsies, CNRS UPRES-A 6020, Faculté de Médecine, Université de la Méditerranée, 13385 Marseille, France
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47
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Abstract
Viruses of Sulfolobus are highly unusual in their morphology, and genome structure and sequence. Certain characteristics of the replication strategies of these viruses and the virus-host interactions suggest relationships with eukaryal and bacterial viruses, and the primeval existence of common ancestors. Moreover, studying these viruses led to the discovery of archaeal promoters and has provided tools for the development of the molecular genetics of these organisms. The Sulfolobus viruses contain unique regulatory features and structures that undoubtedly hold surprises for researchers in the future.
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Affiliation(s)
- D Prangishvili
- Universität Regensburg, Lehrstuhl für Mikrobiologie--Archaeenzentrum, Universitätsstrasse 31, 93053 Regensburg, Germany.
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48
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Renesto P, Gautheret D, Drancourt M, Raoult D. Determination of the rpoB gene sequences of Bartonella henselae and Bartonella quintana for phylogenic analysis. Res Microbiol 2000; 151:831-6. [PMID: 11191808 DOI: 10.1016/s0923-2508(00)01149-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Using the Genome Walker procedure, which allows PCR amplification of genomic DNA using a single gene-specific primer and direct automated sequencing methodology, we obtained the nucleotide sequence of the RNA polymerase beta subunit (rpoB) from Bartonella henselae and Bartonella quintana. A phylogenetic tree constructed from these data and other rpoB sequences available in GenBank is, in part, consistent with those previously derived from 16S rRNA gene sequences and confirms the position of Bartonella within the alpha subdivision of Proteobacteria. In fact, this analysis showed that rpoB data are similar to 16S rRNA data for the alpha, beta and gamma subdivisions of Proteobacteria. In contrast, concerning other bacteria included in our study, the topologies of phylogenetic trees were different. Based on the bootstrap values derived from rpoB phylogenic analysis, we believe that this molecule should contribute to better understanding the evolutionary process.
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Affiliation(s)
- P Renesto
- Unité des rickettsies, CNRS-UPRES-A 6020, Université de la Mediterranée, Marseille, France
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49
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Naryshkina T, Rogulja D, Golub L, Severinov K. Inter- and intrasubunit interactions during the formation of RNA polymerase assembly intermediate. J Biol Chem 2000; 275:31183-90. [PMID: 10906130 DOI: 10.1074/jbc.m003884200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We used yeast two-hybrid and in vitro co-immobilization assays to study the interaction between the Escherichia coli RNA polymerase (RNAP) alpha and beta subunits during the formation of alpha(2)beta, a physiological RNAP assembly intermediate. We show that a 430-amino acid-long fragment containing beta conserved segments F, G, H, and a short part of segment I forms a minimal domain capable of specific interaction with alpha. The alpha-interacting domain is held together by protein-protein interactions between beta segments F and I. Residues in catalytically important beta segments H and I directly participate in alpha binding; substitutions of strictly conserved segment H Asp(1084) and segment I Gly(1215) abolish alpha(2)beta formation in vitro and are lethal in vivo. The importance of these beta amino acids in alpha binding is fully supported by the structural model of the Thermus aquaticus RNAP core enzyme. We also demonstrate that determinants of RNAP assembly are conserved, and that a homologue of beta Asp(1084) in A135, the beta-like subunit of yeast RNAP I, is responsible for interaction with AC40, the largest alpha-like subunit. However, the A135-AC40 interaction is weak compared with the E. coli alpha-beta interaction, and A135 mutation that abolishes the interaction is phenotypically silent. The results suggest that in eukaryotes additional RNAP subunits orchestrate the enzyme assembly by stabilizing weak, but specific interactions of core subunits.
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Affiliation(s)
- T Naryshkina
- Waksman Institute for Microbiology and the Department of Genetics, Rutgers, State University of New Jersey, Piscataway, New Jersey 08854, USA
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50
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Abstract
An extrachromosomal genome of between 27 and 35 kb has been described in several apicomplexan parasites including Plasmodium falciparum and Toxoplasma gondii. Examination of sequence data proved the genomes to be a remnant plastid genome, from which all genes encoding photosynthetic functions had been lost. Localisation studies had shown that the genome was located within a multi-walled organelle, anterior to the nucleus. This organelle had been previously described in ultrastructural studies of several genera of apicomplexa, but no function had been attributed to it. This invited review describes the evolution of knowledge on the apicomplexan plastid, then discusses current research findings on the likely role of the plastid in the Apicomplexa. How the plastid may be used to effect better drug treatments for apicomplexan diseases, and its potential as a marker for investigating phylogenetic relationships among the Apicomplexa, are discussed.
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Affiliation(s)
- M T Gleeson
- Department of Cell and Molecular Biology, Faculty of Science, University of Technology, Westbourne Street, Gore Hill NSW 2065, Sydney, Australia.
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