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Tse C, Ma K. A novel alcohol dehydrogenase in the hyperthermophilic crenarchaeon Hyperthermus butylicus. MLIFE 2024; 3:317-325. [PMID: 38948144 PMCID: PMC11211662 DOI: 10.1002/mlf2.12126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/25/2024] [Accepted: 03/19/2024] [Indexed: 07/02/2024]
Abstract
Hyperthermus butylicus is a hyperthermophilic crenarchaeon that produces 1-butanol as an end product. A thermostable alcohol dehydrogenase (ADH) must be present in H. butylicus to act as the key enzyme responsible for this production; however, the gene that encodes the ADH has not yet been identified. A novel ADH, HbADH2, was purified from a cell-free extract of H. butylicus, and its characteristics were determined. The gene that encodes HbADH2 was demonstrated to be HBUT_RS04850 and annotated as a hypothetical protein in H. butylicus. HbADH2 was found to be a primary-secondary ADH capable of using a wide range of substrates, including butyraldehyde and butanol. Butyraldehyde had the highest specificity constant, calculated as k c at/K m, with k cat and apparent K m values of 8.00 ± 0.22 s-1 and 0.59 ± 0.07 mM, respectively. The apparent K m values for other substrates, including ethanol, 1-propanol, 2-propanol, butanol, acetaldehyde, propanal, and acetone, were 4.36 ± 0.42, 4.69 ± 0.41, 3.74 ± 0.46, 2.44 ± 0.30, 1.27 ± 0.18, 1.55 ± 0.20, and 0.68 ± 0.04 mM, respectively. The optimal pH values for catalyzing aldehyde reduction and alcohol oxidation were 6.0 and 9.0, respectively, while the optimal temperature was higher than 90°C due to the increase in enzymatic activity from 60°C to 90°C. Based on its substrate specificity, enzyme kinetics, and thermostability, HbADH2 may be the ADH that catalyzes the production of 1-butanol in H. butylicus. The putative conserved motif sites for NAD(P)+ and iron binding were identified by aligning HbADH2 with previously characterized Fe-containing ADHs.
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Affiliation(s)
- Ching Tse
- Department of BiologyUniversity of WaterlooWaterlooOntarioCanada
| | - Kesen Ma
- Department of BiologyUniversity of WaterlooWaterlooOntarioCanada
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Bundela R, Keown J, Watkin S, Pearce FG. Structure of a hyperthermostable dimeric archaeal Rubisco from Hyperthermus butylicus. Acta Crystallogr D Struct Biol 2019; 75:536-544. [DOI: 10.1107/s2059798319006466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/07/2019] [Indexed: 11/11/2022] Open
Abstract
The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from the hyperthermophilic archaeonHyperthermus butylicusis presented at 1.8 Å resolution. Previous structures of archaeal Rubisco have been found to assemble into decamers, and this oligomerization was thought to be required for a highly thermally stable enzyme. In the current study,H. butylicusRubisco is shown to exist as a dimer in solution, yet has a thermal denaturation midpoint of 114°C, suggesting that high thermal stability can be achieved without an increased oligomeric state. This increased thermal stability appears to be due to an increased number of electrostatic interactions within the monomeric subunit. As such,H. butylicusRubisco presents a well characterized system in which to investigate the role of assembly and thermal stability in enzyme function.
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The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism. Microbiol Mol Biol Rev 2018; 83:83/1/e00040-18. [PMID: 30567937 DOI: 10.1128/mmbr.00040-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ribosyl 1,5-bisphosphate (PRibP) was discovered 65 years ago and was believed to be an important intermediate in ribonucleotide metabolism, a role immediately taken over by its "big brother" phosphoribosyldiphosphate. Only recently has PRibP come back into focus as an important player in the metabolism of ribonucleotides with the discovery of the pentose bisphosphate pathway that comprises, among others, the intermediates PRibP and ribulose 1,5-bisphosphate (cf. ribose 5-phosphate and ribulose 5-phosphate of the pentose phosphate pathway). Enzymes of several pathways produce and utilize PRibP not only in ribonucleotide metabolism but also in the catabolism of phosphonates, i.e., compounds containing a carbon-phosphorus bond. Pathways for PRibP metabolism are found in all three domains of life, most prominently among organisms of the archaeal domain, where they have been identified either experimentally or by bioinformatic analysis within all of the four main taxonomic groups, Euryarchaeota, TACK, DPANN, and Asgard. Advances in molecular genetics of archaea have greatly improved the understanding of the physiology of PRibP metabolism, and reconciliation of molecular enzymology and three-dimensional structure analysis of enzymes producing or utilizing PRibP emphasize the versatility of the compound. Finally, PRibP is also an effector of several metabolic activities in many organisms, including higher organisms such as mammals. In the present review, we describe all aspects of PRibP metabolism, with emphasis on the biochemical, genetic, and physiological aspects of the enzymes that produce or utilize PRibP. The inclusion of high-resolution structures of relevant enzymes that bind PRibP provides evidence for the flexibility and importance of the compound in metabolism.
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Ionescu MI, Oniga O. Molecular Docking Evaluation of ( E)-5-arylidene-2-thioxothiazolidin-4-one Derivatives as Selective Bacterial Adenylate Kinase Inhibitors. Molecules 2018; 23:molecules23051076. [PMID: 29751552 PMCID: PMC6102543 DOI: 10.3390/molecules23051076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
Multi-drug resistant microorganism infections with emerging problems that require not only a prevention strategy, but also the development of new inhibitory compounds. Six previously synthesized 5-arylidene-2-thioxothiazolidin-4-one derivatives 1a–f, were screened for inhibitory activity on adenylate kinases of different origins by molecular docking. The compounds 1c and 1d were the most efficient inhibitors of bacterial and some archean adenylate kinases. Hydrogen bond interactions were observed with the residues belonging to the ATP binding site. Moreover human adenylate kinases are poor targets, suggesting that this selectivity offers promising prospectives for refining the structure of our compounds.
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Affiliation(s)
- Mihaela Ileana Ionescu
- Department of Microbiology, Iuliu Hațieganu University of Medicine and Pharmacy, 400349 Cluj-Napoca, Romania.
- Department of Microbiology, County Emergency Clinical Hospital, 400006 Cluj-Napoca, Romania.
| | - Ovidiu Oniga
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Iuliu Hațieganu University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania.
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Demey LM, Miller CR, Manzella MP, Spurbeck RR, Sandhu SK, Reguera G, Kashefi K. The draft genome of the hyperthermophilic archaeon Pyrodictium delaneyi strain hulk, an iron and nitrate reducer, reveals the capacity for sulfate reduction. Stand Genomic Sci 2017; 12:47. [PMID: 28814988 PMCID: PMC5556600 DOI: 10.1186/s40793-017-0260-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 08/08/2017] [Indexed: 01/01/2023] Open
Abstract
Pyrodictium delaneyi strain Hulk is a newly sequenced strain isolated from chimney samples collected from the Hulk sulfide mound on the main Endeavour Segment of the Juan de Fuca Ridge (47.9501 latitude, -129.0970 longitude, depth 2200 m) in the Northeast Pacific Ocean. The draft genome of strain Hulk shared 99.77% similarity with the complete genome of the type strain Su06T, which shares with strain Hulk the ability to reduce iron and nitrate for respiration. The annotation of the genome of strain Hulk identified genes for the reduction of several sulfur-containing electron acceptors, an unsuspected respiratory capability in this species that was experimentally confirmed for strain Hulk. This makes P. delaneyi strain Hulk the first hyperthermophilic archaeon known to gain energy for growth by reduction of iron, nitrate, and sulfur-containing electron acceptors. Here we present the most notable features of the genome of P. delaneyi strain Hulk and identify genes encoding proteins critical to its respiratory versatility at high temperatures. The description presented here corresponds to a draft genome sequence containing 2,042,801 bp in 9 contigs, 2019 protein-coding genes, 53 RNA genes, and 1365 hypothetical genes.
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Affiliation(s)
- Lucas M. Demey
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Caitlin R. Miller
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Michael P Manzella
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
- Present address: Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado, USA
| | - Rachel R. Spurbeck
- Applied Genomics and Biology Group, Department of CBRNE Defense, Battelle Memorial Institute, Columbus, OH USA
| | | | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
| | - Kazem Kashefi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI USA
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Yu Z, Ma Y, Zhong W, Qiu J, Li J. Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles. Front Microbiol 2017; 8:1278. [PMID: 28744269 PMCID: PMC5504354 DOI: 10.3389/fmicb.2017.01278] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/26/2017] [Indexed: 12/22/2022] Open
Abstract
Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.
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Affiliation(s)
- Zhiliang Yu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Yunting Ma
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Weihong Zhong
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Juanping Qiu
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China
| | - Jun Li
- Department of Applied Biology, College of Biotechnology and Bioengineering, Zhejiang University of TechnologyHangzhou, China.,State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong UniversityShanghai, China
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Poehlein A, Solano JDM, Flitsch SK, Krabben P, Winzer K, Reid SJ, Jones DT, Green E, Minton NP, Daniel R, Dürre P. Microbial solvent formation revisited by comparative genome analysis. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:58. [PMID: 28286553 PMCID: PMC5343299 DOI: 10.1186/s13068-017-0742-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Accepted: 02/28/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microbial formation of acetone, isopropanol, and butanol is largely restricted to bacteria belonging to the genus Clostridium. This ability has been industrially exploited over the last 100 years. The solvents are important feedstocks for the chemical and biofuel industry. However, biological synthesis suffers from high substrate costs and competition from chemical synthesis supported by the low price of crude oil. To render the biotechnological production economically viable again, improvements in microbial and fermentation performance are necessary. However, no comprehensive comparisons of respective species and strains used and their specific abilities exist today. RESULTS The genomes of a total 30 saccharolytic Clostridium strains, representative of the species Clostridium acetobutylicum, C. aurantibutyricum, C. beijerinckii, C. diolis, C. felsineum, C. pasteurianum, C. puniceum, C. roseum, C. saccharobutylicum, and C. saccharoperbutylacetonicum, have been determined; 10 of them completely, and compared to 14 published genomes of other solvent-forming clostridia. Two major groups could be differentiated and several misclassified species were detected. CONCLUSIONS Our findings represent a comprehensive study of phylogeny and taxonomy of clostridial solvent producers that highlights differences in energy conservation mechanisms and substrate utilization between strains, and allow for the first time a direct comparison of sequentially selected industrial strains at the genetic level. Detailed data mining is now possible, supporting the identification of new engineering targets for improved solvent production.
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Affiliation(s)
- Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - José David Montoya Solano
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Stefanie K. Flitsch
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Preben Krabben
- Green Biologics Ltd., 45A Western Avenue, Milton Park, Abingdon, Oxfordshire OX14 4RU UK
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Sharon J. Reid
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town, 7701 South Africa
| | - David T. Jones
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9010 New Zealand
| | - Edward Green
- CHAIN Biotechnology Ltd., Imperial College Incubator, Level 1 Bessemer Building, Imperial College London, London, SW7 2AZ UK
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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Genome-Scale Modeling of Thermophilic Microorganisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016. [PMID: 27913830 DOI: 10.1007/10_2016_45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Thermophilic microorganisms are of increasing interest for many industries as their enzymes and metabolisms are highly efficient at elevated temperatures. However, their metabolic processes are often largely different from their mesophilic counterparts. These differences can lead to metabolic engineering strategies that are doomed to fail. Genome-scale metabolic modeling is an effective and highly utilized way to investigate cellular phenotypes and to test metabolic engineering strategies. In this review we chronicle a number of thermophilic organisms that have recently been studied with genome-scale models. The microorganisms spread across archaea and bacteria domains, and their study gives insights that can be applied in a broader context than just the species they describe. We end with a perspective on the future development and applications of genome-scale models of thermophilic organisms.
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Lin TJ, El Sebae G, Jung JH, Jung DH, Park CS, Holden JF. Pyrodictium delaneyi sp. nov., a hyperthermophilic autotrophic archaeon that reduces Fe(III) oxide and nitrate. Int J Syst Evol Microbiol 2016; 66:3372-3376. [PMID: 27260263 DOI: 10.1099/ijsem.0.001201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A hyperthermophilic, autotrophic iron and nitrate reducer, strain Su06T, was isolated from an active deep-sea hydrothermal vent chimney on the Endeavour Segment in the north-eastern Pacific Ocean. It was obligately anaerobic, hydrogenotrophic and reduced Fe(III) oxide to magnetite and NO3- to N2. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain was more than 97 % similar to other species of the genera Pyrodictium and Hyperthermus. Therefore, overall genome relatedness index analyses were performed to establish whether strain Su06T represents a novel species. For each analysis, strain Su06T was most similar to Pyrodictium occultum PL-19T. Relative to this strain, the average nucleotide identity score for strain Su06T was 72 %, the genome-to-genome direct comparison score was 13-19 % and the species identification score at the protein level was 89 %. For each analysis, strain Su06T was below the species delineation cutoff. Based on its whole genome sequence and its unique phenotypic characteristics, strain Su06T is suggested to represent a novel species of the genus Pyrodictium, for which the name Pyrodictium delaneyi is proposed. The type strain is Su06T (=DSM 28599T=ATCC BAA-2559T).
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Affiliation(s)
- T Jennifer Lin
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Gabriel El Sebae
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Jong-Hyun Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Republic of Korea
| | - Dong-Hyun Jung
- Graduate School of Biotechnology, Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Cheon-Seok Park
- Graduate School of Biotechnology, Institute of Life Science and Resources, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - James F Holden
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
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Lebedinsky AV, Mardanov AV, Kublanov IV, Gumerov VM, Beletsky AV, Perevalova AA, Bidzhieva SK, Bonch-Osmolovskaya EA, Skryabin KG, Ravin NV. Analysis of the complete genome of Fervidococcus fontis confirms the distinct phylogenetic position of the order Fervidicoccales and suggests its environmental function. Extremophiles 2013; 18:295-309. [DOI: 10.1007/s00792-013-0616-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/05/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Alexander V Lebedinsky
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-let Oktyabrya, 7/2, Moscow, 117312, Russia,
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11
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Baldridge KC, Contreras LM. Functional implications of ribosomal RNA methylation in response to environmental stress. Crit Rev Biochem Mol Biol 2013; 49:69-89. [PMID: 24261569 DOI: 10.3109/10409238.2013.859229] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The study of post-transcriptional RNA modifications has long been focused on the roles these chemical modifications play in maintaining ribosomal function. The field of ribosomal RNA modification has reached a milestone in recent years with the confirmation of the final unknown ribosomal RNA methyltransferase in Escherichia coli in 2012. Furthermore, the last 10 years have brought numerous discoveries in non-coding RNAs and the roles that post-transcriptional modification play in their functions. These observations indicate the need for a revitalization of this field of research to understand the role modifications play in maintaining cellular health in a dynamic environment. With the advent of high-throughput sequencing technologies, the time is ripe for leaps and bounds forward. This review discusses ribosomal RNA methyltransferases and their role in responding to external stress in Escherichia coli, with a specific focus on knockout studies and on analysis of transcriptome data with respect to rRNA methyltransferases.
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Affiliation(s)
- Kevin C Baldridge
- McKetta Department of Chemical Engineering, The University of Texas at Austin , Austin, TX , USA
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Predominant Acidilobus-like populations from geothermal environments in yellowstone national park exhibit similar metabolic potential in different hypoxic microbial communities. Appl Environ Microbiol 2013; 80:294-305. [PMID: 24162572 DOI: 10.1128/aem.02860-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
High-temperature (>70°C) ecosystems in Yellowstone National Park (YNP) provide an unparalleled opportunity to study chemotrophic archaea and their role in microbial community structure and function under highly constrained geochemical conditions. Acidilobus spp. (order Desulfurococcales) comprise one of the dominant phylotypes in hypoxic geothermal sulfur sediment and Fe(III)-oxide environments along with members of the Thermoproteales and Sulfolobales. Consequently, the primary goals of the current study were to analyze and compare replicate de novo sequence assemblies of Acidilobus-like populations from four different mildly acidic (pH 3.3 to 6.1) high-temperature (72°C to 82°C) environments and to identify metabolic pathways and/or protein-encoding genes that provide a detailed foundation of the potential functional role of these populations in situ. De novo assemblies of the highly similar Acidilobus-like populations (>99% 16S rRNA gene identity) represent near-complete consensus genomes based on an inventory of single-copy genes, deduced metabolic potential, and assembly statistics generated across sites. Functional analysis of coding sequences and confirmation of gene transcription by Acidilobus-like populations provide evidence that they are primarily chemoorganoheterotrophs, generating acetyl coenzyme A (acetyl-CoA) via the degradation of carbohydrates, lipids, and proteins, and auxotrophic with respect to several external vitamins, cofactors, and metabolites. No obvious pathways or protein-encoding genes responsible for the dissimilatory reduction of sulfur were identified. The presence of a formate dehydrogenase (Fdh) and other protein-encoding genes involved in mixed-acid fermentation supports the hypothesis that Acidilobus spp. function as degraders of complex organic constituents in high-temperature, mildly acidic, hypoxic geothermal systems.
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Variation of the virus-related elements within syntenic genomes of the hyperthermophilic Archaeon Aeropyrum. Appl Environ Microbiol 2013; 79:5891-8. [PMID: 23872576 DOI: 10.1128/aem.01089-13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The increasing number of genome sequences of archaea and bacteria show their adaptation to different environmental conditions at the genomic level. Aeropyrum spp. are aerobic and hyperthermophilic archaea. Aeropyrum camini was isolated from a deep-sea hydrothermal vent, and Aeropyrum pernix was isolated from a coastal solfataric vent. To investigate the adaptation strategy in each habitat, we compared the genomes of the two species. Shared genome features were a small genome size, a high GC content, and a large portion of orthologous genes (86 to 88%). The genomes also showed high synteny. These shared features may have been derived from the small number of mobile genetic elements and the lack of a RecBCD system, a recombinational enzyme complex. In addition, the specialized physiology (aerobic and hyperthermophilic) of Aeropyrum spp. may also contribute to the entire-genome similarity. Despite having stable genomes, interference of synteny occurred with two proviruses, A. pernix spindle-shaped virus 1 (APSV1) and A. pernix ovoid virus 1 (APOV1), and clustered regularly interspaced short palindromic repeat (CRISPR) elements. Spacer sequences derived from the A. camini CRISPR showed significant matches with protospacers of the two proviruses infecting A. pernix, indicating that A. camini interacted with viruses closely related to APSV1 and APOV1. Furthermore, a significant fraction of the nonorthologous genes (41 to 45%) were proviral genes or ORFans probably originating from viruses. Although the genomes of A. camini and A. pernix were conserved, we observed nonsynteny that was attributed primarily to virus-related elements. Our findings indicated that the genomic diversification of Aeropyrum spp. is substantially caused by viruses.
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Kim JH, Lee KK, Sun Y, Seo GJ, Cho SS, Kwon SH, Kwon ST. Broad nucleotide cofactor specificity of DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus and its evolutionary significance. Extremophiles 2013; 17:515-22. [PMID: 23546841 DOI: 10.1007/s00792-013-0536-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/14/2013] [Indexed: 12/30/2022]
Abstract
The nucleotide cofactor specificity of the DNA ligase from the hyperthermophilic crenarchaeon Hyperthermus butylicus (Hbu) was studied to investigate the evolutionary relationship of DNA ligases. The Hbu DNA ligase gene was expressed under control of the T7lac promoter of pTARG in Escherichia coli BL21-CodonPlus(DE3)-RIL. The expressed enzyme was purified using the IMPACT™-CN system (intein-mediated purification with an affinity chitin-binding tag) and cation-ion (Arg-tag) chromatography. The optimal temperature for Hbu DNA ligase activity was 75 °C, and the optimal pH was 8.0 in Tris-HCl. The activity was highly dependent on MgCl2 or MnCl2 with maximal activity above 5 mM MgCl2 and 2 mM MnCl2. Notably, Hbu DNA ligase can use ADP and GTP in addition to ATP. The broad nucleotide cofactor specificity of Hbu DNA ligase might exemplify an undifferentiated ancestral stage in the evolution of DNA ligases. This study provides new evidence for possible evolutionary relationships among DNA ligases.
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Affiliation(s)
- Jun-Hwan Kim
- Department of Genetic Engineering, Sungkyunkwan University, 300 Cheoncheon-dong, Jangan-gu, Suwon 440-746, Korea
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Kenchappa CS, Heidarsson PO, Kragelund BB, Garrett RA, Poulsen FM. Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2. Nucleic Acids Res 2013; 41:3424-35. [PMID: 23325851 PMCID: PMC3597662 DOI: 10.1093/nar/gks1465] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) form the basis of diverse adaptive immune systems directed primarily against invading genetic elements of archaea and bacteria. Cbp1 of the crenarchaeal thermoacidophilic order Sulfolobales, carrying three imperfect repeats, binds specifically to CRISPR DNA repeats and has been implicated in facilitating production of long transcripts from CRISPR loci. Here, a second related class of CRISPR DNA repeat-binding protein, denoted Cbp2, is characterized that contains two imperfect repeats and is found amongst members of the crenarchaeal thermoneutrophilic order Desulfurococcales. DNA repeat-binding properties of the Hyperthermus butylicus protein Cbp2Hb were characterized and its three-dimensional structure was determined by NMR spectroscopy. The two repeats generate helix-turn-helix structures separated by a basic linker that is implicated in facilitating high affinity DNA binding of Cbp2 by tethering the two domains. Structural studies on mutant proteins provide support for Cys(7) and Cys(28) enhancing high thermal stability of Cbp2Hb through disulphide bridge formation. Consistent with their proposed CRISPR transcriptional regulatory role, Cbp2Hb and, by inference, other Cbp1 and Cbp2 proteins are closely related in structure to homeodomain proteins with linked helix-turn-helix (HTH) domains, in particular the paired domain Pax and Myb family proteins that are involved in eukaryal transcriptional regulation.
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Affiliation(s)
- Chandra S Kenchappa
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
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Schut GJ, Boyd ES, Peters JW, Adams MWW. The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol Rev 2012; 37:182-203. [PMID: 22713092 DOI: 10.1111/j.1574-6976.2012.00346.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 05/30/2012] [Accepted: 06/08/2012] [Indexed: 12/01/2022] Open
Abstract
Hydrogen production is a vital metabolic process for many anaerobic organisms, and the enzyme responsible, hydrogenase, has been studied since the 1930s. A novel subfamily with unique properties was recently recognized, represented by the 14-subunit membrane-bound [NiFe] hydrogenase from the archaeon Pyrococcus furiosus. This so-called energy-converting hydrogenase links the thermodynamically favorable oxidation of ferredoxin with the formation of hydrogen and conserves energy in the form of an ion gradient. It is therefore a simple respiratory system within a single complex. This hydrogenase shows a modular composition represented by a Na(+)/H(+) antiporter domain (Mrp) and a [NiFe] hydrogenase domain (Mbh). An analysis of the large number of microbial genome sequences available shows that homologs of Mbh and Mrp tend to be clustered within the genomes of a limited number of archaeal and bacterial species. In several instances, additional genes are associated with the Mbh and Mrp gene clusters that encode proteins that catalyze the oxidation of formate, CO or NAD(P)H. The Mbh complex also shows extensive homology to a number of subunits within the NADH quinone oxidoreductase or complex I family. The respiratory-type membrane-bound hydrogenase complex appears to be closely related to the common ancestor of complex I and [NiFe] hydrogenases in general.
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Affiliation(s)
- Gerrit J Schut
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA 30602, USA
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Zhao H, Yu S, Liu H, Si W, Wang C, Liu S. Identification of antigenic epitopes of the SapA protein of Campylobacter fetus using a phage display peptide library. Res Vet Sci 2012; 93:1274-80. [PMID: 22424885 DOI: 10.1016/j.rvsc.2012.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 02/06/2012] [Accepted: 02/12/2012] [Indexed: 11/27/2022]
Abstract
In this study, we immunized mice with prokaryotically expressed recombinant surface layer protein, SapA, of Campylobacter fetus, generated hybridomas secreting mouse monoclonal antibodies (mAb) targeting SapA, and purified the mAb A2D5 from mouse ascites using saturated ammonium sulfate solution. The mAb A2D5, coated onto ELISA plates, was used to screen the phage random 12-peptide library through three rounds of panning. Following panning, 15 phage clones were randomly chosen and tested for reactivity with mAb A2D5 by indirect ELISA. Single-stranded DNA from positive clones was sequenced and compared with the sequence of SapA to predict the key epitope. ELISA and/or Western blot analyses further validated that synthetic peptides and recombinant peptide mimotopes all interact with mAb A2D5. Nine of ten positive phage clones identified by screening were sequenced successfully. Seven clones shared the same sequence HYDRHNYHWWHT; one had the sequence LSKNLPLTALGN; and the final one had the sequence SGMKEPELRSYS. These three sequences shared high homology with SapA J05577 in the region GNEKDFVTKIYSIALGNTSDVDGINYW, in which the underlined amino acids may serve as key residues in the epitope. ELISA and/or Western blot analyses showed that mAb A2D5 not only interacted with the four synthetic peptide mimotopes, but also with 14 prokaryotically expressed recombinant peptide mimotopes. The mimotopes identified in this study will aid future studies into the pathological processes and immune mechanisms of the SapA protein of C. fetus.
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Affiliation(s)
- Hailing Zhao
- Division of Bacterial Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 15000, PR China
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Deng L, Kenchappa CS, Peng X, She Q, Garrett RA. Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus. Nucleic Acids Res 2012; 40:2470-80. [PMID: 22139923 PMCID: PMC3315313 DOI: 10.1093/nar/gkr1111] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/04/2011] [Accepted: 11/06/2011] [Indexed: 11/29/2022] Open
Abstract
CRISPR loci are essential components of the adaptive immune system of archaea and bacteria. They consist of long arrays of repeats separated by DNA spacers encoding guide RNAs (crRNA), which target foreign genetic elements. Cbp1 (CRISPR DNA repeat binding protein) binds specifically to the multiple direct repeats of CRISPR loci of members of the acidothermophilic, crenarchaeal order Sulfolobales. cbp1 gene deletion from Sulfolobus islandicus REY15A produced a strong reduction in pre-crRNA yields from CRISPR loci but did not inhibit the foreign DNA targeting capacity of the CRISPR/Cas system. Conversely, overexpression of Cbp1 in S. islandicus generated an increase in pre-crRNA yields while the level of reverse strand transcripts from CRISPR loci remained unchanged. It is proposed that Cbp1 modulates production of longer pre-crRNA transcripts from CRISPR loci. A possible mechanism is that it minimizes interference from potential transcriptional signals carried on spacers deriving from A-T-rich genetic elements and, occasionally, on DNA repeats. Supporting evidence is provided by microarray and northern blotting analyses, and publicly available whole-transcriptome data for S. solfataricus P2.
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Affiliation(s)
| | | | | | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200N Copenhagen K, Denmark
| | - Roger A. Garrett
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200N Copenhagen K, Denmark
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Moriscot C, Gribaldo S, Jault JM, Krupovic M, Arnaud J, Jamin M, Schoehn G, Forterre P, Weissenhorn W, Renesto P. Crenarchaeal CdvA forms double-helical filaments containing DNA and interacts with ESCRT-III-like CdvB. PLoS One 2011; 6:e21921. [PMID: 21760923 PMCID: PMC3132758 DOI: 10.1371/journal.pone.0021921] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 06/09/2011] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The phylum Crenarchaeota lacks the FtsZ cell division hallmark of bacteria and employs instead Cdv proteins. While CdvB and CdvC are homologues of the eukaryotic ESCRT-III and Vps4 proteins, implicated in membrane fission processes during multivesicular body biogenesis, cytokinesis and budding of some enveloped viruses, little is known about the structure and function of CdvA. Here, we report the biochemical and biophysical characterization of the three Cdv proteins from the hyperthermophilic archaeon Metallospherae sedula. METHODOLOGY/PRINCIPAL FINDINGS Using sucrose density gradient ultracentrifugation and negative staining electron microscopy, we evidenced for the first time that CdvA forms polymers in association with DNA, similar to known bacterial DNA partitioning proteins. We also observed that, in contrast to full-lengh CdvB that was purified as a monodisperse protein, the C-terminally deleted CdvB construct forms filamentous polymers, a phenomenon previously observed with eukaryotic ESCRT-III proteins. Based on size exclusion chromatography data combined with detection by multi-angle laser light scattering analysis, we demonstrated that CdvC assembles, in a nucleotide-independent way, as homopolymers resembling dodecamers and endowed with ATPase activity in vitro. The interactions between these putative cell division partners were further explored. Thus, besides confirming the previous observations that CdvB interacts with both CdvA and CdvC, our data demonstrate that CdvA/CdvB and CdvC/CdvB interactions are not mutually exclusive. CONCLUSIONS/SIGNIFICANCE Our data reinforce the concept that Cdv proteins are closely related to the eukaryotic ESCRT-III counterparts and suggest that the organization of the ESCRT-III machinery at the Crenarchaeal cell division septum is organized by CdvA an ancient cytoskeleton protein that might help to coordinate genome segregation.
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Affiliation(s)
- Christine Moriscot
- CNRS-EMBL-UJF, Unit of Virus Host Cell Interactions (UVHCI)-UMI 3265, Grenoble, France
- CEA-CNRS-UJF, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Grenoble, France
| | - Simonetta Gribaldo
- Biologie Moléculaire du gène chez les Extrêmophiles (BMGE), Institut Pasteur, Paris, France
| | - Jean-Michel Jault
- CEA-CNRS-UJF, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Grenoble, France
| | - Mart Krupovic
- Biologie Moléculaire du gène chez les Extrêmophiles (BMGE), Institut Pasteur, Paris, France
| | - Julie Arnaud
- CNRS-EMBL-UJF, Unit of Virus Host Cell Interactions (UVHCI)-UMI 3265, Grenoble, France
| | - Marc Jamin
- CNRS-EMBL-UJF, Unit of Virus Host Cell Interactions (UVHCI)-UMI 3265, Grenoble, France
| | - Guy Schoehn
- CNRS-EMBL-UJF, Unit of Virus Host Cell Interactions (UVHCI)-UMI 3265, Grenoble, France
- CEA-CNRS-UJF, Institut de Biologie Structurale Jean-Pierre Ebel, UMR 5075, Grenoble, France
| | - Patrick Forterre
- Biologie Moléculaire du gène chez les Extrêmophiles (BMGE), Institut Pasteur, Paris, France
- Univ Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR 8621, Orsay, France
| | - Winfried Weissenhorn
- CNRS-EMBL-UJF, Unit of Virus Host Cell Interactions (UVHCI)-UMI 3265, Grenoble, France
| | - Patricia Renesto
- CNRS-EMBL-UJF, Unit of Virus Host Cell Interactions (UVHCI)-UMI 3265, Grenoble, France
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Anderson I, Göker M, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Huntemann M, Liolios K, Ivanova N, Pagani I, Mavromatis K, Ovchinikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Brambilla EM, Huber H, Yasawong M, Rohde M, Spring S, Abt B, Sikorski J, Wirth R, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lapidus A. Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1A). Stand Genomic Sci 2011; 4:381-92. [PMID: 21886865 PMCID: PMC3156397 DOI: 10.4056/sigs.2014648] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pyrolobus fumarii Blöchl et al. 1997 is the type species of the genus Pyrolobus, which belongs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motile crenarchaeon. It is of interest because of its isolated phylogenetic location in the tree of life and because it is a hyperthermophilic chemolithoautotroph known as the primary producer of organic matter at deep-sea hydrothermal vents. P. fumarii exhibits currently the highest optimal growth temperature of all life forms on earth (106°C). This is the first completed genome sequence of a member of the genus Pyrolobus to be published and only the second genome sequence from a member of the family Pyrodictiaceae. Although Diversa Corporation announced the completion of sequencing of the P. fumarii genome on September 25, 2001, this sequence was never released to the public. The 1,843,267 bp long genome with its 1,986 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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21
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Wirth R, Chertkov O, Held B, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Han C, Goodwin L, Pitluck S, Liolios K, Ioanna P, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Bilek Y, Hader T, Rohde M, Spring S, Sikorski J, Göker M, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Desulfurococcus mucosus type strain (O7/1). Stand Genomic Sci 2011; 4:173-82. [PMID: 21677854 PMCID: PMC3111991 DOI: 10.4056/sigs.1644004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Desulfurococcus mucosus Zillig and Stetter 1983 is the type species of the genus Desulfurococcus, which belongs to the crenarchaeal family Desulfurococcaceae. The species is of interest because of its position in the tree of life, its ability for sulfur respiration, and several biotechnologically relevant thermostable and thermoactive extracellular enzymes. This is the third completed genome sequence of a member of the genus Desulfurococcus and already the 8(th) sequence from a member the family Desulfurococcaceae. The 1,314,639 bp long genome with its 1,371 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Mavromatis K, Sikorski J, Pabst E, Teshima H, Lapidus A, Lucas S, Nolan M, Glavina Del Rio T, Cheng JF, Bruce D, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Spring S, Göker M, Wirth R, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Vulcanisaeta distributa type strain (IC-017). Stand Genomic Sci 2010; 3:117-25. [PMID: 21304741 PMCID: PMC3035369 DOI: 10.4056/sigs.1113067] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum Crenarchaeota. The genus Vulcanisaeta is characterized by a global distribution in hot and acidic springs. This is the first genome sequence from a member of the genus Vulcanisaeta and seventh genome sequence in the family Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteriaand Archaea project.
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23
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Göker M, Held B, Lapidus A, Nolan M, Spring S, Yasawong M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Tapia R, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Brambilla E, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP. Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1). Stand Genomic Sci 2010; 3:66-75. [PMID: 21304693 PMCID: PMC3035270 DOI: 10.4056/sigs.1072907] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Ignisphaera aggregans Niederberger et al. 2006 is the type and sole species of genus Ignisphaera. This archaeal species is characterized by a coccoid-shape and is strictly anaerobic, moderately acidophilic, heterotrophic hyperthermophilic and fermentative. The type strain AQ1.S1(T) was isolated from a near neutral, boiling spring in Kuirau Park, Rotorua, New Zealand. This is the first completed genome sequence of the genus Ignisphaera and the fifth genome (fourth type strain) sequence in the family Desulfurococcaceae. The 1,875,953 bp long genome with its 2,009 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Inskeep WP, Rusch DB, Jay ZJ, Herrgard MJ, Kozubal MA, Richardson TH, Macur RE, Hamamura N, Jennings RD, Fouke BW, Reysenbach AL, Roberto F, Young M, Schwartz A, Boyd ES, Badger JH, Mathur EJ, Ortmann AC, Bateson M, Geesey G, Frazier M. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function. PLoS One 2010; 5:e9773. [PMID: 20333304 PMCID: PMC2841643 DOI: 10.1371/journal.pone.0009773] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Accepted: 02/25/2010] [Indexed: 01/07/2023] Open
Abstract
The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O2) control microbial community structure and function in YNP geothermal springs.
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Affiliation(s)
- William P. Inskeep
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
- * E-mail: (WPI); (DBR)
| | - Douglas B. Rusch
- J. Craig Venter Institute, Rockville, Maryland, United States of America
- * E-mail: (WPI); (DBR)
| | - Zackary J. Jay
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | | | - Mark A. Kozubal
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | | | - Richard E. Macur
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Natsuko Hamamura
- Center for Marine Environmental Studies, Ehime University, Matsuyama, Japan
| | - Ryan deM. Jennings
- Thermal Biology Institute and Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Bruce W. Fouke
- University of Illinois, Urbana, Illinois, United States of America
| | | | - Frank Roberto
- Idaho National Laboratory, Idaho Falls, Idaho, United States of America
| | - Mark Young
- Thermal Biology Institute and Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
| | - Ariel Schwartz
- Synthetic Genomics Inc., La Jolla, California, United States of America
| | - Eric S. Boyd
- Thermal Biology Institute and Department of Microbiology, Montana State University, Bozeman, Montana, United States of America
| | - Jonathan H. Badger
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Eric J. Mathur
- Synthetic Genomics Inc., La Jolla, California, United States of America
| | - Alice C. Ortmann
- Department of Marine Science, University of South Alabama, Mobile, Alabama, United States of America
| | - Mary Bateson
- Thermal Biology Institute and Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, United States of America
| | - Gill Geesey
- Thermal Biology Institute and Department of Microbiology, Montana State University, Bozeman, Montana, United States of America
| | - Marvin Frazier
- J. Craig Venter Institute, Rockville, Maryland, United States of America
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Tatusova T. Genomic databases and resources at the National Center for Biotechnology Information. Methods Mol Biol 2010; 609:17-44. [PMID: 20221911 DOI: 10.1007/978-1-60327-241-4_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The National Center for Biotechnology Information (NCBI), as a primary public repository of genomic sequence data, collects and maintains enormous amounts of heterogeneous data. Data for genomes, genes, gene expressions, gene variation, gene families, proteins, and protein domains are integrated with the analytical, search, and retrieval resources through the NCBI Web site. Entrez, a text-based search and retrieval system, provides a fast and easy way to navigate across diverse biological databases.Customized genomic BLAST enables sequence similarity searches against a special collection of organism-specific sequence data and viewing the resulting alignments within a genomic context using NCBI's genome browser, Map Viewer.Comparative genome analysis tools lead to further understanding of evolutionary processes, quickening the pace of discovery.
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Study of the distribution of autotrophic CO2 fixation cycles in Crenarchaeota. Microbiology (Reading) 2010; 156:256-269. [DOI: 10.1099/mic.0.034298-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Two new autotrophic carbon fixation cycles have been recently described in Crenarchaeota. The 3-hydroxypropionate/4-hydroxybutyrate cycle using acetyl-coenzyme A (CoA)/propionyl-CoA carboxylase as the carboxylating enzyme has been identified for (micro)aerobic members of the Sulfolobales. The dicarboxylate/4-hydroxybutyrate cycle using oxygen-sensitive pyruvate synthase and phosphoenolpyruvate carboxylase as carboxylating enzymes has been found in members of the anaerobic Desulfurococcales and Thermoproteales. However, Sulfolobales include anaerobic and Desulfurococcales aerobic autotrophic representatives, raising the question of which of the two cycles they use. We studied the mechanisms of autotrophic CO2 fixation in the strictly anaerobic Stygiolobus azoricus (Sulfolobales) and in the facultatively aerobic Pyrolobus fumarii (Desulfurococcales). The activities of all enzymes of the 3-hydroxypropionate/4-hydroxybutyrate cycle were found in the anaerobic S. azoricus. In contrast, the aerobic or denitrifying P. fumarii possesses all enzyme activities of the dicarboxylate/4-hydroxybutyrate cycle. We conclude that autotrophic Crenarchaeota use one of the two cycles, and that their distribution correlates with the 16S rRNA-based phylogeny of this group, rather than with the aerobic or anaerobic lifestyle.
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Yokobori SI, Itoh T, Yoshinari S, Nomura N, Sako Y, Yamagishi A, Oshima T, Kita K, Watanabe YI. Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene. BMC Evol Biol 2009; 9:198. [PMID: 19671140 PMCID: PMC2738675 DOI: 10.1186/1471-2148-9-198] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Accepted: 08/11/2009] [Indexed: 01/13/2023] Open
Abstract
Background We previously found the first examples of splicing of archaeal pre-mRNAs for homologs of the eukaryotic CBF5 protein (also known as dyskerin in humans) in Aeropyrum pernix, Sulfolobus solfataricus, S. tokodaii, and S. acidocaldarirus, and also showed that crenarchaeal species in orders Desulfurococcales and Sulfolobales, except for Hyperthermus butylicus, Pyrodictium occultum, Pyrolobus fumarii, and Ignicoccus islandicus, contain the (putative) cbf5 intron. However, the exact timing of the intron insertion was not determined and verification of the putative secondary loss of the intron in some lineages was not performed. Results In the present study, we determined approximately two-thirds of the entire coding region of crenarchaeal Cbf5 sequences from 43 species. A phylogenetic analysis of our data and information from the available genome sequences suggested that the (putative) cbf5 intron existed in the common ancestor of the orders Desulfurococcales and Sulfolobales and that probably at least two independent lineages in the order Desulfurococcales lost the (putative) intron. Conclusion This finding is the first observation of a lineage-specific loss of a pre-mRNA intron in Archaea. As the insertion or deletion of introns in protein-coding genes in Archaea has not yet been seriously considered, our finding suggests the possible difficulty of accurately and completely predicting protein-coding genes in Archaea.
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Affiliation(s)
- Shin-ichi Yokobori
- Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo 192-0392, Japan.
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Cerdeño-Tárraga AM. Genome watch: What a scorcher! Nat Rev Microbiol 2009; 7:408-9. [PMID: 19444245 DOI: 10.1038/nrmicro2154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This month's Genome Watch looks at the publication of four hyperthermophilic archaeal genomes, three of which belong to the Crenarchaeota phylum and one of which belongs to the newly defined Nanoarchaeota phylum.
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Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J, Kyrpides N. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics 2009; 10:145. [PMID: 19341479 PMCID: PMC2678158 DOI: 10.1186/1471-2164-10-145] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Accepted: 04/02/2009] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Staphylothermus marinus is an anaerobic, sulfur-reducing peptide fermenter of the archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the three genomes. RESULTS The 1.57 Mbp genome of the hyperthermophilic crenarchaeote Staphylothermus marinus has been completely sequenced. The main energy generating pathways likely involve 2-oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. S. marinus possesses several enzymes not present in other crenarchaeotes including a sodium ion-translocating decarboxylase likely to be involved in amino acid degradation. S. marinus lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that have been sequenced -- Thermofilum pendens and Hyperthermus butylicus. Instead it has three operons similar to the mbh and mbx operons of Pyrococcus furiosus, which may play a role in sulfur reduction and/or hydrogen production. The two marine organisms, S. marinus and H. butylicus, possess more sodium-dependent transporters than T. pendens and use symporters for potassium uptake while T. pendens uses an ATP-dependent potassium transporter. T. pendens has adapted to a nutrient-rich environment while H. butylicus is adapted to a nutrient-poor environment, and S. marinus lies between these two extremes. CONCLUSION The three heterotrophic sulfur-reducing crenarchaeotes have adapted to their habitats, terrestrial vs. marine, via their transporter content, and they have also adapted to environments with differing levels of nutrients. Despite the fact that they all use sulfur as an electron acceptor, they are likely to have different pathways for sulfur reduction.
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Affiliation(s)
- Iain J Anderson
- Genome Biology Program, Joint Genome Institute, Walnut Creek, USA.
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Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, Chen W, Deciu C, Hutchison D, Eads JR, Anderson A, Fernandes F, Szeto E, Lapidus A, Kyrpides NC, Saier MH, Richardson PM, Rachel R, Huber H, Eisen JA, Koonin EV, Keller M, Stetter KO. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol 2008; 9:R158. [PMID: 19000309 PMCID: PMC2614490 DOI: 10.1186/gb-2008-9-11-r158] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 10/21/2008] [Accepted: 11/10/2008] [Indexed: 01/03/2023] Open
Abstract
Sequencing of the complete genome of Ignicoccus hospitalis gives insight into its association with another species of Archaea, Nanoarchaeum equitans. Background The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea. Little is known about the mechanisms that enable this relationship. Results We sequenced the complete genome of I. hospitalis and found it to be the smallest among independent, free-living organisms. A comparative genomic reconstruction suggests that the I. hospitalis lineage has lost most of the genes associated with a heterotrophic metabolism that is characteristic of most of the Crenarchaeota. A streamlined genome is also suggested by a low frequency of paralogs and fragmentation of many operons. However, this process appears to be partially balanced by lateral gene transfer from archaeal and bacterial sources. Conclusions A combination of genomic and cellular features suggests highly efficient adaptation to the low energy yield of sulfur-hydrogen respiration and efficient inorganic carbon and nitrogen assimilation. Evidence of lateral gene exchange between N. equitans and I. hospitalis indicates that the relationship has impacted both genomes. This association is the simplest symbiotic system known to date and a unique model for studying mechanisms of interspecific relationships at the genomic and metabolic levels.
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Affiliation(s)
- Mircea Podar
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA.
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31
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Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct 2007; 2:33. [PMID: 18042280 PMCID: PMC2222616 DOI: 10.1186/1745-6150-2-33] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2007] [Accepted: 11/27/2007] [Indexed: 12/29/2022] Open
Abstract
Background An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in Clusters of Orthologous Groups of proteins (COGs). Rapid accumulation of genome sequences creates opportunities for refining COGs but also represents a challenge because of error amplification. One of the practical strategies involves construction of refined COGs for phylogenetically compact subsets of genomes. Results New Archaeal Clusters of Orthologous Genes (arCOGs) were constructed for 41 archaeal genomes (13 Crenarchaeota, 27 Euryarchaeota and one Nanoarchaeon) using an improved procedure that employs a similarity tree between smaller, group-specific clusters, semi-automatically partitions orthology domains in multidomain proteins, and uses profile searches for identification of remote orthologs. The annotation of arCOGs is a consensus between three assignments based on the COGs, the CDD database, and the annotations of homologs in the NR database. The 7538 arCOGs, on average, cover ~88% of the genes in a genome compared to a ~76% coverage in COGs. The finer granularity of ortholog identification in the arCOGs is apparent from the fact that 4538 arCOGs correspond to 2362 COGs; ~40% of the arCOGs are new. The archaeal gene core (protein-coding genes found in all 41 genome) consists of 166 arCOGs. The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. The Last Archaeal Common Ancestor (LACA) is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for the last common ancestors of Crenarchaeota and Euryarchaeota, respectively. It is inferred that LACA was a chemoautotrophic hyperthermophile that, in addition to the core archaeal functions, encoded more idiosyncratic systems, e.g., the CASS systems of antivirus defense and some toxin-antitoxin systems. Conclusion The arCOGs provide a convenient, flexible framework for functional annotation of archaeal genomes, comparative genomics and evolutionary reconstructions. Genomic reconstructions suggest that the last common ancestor of archaea might have been (nearly) as advanced as the modern archaeal hyperthermophiles. ArCOGs and related information are available at: . Reviewers This article was reviewed by Peer Bork, Patrick Forterre, and Purificacion Lopez-Garcia.
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Affiliation(s)
- Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Galperin MY. Mycobacterial genomes for all tastes: from BCG to biodegradation of naphtalene and pyrene. Environ Microbiol 2007; 9:839-45. [PMID: 17359256 DOI: 10.1111/j.1462-2920.2007.01275.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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Robinson NP, Bell SD. Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes. Proc Natl Acad Sci U S A 2007; 104:5806-11. [PMID: 17392430 PMCID: PMC1851573 DOI: 10.1073/pnas.0700206104] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In all three domains of life, DNA replication begins at specialized loci termed replication origins. In bacteria, replication initiates from a single, clearly defined site. In contrast, eukaryotic organisms exploit a multitude of replication origins, dividing their genomes into an array of short contiguous units. Recently, the multiple replication origin paradigm has also been demonstrated within the archaeal domain of life, with the discovery that the hyperthermophilic archaeon Sulfolobus has three replication origins. However, the evolutionary mechanism driving the progression from single to multiple origin usage remains unclear. Here, we demonstrate that Aeropyrum pernix, a distant relative of Sulfolobus, has two origins. Comparison with the Sulfolobus origins provides evidence for evolution of replicon complexity by capture of extrachromosomal genetic elements. We additionally identify a previously unrecognized candidate archaeal initiator protein that is distantly related to eukaryotic Cdt1. Our data thus provide evidence that horizontal gene transfer, in addition to its well-established role in contributing to the information content of chromosomes, may fundamentally alter the manner in which the host chromosome is replicated.
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Affiliation(s)
- Nicholas P. Robinson
- Medical Research Council Cancer Cell Unit, Hutchison Medical Research Council Research Center, Hills Road, Cambridge CB2 0XZ, United Kingdom
- To whom correspondence may be addressed. E-mail: or
| | - Stephen D. Bell
- Medical Research Council Cancer Cell Unit, Hutchison Medical Research Council Research Center, Hills Road, Cambridge CB2 0XZ, United Kingdom
- To whom correspondence may be addressed. E-mail: or
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