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Singh S, Zhang J, Huber TD, Sunkara M, Hurley K, Goff RD, Wang G, Zhang W, Liu C, Rohr J, Van Lanen SG, Morris AJ, Thorson JS. Facile Chemoenzymatic Strategies for the Synthesis and Utilization ofS-Adenosyl-L-Methionine Analogues. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308272] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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152
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Randich AM, Cuello LG, Wanderling SS, Perozo E. Biochemical and structural analysis of the hyperpolarization-activated K(+) channel MVP. Biochemistry 2014; 53:1627-36. [PMID: 24490868 PMCID: PMC3985891 DOI: 10.1021/bi4014243] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
In
contrast to the majority of voltage-gated ion channels, hyperpolarization-activated
channels remain closed at depolarizing potentials and are activated
at hyperpolarizing potentials. The basis for this reverse polarity
is thought to be a result of differences in the way the voltage-sensing
domain (VSD) couples to the pore domain. In the absence of structural
data, the molecular mechanism of this reverse polarity coupling remains
poorly characterized. Here we report the characterization of the structure
and local dynamics of the closed activation gate (lower S6 region)
of MVP, a hyperpolarization-activated potassium channel from Methanococcus jannaschii, by electron paramagnetic resonance
(EPR) spectroscopy. We show that a codon-optimized version of MVP
has high expression levels in Escherichia coli, is
purified as a stable tetramer, and exhibits expected voltage-dependent
activity when reconstituted in liposomes. EPR analysis of the mid
to lower S6 region revealed positions exhibiting strong spin–spin
coupling, indicating that the activation gate of MVP is closed at
0 mV. A comparison of local environmental parameters along the activation
gate for MVP and KcsA indicates that MVP adopts a different closed
conformation. These structural details set the stage for future evaluations
of reverse electromechanical coupling in MVP.
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Affiliation(s)
- Amelia M Randich
- Department of Biochemistry and Molecular Biology, The University of Chicago , Chicago, Illinois 60637, United States
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153
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Towards a computational model of a methane producing archaeum. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:898453. [PMID: 24729742 PMCID: PMC3960522 DOI: 10.1155/2014/898453] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 12/18/2013] [Indexed: 11/17/2022]
Abstract
Progress towards a complete model of the methanogenic archaeum Methanosarcina acetivorans is reported. We characterized size distribution of the cells using differential interference contrast microscopy, finding them to be ellipsoidal with mean length and width of 2.9 μm and 2.3 μm, respectively, when grown on methanol and 30% smaller when grown on acetate. We used the single molecule pull down (SiMPull) technique to measure average copy number of the Mcr complex and ribosomes. A kinetic model for the methanogenesis pathways based on biochemical studies and recent metabolic reconstructions for several related methanogens is presented. In this model, 26 reactions in the methanogenesis pathways are coupled to a cell mass production reaction that updates enzyme concentrations. RNA expression data (RNA-seq) measured for cell cultures grown on acetate and methanol is used to estimate relative protein production per mole of ATP consumed. The model captures the experimentally observed methane production rates for cells growing on methanol and is most sensitive to the number of methyl-coenzyme-M reductase (Mcr) and methyl-tetrahydromethanopterin:coenzyme-M methyltransferase (Mtr) proteins. A draft transcriptional regulation network based on known interactions is proposed which we intend to integrate with the kinetic model to allow dynamic regulation.
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154
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Archaeal genome guardians give insights into eukaryotic DNA replication and damage response proteins. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:206735. [PMID: 24701133 PMCID: PMC3950489 DOI: 10.1155/2014/206735] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 09/27/2013] [Accepted: 11/29/2013] [Indexed: 12/28/2022]
Abstract
As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.
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155
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Borodovsky M, Lomsadze A. Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite. ACTA ACUST UNITED AC 2014; 32:Unit 1E.7.. [PMID: 24510847 DOI: 10.1002/9780471729259.mc01e07s32] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This unit describes how to use several gene-finding programs from the GeneMark line developed for finding protein-coding ORFs in genomic DNA of prokaryotic species, in genomic DNA of eukaryotic species with intronless genes, in genomes of viruses and phages, and in prokaryotic metagenomic sequences, as well as in EST sequences with spliced-out introns. These bioinformatics tools were demonstrated to have state-of-the-art accuracy, and have been frequently used for gene annotation in novel nucleotide sequences. An additional advantage of these sequence-analysis tools is that the problem of algorithm parameterization is solved automatically, with parameters estimated by iterative self-training (unsupervised training).
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157
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Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206-14. [PMID: 24293654 PMCID: PMC3965101 DOI: 10.1093/nar/gkt1226] [Citation(s) in RCA: 3141] [Impact Index Per Article: 314.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/04/2013] [Accepted: 11/05/2013] [Indexed: 01/12/2023] Open
Abstract
In 2004, the SEED (http://pubseed.theseed.org/) was created to provide consistent and accurate genome annotations across thousands of genomes and as a platform for discovering and developing de novo annotations. The SEED is a constantly updated integration of genomic data with a genome database, web front end, API and server scripts. It is used by many scientists for predicting gene functions and discovering new pathways. In addition to being a powerful database for bioinformatics research, the SEED also houses subsystems (collections of functionally related protein families) and their derived FIGfams (protein families), which represent the core of the RAST annotation engine (http://rast.nmpdr.org/). When a new genome is submitted to RAST, genes are called and their annotations are made by comparison to the FIGfam collection. If the genome is made public, it is then housed within the SEED and its proteins populate the FIGfam collection. This annotation cycle has proven to be a robust and scalable solution to the problem of annotating the exponentially increasing number of genomes. To date, >12 000 users worldwide have annotated >60 000 distinct genomes using RAST. Here we describe the interconnectedness of the SEED database and RAST, the RAST annotation pipeline and updates to both resources.
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Affiliation(s)
- Ross Overbeek
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Robert Olson
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Gordon D. Pusch
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Gary J. Olsen
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - James J. Davis
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Terry Disz
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Robert A. Edwards
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Svetlana Gerdes
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Bruce Parrello
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Maulik Shukla
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Veronika Vonstein
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Alice R. Wattam
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Fangfang Xia
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
| | - Rick Stevens
- Fellowship for Interpretation of Genomes, Burr Ridge, IL 60527, USA, Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA, Computation Institute, University of Chicago, Chicago, IL 60637, USA, Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA, Department of Computer Science, San Diego State University, San Diego, CA 92182, USA, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24060, USA, Computing, Environment and Life Sciences, Argonne National Laboratory, Argonne, IL 60439, USA and Department of Computer Science, University of Chicago, Chicago, IL 60637, USA
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158
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Vöhringer-Martinez E, Link O, Lugovoy E, Siefermann KR, Wiederschein F, Grubmüller H, Abel B. Hydrogen bond dynamics of superheated water and methanol by ultrafast IR-pump and EUV-photoelectron probe spectroscopy. Phys Chem Chem Phys 2014; 16:19365-75. [DOI: 10.1039/c4cp02063d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Snapshot of superheated water 40 ps after fs-IR laser excitation; representative aggregates formed during the simulation (close-up) compared to one obtained from superheated methanol phase (inset).
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Affiliation(s)
- E. Vöhringer-Martinez
- Departamento de Físico-Química
- Facultad de Ciencias Químicas
- Universidad de Concepción
- Concepción, Chile
| | - O. Link
- Institut für Physikalische Chemie
- Georg August Universität Göttingen
- Göttingen, Germany
| | - E. Lugovoy
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig, Germany
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
- 04103 Leipzig, Germany
| | - K. R. Siefermann
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig, Germany
| | - F. Wiederschein
- Max-Planck-Institut für biophysikalische Chemie
- 37077 Göttingen, Germany
| | - H. Grubmüller
- Max-Planck-Institut für biophysikalische Chemie
- 37077 Göttingen, Germany
| | - B. Abel
- Leibniz-Institute of Surface Modification (IOM)
- 04318 Leipzig, Germany
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie
- Universität Leipzig
- 04103 Leipzig, Germany
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159
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Identification of a 5'-deoxyadenosine deaminase in Methanocaldococcus jannaschii and its possible role in recycling the radical S-adenosylmethionine enzyme reaction product 5'-deoxyadenosine. J Bacteriol 2013; 196:1064-72. [PMID: 24375099 DOI: 10.1128/jb.01308-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterize here the MJ1541 gene product from Methanocaldococcus jannaschii, an enzyme that was annotated as a 5'-methylthioadenosine/S-adenosylhomocysteine deaminase (EC 3.5.4.31/3.5.4.28). The MJ1541 gene product catalyzes the conversion of 5'-deoxyadenosine to 5'-deoxyinosine as its major product but will also deaminate 5'-methylthioadenosine, S-adenosylhomocysteine, and adenosine to a small extent. On the basis of these findings, we are naming this new enzyme 5'-deoxyadenosine deaminase (DadD). The Km for 5'-deoxyadenosine was found to be 14.0 ± 1.2 μM with a kcat/Km of 9.1 × 10(9) M(-1) s(-1). Radical S-adenosylmethionine (SAM) enzymes account for nearly 2% of the M. jannaschii genome, where the major SAM derived products is 5'-deoxyadenosine. Since 5'-dA has been demonstrated to be an inhibitor of radical SAM enzymes; a pathway for removing this product must be present. We propose here that DadD is involved in the recycling of 5'-deoxyadenosine, whereupon the 5'-deoxyribose moiety of 5'-deoxyinosine is further metabolized to deoxyhexoses used for the biosynthesis of aromatic amino acids in methanogens.
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160
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Ereño-Orbea J, Oyenarte I, Martínez-Cruz LA. CBS domains: Ligand binding sites and conformational variability. Arch Biochem Biophys 2013; 540:70-81. [DOI: 10.1016/j.abb.2013.10.008] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/08/2013] [Accepted: 10/11/2013] [Indexed: 02/07/2023]
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161
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Maus I, Wibberg D, Stantscheff R, Cibis K, Eikmeyer FG, König H, Pühler A, Schlüter A. Complete genome sequence of the hydrogenotrophic Archaeon Methanobacterium sp. Mb1 isolated from a production-scale biogas plant. J Biotechnol 2013; 168:734-6. [DOI: 10.1016/j.jbiotec.2013.10.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 10/09/2013] [Indexed: 10/26/2022]
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162
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Pire C, Martínez-Espinosa RM, Pérez-Pomares F, Esclapez J, Bonete MJ. Ferredoxin-dependent glutamate synthase: involvement in ammonium assimilation in Haloferax mediterranei. Extremophiles 2013; 18:147-59. [DOI: 10.1007/s00792-013-0606-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 11/14/2013] [Indexed: 11/28/2022]
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163
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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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164
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Wang X, Yuan Y, Teng M, Niu L, Gao Y. Crystallization and preliminary X-ray diffraction analysis of MJ0458, an adenylate kinase from Methanocaldococcus jannaschii. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1272-4. [PMID: 24192367 DOI: 10.1107/s1744309113026638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 09/26/2013] [Indexed: 11/10/2022]
Abstract
Adenylate kinase plays a very important role in regulating adenylate species in the cell. Methanocaldococcus jannaschii is a rich resource of unique enzymes. Here, MJ0458, an adenylate kinase from M. jannaschii, was crystallized. A set of X-ray diffraction data to 2.70 Å resolution was collected on beamline BL-17U of the Shanghai Synchrotron Radiation Facility (SSRF). The crystal belonged to space group P4(1)2(1)2 or P4(3)2(1)2. The unit-cell parameters were a = b = 76.18, c = 238.70 Å, α = β = γ = 90°.
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Affiliation(s)
- Xiao Wang
- School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, People's Republic of China
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165
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Parthasarathy A, Kahnt J, Chowdhury NP, Buckel W. Phenylalanine catabolism in Archaeoglobus fulgidus VC-16. Arch Microbiol 2013; 195:781-97. [DOI: 10.1007/s00203-013-0925-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/29/2013] [Accepted: 08/31/2013] [Indexed: 01/06/2023]
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166
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Mardanov AV, Ravin NV. The impact of genomics on research in diversity and evolution of archaea. BIOCHEMISTRY (MOSCOW) 2013; 77:799-812. [PMID: 22860902 DOI: 10.1134/s0006297912080019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Since the definition of archaea as a separate domain of life along with bacteria and eukaryotes, they have become one of the most interesting objects of modern microbiology, molecular biology, and biochemistry. Sequencing and analysis of archaeal genomes were especially important for studies on archaea because of a limited availability of genetic tools for the majority of these microorganisms and problems associated with their cultivation. Fifteen years since the publication of the first genome of an archaeon, more than one hundred complete genome sequences of representatives of different phylogenetic groups have been determined. Analysis of these genomes has expanded our knowledge of biology of archaea, their diversity and evolution, and allowed identification and characterization of new deep phylogenetic lineages of archaea. The development of genome technologies has allowed sequencing the genomes of uncultivated archaea directly from enrichment cultures, metagenomic samples, and even from single cells. Insights have been gained into the evolution of key biochemical processes in archaea, such as cell division and DNA replication, the role of horizontal gene transfer in the evolution of archaea, and new relationships between archaea and eukaryotes have been revealed.
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Affiliation(s)
- A V Mardanov
- Laboratory of Molecular Cloning, Centre Bioengineering, Russian Academy of Sciences, pr. 60-let Oktyabrya 7-1, 117312 Moscow, Russia
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167
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Xiao KQ, Bao P, Bao QL, Jia Y, Huang FY, Su JQ, Zhu YG. Quantitative analyses of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large-subunit genes (cbbL) in typical paddy soils. FEMS Microbiol Ecol 2013; 87:89-101. [DOI: 10.1111/1574-6941.12193] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/12/2013] [Accepted: 08/20/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Ke-Qing Xiao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Peng Bao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Qiong-Li Bao
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
| | - Yan Jia
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- University of Chinese Academy of Sciences; Beijing China
| | - Fu-Yi Huang
- University of Chinese Academy of Sciences; Beijing China
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology; Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; Beijing China
- Key Lab of Urban Environment and Health; Institute of Urban Environment; Chinese Academy of Sciences; Xiamen China
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168
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Shen-Miller J, Lindner P, Xie Y, Villa S, Wooding K, Clarke SG, Loo RRO, Loo JA. Thermal-stable proteins of fruit of long-living Sacred Lotus Nelumbo nucifera Gaertn var. China Antique. TROPICAL PLANT BIOLOGY 2013; 6:10.1007/s12042-013-9124-2. [PMID: 24363819 PMCID: PMC3869599 DOI: 10.1007/s12042-013-9124-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Single-seeded fruit of the sacred lotus Nelumbo nucifera Gaertn var. China Antique from NE China have viability as long as ~1300 years determined by direct radiocarbon-dating, having a germination rate of 84%. The pericarp, a fruit tissue that encloses the single seeds of Nelumbo, is considered one of the major factors that contribute to fruit longevity. Proteins that are heat stable and have protective function may be equally important to seed viability. We show proteins of Nelumbo fruit that are able to withstand heating, 31% of which remained soluble in the 110°C-treated embryo-axis of a 549-yr-old fruit and 76% retained fluidity in its cotyledons. Genome of Nelumbo is published. The amino-acid sequences of 11 "thermal proteins" (soluble at 100°C) of modern Nelumbo embryo-axes and cotyledons, identified by mass spectrometry, Western blot and bioassay, are assembled and aligned with those of an archaeal-hyperthermophile Methancaldococcus jannaschii (Mj; an anaerobic methanogen having a growth optimum of 85°C) and with five mesophile angiosperms. These thermal proteins have roles in protection and repair under stress. More than half of the Nelumbo thermal proteins (55%) are present in the archaean Mj, indicating their long-term durability and history. One Nelumbo protein-repair enzyme exhibits activity at 100°C, having a higher heat-tolerance than that of Arabidopsis. A list of 30 sequenced but unassembled thermal proteins of Nelumbo is supplemented.
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Affiliation(s)
- J Shen-Miller
- IGPP Center for the Study of Evolution and Origin of Life, Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Geology Building, Room 5676, 595 Charles E. Young Drive East, Los Angeles, CA 90095-1567, USA, Telephone: (310) 825-2891, ,
| | - Petra Lindner
- Lehrstuhl Mikrobiologie Regensburg University Universitat Str. 31 93053 Regensburg, Germany
| | - Yongming Xie
- Department of Chemistry and Biochemistry University of California, Los Angeles 402 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1569, USA
| | - Sarah Villa
- Department of Chemistry and Biochemistry University of California, Los Angeles 640 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1570, USA
| | - Kerry Wooding
- Department of Chemistry and Biochemistry University of California, Los Angeles 402 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1569, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry University of California, Los Angeles 640 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1570, USA
| | - Rachel R O Loo
- Department of Chemistry and Biochemistry University of California, Los Angeles 402 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1569, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry University of California, Los Angeles 402 Boyer Hall, Hilgard Avenue Los Angeles, CA 90095-1569, USA
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169
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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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170
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Padmanabhan B, Yokoyama S, Bessho Y. Crystal structure of putative CbiT from Methanocaldococcus jannaschii: an intermediate enzyme activity in cobalamin (vitamin B12) biosynthesis. BMC STRUCTURAL BIOLOGY 2013; 13:10. [PMID: 23688113 PMCID: PMC3672029 DOI: 10.1186/1472-6807-13-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 05/10/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND In the anaerobic pathway of cobalamin (vitamin B12) synthesis, the CbiT enzyme plays two roles, as a cobalt-precorrin-7 C15-methyltransferase and a C12-decarboxylase, to produce the intermediate, cobalt-precorrin 8. RESULTS The primary structure of the hypothetical protein MJ0391, from Methanocaldococcus jannaschii, suggested that MJ0391 is a putative CbiT. Here, we report the crystal structure of MJ0391, solved by the MAD procedure and refined to final R-factor and R-free values of 19.8 & 27.3%, respectively, at 2.3 Å resolution. The asymmetric unit contains two NCS molecules, and the intact tetramer generated by crystallographic symmetry may be functionally important. The overall tertiary structure and the tetrameric arrangements are highly homologous to those found in MT0146/CbiT from Methanobacterium thermoautotrophicum. CONCLUSIONS The conservation of functional residues in the binding site for the co-factor, AdoMet, and in the putative precorrin-7 binding pocket suggested that MJ0391 may also possess CbiT activity. The putative function of MJ0391 is discussed, based on structural homology.
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Affiliation(s)
- Balasundaram Padmanabhan
- Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bangalore 560029, India,RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Shigeyuki Yokoyama
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan,Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshitaka Bessho
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan,RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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171
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Blainey PC. The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev 2013; 37:407-27. [PMID: 23298390 PMCID: PMC3878092 DOI: 10.1111/1574-6976.12015] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 11/28/2012] [Accepted: 12/20/2012] [Indexed: 01/08/2023] Open
Abstract
Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. Experimental strategies transcending specific methodologies are identified and organized as a road map for future studies in single-cell genomics of environmental microorganisms. Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology.
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172
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Lee SJ, Lee SJ, Lee DW. Design and development of synthetic microbial platform cells for bioenergy. Front Microbiol 2013; 4:92. [PMID: 23626588 PMCID: PMC3630320 DOI: 10.3389/fmicb.2013.00092] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 04/03/2013] [Indexed: 12/26/2022] Open
Abstract
The finite reservation of fossil fuels accelerates the necessity of development of renewable energy sources. Recent advances in synthetic biology encompassing systems biology and metabolic engineering enable us to engineer and/or create tailor made microorganisms to produce alternative biofuels for the future bio-era. For the efficient transformation of biomass to bioenergy, microbial cells need to be designed and engineered to maximize the performance of cellular metabolisms for the production of biofuels during energy flow. Toward this end, two different conceptual approaches have been applied for the development of platform cell factories: forward minimization and reverse engineering. From the context of naturally minimized genomes,non-essential energy-consuming pathways and/or related gene clusters could be progressively deleted to optimize cellular energy status for bioenergy production. Alternatively, incorporation of non-indigenous parts and/or modules including biomass-degrading enzymes, carbon uptake transporters, photosynthesis, CO2 fixation, and etc. into chassis microorganisms allows the platform cells to gain novel metabolic functions for bioenergy. This review focuses on the current progress in synthetic biology-aided pathway engineering in microbial cells and discusses its impact on the production of sustainable bioenergy.
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Affiliation(s)
- Sang Jun Lee
- Systems and Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology Daejeon, South Korea
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173
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Living side by side with a virus: characterization of two novel plasmids from Thermococcus prieurii, a host for the spindle-shaped virus TPV1. Appl Environ Microbiol 2013; 79:3822-8. [PMID: 23584787 DOI: 10.1128/aem.00525-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial cells often serve as an evolutionary battlefield for different types of mobile genetic elements, such as viruses and plasmids. Here, we describe the isolation and characterization of two new archaeal plasmids which share the host with the spindle-shaped Thermococcus prieurii virus 1 (TPV1). The two plasmids, pTP1 and pTP2, were isolated from the hyperthermophilic archaeon Thermococcus prieurii (phylum Euryarchaeota), a resident of a deep-sea hydrothermal vent located at the East Pacific Rise at 2,700-m depth (7°25'24 S, 107°47'66 W). pTP1 (3.1 kb) and pTP2 (2.0 kb) are among the smallest known plasmids of hyperthermophilic archaea, and both are predicted to replicate via the rolling-circle mechanism. The two plasmids and the virus TPV1 do not have a single gene in common and stably propagate in infected cells without any apparent antagonistic effect on each other. The compatibility of the three genetic elements and the high copy number of pTP1 and pTP2 plasmids (50 copies/cell) might be useful for developing new genetic tools for studying hyperthermophilic euryarchaea and their viruses.
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174
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Cai F, Axen SD, Kerfeld CA. Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. RNA Biol 2013; 10:687-93. [PMID: 23628889 DOI: 10.4161/rna.24571] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Members of the phylum Cyanobacteria inhabit ecologically diverse environments. However, the CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPR associated genes), an extremely adaptable defense system, has not been surveyed in this phylum. We analyzed 126 cyanobacterial genomes and, surprisingly, found CRISPR-Cas in the majority except the marine subclade (Synechococcus and Prochlorococcus), in which cyanophages are a known force shaping their evolution. Multiple observations of CRISPR loci in the absence of cas1/cas2 genes may represent an early stage of losing a CRISPR-Cas locus. Our findings reveal the widespread distribution of their role in the phylum Cyanobacteria and provide a first step to systematically understanding CRISPR-Cas systems in cyanobacteria.
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Affiliation(s)
- Fei Cai
- U.S. Department of Energy-Joint Genome Institute, Walnut Creek, CA, USA
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175
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Quinlan RA, Zhang Y, Lansbury A, Williamson I, Pohl E, Sun F. Changes in the quaternary structure and function of MjHSP16.5 attributable to deletion of the IXI motif and introduction of the substitution, R107G, in the α-crystallin domain. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120327. [PMID: 23530263 PMCID: PMC3638399 DOI: 10.1098/rstb.2012.0327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The archael small heat-shock protein (sHSP), MjHSP16.5, forms a 24-subunit oligomer with octahedral symmetry. Here, we demonstrate that the IXI motif present in the C-terminal domain is necessary for the oligomerization of MjHSP16.5. Removal increased the in vitro chaperone activity with citrate synthase as the client protein. Less predictable were the effects of the R107G substitution in MjHSP16.5 because of the differences in the oligomerization of metazoan and non-metazoan sHSPs. We present the crystal structure for MjHSP16.5 R107G and compare this with an improved (2.5 Å) crystal structure for wild-type (WT) MjHSP16.5. Although no significant structural differences were found in the crystal, using cryo-electron microscopy, we identified two 24mer species with octahedral symmetry for the WT MjHSP16.5 both at room temperature and at 60°C, all showing two major species with the same diameter of 12.4 nm. Similarly, at room temperature, there are also two kinds of 12.4 nm oligomers for R107G MjHSP16.5, but in the 60°C sample, a larger 24mer species with a diameter of 13.6 nm was observed with significant changes in the fourfold symmetry axis and dimer–dimer interface. This highly conserved arginine, therefore, contributes to the quaternary organization of non-metazoan sHSP oligomers. Potentially, the R107G substitution has functional consequences as R107G MjHSP16.5 was far superior to the WT protein in protecting βL-crystallin against heat-induced aggregation.
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Affiliation(s)
- Roy A Quinlan
- Biophysical Sciences Institute, University of Durham, , South Road, Durham DH1 LE, UK
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176
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Ribonucleoproteins in archaeal pre-rRNA processing and modification. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:614735. [PMID: 23554567 PMCID: PMC3608112 DOI: 10.1155/2013/614735] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/09/2013] [Accepted: 01/15/2013] [Indexed: 12/27/2022]
Abstract
Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures.
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177
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Guo X, Yin H, Cong J, Dai Z, Liang Y, Liu X. RubisCO gene clusters found in a metagenome microarray from acid mine drainage. Appl Environ Microbiol 2013; 79:2019-26. [PMID: 23335778 PMCID: PMC3592212 DOI: 10.1128/aem.03400-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 01/11/2013] [Indexed: 11/20/2022] Open
Abstract
The enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (cbbL). Forty-six cbbL-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities of cbbL and the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny.
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Affiliation(s)
- Xue Guo
- School of Mineral Processing and Bioengineering, Central South University, Changsha, People's Republic of China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, People's Republic of China
| | - Huaqun Yin
- School of Mineral Processing and Bioengineering, Central South University, Changsha, People's Republic of China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, People's Republic of China
| | - Jing Cong
- School of Mineral Processing and Bioengineering, Central South University, Changsha, People's Republic of China
| | - Zhimin Dai
- School of Mineral Processing and Bioengineering, Central South University, Changsha, People's Republic of China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, People's Republic of China
| | - Yili Liang
- School of Mineral Processing and Bioengineering, Central South University, Changsha, People's Republic of China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, People's Republic of China
| | - Xueduan Liu
- School of Mineral Processing and Bioengineering, Central South University, Changsha, People's Republic of China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, People's Republic of China
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178
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Wrede C, Walbaum U, Ducki A, Heieren I, Hoppert M. Localization of Methyl-Coenzyme M reductase as metabolic marker for diverse methanogenic Archaea. ARCHAEA (VANCOUVER, B.C.) 2013; 2013:920241. [PMID: 23533332 PMCID: PMC3596918 DOI: 10.1155/2013/920241] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/09/2013] [Indexed: 11/23/2022]
Abstract
Methyl-Coenzyme M reductase (MCR) as key enzyme for methanogenesis as well as for anaerobic oxidation of methane represents an important metabolic marker for both processes in microbial biofilms. Here, the potential of MCR-specific polyclonal antibodies as metabolic marker in various methanogenic Archaea is shown. For standard growth conditions in laboratory culture, the cytoplasmic localization of the enzyme in Methanothermobacter marburgensis, Methanothermobacter wolfei, Methanococcus maripaludis, Methanosarcina mazei, and in anaerobically methane-oxidizing biofilms is demonstrated. Under growth limiting conditions on nickel-depleted media, at low linear growth of cultures, a fraction of 50-70% of the enzyme was localized close to the cytoplasmic membrane, which implies "facultative" membrane association of the enzyme. This feature may be also useful for assessment of growth-limiting conditions in microbial biofilms.
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Affiliation(s)
- Christoph Wrede
- Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
- Hannover Medical School, Institute of Functional and Applied Anatomy, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Ulrike Walbaum
- Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
- Behavioral Ecology and Sociobiology Unit, German Primate Center, Kellnerweg 4, 37077 Göttingen, Germany
| | - Andrea Ducki
- Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
- School of Veterinary and Biomedical Sciences, Murdoch University, 90 South Street Murdoch, WA 6150, Australia
| | - Iris Heieren
- Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
| | - Michael Hoppert
- Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
- Courant Centre Geobiology, Georg-August-Universität Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany
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179
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Saengkerdsub S, Ricke SC. Ecology and characteristics of methanogenic archaea in animals and humans. Crit Rev Microbiol 2013; 40:97-116. [PMID: 23425063 DOI: 10.3109/1040841x.2013.763220] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, the molecular techniques used in animal-based-methanogen studies will be discussed along with how methanogens interact not only with other microorganisms but with their animal hosts as well. These methods not only indicate the diversity and levels of methanogens, but also provide insight on their ecological functions. Most molecular techniques have been based on either 16S rRNA genes or methyl-coenzyme M reductase, a ubiquitous enzyme in methanogens. The most predominant methanogens in animals belong to the genus Methanobrevibacter. Besides methanogens contributing to overall H2 balance, methanogens also have mutual interactions with other bacteria. In addition to shared metabolic synergism, the host animal retrieves additional energy from the diet when methanogens are co-colonized with other normal flora. By comparing genes in methanogens with other bacteria, possible gene transfer between methanogens and other bacteria in the same environments appears to occur. Finally, diets in conjunction with the genetics of methanogens and hosts may represent the biological framework that dictate the extent of methanogen prevalence in these ecosystems. In addition, host evolution including the immune system could serve as an additional selective pressure for methanogen colonization.
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Affiliation(s)
- Suwat Saengkerdsub
- Department of Food Science, Center for Food Safety, University of Arkansas , Fayetteville, AR , USA , and
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180
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Shi W, Xie S, Chen X, Sun S, Zhou X, Liu L, Gao P, Kyrpides NC, No EG, Yuan JS. Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications. PLoS Genet 2013; 9:e1003131. [PMID: 23326236 PMCID: PMC3542064 DOI: 10.1371/journal.pgen.1003131] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 10/15/2012] [Indexed: 02/01/2023] Open
Abstract
Metagenome analysis of the gut symbionts of three different insects was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. Grasshopper and cutworm gut symbionts were sequenced and compared with the previously identified metagenome of termite gut microbiota. These insect hosts represent three different insect orders and specialize on different food types. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH) enzymes relevant to lignocellulosic biomass degradation. Moreover, termite gut metabolome was more enriched with nitrogen fixation genes than those of grasshopper and cutworm gut, presumably due to the termite's adaptation to the high fiber and less nutritious food types. In order to evaluate and exploit the insect symbionts for biotechnology applications, we cloned and further characterized four biomass-degrading enzymes including one endoglucanase and one xylanase from both the grasshopper and cutworm gut symbionts. The results indicated that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host diet, and suggested that this relationship could be exploited for the discovery of symbionts and biocatalysts useful for biorefinery applications.
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Affiliation(s)
- Weibing Shi
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Shangxian Xie
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
- School of Life Sciences and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xueyan Chen
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
- Department of Veterinary Pathology, Texas A&M University, College Station, Texas, United States of America
| | - Su Sun
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Xin Zhou
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Lantao Liu
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Peng Gao
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Nikos C. Kyrpides
- DOE Joint Genomes Institute, Walnut Creek, California, United States of America
| | - En-Gyu No
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
| | - Joshua S. Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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181
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Jia B, Cheong GW, Zhang S. Multifunctional enzymes in archaea: promiscuity and moonlight. Extremophiles 2013; 17:193-203. [PMID: 23283522 DOI: 10.1007/s00792-012-0509-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 12/17/2012] [Indexed: 10/27/2022]
Abstract
Enzymes from many archaea colonizing extreme environments are of great interest because of their potential for various biotechnological processes and scientific value of evolution. Many enzymes from archaea have been reported to catalyze promiscuous reactions or moonlight in different functions. Here, we summarize known archaeal enzymes of both groups that include different kinds of proteins. Knowledge of their biochemical properties and three-dimensional structures has proved invaluable in understanding mechanism, application, and evolutionary implications of this manifestation. In addition, the review also summarizes the methods to unravel the extra function which almost was discovered serendipitously. The study of these amazing enzymes will provide clues to optimize protein engineering applications and how enzymes might have evolved on Earth.
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Affiliation(s)
- Baolei Jia
- College of Plant Sciences, Jilin University, Changchun, China.
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182
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Abstract
The aminoacyl-tRNA synthetases (aaRSs) are essential components of the protein synthesis machinery responsible for defining the genetic code by pairing the correct amino acids to their cognate tRNAs. The aaRSs are an ancient enzyme family believed to have origins that may predate the last common ancestor and as such they provide insights into the evolution and development of the extant genetic code. Although the aaRSs have long been viewed as a highly conserved group of enzymes, findings within the last couple of decades have started to demonstrate how diverse and versatile these enzymes really are. Beyond their central role in translation, aaRSs and their numerous homologs have evolved a wide array of alternative functions both inside and outside translation. Current understanding of the emergence of the aaRSs, and their subsequent evolution into a functionally diverse enzyme family, are discussed in this chapter.
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183
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Abstract
Archaea contain, both a functional proteasome and an ubiquitin-like protein conjugation system (termed sampylation) that is related to the ubiquitin proteasome system (UPS) of eukaryotes. Archaeal proteasomes have served as excellent models for understanding how proteins are degraded by the central energy-dependent proteolytic machine of eukaryotes, the 26S proteasome. While sampylation has only recently been discovered, it is thought to be linked to proteasome-mediated degradation in archaea. Unlike eukaryotes, sampylation only requires an E1 enzyme homolog of the E1-E2-E3 ubiquitylation cascade to mediate protein conjugation. Furthermore, recent evidence suggests that archaeal and eurkaryotic E1 enzyme homologs can serve dual roles in mediating protein conjugation and activating sulfur for incorporation into biomolecules. The focus of this book chapter is the energy-dependent proteasome and sampylation systems of Archaea.
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Affiliation(s)
- Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611-0700, USA,
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184
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Jugder BE, Welch J, Aguey-Zinsou KF, Marquis CP. Fundamentals and electrochemical applications of [Ni–Fe]-uptake hydrogenases. RSC Adv 2013. [DOI: 10.1039/c3ra22668a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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185
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Robb FT, Lowe TM, Kelman Z. The modern "3G" age of archaeal molecular biology. Front Microbiol 2012; 3:430. [PMID: 23267357 PMCID: PMC3527003 DOI: 10.3389/fmicb.2012.00430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 12/06/2012] [Indexed: 11/13/2022] Open
Affiliation(s)
- Frank T Robb
- Institute of Marine and Environmental Technology Baltimore, MD, USA ; University of Maryland School of Medicine Baltimore, MD, USA
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186
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Wang Y, Xie JJ, Han Z, Liu JH, Liu XP. Expression, purification and biochemical characterization of Methanocaldococcus jannaschii DNA ligase. Protein Expr Purif 2012; 87:79-86. [PMID: 23147204 DOI: 10.1016/j.pep.2012.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 10/20/2012] [Accepted: 10/31/2012] [Indexed: 10/27/2022]
Abstract
We describe the biochemical characterization of Methanocaldococcus jannaschii (M. jannaschii) DNA ligase and its potential application in single nucleotide polymorphism (SNP) genotyping. The recombinant M. jannaschii DNA ligase is an ATP-dependent ligase. The ligase activity was dependent on metal ions of Mg(2+) and Mn(2+). The optimal concentrations of ATP cofactor and Mg(2+) ion were 0.01-2 and 10 mM, respectively. The optimal pH value for DNA ligation was 8.5. High concentrations of NaCl inhibited DNA ligation. The effects of mismatches on joining short oligonucleotides by M. jannaschii DNA ligase were fully characterized. The mismatches at the first position 5' to the nick inhibited ligation more than those at the first position 3' to the nick. The mismatches at other positions 5' to the nick (3rd to 7th sites) exhibited less inhibition on ligation. However, the introduction of a C/C mismatch at the third position 5' to the nick could completely inhibit the ligation of the terminal-mismatched nick of an oligonucleotide duplex by M. jannaschii DNA ligase. Therefore, introducing an additional mismatch at the third position 5' to the SNP site is a more effective approach in genotyping by M. jannaschii DNA ligase.
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Affiliation(s)
- You Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
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187
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Abstract
Extremely thermophilic microorganisms have been sources of thermostable and thermoactive enzymes for over 30 years. However, information and insights gained from genome sequences, in conjunction with new tools for molecular genetics, have opened up exciting new possibilities for biotechnological opportunities based on extreme thermophiles that go beyond single-step biotransformations. Although the pace for discovering novel microorganisms has slowed over the past two decades, genome sequence data have provided clues to novel biomolecules and metabolic pathways, which can be mined for a range of new applications. Furthermore, recent advances in molecular genetics for extreme thermophiles have made metabolic engineering for high temperature applications a reality.
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Affiliation(s)
- Andrew D Frock
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905
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188
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Popa E, Perera N, Kibédi-Szabó CZ, Guy-Evans H, Evans DR, Purcarea C. The smallest active carbamoyl phosphate synthetase was identified in the human gut archaeon Methanobrevibacter smithii. J Mol Microbiol Biotechnol 2012; 22:287-99. [PMID: 23107800 PMCID: PMC6158779 DOI: 10.1159/000342520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The genome of the major intestinal archaeon Methanobrevibacter smithii contains a complex gene system coding for carbamoyl phosphate synthetase (CPSase) composed of both full-length and reduced-size synthetase subunits. These ammonia-metabolizing enzymes could play a key role in controlling ammonia assimilation in M. smithii, affecting the metabolism of gut bacterial microbiota, with an impact on host obesity. In this study, we isolated and characterized the small (41 kDa) CPSase homolog from M. smithii. The gene was cloned and overexpressed in Escherichia coli, and the recombinant enzyme was purified in one step. Chemical cross-linking and size exclusion chromatography indicated a homodimeric/tetrameric structure, in accordance with a dimer-based CPSase activity and reaction mechanism. This small enzyme, MS-s, synthesized carbamoyl phosphate from ATP, bicarbonate, and ammonia and catalyzed the same ATP-dependent partial reactions observed for full-length CPSases. Steady-state kinetics revealed a high apparent affinity for ATP and ammonia. Sequence comparisons, molecular modeling, and kinetic studies suggest that this enzyme corresponds to one of the two synthetase domains of the full-length CPSase that catalyze the ATP-dependent phosphorylations involved in the three-step synthesis of carbamoyl phosphate. This protein represents the smallest naturally occurring active CPSase characterized thus far. The small M. smithii CPSase appears to be specialized for carbamoyl phosphate metabolism in methanogens.
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Affiliation(s)
- Elena Popa
- Department of Microbiology, Institute of Biology Bucharest, Romanian Academy, Bucharest 060031, Romania
| | - Nirosha Perera
- Department of Chemistry, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - Csaba Z. Kibédi-Szabó
- Department of Microbiology, Institute of Biology Bucharest, Romanian Academy, Bucharest 060031, Romania
| | - Hedeel Guy-Evans
- Department of Chemistry, Eastern Michigan University, Ypsilanti, MI 48197, USA
| | - David R. Evans
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Cristina Purcarea
- Department of Microbiology, Institute of Biology Bucharest, Romanian Academy, Bucharest 060031, Romania
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189
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Abstract
Archaea were, until recently, considered to be confined to specialized environments including those at high temperature, high salinity, extremes of pH and ambients that permit methanogenesis. Recently developed molecular methods for studying microbial ecology, which do not necessitate cell culturing, have demonstrated their presence in a wide variety of temperate and cold environments including agricultural and forest soils, fresh water lake sediments, marine picoplankton and deep-sea locations. These discoveries mark the beginning of a new era for investigating the Archaea and in particular their physiological and metabolic properties and their biological roles in complex microbial populations.
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190
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Crécy-Lagard VD, Phillips G, Grochowski LL, Yacoubi BE, Jenney F, Adams MWW, Murzin AG, White RH. Comparative genomics guided discovery of two missing archaeal enzyme families involved in the biosynthesis of the pterin moiety of tetrahydromethanopterin and tetrahydrofolate. ACS Chem Biol 2012; 7:1807-16. [PMID: 22931285 PMCID: PMC3500442 DOI: 10.1021/cb300342u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
C-1 carriers are essential cofactors in all domains of
life, and
in Archaea, these can be derivatives of tetrahydromethanopterin (H4-MPT) or tetrahydrofolate (H4-folate). Their synthesis
requires 6-hydroxymethyl-7,8-dihydropterin diphosphate (6-HMDP) as
the precursor, but the nature of pathways that lead to its formation
were unknown until the recent discovery of the GTP cyclohydrolase
IB/MptA family that catalyzes the first step, the conversion of GTP
to dihydroneopterin 2′,3′-cyclic phosphate or 7,8-dihydroneopterin
triphosphate [El Yacoubi, B.; et al. (2006) J. Biol. Chem., 281, 37586–37593
and Grochowski, L. L.; et al. (2007) Biochemistry46, 6658–6667]. Using a combination of comparative
genomics analyses, heterologous complementation tests, and in vitro assays, we show that the archaeal protein families
COG2098 and COG1634 specify two of the missing 6-HMDP synthesis enzymes.
Members of the COG2098 family catalyze the formation of 6-hydroxymethyl-7,8-dihydropterin
from 7,8-dihydroneopterin, while members of the COG1634 family catalyze
the formation of 6-HMDP from 6-hydroxymethyl-7,8-dihydropterin. The
discovery of these missing genes solves a long-standing mystery and
provides novel examples of convergent evolutions where proteins of
dissimilar architectures perform the same biochemical function.
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Affiliation(s)
- Valérie de Crécy-Lagard
- Department of Microbiology and
Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700,
United States
| | - Gabriela Phillips
- Department of Microbiology and
Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700,
United States
| | - Laura L. Grochowski
- Department
of Biochemistry (0308), Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United
States
| | - Basma El Yacoubi
- Department of Microbiology and
Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700,
United States
| | - Francis Jenney
- Department of Basic
Sciences,
Georgia Campus, Philadelphia College of Osteopathic Medicine, Suwanee, Georgia 30024, United States
| | - Michael W. W. Adams
- Department of Biochemistry and
Molecular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Alexey G. Murzin
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH,
U.K
| | - Robert H. White
- Department
of Biochemistry (0308), Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United
States
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191
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Ownership and sharing in synthetic biology: A ‘diverse ecology’ of the open and the proprietary? BIOSOCIETIES 2012. [DOI: 10.1057/biosoc.2012.3] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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192
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Unal B, Perry VR, Sheth M, Gomez-Alvarez V, Chin KJ, Nüsslein K. Trace elements affect methanogenic activity and diversity in enrichments from subsurface coal bed produced water. Front Microbiol 2012; 3:175. [PMID: 22590465 PMCID: PMC3349271 DOI: 10.3389/fmicb.2012.00175] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Accepted: 04/20/2012] [Indexed: 12/01/2022] Open
Abstract
Microbial methane from coal beds accounts for a significant and growing percentage of natural gas worldwide. Our knowledge of physical and geochemical factors regulating methanogenesis is still in its infancy. We hypothesized that in these closed systems, trace elements (as micronutrients) are a limiting factor for methanogenic growth and activity. Trace elements are essential components of enzymes or cofactors of metabolic pathways associated with methanogenesis. This study examined the effects of eight trace elements (iron, nickel, cobalt, molybdenum, zinc, manganese, boron, and copper) on methane production, on mcrA transcript levels, and on methanogenic community structure in enrichment cultures obtained from coal bed methane (CBM) well produced water samples from the Powder River Basin, Wyoming. Methane production was shown to be limited both by a lack of additional trace elements as well as by the addition of an overly concentrated trace element mixture. Addition of trace elements at concentrations optimized for standard media enhanced methane production by 37%. After 7 days of incubation, the levels of mcrA transcripts in enrichment cultures with trace element amendment were much higher than in cultures without amendment. Transcript levels of mcrA correlated positively with elevated rates of methane production in supplemented enrichments (R2 = 0.95). Metabolically active methanogens, identified by clone sequences of mcrA mRNA retrieved from enrichment cultures, were closely related to Methanobacterium subterraneum and Methanobacterium formicicum. Enrichment cultures were dominated by M. subterraneum and had slightly higher predicted methanogenic richness, but less diversity than enrichment cultures without amendments. These results suggest that varying concentrations of trace elements in produced water from different subsurface coal wells may cause changing levels of CBM production and alter the composition of the active methanogenic community.
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Affiliation(s)
- Burcu Unal
- Department of Microbiology, University of Massachusetts Amherst, MA, USA
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193
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Huang L. Unveiling the beauty of Archaea. SCIENCE CHINA. LIFE SCIENCES 2012; 55:375-6. [PMID: 22645081 DOI: 10.1007/s11427-012-4323-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Indexed: 11/30/2022]
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194
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Nau-Wagner G, Opper D, Rolbetzki A, Boch J, Kempf B, Hoffmann T, Bremer E. Genetic control of osmoadaptive glycine betaine synthesis in Bacillus subtilis through the choline-sensing and glycine betaine-responsive GbsR repressor. J Bacteriol 2012; 194:2703-14. [PMID: 22408163 PMCID: PMC3347207 DOI: 10.1128/jb.06642-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 02/27/2012] [Indexed: 11/20/2022] Open
Abstract
Synthesis of the compatible solute glycine betaine confers a considerable degree of osmotic stress tolerance to Bacillus subtilis. This osmoprotectant is produced through the uptake of the precursor choline via the osmotically inducible OpuB and OpuC ABC transporters and a subsequent two-step oxidation process by the GbsB and GbsA enzymes. We characterized a regulatory protein, GbsR, controlling the transcription of both the structural genes for the glycine betaine biosynthetic enzymes (gbsAB) and those for the choline-specific OpuB transporter (opuB) but not of that for the promiscuous OpuC transporter. GbsR acts genetically as a repressor and functions as an intracellular choline sensor. Spectroscopic analysis of the purified GbsR protein showed that it binds the inducer choline with an apparent K(D) (equilibrium dissociation constant) of approximately 165 μM. Based on the X-ray structure of a protein (Mj223) from Methanococcus jannaschii, a homology model for GbsR was derived. Inspection of this GbsR in silico model revealed a possible ligand-binding pocket for choline resembling those of known choline-binding sites present in solute receptors of microbial ABC transporters, e.g., that of the OpuBC ligand-binding protein of the OpuB ABC transporter. GbsR was not only needed to control gbsAB and opuB expression in response to choline availability but also required to genetically tune down glycine betaine production once cellular adjustment to high osmolarity has been achieved. The GbsR regulatory protein from B. subtilis thus records and integrates cellular and environmental signals for both the onset and the repression of the synthesis of the osmoprotectant glycine betaine.
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Affiliation(s)
- Gabriele Nau-Wagner
- Philipps-University Marburg, Department of Biology, Laboratory for Microbiology, Marburg, Germany
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195
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De Vrieze J, Hennebel T, Boon N, Verstraete W. Methanosarcina: the rediscovered methanogen for heavy duty biomethanation. BIORESOURCE TECHNOLOGY 2012; 112:1-9. [PMID: 22418081 DOI: 10.1016/j.biortech.2012.02.079] [Citation(s) in RCA: 435] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 02/13/2012] [Accepted: 02/16/2012] [Indexed: 05/07/2023]
Abstract
Anaerobic digestion is an important technology in the framework of renewable energy production. The anaerobic digestion system is susceptible to perturbations due to the sensitivity of the methanogens towards environmental factors. Currently, technology is evolving from conventional waste treatment, i.e. the removal of pollutants, to very intensive biogas production from concentrated wastes, in the framework of bio-energy production. In the latter configuration Methanosarcina species appear to be of crucial importance. Methanosarcina sp. are, compared to other methanogens, quite robust towards different impairments. They are reported to be tolerant to total ammonium concentrations up to 7000 mg L(-1), salt concentrations up to 18,000 mg Na(+)L(-1), a pH shock of 0.8-1.0 units and acetate concentrations up to 15,000 mg CODL(-1). The possibilities of Methanosarcina sp. as key organisms in specific types of anaerobic digestion systems are demonstrated in this review.
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Affiliation(s)
- Jo De Vrieze
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
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196
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Sequence fingerprints of enzyme specificities from the glycoside hydrolase family GH57. Extremophiles 2012; 16:497-506. [PMID: 22527043 DOI: 10.1007/s00792-012-0449-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 04/02/2012] [Indexed: 10/28/2022]
Abstract
The glycoside hydrolase family 57 (GH57) contains five well-established enzyme specificities: α-amylase, amylopullulanase, branching enzyme, 4-α-glucanotransferase and α-galactosidase. Around 700 GH57 members originate from Bacteria and Archaea, a substantial number being produced by thermophiles. An intriguing feature of family GH57 is that only slightly more than 2 % of its members (i.e., less than 20 enzymes) have already been biochemically characterized. The main goal of the present bioinformatics study was to retrieve from databases, and analyze in detail, sequences having clear features of the five GH57 enzyme specificities mentioned above. Of the 367 GH57 sequences, 56 were evaluated as α-amylases, 99 as amylopullulanases, 158 as branching enzymes, 46 as 4-α-glucanotransferases and 8 as α-galactosidases. Based on the analysis of collected sequences, sequence logos were created for each specificity and unique sequence features were identified within the logos. These features were proposed to define the so-called sequence fingerprints of GH57 enzyme specificities. Domain arrangements characteristic of the individual enzyme specificities as well as evolutionary relationships within the family GH57 are also discussed. The results of this study could find use in rational protein design of family GH57 amylolytic enzymes and also in the possibility of assigning a GH57 specificity to a hypothetical GH57 member prior to its biochemical characterization.
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197
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Baird NJ, Zhang J, Hamma T, Ferré-D'Amaré AR. YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops. RNA (NEW YORK, N.Y.) 2012; 18:759-70. [PMID: 22355167 PMCID: PMC3312563 DOI: 10.1261/rna.031518.111] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 12/24/2011] [Indexed: 05/20/2023]
Abstract
The archaeal protein L7Ae and eukaryotic homologs such as L30e and 15.5kD comprise the best characterized family of K-turn-binding proteins. K-turns are an RNA motif comprised of a bulge flanked by canonical and noncanonical helices. They are widespread in cellular RNAs, including bacterial gene-regulatory RNAs such as the c-di-GMP-II, lysine, and SAM-I riboswitches, and the T-box. The existence in bacteria of K-turn-binding proteins of the L7Ae family has not been proven, although two hypothetical proteins, YbxF and YlxQ, have been proposed to be L7Ae homologs based on sequence conservation. Using purified, recombinant proteins, we show that Bacillus subtilis YbxF and YlxQ bind K-turns (K(d) ~270 nM and ~2300 nM, respectively). Crystallographic structure determination demonstrates that both YbxF and YlxQ adopt the same overall fold as L7Ae. Unlike the latter, neither bacterial protein recognizes K-loops, a structural motif that lacks the canonical helix of the K-turn. This property is shared between the bacterial and eukaryal family members. Comparison of our structure of YbxF in complex with the K-turn of the SAM-I riboswitch and previously determined structures of archaeal and eukaryal homologs bound to RNA indicates that L7Ae approaches the K-turn at a unique angle, which results in a considerably larger RNA-protein interface dominated by interactions with the noncanonical helix of the K-turn. Thus, the inability of the bacterial and eukaryal L7Ae homologs to bind K-loops probably results from their reliance on interactions with the canonical helix. The biological functions of YbxF and YlxQ remain to be determined.
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Affiliation(s)
- Nathan J. Baird
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Jinwei Zhang
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Tomoko Hamma
- Pacific Northwest University of Health Sciences, Yakima, Washington 98901, USA
| | - Adrian R. Ferré-D'Amaré
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
- Corresponding author.E-mail .
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198
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Park HC, Park JS, Choi JD, Dabrowski M, Atkins WM, Yoon MY. Kinetic mechanism of fuculose-1-phosphate aldolase from the hyperthermophilic Archaeon Methanococcus jannaschii. Enzyme Microb Technol 2012; 50:209-14. [DOI: 10.1016/j.enzmictec.2012.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 12/28/2011] [Accepted: 01/09/2012] [Indexed: 11/15/2022]
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199
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Miller D, Xu H, White RH. A New Subfamily of Agmatinases Present in Methanogenic Archaea Is Fe(II) Dependent. Biochemistry 2012; 51:3067-78. [DOI: 10.1021/bi300039f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Danielle Miller
- Department
of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
24061, United States
| | - Huimin Xu
- Department
of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
24061, United States
| | - Robert H. White
- Department
of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
24061, United States
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200
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Oza JP, Sowers KR, Perona JJ. Linking energy production and protein synthesis in hydrogenotrophic methanogens. Biochemistry 2012; 51:2378-89. [PMID: 22401293 DOI: 10.1021/bi300106p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogenotrophic methanogens possessing the hydrogen-dependent dehydrogenase Hmd also encode paralogs of this protein whose function is poorly understood. Here we present biochemical evidence that the two inactive Hmd paralogs of Methanocaldococcus jannaschii, HmdII and HmdIII, form binary and ternary complexes with several components of the protein translation apparatus. HmdII and HmdIII, but not the active dehydrogenase Hmd, bind with micromolar binding affinities to a number of tRNAs and form ternary complexes with tRNA(Pro) and prolyl-tRNA synthetase (ProRS). Fluorescence spectroscopy experiments also suggest that binding of HmdII and ProRS involves distinct binding determinants on the tRNA. These biochemical data suggest the possibility of a regulatory link between energy production and protein translation pathways that may allow a rapid cellular response to altered environmental conditions.
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Affiliation(s)
- Javin P Oza
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, Santa Barbara, California 93106-9510, United States
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