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Colucci E, Anshari ZR, Patiño-Ruiz MF, Nemchinova M, Whittaker J, Slotboom DJ, Guskov A. Mutation in glutamate transporter homologue GltTk provides insights into pathologic mechanism of episodic ataxia 6. Nat Commun 2023; 14:1799. [PMID: 37002226 PMCID: PMC10066184 DOI: 10.1038/s41467-023-37503-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
Episodic ataxias (EAs) are rare neurological conditions affecting the nervous system and typically leading to motor impairment. EA6 is linked to the mutation of a highly conserved proline into an arginine in the glutamate transporter EAAT1. In vitro studies showed that this mutation leads to a reduction in the substrates transport and an increase in the anion conductance. It was hypothesised that the structural basis of these opposed functional effects might be the straightening of transmembrane helix 5, which is kinked in the wild-type protein. In this study, we present the functional and structural implications of the mutation P208R in the archaeal homologue of glutamate transporters GltTk. We show that also in GltTk the P208R mutation leads to reduced aspartate transport activity and increased anion conductance, however a cryo-EM structure reveals that the kink is preserved. The arginine side chain of the mutant points towards the lipidic environment, where it may engage in interactions with the phospholipids, thereby potentially interfering with the transport cycle and contributing to stabilisation of an anion conducting state.
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Affiliation(s)
- Emanuela Colucci
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - Zaid R Anshari
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - Miyer F Patiño-Ruiz
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - Mariia Nemchinova
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - Jacob Whittaker
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - Dirk J Slotboom
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands.
| | - Albert Guskov
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands.
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2
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Sakrikar S, Schmid A. An archaeal histone-like protein regulates gene expression in response to salt stress. Nucleic Acids Res 2021; 49:12732-12743. [PMID: 34883507 PMCID: PMC8682779 DOI: 10.1093/nar/gkab1175] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 12/21/2022] Open
Abstract
Histones, ubiquitous in eukaryotes as DNA-packing proteins, find their evolutionary origins in archaea. Unlike the characterized histone proteins of a number of methanogenic and themophilic archaea, previous research indicated that HpyA, the sole histone encoded in the model halophile Halobacterium salinarum, is not involved in DNA packaging. Instead, it was found to have widespread but subtle effects on gene expression and to maintain wild type cell morphology. However, the precise function of halophilic histone-like proteins remain unclear. Here we use quantitative phenotyping, genetics, and functional genomics to investigate HpyA function. These experiments revealed that HpyA is important for growth and rod-shaped morphology in reduced salinity. HpyA preferentially binds DNA at discrete genomic sites under low salt to regulate expression of ion uptake, particularly iron. HpyA also globally but indirectly activates other ion uptake and nucleotide biosynthesis pathways in a salt-dependent manner. Taken together, these results demonstrate an alternative function for an archaeal histone-like protein as a transcriptional regulator, with its function tuned to the physiological stressors of the hypersaline environment.
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Affiliation(s)
- Saaz Sakrikar
- Biology Department, Duke University, Durham, NC27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC27708, USA
| | - Amy K Schmid
- Biology Department, Duke University, Durham, NC27708, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC27708, USA
- Center for Genomics and Computational Biology, Duke University, Durham, NC27708, USA
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3
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Li Z, Rodriguez‐Franco M, Albers S, Quax TEF. The switch complex ArlCDE connects the chemotaxis system and the archaellum. Mol Microbiol 2020; 114:468-479. [PMID: 32416640 PMCID: PMC7534055 DOI: 10.1111/mmi.14527] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/06/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022]
Abstract
Cells require a sensory system and a motility structure to achieve directed movement. Bacteria and archaea possess rotating filamentous motility structures that work in concert with the sensory chemotaxis system. This allows microorganisms to move along chemical gradients. The central response regulator protein CheY can bind to the motor of the motility structure, the flagellum in bacteria, and the archaellum in archaea. Both motility structures have a fundamentally different protein composition and structural organization. Yet, both systems receive input from the chemotaxis system. So far, it was unknown how the signal is transferred from the archaeal CheY to the archaellum motor to initiate motor switching. We applied a fluorescent microscopy approach in the model euryarchaeon Haloferax volcanii and shed light on the sequence order in which signals are transferred from the chemotaxis system to the archaellum. Our findings indicate that the euryarchaeal-specific ArlCDE are part of the archaellum motor and that they directly receive input from the chemotaxis system via the adaptor protein CheF. Hence, ArlCDE are an important feature of the archaellum of euryarchaea, are essential for signal transduction during chemotaxis and represent the archaeal switch complex.
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Affiliation(s)
- Zhengqun Li
- Molecular Biology of Archaea, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | | | - Sonja‐Verena Albers
- Molecular Biology of Archaea, Faculty of BiologyUniversity of FreiburgFreiburgGermany
| | - Tessa E. F. Quax
- Archaeal Virus–Host Interactions, Faculty of BiologyUniversity of FreiburgFreiburgGermany
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4
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Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P, Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques R, Snijders AP, Šarić A, Lindås AC, Robinson NP, Baum B. The proteasome controls ESCRT-III-mediated cell division in an archaeon. Science 2020; 369:eaaz2532. [PMID: 32764038 PMCID: PMC7116001 DOI: 10.1126/science.aaz2532] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/30/2020] [Accepted: 06/11/2020] [Indexed: 12/28/2022]
Abstract
Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III-mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control.
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Affiliation(s)
- Gabriel Tarrason Risa
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Fredrik Hurtig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sian Bray
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Anne E Hafner
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Lena Harker-Kirschneck
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Peter Faull
- Proteomics Platform, The Francis Crick Institute, London, UK
| | - Colin Davis
- Proteomics Platform, The Francis Crick Institute, London, UK
| | - Dimitra Papatziamou
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Delyan R Mutavchiev
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Catherine Fan
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Leticia Meneguello
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | | | - Gautam Dey
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Mairi Kilkenny
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Diorge P Souza
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Luca Pellegrini
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Robertus A M de Bruin
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | | | - Anđela Šarić
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Nicholas P Robinson
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK.
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK.
- Institute for the Physics of Living Systems, UCL, London, UK
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5
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Iwata S, Kinosita Y, Uchida N, Nakane D, Nishizaka T. Motor torque measurement of Halobacterium salinarum archaellar suggests a general model for ATP-driven rotary motors. Commun Biol 2019; 2:199. [PMID: 31149643 PMCID: PMC6534597 DOI: 10.1038/s42003-019-0422-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 04/05/2019] [Indexed: 02/06/2023] Open
Abstract
It is unknown how the archaellum-the rotary propeller used by Archaea for motility-works. To further understand the molecular mechanism by which the hexameric ATPase motor protein FlaI drives rotation of the membrane-embedded archaellar motor, we determined motor torque by imposition of various loads on Halobacterium salinarum archaella. Markers of different sizes were attached to single archaella, and their trajectories were quantified using three-dimensional tracking and high-speed recording. We show that rotation slows as the viscous drag of markers increases, but torque remains constant at 160 pN·nm independent of rotation speed. Notably, the estimated work done in a single rotation is twice the expected energy that would come from hydrolysis of six ATP molecules in the hexamer, indicating that more ATP molecules are required for one rotation of archaellum. To reconcile the apparent contradiction, we suggest a new and general model for the mechanism of ATP-driven rotary motors.
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Affiliation(s)
- Seiji Iwata
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
| | - Yoshiaki Kinosita
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
| | - Nariya Uchida
- Department of Physics, Tohoku University, Sendai, 980-8578 Japan
| | - Daisuke Nakane
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
| | - Takayuki Nishizaka
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588 Japan
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6
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Tian Y, Gu H, Fan Z, Shi G, Yuan J, Wei F, Yang Y, Tian B, Cao G, Huang J. Role of a cotton endoreduplication-related gene, GaTOP6B, in response to drought stress. Planta 2019; 249:1119-1132. [PMID: 30552583 DOI: 10.1007/s00425-018-3067-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/10/2018] [Indexed: 05/24/2023]
Abstract
Cotton GaTOP6B is involved in cellular endoreduplication and a positive response to drought stress via promoting plant leaf and root growth. Drought is deemed as one of adverse conditions that could cause substantial reductions in crop yields worldwide. Since cotton exhibits a moderate-tolerant phenotype under water-deficit conditions, the plant could therefore be used to characterize potential new genes regulating drought tolerance in crop plants. In this work, GaTOP6B, encoding DNA topoisomerase VI subunit B, was identified in Asian cotton (Gossypium arboreum). Virus-induced gene silencing (VIGS) and overexpression (OE) were used to investigate the biological function of GaTOP6B in G. arboreum and Arabidopsis thaliana under drought stress. The GaTOP6B-silencing plants showed a reduced ploidy level, and displayed a compromised tolerance phenotype including lowered relative water content (RWC), decreased proline content and antioxidative enzyme activity, and an increased malondialdehyde (MDA) content under drought stress. GaTOP6B-overexpressing Arabidopsis lines, however, had increased ploidy levels, and were more tolerant to drought treatment, associated with improved RWC maintenance, higher proline accumulation, and reduced stomatal aperture under drought stress. Transcriptome analysis showed that genes involved in the processes like cell cycle, transcription and signal transduction, were substantially up-regulated in GaTOP6B-overexpressing Arabidopsis, promoting plant growth and development. More specifically, under drought stress, the genes involved in the biosynthesis of secondary metabolites such as phenylpropanoid, starch and sucrose were selectively enhanced to improve tolerance in plants. Taken together, the results demonstrated that GaTOP6B could coordinately regulate plant leaf and root growth via cellular endoreduplication, and positively respond to drought stress. Thus, GaTOP6B could be a competent candidate gene for improvement of drought tolerance in crop species.
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Affiliation(s)
- Yanfei Tian
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Huihui Gu
- School of Chemical Engineering and Energy, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Zhuxuan Fan
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Gongyao Shi
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Jiachen Yuan
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Fang Wei
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
| | - Yan Yang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Baoming Tian
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
| | - Gangqiang Cao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China
| | - Jinyong Huang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
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7
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Abstract
Molecular chaperones promote the correct folding of proteins in aggregation-prone cellular environments by stabilizing nascent polypeptide chains and providing appropriate folding conditions. Prefoldins (PFDs) are molecular chaperones found in archaea and eukaryotes, generally characterized by a unique jellyfish-like hexameric structure consisting of a rigid beta-barrel backbone with protruding flexible coiled-coils. Unlike eukaryotic PFDs that mainly interact with cytoskeletal components, archaeal PFDs can stabilize a wide range of substrates; such versatility reflects PFD's role as a key element in archaeal chaperone systems, which often lack general nascent-chain binding chaperone components such as Hsp70. While archaeal PFDs mainly exist as hexameric complexes, their structural diversity ranges from tetramers to filamentous oligomers. PFDs bind and stabilize nonnative proteins using varying numbers of coiled-coils, and subsequently transfer the substrate to a group II chaperonin (CPN) for refolding. The distinct structure and specific function of archaeal PFDs have been exploited for a broad range of applications in biotechnology; furthermore, a filament-forming variant of PFD has been used to fabricate nanoscale architectures of defined shapes, demonstrating archaeal PFDs' potential applicability in nanotechnology.
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Affiliation(s)
- Samuel Lim
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA
| | - Dominic J Glover
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Douglas S Clark
- Department of Chemical and Biological Engineering, University of California, Berkeley, CA, USA.
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8
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van Tran N, Muller L, Ross RL, Lestini R, Létoquart J, Ulryck N, Limbach PA, de Crécy-Lagard V, Cianférani S, Graille M. Evolutionary insights into Trm112-methyltransferase holoenzymes involved in translation between archaea and eukaryotes. Nucleic Acids Res 2018; 46:8483-8499. [PMID: 30010922 PMCID: PMC6144793 DOI: 10.1093/nar/gky638] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 06/25/2018] [Accepted: 07/04/2018] [Indexed: 12/22/2022] Open
Abstract
Protein synthesis is a complex and highly coordinated process requiring many different protein factors as well as various types of nucleic acids. All translation machinery components require multiple maturation events to be functional. These include post-transcriptional and post-translational modification steps and methylations are the most frequent among these events. In eukaryotes, Trm112, a small protein (COG2835) conserved in all three domains of life, interacts and activates four methyltransferases (Bud23, Trm9, Trm11 and Mtq2) that target different components of the translation machinery (rRNA, tRNAs, release factors). To clarify the function of Trm112 in archaea, we have characterized functionally and structurally its interaction network using Haloferax volcanii as model system. This led us to unravel that methyltransferases are also privileged Trm112 partners in archaea and that this Trm112 network is much more complex than anticipated from eukaryotic studies. Interestingly, among the identified enzymes, some are functionally orthologous to eukaryotic Trm112 partners, emphasizing again the similarity between eukaryotic and archaeal translation machineries. Other partners display some similarities with bacterial methyltransferases, suggesting that Trm112 is a general partner for methyltransferases in all living organisms.
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Affiliation(s)
- Nhan van Tran
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
| | - Leslie Muller
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Robert L Ross
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
| | - Roxane Lestini
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645-INSERM U1182 91128, Palaiseau Cedex, France
| | - Juliette Létoquart
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
| | - Nathalie Ulryck
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, Cincinnati, OH 45221-0172, USA
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Marc Graille
- Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, F-91128 Palaiseau cedex, France
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9
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Brooks C, Snoberger A, Belcastro M, Murphy J, Kisselev OG, Smith DM, Sokolov M. Archaeal Unfoldase Counteracts Protein Misfolding Retinopathy in Mice. J Neurosci 2018; 38:7248-7254. [PMID: 30012684 PMCID: PMC6096037 DOI: 10.1523/jneurosci.0905-18.2018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/08/2018] [Accepted: 06/30/2018] [Indexed: 11/21/2022] Open
Abstract
Deregulation of cellular proteostasis due to the failure of the ubiquitin proteasome system to dispose of misfolded aggregation-prone proteins is a hallmark of various neurodegenerative diseases in humans. Microorganisms have evolved to survive massive protein misfolding and aggregation triggered by heat shock using their protein-unfolding ATPases (unfoldases) from the Hsp100 family. Because the Hsp100 chaperones are absent in homoeothermic mammals, we hypothesized that the vulnerability of mammalian neurons to misfolded proteins could be mitigated by expressing a xenogeneic unfoldase. To test this idea, we expressed proteasome-activating nucleotidase (PAN), a protein-unfolding ATPase from thermophilic Archaea, which is homologous to the 19S eukaryotic proteasome and similar to the Hsp100 family chaperones in rod photoreceptors of mice. We found that PAN had no obvious effect in healthy rods; however, it effectively counteracted protein-misfolding retinopathy in Gγ1 knock-out mice. We conclude that archaeal PAN can rescue a protein-misfolding neurodegenerative disease, likely by recognizing misfolded mammalian proteins.SIGNIFICANCE STATEMENT This study demonstrates successful therapeutic application of an archaeal molecular chaperone in an animal model of neurodegenerative disease. Introducing the archaeal protein-unfolding ATPase proteasome-activating nucleotidase (PAN) into the retinal photoreceptors of mice protected these neurons from the cytotoxic effect of misfolded proteins. We propose that xenogeneic protein-unfolding chaperones could be equally effective against other types of neurodegenerative diseases of protein-misfolding etiology.
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Affiliation(s)
| | - Aaron Snoberger
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, and
| | | | | | - Oleg G Kisselev
- Department of Ophthalmology, St. Louis University, St. Louis, Missouri 63104
| | - David M Smith
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, and
| | - Maxim Sokolov
- Department of Ophthalmology,
- Department of Biochemistry, West Virginia University, Morgantown, West Virginia 26506, and
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10
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Abstract
Organisms within the archaeal domain of life possess a simplified version of the eukaryotic DNA replication machinery. While some archaea possess a bacterial-like mode of DNA replication with single origins of replication per chromosome, the majority of species characterized to date possess chromosomes with multiple replication origins. Genetic, structural, and biochemical studies have revealed the nature of archaeal origin specification. Recent work has begun to shed light on the mechanisms of replication initiation in these organisms.
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Affiliation(s)
- Stephen D Bell
- Department of Molecular and Cellular Biochemistry, Department of Biology, Indiana University, Bloomington, IN, USA.
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11
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Chang YC, Hu Z, Rachlin J, Anton BP, Kasif S, Roberts RJ, Steffen M. COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps. Nucleic Acids Res 2015; 44:D330-5. [PMID: 26635392 PMCID: PMC4702925 DOI: 10.1093/nar/gkv1324] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/11/2015] [Indexed: 02/06/2023] Open
Abstract
The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue.
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Affiliation(s)
- Yi-Chien Chang
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Zhenjun Hu
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | | | | | - Simon Kasif
- Bioinformatics Program, Boston University, Boston, MA 02215, USA Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Martin Steffen
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA 02118, USA
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12
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Benda C, Ebert J, Scheltema RA, Schiller HB, Baumgärtner M, Bonneau F, Mann M, Conti E. Structural model of a CRISPR RNA-silencing complex reveals the RNA-target cleavage activity in Cmr4. Mol Cell 2014; 56:43-54. [PMID: 25280103 DOI: 10.1016/j.molcel.2014.09.002] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/29/2014] [Accepted: 08/29/2014] [Indexed: 12/26/2022]
Abstract
The Cmr complex is an RNA-guided endonuclease that cleaves foreign RNA targets as part of the CRISPR prokaryotic defense system. We investigated the molecular architecture of the P. furiosus Cmr complex using an integrative structural biology approach. We determined crystal structures of P. furiosus Cmr1, Cmr2, Cmr4, and Cmr6 and combined them with known structural information to interpret the cryo-EM map of the complex. To support structure determination, we obtained residue-specific interaction data using protein crosslinking and mass spectrometry. The resulting pseudoatomic model reveals how the superhelical backbone of the complex is defined by the polymerizing principles of Cmr4 and Cmr5 and how it is capped at the extremities by proteins of similar folds. The inner surface of the superhelix exposes conserved residues of Cmr4 that we show are required for target-cleavage activity. The structural and biochemical data thus identify Cmr4 as the conserved endoribonuclease of the Cmr complex.
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Affiliation(s)
- Christian Benda
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Judith Ebert
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Richard A Scheltema
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Herbert B Schiller
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Marc Baumgärtner
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Fabien Bonneau
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
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13
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Grüber G, Manimekalai MSS, Mayer F, Müller V. ATP synthases from archaea: the beauty of a molecular motor. Biochim Biophys Acta 2014; 1837:940-52. [PMID: 24650628 DOI: 10.1016/j.bbabio.2014.03.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 03/07/2014] [Accepted: 03/11/2014] [Indexed: 11/18/2022]
Abstract
Archaea live under different environmental conditions, such as high salinity, extreme pHs and cold or hot temperatures. How energy is conserved under such harsh environmental conditions is a major question in cellular bioenergetics of archaea. The key enzymes in energy conservation are the archaeal A1AO ATP synthases, a class of ATP synthases distinct from the F1FO ATP synthase ATP synthase found in bacteria, mitochondria and chloroplasts and the V1VO ATPases of eukaryotes. A1AO ATP synthases have distinct structural features such as a collar-like structure, an extended central stalk, and two peripheral stalks possibly stabilizing the A1AO ATP synthase during rotation in ATP synthesis/hydrolysis at high temperatures as well as to provide the storage of transient elastic energy during ion-pumping and ATP synthesis/-hydrolysis. High resolution structures of individual subunits and subcomplexes have been obtained in recent years that shed new light on the function and mechanism of this unique class of ATP synthases. An outstanding feature of archaeal A1AO ATP synthases is their diversity in size of rotor subunits and the coupling ion used for ATP synthesis with H(+), Na(+) or even H(+) and Na(+) using enzymes. The evolution of the H(+) binding site to a Na(+) binding site and its implications for the energy metabolism and physiology of the cell are discussed.
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Affiliation(s)
- Gerhard Grüber
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
| | | | - Florian Mayer
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Volker Müller
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany.
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14
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Reindl S, Ghosh A, Williams GJ, Lassak K, Neiner T, Henche AL, Albers SV, Tainer JA. Insights into FlaI functions in archaeal motor assembly and motility from structures, conformations, and genetics. Mol Cell 2013; 49:1069-82. [PMID: 23416110 DOI: 10.1016/j.molcel.2013.01.014] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 10/23/2012] [Accepted: 01/10/2013] [Indexed: 11/29/2022]
Abstract
Superfamily ATPases in type IV pili, type 2 secretion, and archaella (formerly archaeal flagella) employ similar sequences for distinct biological processes. Here, we structurally and functionally characterize prototypical superfamily ATPase FlaI in Sulfolobus acidocaldarius, showing FlaI activities in archaeal swimming-organelle assembly and movement. X-ray scattering data of FlaI in solution and crystal structures with and without nucleotide reveal a hexameric crown assembly with key cross-subunit interactions. Rigid building blocks form between N-terminal domains (points) and neighboring subunit C-terminal domains (crown ring). Upon nucleotide binding, these six cross-subunit blocks move with respect to each other and distinctly from secretion and pilus ATPases. Crown interactions and conformations regulate assembly, motility, and force direction via a basic-clamp switching mechanism driving conformational changes between stable, backbone-interconnected moving blocks. Collective structural and mutational results identify in vivo functional components for assembly and motility, phosphate-triggered rearrangements by ATP hydrolysis, and molecular predictors for distinct ATPase superfamily functions.
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Affiliation(s)
- Sophia Reindl
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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15
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Yelton AP, Thomas BC, Simmons SL, Wilmes P, Zemla A, Thelen MP, Justice N, Banfield JF. A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes. PLoS Comput Biol 2011; 7:e1002230. [PMID: 22028637 PMCID: PMC3197636 DOI: 10.1371/journal.pcbi.1002230] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 08/30/2011] [Indexed: 11/19/2022] Open
Abstract
During microbial evolution, genome rearrangement increases with increasing sequence divergence. If the relationship between synteny and sequence divergence can be modeled, gene clusters in genomes of distantly related organisms exhibiting anomalous synteny can be identified and used to infer functional conservation. We applied the phylogenetic pairwise comparison method to establish and model a strong correlation between synteny and sequence divergence in all 634 available Archaeal and Bacterial genomes from the NCBI database and four newly assembled genomes of uncultivated Archaea from an acid mine drainage (AMD) community. In parallel, we established and modeled the trend between synteny and functional relatedness in the 118 genomes available in the STRING database. By combining these models, we developed a gene functional annotation method that weights evolutionary distance to estimate the probability of functional associations of syntenous proteins between genome pairs. The method was applied to the hypothetical proteins and poorly annotated genes in newly assembled acid mine drainage Archaeal genomes to add or improve gene annotations. This is the first method to assign possible functions to poorly annotated genes through quantification of the probability of gene functional relationships based on synteny at a significant evolutionary distance, and has the potential for broad application.
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Affiliation(s)
- Alexis P. Yelton
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America
| | - Brian C. Thomas
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America
| | - Sheri L. Simmons
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
| | - Paul Wilmes
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
| | - Adam Zemla
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Michael P. Thelen
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, United States of America
| | - Nicholas Justice
- Department of Plant and Microbial Biology, University of California, Berkeley, California, United States of America
| | - Jillian F. Banfield
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
- * E-mail:
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16
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Ishino Y. [Structure, functions, and application of the proteins from extremophiles]. Seikagaku 2009; 81:1035-1037. [PMID: 20077845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Yoshizumi Ishino
- Graduate School of Bioresource & Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka 812-8581, Japan
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17
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Kimura M. [Structure-function relationship and thermostability of ribonucleoprotein enzyme from hyperthermophilic archaeon]. Seikagaku 2009; 81:1038-1048. [PMID: 20077846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Makoto Kimura
- Graduate School of Bioresource & Bioenvironmental Sciences, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan
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18
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Hirata A. [Archaeal transcriptional machinery]. Seikagaku 2009; 81:377-381. [PMID: 19522293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Akira Hirata
- Department of Material Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Bunkyo 3, Matsuyama 790-8577, Japan
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19
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Ishino S, Ishino Y. [DNA transactions in Archaea]. Tanpakushitsu Kakusan Koso 2009; 54:141-147. [PMID: 19205349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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20
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Bowyer A, Mikolajek H, Wright JN, Coker A, Erskine PT, Cooper JB, Bashir Q, Rashid N, Jamil F, Akhtar M. Crystallization and preliminary X-ray diffraction analysis of L-threonine dehydrogenase (TDH) from the hyperthermophilic archaeon Thermococcus kodakaraensis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:828-30. [PMID: 18765916 PMCID: PMC2531275 DOI: 10.1107/s1744309108025384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 08/06/2008] [Indexed: 11/10/2022]
Abstract
The enzyme L-threonine dehydrogenase catalyses the NAD(+)-dependent conversion of L-threonine to 2-amino-3-ketobutyrate, which is the first reaction of a two-step biochemical pathway involved in the metabolism of threonine to glycine. Here, the crystallization and preliminary crystallographic analysis of L-threonine dehydrogenase (Tk-TDH) from the hyperthermophilic organism Thermococcus kodakaraensis KOD1 is reported. This threonine dehydrogenase consists of 350 amino acids, with a molecular weight of 38 kDa, and was prepared using an Escherichia coli expression system. The purified native protein was crystallized using the hanging-drop vapour-diffusion method and crystals grew in the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = b = 124.5, c = 271.1 A. Diffraction data were collected to 2.6 A resolution and preliminary analysis indicates that there are four molecules in the asymmetric unit of the crystal.
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Affiliation(s)
- A. Bowyer
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
| | - H. Mikolajek
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
| | - J. N. Wright
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
| | - A. Coker
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Department of Medicine (Hampstead Campus), Rowland Hill Street, London NW3 2PF, England
| | - P. T. Erskine
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Department of Medicine (Hampstead Campus), Rowland Hill Street, London NW3 2PF, England
| | - J. B. Cooper
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
- Laboratory of Protein Crystallography, Centre for Amyloidosis and Acute Phase Proteins, UCL Department of Medicine (Hampstead Campus), Rowland Hill Street, London NW3 2PF, England
| | - Q. Bashir
- School of Biological Sciences, University of Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - N. Rashid
- School of Biological Sciences, University of Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - F. Jamil
- School of Biological Sciences, University of Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - M. Akhtar
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, England
- School of Biological Sciences, University of Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
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21
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Ding X, Lv ZM, Zhao Y, Min H, Yang WJ. MTH1745, a protein disulfide isomerase-like protein from thermophilic archaea, Methanothermobacter thermoautotrophicum involving in stress response. Cell Stress Chaperones 2008; 13:239-46. [PMID: 18759006 PMCID: PMC2673884 DOI: 10.1007/s12192-008-0026-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 01/23/2008] [Accepted: 01/25/2008] [Indexed: 01/20/2023] Open
Abstract
MTH1745 is a putative protein disulfide isomerase characterized with 151 amino acid residues and a CPAC active-site from the anaerobic archaea Methanothermobacter thermoautotrophicum. The potential functions of MTH1745 are not clear. In the present study, we show a crucial role of MTH1745 in protecting cells against stress which may be related to its functions as a disulfide isomerase and its chaperone properties. Using real-time polymerase chain reaction analyses, the level of MTH1745 messenger RNA (mRNA) in the thermophilic archaea M. thermoautotrophicum was found to be stress-induced in that it was significantly higher under low (50 degrees C) and high (70 degrees C) growth temperatures than under the optimal growth temperature for the organism (65 degrees C). Additionally, the expression of MTH1745 mRNA was up-regulated by cold shock (4 degrees C). Furthermore, the survival of MTH1745 expressing Escherichia coli cells was markedly higher than that of control cells in response to heat shock (51.0 degrees C). These results indicated that MTH1745 plays an important role in the resistance of stress. By assay of enzyme activities in vitro, MTH1745 also exhibited a chaperone function by promoting the functional folding of citrate synthase after thermodenaturation. On the other hand, MTH1745 was also shown to function as a disulfide isomerase on the refolding of denatured and reduced ribonuclease A. On the basis of its single thioredoxin domain, function as a disulfide isomerase, and its chaperone activity, we suggest that MTH1745 may be an ancient protein disulfide isomerase. These studies may provide clues to the understanding of the function of protein disulfide isomerase in archaea.
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Affiliation(s)
- Xia Ding
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
- College of Life Sciences, Nanchang University, Nanchang, Jiangxi 330000 China
| | - Zhen-Mei Lv
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Yang Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
| | - Hang Min
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
- Room 223, College of Life Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang China 310030
| | - Wei-Jun Yang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058 China
- Room 317, College of Life Sciences, Zijingang Campus, Zhejiang University, Hangzhou, Zhejiang China 310030
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22
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Vesteg M, Krajcovic J. On the origin of eukaryotic cytoskeleton. Riv Biol 2008; 101:109-118. [PMID: 18600633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The origin of eukaryote-specific cytoskeletal proteins is an issue which is closely related to the origin of the domain Eukarya. As nearly all of these proteins are not found in prokaryotes, the prokaryotic origin of eukaryotic cytoskeletal network suggested by most models is questionable. Eukaryotic cytoskeletal proteins might descend from subpopulations of pre-cells co-existing with Bacteria and Archaea prior to the origin of eukaryotes. The pre-karyote (the host for a-proteobacterial ancestors of mitochondria) might have already possessed eukaryotic-like cytoskeleton. A possible role for viruses in the origin of eukaryotic cytoskeletal proteins is discussed. Viruses parasitizing on pre-cells and/or on the pre-karyote might have themselves used several eukaryotic-like cytoskeletal proteins for segregation and packing of their genomes.
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Affiliation(s)
- Matej Vesteg
- Institute of Cell Biology, Faculty of Natural Sciences, Comenius University, Mlynska dolina, 842 15 Bratislava, Slovakia.
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23
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Chaban B, Ng SYM, Kanbe M, Saltzman I, Nimmo G, Aizawa SI, Jarrell KF. Systematic deletion analyses of the fla genes in the flagella operon identify several genes essential for proper assembly and function of flagella in the archaeon, Methanococcus maripaludis. Mol Microbiol 2007; 66:596-609. [PMID: 17887963 DOI: 10.1111/j.1365-2958.2007.05913.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The archaeal flagellum is a unique motility apparatus in the prokaryotic domain, distinct from the bacterial flagellum. Most of the currently recognized archaeal flagella-associated genes fall into a single fla operon that contains the genes for the flagellin proteins (two or more genes designated as flaA or flaB), some variation of a set of conserved proteins of unknown function (flaC, flaD, flaE, flaF, flaG and flaH), an ATPase (flaI) and a membrane protein (flaJ). In addition, the flaD gene has been demonstrated to encode two proteins: a full-length gene product and a truncated product derived from an alternate, internal start site. A systematic deletion approach was taken using the methanogen Methanococcus maripaludis to investigate the requirement and a possible role for these proposed flagella-associated genes. Markerless in-frame deletion strains were created for most of the genes in the M. maripaludis fla operon. In addition, a strain lacking the truncated FlaD protein [FlaD M(191)I] was also created. DNA sequencing and Southern blot analysis confirmed each mutant strain, and the integrity of the remaining operon was confirmed by immunoblot. With the exception of the DeltaFlaB3 and FlaD M(191)I strains, all mutants were non-motile by light microscopy and non-flagellated by electron microscopy. A detailed examination of the DeltaFlaB3 mutant flagella revealed that these structures had no hook region, while the FlaD M(191)I strain appeared identical to wild type. Each deletion strain was complemented, and motility and flagellation was restored. Collectively, these results demonstrate for first time that these fla operon genes are directly involved and critically required for proper archaeal flagella assembly and function.
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Affiliation(s)
- Bonnie Chaban
- Department of Microbiology and Immunology, Queen's University, Kingston, Ontario, Canada, K7L3 N6
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24
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Gnanamani M, Kumar N, Ramachandran S. ARC: automated resource classifier for agglomerative functional classification of prokaryotic proteins using annotation texts. J Biosci 2007; 32:937-45. [PMID: 17914236 DOI: 10.1007/s12038-007-0094-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Functional classification of proteins is central to comparative genomics. The need for algorithms tuned to enable integrative interpretation of analytical data is felt globally. The availability of a general,automated software with built-in flexibility will significantly aid this activity. We have prepared ARC (Automated Resource Classifier), which is an open source software meeting the user requirements of flexibility. The default classification scheme based on keyword match is agglomerative and directs entries into any of the 7 basic non-overlapping functional classes: Cell wall, Cell membrane and Transporters (C), Cell division (D), Information (I), Translocation (L), Metabolism (M), Stress(R), Signal and communication (S) and 2 ancillary classes: Others (O) and Hypothetical (H). The keyword library of ARC was built serially by first drawing keywords from Bacillus subtilis and Escherichia coli K12. In subsequent steps,this library was further enriched by collecting terms from archaeal representative Archaeoglobus fulgidus, Gene Ontology, and Gene Symbols. ARC is 94.04% successful on 6,75,663 annotated proteins from 348 prokaryotes. Three examples are provided to illuminate the current perspectives on mycobacterial physiology and costs of proteins in 333 prokaryotes. ARC is available at http://arc.igib.res.in.
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Affiliation(s)
- Muthiah Gnanamani
- G N Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
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25
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Abstract
Much of the current information about the archaeal cell cycle has been generated through studies of the genus Sulfolobus. The overall organization of the cell cycle in these species is well understood, and information about the regulatory principles that govern cell cycle progression is rapidly accumulating. Exciting progress regarding the control and molecular details of the chromosome replication process is evident, and the first insights into the elusive crenarchaeal mitosis and cytokinesis machineries are within reach.
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Affiliation(s)
- Rolf Bernander
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala, Sweden.
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26
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Chen LT, Ko TP, Chang YW, Lin KA, Wang AHJ, Wang TF. Structural and functional analyses of five conserved positively charged residues in the L1 and N-terminal DNA binding motifs of archaeal RADA protein. PLoS One 2007; 2:e858. [PMID: 17848989 PMCID: PMC1964548 DOI: 10.1371/journal.pone.0000858] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Accepted: 08/16/2007] [Indexed: 12/29/2022] Open
Abstract
RecA family proteins engage in an ATP-dependent DNA strand exchange reaction that includes a ssDNA nucleoprotein helical filament and a homologous dsDNA sequence. In spite of more than 20 years of efforts, the molecular mechanism of homology pairing and strand exchange is still not fully understood. Here we report a crystal structure of Sulfolobus solfataricus RadA overwound right-handed filament with three monomers per helical pitch. This structure reveals conformational details of the first ssDNA binding disordered loop (denoted L1 motif) and the dsDNA binding N-terminal domain (NTD). L1 and NTD together form an outwardly open palm structure on the outer surface of the helical filament. Inside this palm structure, five conserved basic amino acid residues (K27, K60, R117, R223 and R229) surround a 25 A pocket that is wide enough to accommodate anionic ssDNA, dsDNA or both. Biochemical analyses demonstrate that these five positively charged residues are essential for DNA binding and for RadA-catalyzed D-loop formation. We suggest that the overwound right-handed RadA filament represents a functional conformation in the homology search and pairing reaction. A new structural model is proposed for the homologous interactions between a RadA-ssDNA nucleoprotein filament and its dsDNA target.
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Affiliation(s)
- Li-Tzu Chen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yu-Wei Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kuei-An Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Department of Life Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- National Core Facility of High-Throughput Protein Crystallography, Academia Sinica, Taipei, Taiwan
- * To whom correspondence should be addressed. E-mail: (AW); (TW)
| | - Ting-Fang Wang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- * To whom correspondence should be addressed. E-mail: (AW); (TW)
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27
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Zhang H, Lin L, Zeng C, Shen P, Huang YP. Cloning and characterization of a haloarchaeal heat shock protein 70 functionally expressed in Escherichia coli. FEMS Microbiol Lett 2007; 275:168-74. [PMID: 17711453 DOI: 10.1111/j.1574-6968.2007.00881.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Hsp70 molecular chaperone machine is constituted by the 70-kDa heat shock protein Hsp70 (DnaK), cochaperone protein Hsp40 (DnaJ) and a nucleotide-exchange factor GrpE. Although it is one of the best-characterized molecular chaperone machines, little is known about it in archaea. A 5.2-kb region containing the hsp70 (dnaK) gene was cloned from Natrinema sp. J7 strain and sequenced. It contained the Hsp70 chaperone machine gene locus arranged unidirectionally in the order of grpE, hsp70 and hsp40 (dnaJ). The hsp70 gene from Natrinema sp. J7 was overexpressed in Escherichia coli BL21 (DE3). The recombinant Hsp70 protein was in a soluble and active form, and its ATPase activity was optimally active in 2.0 M KCl, whereas NaCl had less effect. In vivo, the haloarchaeal hsp70 gene allowed an E. coli dnak-null mutant to propagate lambda phages and grow at 42 degrees C. The results suggested that haloarchaeal Hsp70 should be beneficial for extreme halophiles survival in low-salt environments.
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Affiliation(s)
- Hao Zhang
- Laboratory of Microbial Genetics, College of Life Sciences, Wuhan University, Wuhan, China
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Giaquinto L, Curmi PMG, Siddiqui KS, Poljak A, DeLong E, DasSarma S, Cavicchioli R. Structure and function of cold shock proteins in archaea. J Bacteriol 2007; 189:5738-48. [PMID: 17545280 PMCID: PMC1951829 DOI: 10.1128/jb.00395-07] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Accepted: 05/20/2007] [Indexed: 11/20/2022] Open
Abstract
Archaea are abundant and drive critical microbial processes in the Earth's cold biosphere. Despite this, not enough is known about the molecular mechanisms of cold adaptation and no biochemical studies have been performed on stenopsychrophilic archaea (e.g., Methanogenium frigidum). This study examined the structural and functional properties of cold shock proteins (Csps) from archaea, including biochemical analysis of the Csp from M. frigidum. csp genes are present in most bacteria and some eucarya but absent from most archaeal genome sequences, most notably, those of all archaeal thermophiles and hyperthermophiles. In bacteria, Csps are small, nucleic acid binding proteins involved in a variety of cellular processes, such as transcription. In this study, archaeal Csp function was assessed by examining the ability of csp genes from psychrophilic and mesophilic Euryarchaeota and Crenarchaeota to complement a cold-sensitive growth defect in Escherichia coli. In addition, an archaeal gene with a cold shock domain (CSD) fold but little sequence identity to Csps was also examined. Genes encoding Csps or a CSD structural analog from three psychrophilic archaea rescued the E. coli growth defect. The three proteins were predicted to have a higher content of solvent-exposed basic residues than the noncomplementing proteins, and the basic residues were located on the nucleic acid binding surface, similar to their arrangement in E. coli CspA. The M. frigidum Csp was purified and found to be a single-domain protein that folds by a reversible two-state mechanism and to exhibit a low conformational stability typical of cold-adapted proteins. Moreover, M. frigidum Csp was characterized as binding E. coli single-stranded RNA, consistent with its ability to complement function in E. coli. The studies show that some Csp and CSD fold proteins have retained sufficient similarity throughout evolution in the Archaea to be able to function effectively in the Bacteria and that the function of the archaeal proteins relates to cold adaptation. The initial biochemical analysis of M. frigidum Csp has developed a platform for further characterization and demonstrates the potential for expanding molecular studies of proteins from this important archaeal stenopsychrophile.
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Affiliation(s)
- Laura Giaquinto
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales 2052, Australia
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29
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Abstract
NrpR is a transcriptional repressor of nitrogen assimilation genes that was recently discovered and characterized in the methanogenic archaeon Methanococcus maripaludis. NrpR homologues are widely distributed in Euryarchaeota and present in a few bacterial species. They exist in three different domain configurations: a single ORF encoding one NrpR domain following an N-terminal helix-turn-helix (HTH); a single ORF encoding two NrpR domains fused in tandem following an N-terminal HTH; and two separate ORFs, one with a single domain following an N-terminal HTH and one with a single domain without a HTH. Phylogenetic analysis indicated that the NrpR family forms five distinct groups: the single domain HTH type, the two domains of the double domain HTH type and the two separately encoded domains. To determine the function of diverse NrpR homologues, representative genes in were expressed an Methanococcus maripaludis nrpR deletion mutant. Homologues from species that possess a single gene restored regulated repression, regardless of domain structure. In the case of Methanosarcina acetivorans that contains two genes, both were required. The results show that distantly related NrpR homologues that are present in widely dispersed phyla regulate the expression of nitrogen assimilation genes in a similar fashion.
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Affiliation(s)
- Thomas J Lie
- Department of Microbiology, University of Washington, Seattle, WA 98195-7242, USA
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Abstract
Sco proteins are widespread proteins found in eukaryotic as well as in many prokaryotic organisms. The 3D structure of representatives from human, yeast, and Bacillus subtilis has been determined, showing a thioredoxin-like fold. Sco proteins have been implicated mainly as copper transporters involved in the assembly of the CuA cofactor in cytochrome c oxidase. Some mutations have been identified in humans that lead to defective cytochrome c oxidase formation and thus to fatal illnesses. However, it appears that the physiological function of Sco proteins goes beyond assembly of the CuA cofactor. Extensive analysis of completely sequenced prokaryotic genomes reveals that 18% of them contain either Sco proteins but not CuA-containing proteins or vice versa. In addition, in several cases, multiple Sco-encoding genes occur even if only a single potential Sco target is encoded in the genome. Genomic context analysis indeed points to a more general role for Sco proteins in copper transport, also to copper enzymes lacking a CuA cofactor. To obtain further insight into the possible role of Sco in the assembly of other cofactors, a search for Cox11 proteins, which are important for CuB biosynthesis, was also performed. A general framework for the action of Sco proteins is proposed, based on the hypothesis that they can couple metal transport and thiol/disulfide-based oxidoreductase activity, as well as select between either of these two cellular functions. This model reconciles the variety of experimental observations made on these proteins over the years, and can constitute a basis for further studies.
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Affiliation(s)
- Lucia Banci
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy
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31
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Abstract
Eukaryotes and archaea use two sets of specialized ribonucleoproteins (RNPs) to carry out sequence-specific methylation and pseudouridylation of RNA, the two most abundant types of modifications of cellular RNAs. In eukaryotes, these protein–RNA complexes localize to the nucleolus and are called small nucleolar RNPs (snoRNPs), while in archaea they are known as small RNPs (sRNP). The C/D class of sno(s)RNPs carries out ribose-2′-O-methylation, while the H/ACA class is responsible for pseudouridylation of their RNA targets. Here, we review the recent advances in the structure, assembly and function of the conserved C/D and H/ACA sno(s)RNPs. Structures of each of the core archaeal sRNP proteins have been determined and their assembly pathways delineated. Furthermore, the recent structure of an H/ACA complex has revealed the organization of a complete sRNP. Combined with current biochemical data, these structures offer insight into the highly homologous eukaryotic snoRNPs.
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Affiliation(s)
- Steve L. Reichow
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
| | - Tomoko Hamma
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
| | - Adrian R. Ferré-D'Amaré
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA and Department of Biochemistry, University of WA, Box 357350, Seattle, WA 98195-7350, USA
- *To whom correspondence should be addressed. +(206) 543 1610+(206) 685 8665
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32
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Son HJ, Shin EJ, Nam SW, Kim DE, Jeon SJ. Properties of the α subunit of a Chaperonin from the hyperthermophilic CrenarchaeonAeropyrum pernixK1. FEMS Microbiol Lett 2007; 266:103-9. [PMID: 17092293 DOI: 10.1111/j.1574-6968.2006.00513.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The gene encoding for a putative thermosome from the hyperthermophilic crenarchaeon Aeropyrum pernix K1 (ApcpnA) was cloned and the biochemical characteristics of the resulting recombinant protein were examined. The gene (accession no. APE0907) from A. pernix K1 showed some homology with other group II chaperonins from archaea. The recombinant ApcpnA protein has a molecular mass of 60 kDa, determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and exhibited ATPase activity with an optimum temperature and pH of 90 degrees C and 5.0, respectively. The ATPase activity was found to be dependent on manganese and potassium ions, but not magnesium ion. The K(m) for ATP at pH 5.0 and 90 degrees C was 10.04 (+/- 1.31) microM, and k(cat) was determined to be 2.21 (+/- 0.11) min(-1) for the ApcpnA monomer. The recombinant ApcpnA prevents thermal aggregation of bovine rhodanese and enhances the thermal stability of alcohol dehydrogenase in vitro, indicating that the protein is suitable as a molecular chaperonin in the high-temperature environment.
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Affiliation(s)
- Hae-Jin Son
- Department of Biotechnology and Bioengineering, Dong-Eui University, Busan, Korea
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33
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Santangelo TJ, Čuboňová L, James CL, Reeve JN. TFB1 or TFB2 is sufficient for Thermococcus kodakaraensis viability and for basal transcription in vitro. J Mol Biol 2006; 367:344-57. [PMID: 17275836 PMCID: PMC1855253 DOI: 10.1016/j.jmb.2006.12.069] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 12/22/2006] [Accepted: 12/27/2006] [Indexed: 11/18/2022]
Abstract
Archaeal RNA polymerases (RNAPs) are most similar to eukaryotic RNAP II (Pol II) but require the support of only two archaeal general transcription factors, TBP (TATA-box binding protein) and TFB (archaeal homologue of the eukaryotic general transcription factor TFIIB) to initiate basal transcription. However, many archaeal genomes encode more than one TFB and/or TBP leading to the hypothesis that different TFB/TBP combinations may be employed to direct initiation from different promoters in Archaea. As a first test of this hypothesis, we have determined the ability of RNAP purified from Thermococcus kodakaraensis (T.k.) to initiate transcription from a variety of T.k. promoters in vitro when provided with T.k. TBP and either TFB1 or TFB2, the two TFBs encoded in the T.k. genome. With every promoter active in vitro, transcription initiation occurred with either TFB1 or TFB2 although the optimum salt concentration for initiation was generally higher for TFB2 (approximately 250 mM K(+)) than for TFB1 (approximately 200 mM K(+)). Consistent with this functional redundancy in vitro, T.k. strains have been constructed with the TFB1- (tfb1; TK1280) or TFB2- (tfb2; TK2287) encoding gene deleted. These mutants exhibit no detectable growth defects under laboratory conditions. Domain swapping between TFB1 and TFB2 has identified a central region that contributes to the salt sensitivity of TFB activity, and deleting residues predicted to form the tip of the B-finger region of TFB2 had no detectable effects on promoter recognition or transcription initiation but did eliminate the production of very short (< or =5 nt) abortive transcripts.
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34
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Inoue K, Sasaki J, Spudich JL, Terazima M. Laser-induced transient grating analysis of dynamics of interaction between sensory rhodopsin II D75N and the HtrII transducer. Biophys J 2006; 92:2028-40. [PMID: 17189313 PMCID: PMC1861795 DOI: 10.1529/biophysj.106.097493] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The interaction between sensory rhodopsin II (SRII) and its transducer HtrII was studied by the time-resolved laser-induced transient grating method using the D75N mutant of SRII, which exhibits minimal visible light absorption changes during its photocycle, but mediates normal phototaxis responses. Flash-induced transient absorption spectra of transducer-free D75N and D75N joined to 120 amino-acid residues of the N-terminal part of the SRII transducer protein HtrII (DeltaHtrII) showed only one spectrally distinct K-like intermediate in their photocycles, but the transient grating method resolved four intermediates (K(1)-K(4)) distinct in their volumes. D75N bound to HtrII exhibited one additional slower kinetic species, which persists after complete recovery of the initial state as assessed by absorption changes in the UV-visible region. The kinetics indicate a conformationally changed form of the transducer portion (designated Tr*), which persists after the photoreceptor returns to the unphotolyzed state. The largest conformational change in the DeltaHtrII portion was found to cause a DeltaHtrII-dependent increase in volume rising in 8 micros in the K(4) state and a drastic decrease in the diffusion coefficient (D) of K(4) relatively to those of the unphotolyzed state and Tr*. The magnitude of the decrease in D indicates a large structural change, presumably in the solvent-exposed HAMP domain of DeltaHtrII, where rearrangement of interacting molecules in the solvent would substantially change friction between the protein and the solvent.
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Affiliation(s)
- Keiichi Inoue
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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35
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are responsible for attaching amino acids to their cognate tRNAs during protein synthesis. In eukaryotes aaRSs are commonly found in multi-enzyme complexes, although the role of these complexes is still not completely clear. Associations between aaRSs have also been reported in archaea, including a complex between prolyl-(ProRS) and leucyl-tRNA synthetases (LeuRS) in Methanothermobacter thermautotrophicus that enhances tRNA(Pro) aminoacylation. Yeast two-hybrid screens suggested that lysyl-tRNA synthetase (LysRS) also associates with LeuRS in M. thermautotrophicus. Co-purification experiments confirmed that LeuRS, LysRS, and ProRS associate in cell-free extracts. LeuRS bound LysRS and ProRS with a comparable K(D) of about 0.3-0.9 microm, further supporting the formation of a stable multi-synthetase complex. The steady-state kinetics of aminoacylation by LysRS indicated that LeuRS specifically reduced the Km for tRNA(Lys) over 3-fold, with no additional change seen upon the addition of ProRS. No significant changes in aminoacylation by LeuRS or ProRS were observed upon the addition of LysRS. These findings, together with earlier data, indicate the existence of a functional complex of three aminoacyl-tRNA synthetases in archaea in which LeuRS improves the catalytic efficiency of tRNA aminoacylation by both LysRS and ProRS.
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Affiliation(s)
- Mette Praetorius-Ibba
- Department of Microbiology, The Ohio State University, Columbus, Ohio 43210-1292, USA.
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36
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Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 2006; 35:D260-4. [PMID: 17151080 PMCID: PMC1781115 DOI: 10.1093/nar/gkl1043] [Citation(s) in RCA: 229] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to their specific molecular functions. Most TIGRFAMs models describe ‘equivalog’ families, where both orthology and lateral gene transfer may be part of the evolutionary history, but where a single molecular function has been conserved. The Genome Properties system contains a queriable set of metabolic reconstructions, genome metrics and extractions of information from the scientific literature. Its genome-by-genome assertions of whether or not specific structures, pathways or systems are present provide high-level conceptual descriptions of genomic content. These assertions enable comparative genomics, provide a meaningful biological context to aid in manual annotation, support assignments of Gene Ontology (GO) biological process terms and help validate HMM-based predictions of protein function. The Genome Properties system is particularly useful as a generator of phylogenetic profiles, through which new protein family functions may be discovered. The TIGRFAMs and Genome Properties systems can be accessed at and .
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Affiliation(s)
- Jeremy D Selengut
- TIGR, Bioinformatics Department, 9712 Medical Center Drive, Rockville, MD 20850, USA.
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Kapatai G, Large A, Benesch JLP, Robinson CV, Carrascosa JL, Valpuesta JM, Gowrinathan P, Lund PA. All three chaperonin genes in the archaeon Haloferax volcanii are individually dispensable. Mol Microbiol 2006; 61:1583-97. [PMID: 16968228 DOI: 10.1111/j.1365-2958.2006.05324.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The Hsp60 or chaperonin class of molecular chaperones is divided into two phylogenetic groups: group I, found in bacteria, mitochondria and chloroplasts, and group II, found in eukaryotic cytosol and archaea. Group I chaperonins are generally essential in bacteria, although when multiple copies are found one or more of these are dispensable. Eukaryotes contain eight genes for group II chaperonins, all of which are essential, and it has been shown that these proteins assemble into double-ring complexes with eightfold symmetry where all proteins occupy specific positions in the ring. In archaea, there are one, two or three genes for the group II chaperonins, but whether they are essential for growth is unknown. Here we describe a detailed genetic, structural and biochemical analysis of these proteins in the halophilic archaeon, Haloferax volcanii. This organism contains three genes for group II chaperonins, and we show that all are individually dispensable but at least one must be present for growth. Two of the three possible double mutants can be constructed, but only one of the three genes is capable of fully complementing the stress-dependent phenotypes that these double mutants show. The chaperonin complexes are made up of hetero-oligomers with eightfold symmetry, and the properties of the different combinations of subunits derived from the mutants are distinct. We conclude that, although they are more homologous to eukaryotic than prokaryotic chaperonins, archaeal chaperonins have some redundancy of function.
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Affiliation(s)
- Georgia Kapatai
- School of Biosciences, University of Birmingham, Birmingham, UK
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38
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Ng SYM, Chaban B, Jarrell KF. Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications. J Mol Microbiol Biotechnol 2006; 11:167-91. [PMID: 16983194 DOI: 10.1159/000094053] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The archaeal flagellum is a unique motility organelle. While superficially similar to the bacterial flagellum, several similarities have been reported between the archaeal flagellum and the bacterial type IV pilus system. These include the multiflagellin nature of the flagellar filament, N-terminal sequence similarities between archaeal flagellins and bacterial type IV pilins, as well as the presence of homologous proteins in the two systems. Recent advances in archaeal flagella research add to the growing list of similarities. First, the preflagellin peptidase that is responsible for processing the N-terminal signal peptide in preflagellins has been identified. The preflagellin peptidase is a membrane-bound enzyme topologically similar to its counterpart in the type IV pilus system (prepilin peptidase); the two enzymes are demonstrated to utilize the same catalytic mechanism. Second, it has been suggested that the archaeal flagellum and the bacterial type IV pilus share a similar mode of assembly. While bacterial flagellins and type IV pilins can be modified with O-linked glycans, N-linked glycans have recently been reported on archaeal flagellins. This mode of glycosylation, as well as the observation that the archaeal flagellum lacks a central channel, are both consistent with the proposed assembly model. On the other hand, the failure to identify other genes involved in archaeal flagellation by homology searches likely implies a novel aspect of the archaeal flagellar system. These interesting features remain to be deciphered through continued research. Such knowledge would be invaluable to motility and protein export studies in the Archaea.
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Affiliation(s)
- Sandy Y M Ng
- Department of Microbiology and Immunology, Queen's University, Kingston, Canada
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Madding LS, Michel JK, Shockley KR, Conners SB, Epting KL, Johnson MR, Kelly RM. Role of the beta1 subunit in the function and stability of the 20S proteasome in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 2006; 189:583-90. [PMID: 17114253 PMCID: PMC1797377 DOI: 10.1128/jb.01382-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The hyperthermophilic archaeon Pyrococcus furiosus genome encodes three proteasome component proteins: one alpha protein (PF1571) and two beta proteins (beta1-PF1404 and beta2-PF0159), as well as an ATPase (PF0115), referred to as proteasome-activating nucleotidase. Transcriptional analysis of the P. furiosus dynamic heat shock response (shift from 90 to 105 degrees C) showed that the beta1 gene was up-regulated over twofold within 5 minutes, suggesting a specific role during thermal stress. Consistent with transcriptional data, two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that incorporation of the beta1 protein relative to beta2 into the 20S proteasome (core particle [CP]) increased with increasing temperature for both native and recombinant versions. For the recombinant enzyme, the beta2/beta1 ratio varied linearly with temperature from 3.8, when assembled at 80 degrees C, to 0.9 at 105 degrees C. The recombinant alpha+beta1+beta2 CP assembled at 105 degrees C was more thermostable than either the alpha+beta1+beta2 version assembled at 90 degrees C or the alpha+beta2 version assembled at either 90 degrees C or 105 degrees C, based on melting temperature and the biocatalytic inactivation rate at 115 degrees C. The recombinant CP assembled at 105 degrees C was also found to have different catalytic rates and specificity for peptide hydrolysis, compared to the 90 degrees C assembly (measured at 95 degrees C). Combination of the alpha and beta1 proteins neither yielded a large proteasome complex nor demonstrated any significant activity. These results indicate that the beta1 subunit in the P. furiosus 20S proteasome plays a thermostabilizing role and influences biocatalytic properties, suggesting that beta subunit composition is a factor in archaeal proteasome function during thermal stress, when polypeptide turnover is essential to cell survival.
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Affiliation(s)
- Lara S Madding
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA
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40
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Abstract
SecY is the central channel protein of the SecYEbeta translocon, the structure of which has been determined by X-ray diffraction. Extended (15 ns) MD simulations of the isolated SecY protein in a phospholipid bilayer have been performed to explore the relationship between protein flexibility and the mechanisms of channel gating. In particular, principal components analysis of the simulation trajectory has been used to probe the intrinsic flexibility of the isolated SecY protein in the absence of the gamma-subunit (SecE) clamp. Analysis and visualization of the principal eigenvectors support a "plug and clamshell" model of SecY channel gating. The simulation results also indicate that hydrophobic gating at the central pore ring prevents leakage of water and ions through the channel in the absence of a translocating peptide.
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Affiliation(s)
- Shozeb Haider
- Department of Biochemistry, University of Oxford, UK
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41
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Goede B, Naji S, von Kampen O, Ilg K, Thomm M. Protein-protein interactions in the archaeal transcriptional machinery: binding studies of isolated RNA polymerase subunits and transcription factors. J Biol Chem 2006; 281:30581-92. [PMID: 16885163 DOI: 10.1074/jbc.m605209200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transcription in Archaea is directed by a pol II-like RNA polymerase and homologues of TBP and TFIIB (TFB) but the crystal structure of the archaeal enzyme and the subunits involved in recruitment of RNA polymerase to the promoter-TBP-TFB-complex are unknown. We described here the cloning expression and purification of 11 bacterially expressed subunits of the Pyrococcus furiosus RNAP. Protein interactions of subunits with each other and of archaeal transcription factors TFB and TFB with RNAP subunits were studied by Far-Western blotting and reconstitution of subcomplexes from single subunits in solution. In silico comparison of a consensus sequence of archaeal RNAP subunits with the sequence of yeast pol II subunits revealed a high degree of conservation of domains of the enzymes forming the cleft and catalytic center of the enzyme. Interaction studies with the large subunits were complicated by the low solubility of isolated subunits B, A', and A'', but an interaction network of the smaller subunits of the enzyme was established. Far-Western analyses identified subunit D as structurally important key polypeptide of RNAP involved in interactions with subunits B, L, N, and P and revealed also a strong interaction of subunits E' and F. Stable complexes consisting of subunits E' and F, of D and L and a BDLNP-subcomplex were reconstituted and purified. Gel shift analyses revealed an association of the BDLNP subcomplex with promoter-bound TBP-TFB. These results suggest a major role of subunit B (Rpb2) in RNAP recruitment to the TBP-TFB promoter complex.
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Affiliation(s)
- Bernd Goede
- Lehrstuhl für Allgemeine Mikrobiologie, Universität Kiel, am Botanischen Garten 1-9, 24107 Kiel, Germany
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42
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Abstract
MthK is a calcium-gated, inwardly rectifying, prokaryotic potassium channel. Although little functional information is available for MthK, its high-resolution structure is used as a model for eukaryotic Ca2+-dependent potassium channels. Here we characterize in detail the main gating characteristics of MthK at the single-channel level with special focus on the mechanism of Ca2+ activation. MthK has two distinct gating modes: slow gating affected mainly by Ca2+ and fast gating affected by voltage. Millimolar Ca2+ increases MthK open probability over 100-fold by mainly increasing the frequency of channel opening while leaving the opening durations unchanged. The Ca2+ dose–response curve displays an unusually high Hill coefficient (n = ∼8), suggesting strong coupling between Ca2+ binding and channel opening. Depolarization affects both the fast gate by dramatically reducing the fast flickers, and to a lesser extent, the slow gate, by increasing MthK open probability. We were able to capture the mechanistic features of MthK with a modified MWC model.
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Affiliation(s)
- Brittany Zadek
- Department of Biochemistry and Membrane Biology, University of California, Davis, 95616, USA
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43
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Abstract
The human disease protein, Bestrophin-1, associated with vitelliform macular dystrophy, has recently been shown to be an integral membrane anion channel-forming protein. In this study we have recovered all bestrophin homologues from the NCBI database and analyzed their sequences using bioinformatic approaches. Eukaryotic homologues were found in animals and fungi but not in plants or protozoans, and prokaryotic homologues distantly related to the eukaryotic proteins, were identified in certain Gram-negative bacterial kingdoms but not in Gram-positive bacteria or archaea. Our analyses suggest a uniform 4 TMS topology for most of these homologues with regions of conservation overlapping and preceding the odd numbered TMSs and overlapping and following the even numbered TMSs. Well-conserved motifs were identified in both the eukaryotic and the prokaryotic homologues, and these proved to overlap, suggesting common structural and functional properties. Phylogenetic analyses revealed that the eukaryotic proteins cluster according to organismal type, and that the prokaryotic proteins sometimes (but not always) do so. This suggests that eukaryotic paralogues arose exclusively by recent gene duplication events although both early and late gene duplication events occurred in prokaryotes.
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Affiliation(s)
- Andrew R Hagen
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA, 92093-0116, USA
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44
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Kasiviswanathan R, Shin JH, Kelman Z. DNA binding by the Methanothermobacter thermautotrophicus Cdc6 protein is inhibited by the minichromosome maintenance helicase. J Bacteriol 2006; 188:4577-80. [PMID: 16740965 PMCID: PMC1482948 DOI: 10.1128/jb.00168-06] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Cdc6 proteins from the archaeon Methanothermobacter thermautotrophicus were previously shown to bind double-stranded DNA. It is shown here that the proteins also bind single-stranded DNA. Using minichromosome maintenance (MCM) helicase mutant proteins unable to bind DNA, it was found that the interaction of MCM with Cdc6 inhibits the DNA binding activity of Cdc6.
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Affiliation(s)
- Rajesh Kasiviswanathan
- University of Maryland Biotechnology Institute, Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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Yamada SI, Niwa JI, Ishigaki S, Takahashi M, Ito T, Sone J, Doyu M, Sobue G. Archaeal proteasomes effectively degrade aggregation-prone proteins and reduce cellular toxicities in mammalian cells. J Biol Chem 2006; 281:23842-51. [PMID: 16793767 DOI: 10.1074/jbc.m601274200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 20 S proteasome is a ubiquitous, barrel-shaped protease complex responsible for most of cellular proteolysis, and its reduced activity is thought to be associated with accumulations of aberrant or misfolded proteins, resulting in a number of neurodegenerative diseases, including amyotrophic lateral sclerosis, spinal and bulbar muscular atrophy, Parkinson disease, and Alzheimer disease. The 20 S proteasomes of archaebacteria (archaea) are structurally simple and proteolytically powerful and thought to be an evolutionary precursor to eukaryotic proteasomes. We successfully reproduced the archaeal proteasome in a functional state in mammalian cells, and here we show that the archaeal proteasome effectively accelerated species-specific degradation of mutant superoxide dismutase-1 and the mutant polyglutamine tract-extended androgen receptor, causative proteins of familial amyotrophic lateral sclerosis and spinal and bulbar muscular atrophy, respectively, and reduced the cellular toxicities of these mutant proteins. Further, we demonstrate that archaeal proteasome can also degrade other neurodegenerative disease-associated proteins such as alpha-synuclein and tau. Our study showed that archaeal proteasomes can degrade aggregation-prone proteins whose toxic gain of function causes neurodegradation and reduce protein cellular toxicity.
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Affiliation(s)
- Shin-ichi Yamada
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya-city, Aichi 466-8550, Japan
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Lewalter K, Müller V. Bioenergetics of archaea: ancient energy conserving mechanisms developed in the early history of life. Biochim Biophys Acta 2006; 1757:437-45. [PMID: 16806054 DOI: 10.1016/j.bbabio.2006.04.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 03/23/2006] [Accepted: 04/19/2006] [Indexed: 11/18/2022]
Abstract
A key component in cellular bioenergetics is the ATP synthase. The enzyme from archaea represents a new class of ATPases, the A1AO ATP synthases. They are composed of two domains that function as a pair of rotary motors connected by a central and peripheral stalk(s). The structure of the chemically-driven motor (A1) was solved by small angle X-ray scattering in solution, and the structure of the first A1AO ATP synthases (from methanoarchaea) was obtained recently by single particle analyses. These studies revealed novel structural features such as a second peripheral stalk and a collar-like structure. Interestingly, the membrane-embedded electrically-driven motor (AO) is very different in archaea with sometimes novel, exceptional subunit composition.
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Affiliation(s)
- Kim Lewalter
- Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Campus Riedberg, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
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Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ. Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. PLoS Biol 2006; 4:e11. [PMID: 16379496 PMCID: PMC1325099 DOI: 10.1371/journal.pbio.0040011] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Accepted: 11/01/2005] [Indexed: 12/02/2022] Open
Abstract
7,8-dihydro-8-oxoguanine (oxoG), the predominant lesion formed following oxidative damage of DNA by reactive oxygen species, is processed differently by replicative and bypass polymerases. Our kinetic primer extension studies demonstrate that the bypass polymerase Dpo4 preferentially inserts C opposite oxoG, and also preferentially extends from the oxoG•C base pair, thus achieving error-free bypass of this lesion. We have determined the crystal structures of preinsertion binary, insertion ternary, and postinsertion binary complexes of oxoG-modified template-primer DNA and Dpo4. These structures provide insights into the translocation mechanics of the bypass polymerase during a complete cycle of nucleotide incorporation. Specifically, during noncovalent dCTP insertion opposite oxoG (or G), the little-finger domain–DNA phosphate contacts translocate by one nucleotide step, while the thumb domain–DNA phosphate contacts remain fixed. By contrast, during the nucleotidyl transfer reaction that covalently incorporates C opposite oxoG, the thumb-domain–phosphate contacts are translocated by one nucleotide step, while the little-finger contacts with phosphate groups remain fixed. These stepwise conformational transitions accompanying nucleoside triphosphate binding and covalent nucleobase incorporation during a full replication cycle of Dpo4-catalyzed bypass of the oxoG lesion are distinct from the translocation events in replicative polymerases. Crystal structures of the bypass polymerase Dpo4 at different stages of lesion-bypass reveal how the cell copes with oxidative DNA damage.
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Affiliation(s)
- Olga Rechkoblit
- 1Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Lucy Malinina
- 1Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Yuan Cheng
- 1Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Vitaly Kuryavyi
- 1Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Suse Broyde
- 2Biology Department, New York University, New York, New York, United States of America
| | - Nicholas E Geacintov
- 3Chemistry Department, New York University, New York, New York, United States of America
| | - Dinshaw J Patel
- 1Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
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Abstract
The majority of secretory proteins are translocated into and across hydrophobic membranes via the universally conserved Sec pore. Accessory proteins, including the SecDF-YajC Escherichia coli membrane complex, are required for efficient protein secretion. E. coli SecDF-YajC has been proposed to be involved in the membrane cycling of SecA, the cytoplasmic bacterial translocation ATPase, and in the stabilizing of SecG, a subunit of the Sec pore. While there are no identified archaeal homologs of either SecA or SecG, many archaea possess homologs of SecD and SecF. Here, we present the first study that addresses the function of archaeal SecD and SecF homologs. We show that the SecD and SecF components in the model archaeon Haloferax volcanii form a cytoplasmic membrane complex in the native host. Furthermore, as in E. coli, an H. volcanii deltasecFD mutant strain exhibits both severe cold sensitivity and a Sec-specific protein translocation defect. Taken together, these results demonstrate significant functional conservation among the prokaryotic SecD and SecF homologs despite the distinct composition of their translocation machineries.
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Affiliation(s)
- Nicholas J Hand
- Department of Biology, University of Pennsylvania, 201 Leidy Laboratories, 415 South University Ave., Philadelphia, Pennsylvania 19104, USA
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Abstract
Rh (Rhesus) proteins are homologues of ammonium transport (Amt) proteins. Physiological and structural evidence shows that Amt proteins are gas channels for NH(3), but the substrate of Rh proteins, be it CO2 as shown in green alga, or NH3/NH4+ as shown in mammalian cells, remains disputed. We assembled a large dataset generated of Rh and Amt to explore how Rh originated from and evolved independently of Amt relatives. Analysis of this rich data implies that Rh was split from Amt first to emerge in archaeal species. The Rh ancestor underwent divergence and duplication along speciation, leading to neofunctionalization and subfunctionalization of the Rh family. The characteristic organismal distribution of Rh vs. Amt reflects their early separation and subsequent independent evolution: they coexist in microbes and invertebrates but do not in fungi, vascular plants or vertebrates. Rh gene-duplication was prominent in vertebrates: while epithelial RhBG/RhCG displayed strong purifying selection, erythroid Rh30 and RhAG experienced different episodes of positive selection in each of which adaptive evolution occurred at certain time points and in a few codon sites. Mammalian Rh30 and RhAG were subject to particularly strong positive selection in some codon sites in the lineage from rodents to human. The grounds of this adaptive evolution may be driven by the necessity to increase the surface/volume ratio of biconcave erythrocytes for facilitative gas diffusion. Altogether, these results are consistent with Rh proteins not being the orthologue of Amt proteins but having gained the function for CO2/HCO3- transport, with important roles in systemic pH regulation.
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Affiliation(s)
- J Peng
- Laboratory of Biochemistry and Molecular Genetics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021, USA
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Abstract
X-ray crystallography revealed a similar architecture of the ammonium transport protein AmtB from Escherichia coli and the homologous protein Amt-1 from Archaeoglobus fulgidus. Furthermore, the atomic structures suggest that the proteins conduct ammonia (NH3) rather than ammonium ions (NH4+). These findings indicate that the more than 350 members of the ammonium transporter/methylamine permease/Rhesus (Amt/Mep/Rh) protein family found in archaea, bacteria, fungi, plants and animals are ammonia-conducting channels rather than ammonium ion transporters. The essential part of these proteins is the narrow hydrophobic ammonia-conducting pore with two highly conserved histidine residues located in the middle of the pore. A specific ammonium ion binding site is found at the extracellular entry site of E. coli AmtB. E. coli AmtB and its regulator GlnK form an effective ammonium sensory system that couples intracellular gene regulation by the nitrogen control system to external changes in ammonium availability. Based on structural and functional analysis of various mutants, two conserved histidine residues were found to be essential for substrate conductance also in the functional eukaryotic ammonium transporters. The next big challenge in the field surely is to determine the atomic structure of Rh proteins.
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Affiliation(s)
- X-D Li
- Biomolecular Research, Paul Scherrer Institute, OFLC 104, CH-5232 Villigen, Switzerland.
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