1
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Cooper CR, Lewis AM, Notey JS, Mukherjee A, Willard DJ, Blum PH, Kelly RM. Interplay between transcriptional regulators and VapBC toxin-antitoxin loci during thermal stress response in extremely thermoacidophilic archaea. Environ Microbiol 2023; 25:1200-1215. [PMID: 36752722 PMCID: PMC10580297 DOI: 10.1111/1462-2920.16350] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 09/30/2022] [Accepted: 02/05/2023] [Indexed: 02/09/2023]
Abstract
Thermoacidophilic archaea lack sigma factors and the large inventory of heat shock proteins (HSPs) widespread in bacterial genomes, suggesting other strategies for handling thermal stress are involved. Heat shock transcriptomes for the thermoacidophilic archaeon Saccharolobus (f. Sulfolobus) solfataricus 98/2 revealed genes that were highly responsive to thermal stress, including transcriptional regulators YtrASs (Ssol_2420) and FadRSs (Ssol_0314), as well as type II toxin-antitoxin (TA) loci VapBC6 (Ssol_2337, Ssol_2338) and VapBC22 (Ssol_0819, Ssol_0818). The role, if any, of type II TA loci during stress response in microorganisms, such as Escherichia coli, is controversial. But, when genes encoding YtrASs , FadRSs , VapC22, VapB6, and VapC6 were systematically mutated in Sa. solfataricus 98/2, significant up-regulation of the other genes within this set was observed, implicating an interconnected regulatory network during thermal stress response. VapBC6 and VapBC22 have close homologues in other Sulfolobales, as well as in other archaea (e.g. Pyrococcus furiosus and Archaeoglobus fulgidus), and their corresponding genes were also heat shock responsive. The interplay between VapBC TA loci and heat shock regulators in Sa solfataricus 98/2 not only indicates a cellular mechanism for heat shock response that differs from bacteria but one that could have common features within the thermophilic archaea.
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Affiliation(s)
- Charlotte R. Cooper
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905
| | - April M. Lewis
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905
| | - Jaspreet S. Notey
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905
| | - Arpan Mukherjee
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905
| | - Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905
| | - Paul H. Blum
- Beadle Center for Genetics, University of Nebraska-Lincoln, Lincoln, NE 68588-0666
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905
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2
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Knadler C, Graham V W, Rolfsmeier M, Haseltine CA. Divalent metal cofactors differentially modulate RadA-mediated strand invasion and exchange in Saccharolobus solfataricus. Biosci Rep 2023; 43:BSR20221807. [PMID: 36601994 PMCID: PMC9950535 DOI: 10.1042/bsr20221807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/20/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Central to the universal process of recombination, RecA family proteins form nucleoprotein filaments to catalyze production of heteroduplex DNA between substrate ssDNAs and template dsDNAs. ATP binding assists the filament in assuming the necessary conformation for forming heteroduplex DNA, but hydrolysis is not required. ATP hydrolysis has two identified roles which are not universally conserved: promotion of filament dissociation and enhancing flexibility of the filament. In this work, we examine ATP utilization of the RecA family recombinase SsoRadA from Saccharolobus solfataricus to determine its function in recombinase-mediated heteroduplex DNA formation. Wild-type SsoRadA protein and two ATPase mutant proteins were evaluated for the effects of three divalent metal cofactors. We found that unlike other archaeal RadA proteins, SsoRadA-mediated strand exchange is not enhanced by Ca2+. Instead, the S. solfataricus recombinase can utilize Mn2+ to stimulate strand invasion and reduce ADP-binding stability. Additionally, reduction of SsoRadA ATPase activity by Walker Box mutation or cofactor alteration resulted in a loss of large, complete strand exchange products. Depletion of ADP was found to improve initial strand invasion but also led to a similar loss of large strand exchange events. Our results indicate that overall, SsoRadA is distinct in its use of divalent cofactors but its activity with Mn2+ shows similarity to human RAD51 protein with Ca2+.
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Affiliation(s)
- Corey J. Knadler
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - William J. Graham V
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - Michael L. Rolfsmeier
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
| | - Cynthia A. Haseltine
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-7520, U.S.A
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3
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Romagnoli A, Moretti P, D’Agostino M, Rexha J, Perta N, Piccinini A, Di Marino D, Spinozzi F, La Teana A. Structural–Functional Relationship of the Ribonucleolytic Activity of aIF5A from Sulfolobus solfataricus. Biomolecules 2022; 12:biom12101432. [PMID: 36291641 PMCID: PMC9599864 DOI: 10.3390/biom12101432] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/16/2022] Open
Abstract
The translation factor IF5A is a highly conserved protein playing a well-recognized and well-characterized role in protein synthesis; nevertheless, some of its features as well as its abundance in the cell suggest that it may perform additional functions related to RNA metabolism. Here, we have undertaken a structural and functional characterization of aIF5A from the crenarchaeal Sulfolobus solfataricus model organism. We confirm the association of aIF5A with several RNA molecules in vivo and demonstrate that the protein is endowed with a ribonuclease activity which is specific for long and structured RNA. By means of biochemical and structural approaches we show that aIF5A can exist in both monomeric and dimeric conformations and the monomer formation is favored by the association with RNA. Finally, modelling of the three-dimensional structure of S. solfataricus aIF5A shows an extended positively charged surface which may explain its strong tendency to associate to RNA in vivo.
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Affiliation(s)
- Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- New York-Marche Structural Biology Center (Ny-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Correspondence: (A.R.); (A.L.T.)
| | - Paolo Moretti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Mattia D’Agostino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Jesmina Rexha
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Nunzio Perta
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Astra Piccinini
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- New York-Marche Structural Biology Center (Ny-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Francesco Spinozzi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Anna La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- New York-Marche Structural Biology Center (Ny-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Correspondence: (A.R.); (A.L.T.)
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4
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Cajili MKM, Prieto EI. Interplay between Alba and Cren7 Regulates Chromatin Compaction in Sulfolobus solfataricus. Biomolecules 2022; 12:biom12040481. [PMID: 35454068 PMCID: PMC9030869 DOI: 10.3390/biom12040481] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/03/2022] [Accepted: 03/15/2022] [Indexed: 01/06/2023] Open
Abstract
Chromatin compaction and regulation are essential processes for the normal function of all organisms, yet knowledge on how archaeal chromosomes are packed into higher-order structures inside the cell remains elusive. In this study, we investigated the role of archaeal architectural proteins Alba and Cren7 in chromatin folding and dynamics. Atomic force microscopy revealed that Sulfolobus solfataricus chromatin is composed of 28 nm fibers and 60 nm globular structures. In vitro reconstitution showed that Alba can mediate the formation of folded DNA structures in a concentration-dependent manner. Notably, it was demonstrated that Alba on its own can form higher-order structures with DNA. Meanwhile, Cren7 was observed to affect the formation of Alba-mediated higher-order chromatin structures. Overall, the results suggest an interplay between Alba and Cren7 in regulating chromatin compaction in archaea.
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5
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Abstract
Recruitment of RNA polymerase and initiation factors to the promoter is the only known target for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation are involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Saccharolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.
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Affiliation(s)
- Fabian Blombach
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Thomas Fouqueau
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Dorota Matelska
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Katherine Smollett
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Finn Werner
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK.
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6
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Huang CH, Huang TL, Liu YC, Chen TC, Lin SM, Shaw SY, Chang CC. Overexpression of a multifunctional β-glucosidase gene from thermophilic archaeon Sulfolobus solfataricus in transgenic tobacco could facilitate glucose release and its use as a reporter. Transgenic Res 2020; 29:511-527. [PMID: 32776308 DOI: 10.1007/s11248-020-00212-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 10/18/2019] [Accepted: 07/25/2020] [Indexed: 11/25/2022]
Abstract
The β-glucosidase, which hydrolyzes the β(1-4) glucosidic linkage of disaccharides, oligosaccharides and glucose-substituted molecules, has been used in many biotechnological applications. The current commercial source of β-glucosidase is mainly microbial fermentation. Plants have been developed as bioreactors to produce various kinds of proteins including β-glucosidase because of the potential low cost. Sulfolobus solfataricus is a thermoacidophilic archaeon that can grow optimally at high temperature, around 80 °C, and pH 2-4. We overexpressed the β-glucosidase gene from S. solfataricus in transgenic tobacco via Agrobacteria-mediated transformation. Three transgenic tobacco lines with β-glucosidase gene expression driven by the rbcS promoter were obtained, and the recombinant proteins were accumulated in chloroplasts, endoplasmic reticulum and vacuoles up to 1%, 0.6% and 0.3% of total soluble protein, respectively. By stacking the transgenes via crossing distinct transgenic events, the level of β-glucosidase in plants could further increase. The plant-expressed β-glucosidase had optimal activity at 80 °C and pH 5-6. In addition, the plant-expressed β-glucosidase showed high thermostability; on heat pre-treatment at 80 °C for 2 h, approximately 70% residual activity remained. Furthermore, wind-dried leaf tissues of transgenic plants showed good stability in short-term storage at room temperature, with β-glucosidase activity of about 80% still remaining after 1 week of storage as compared with fresh leaf. Furthermore, we demonstrated the possibility of using the archaebacterial β-glucosidase gene as a reporter in plants based on alternative β-galactosidase activity.
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Affiliation(s)
- Chih-Hao Huang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Tzu-Ling Huang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yu-Chang Liu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ting-Chieh Chen
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shih-Ming Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shyh-Yu Shaw
- Department of Chemistry, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Ching-Chun Chang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
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7
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Begander B, Huber A, Döring M, Sperl J, Sieber V. Development of an Improved Peroxidase-Based High-Throughput Screening for the Optimization of D-Glycerate Dehydratase Activity. Int J Mol Sci 2020; 21:ijms21010335. [PMID: 31947885 PMCID: PMC6982167 DOI: 10.3390/ijms21010335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/22/2019] [Accepted: 12/24/2019] [Indexed: 02/06/2023] Open
Abstract
Successful directed evolution examples span a broad range of improved enzyme properties. Nevertheless, the most challenging step for each single directed evolution approach is an efficient identification of improved variants from a large genetic library. Thus, the development and choice of a proper high-throughput screening is a central key for the optimization of enzymes. The detection of low enzymatic activities is especially complicated when they lead to products that are present in the metabolism of the utilized genetic host. Coupled enzymatic assays based on colorimetric products have enabled the optimization of many of such enzymes, but are susceptible to problems when applied on cell extract samples. The purpose of this study was the development of a high-throughput screening for D-glycerate dehydratase activity in cell lysates. With the aid of an automated liquid handling system, we developed a high-throughput assay that relied on a pre-treatment step of cell extract prior to performing the enzymatic and assay reactions. We could successfully apply our method, which should also be transferable to other cell extract-based peroxidase assays, to identify an improved enzyme for the dehydration of D-glycerate.
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Affiliation(s)
- Benjamin Begander
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, D-94315 Straubing, Germany
| | - Anna Huber
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, D-94315 Straubing, Germany
| | - Manuel Döring
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, D-94315 Straubing, Germany
| | - Josef Sperl
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, D-94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, D-94315 Straubing, Germany
- Catalysis Research Center, Technical University of Munich, 85748 Garching, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
- Correspondence: ; Tel.: +49-9421-187-300
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8
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Johnson T, Payne S, Grove R, McCarthy S, Oeltjen E, Mach C, Adamec J, Wilson MA, Van Cott K, Blum P. Methylation deficiency of chromatin proteins is a non-mutational and epigenetic-like trait in evolved lines of the archaeon Sulfolobus solfataricus. J Biol Chem 2019; 294:7821-7832. [PMID: 30918025 PMCID: PMC6514617 DOI: 10.1074/jbc.ra118.006469] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/01/2019] [Indexed: 11/06/2022] Open
Abstract
Archaea are a distinct and deeply rooted lineage that harbor eukaryotic-like mechanisms, including several that manage chromosome function. In previous work, the thermoacidophilic crenarchaeon, Sulfolobus solfataricus, was subjected to adaptive laboratory evolution to produce three strains, called SARC, with a new heritable trait of super acid resistance. These strains acquired heritable conserved transcriptomes, yet one strain contained no mutations. Homologous recombination without allele replacement at SARC acid resistance genes caused changes in both phenotype and expression of the targeted gene. As recombination displaces chromatin proteins, their involvement was predicted in the SARC trait. Native chromatin proteins are basic and highly abundant and undergo post-translational modification through lysine monomethylation. In this work, their modification states were investigated. In all SARC lines, two chromatin proteins, Cren7 and Sso7d, were consistently undermethylated, whereas other chromatin proteins were unaltered. This pattern was heritable in the absence of selection and independent of transient exposure to acid stress. The bulk of Sso7d was undermethylated at three contiguous N-terminal lysine residues but not at central or C-terminal regions. The N-terminal region formed a solvent-exposed patch located on the opposite side of the binding domain associated with the DNA minor groove. By analogy to eukaryotic histones, this patch could interact with other chromosomal proteins and be modulated by differential post-translational modification. Previous work established an epigenetic-like mechanism of adaptation and inheritance in S. solfataricus The identification of heritable epigenetic marks in this work further supports the occurrence of an epigenetic process in archaea.
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Affiliation(s)
- Tyler Johnson
- From the Beadle Center for Genetics, School of Biological Sciences
| | - Sophie Payne
- From the Beadle Center for Genetics, School of Biological Sciences
| | - Ryan Grove
- the Department of Biochemistry and Redox Biology Center, and
| | - Samuel McCarthy
- From the Beadle Center for Genetics, School of Biological Sciences
| | - Erin Oeltjen
- From the Beadle Center for Genetics, School of Biological Sciences
| | - Collin Mach
- From the Beadle Center for Genetics, School of Biological Sciences
| | - Jiri Adamec
- the Department of Biochemistry and Redox Biology Center, and
| | - Mark A Wilson
- the Department of Biochemistry and Redox Biology Center, and
| | - Kevin Van Cott
- the Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, Nebraska 68588, and
| | - Paul Blum
- From the Beadle Center for Genetics, School of Biological Sciences,
- the Department of Microbiology and Toxicology, University of California, Santa Cruz, California 95064
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9
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Abstract
We theoretically study the effects of non-monotonic response curves in genetic auto-regulation by exploring the possible dynamical behaviors for such systems. Our motivation is twofold: we aim at conceiving the simplest genetic circuits for synthetic biology and at understanding the natural auto-regulation of the LrpB protein of the Sulfolobus solfataricus archaeon which exhibits non-monotonicity. We analyzed three toy models, based on mass-action kinetics, with increasing complexity and sought for oscillations and (fast) bistable switching. We performed large parameter scans and sensitivity analyses, and quantified the quality of the oscillators and switches by computing relative volumes in parameter space reproducing the sought dynamical behavior. All single gene systems need finely tuned parameters in order to oscillate, but bistable switches are more robust against parameter changes. We expected non-monotonic switches to be faster than monotonic ones, however solutions combining both auto-activation and repression in the physiological range to obtain fast switches are scarce. Our analysis shows that the Ss-LrpB system can not provide a bistable switch and that robust oscillations are unlikely. Gillespie simulations suggest that the function of the natural Ss-LrpB system is sensing via a spiking behavior, which is in line with the fact that this protein has a metabolic regulatory function and binds to a ligand.
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Affiliation(s)
- Lana Descheemaeker
- Applied Physics Research Group, Physics Department, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel - Université Libre de Bruxelles, Brussels, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Sophie de Buyl
- Applied Physics Research Group, Physics Department, Vrije Universiteit Brussel, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel - Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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10
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Abstract
Type III CRISPR effector complexes utilize a bound CRISPR RNA (crRNA) to detect the presence of RNA from invading mobile genetic elements in the cell. This RNA binding results in the activation of two enzymatic domains of the Cas10 subunit-the HD nuclease domain, which degrades DNA, and PALM/cyclase domain. The latter synthesizes cyclic oligoadenylate (cOA) molecules by polymerizing ATP, and cOA acts as a second messenger in the cell, switching on the antiviral response by activating host ribonucleases and other proteins. In this chapter, we focus on the methods required to study the biochemistry of this recently discovered cOA signaling pathway. We cover protein expression and purification, synthesis of cOA and its linear analogues, kinetic analysis of cOA synthesis and cOA-stimulated ribonuclease activity, and small molecule detection and identification with thin-layer chromatography and mass spectrometry. The methods described are based on our recent studies of the type III CRISPR system in Sulfolobus solfataricus, but are widely applicable to other type III systems.
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Affiliation(s)
- Christophe Rouillon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Januka S Athukoralage
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom.
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11
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Gadkari VV, Harvey SR, Raper AT, Chu WT, Wang J, Wysocki VH, Suo Z. Investigation of sliding DNA clamp dynamics by single-molecule fluorescence, mass spectrometry and structure-based modeling. Nucleic Acids Res 2018; 46:3103-3118. [PMID: 29529283 PMCID: PMC5888646 DOI: 10.1093/nar/gky125] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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] [Received: 11/03/2017] [Revised: 01/23/2018] [Accepted: 02/12/2018] [Indexed: 12/20/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a trimeric ring-shaped clamp protein that encircles DNA and interacts with many proteins involved in DNA replication and repair. Despite extensive structural work to characterize the monomeric, dimeric, and trimeric forms of PCNA alone and in complex with interacting proteins, no structure of PCNA in a ring-open conformation has been published. Here, we use a multidisciplinary approach, including single-molecule Förster resonance energy transfer (smFRET), native ion mobility-mass spectrometry (IM-MS), and structure-based computational modeling, to explore the conformational dynamics of a model PCNA from Sulfolobus solfataricus (Sso), an archaeon. We found that Sso PCNA samples ring-open and ring-closed conformations even in the absence of its clamp loader complex, replication factor C, and transition to the ring-open conformation is modulated by the ionic strength of the solution. The IM-MS results corroborate the smFRET findings suggesting that PCNA dynamics are maintained in the gas phase and further establishing IM-MS as a reliable strategy to investigate macromolecular motions. Our molecular dynamic simulations agree with the experimental data and reveal that ring-open PCNA often adopts an out-of-plane left-hand geometry. Collectively, these results implore future studies to define the roles of PCNA dynamics in DNA loading and other PCNA-mediated interactions.
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Affiliation(s)
- Varun V Gadkari
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Austin T Raper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P.R. China
- Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY 11794-3400, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Zucai Suo
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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12
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Rollie C, Graham S, Rouillon C, White MF. Prespacer processing and specific integration in a Type I-A CRISPR system. Nucleic Acids Res 2018; 46:1007-1020. [PMID: 29228332 PMCID: PMC5815122 DOI: 10.1093/nar/gkx1232] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [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: 10/31/2017] [Revised: 11/22/2017] [Accepted: 11/29/2017] [Indexed: 12/15/2022] Open
Abstract
The CRISPR-Cas system for prokaryotic adaptive immunity provides RNA-mediated protection from viruses and mobile genetic elements. Adaptation is dependent on the Cas1 and Cas2 proteins along with varying accessory proteins. Here we analyse the process in Sulfolobus solfataricus, showing that while Cas1 and Cas2 catalyze spacer integration in vitro, host factors are required for specificity. Specific integration also requires at least 400 bp of the leader sequence, and is dependent on the presence of hydrolysable ATP, suggestive of an active process that may involve DNA remodelling. Specific spacer integration is associated with processing of prespacer 3' ends in a PAM-dependent manner. This is reflected in PAM-dependent processing of prespacer 3' ends in vitro in the presence of cell lysate or the Cas4 nuclease, in a reaction consistent with PAM-directed binding and protection of prespacer DNA. These results highlight the diverse interplay between CRISPR-Cas elements and host proteins across CRISPR types.
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Affiliation(s)
- Clare Rollie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Christophe Rouillon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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13
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Jacquet P, Hiblot J, Daudé D, Bergonzi C, Gotthard G, Armstrong N, Chabrière E, Elias M. Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase. Sci Rep 2017; 7:16745. [PMID: 29196634 PMCID: PMC5711954 DOI: 10.1038/s41598-017-16841-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [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: 08/29/2017] [Accepted: 11/16/2017] [Indexed: 11/13/2022] Open
Abstract
The redesign of enzyme active sites to alter their function or specificity is a difficult yet appealing challenge. Here we used a structure-based design approach to engineer the lactonase SsoPox from Sulfolobus solfataricus into a phosphotriesterase. The five best variants were characterized and their structure was solved. The most active variant, αsD6 (V27A-Y97W-L228M-W263M) demonstrates a large increase in catalytic efficiencies over the wild-type enzyme, with increases of 2,210-fold, 163-fold, 58-fold, 16-fold against methyl-parathion, malathion, ethyl-paraoxon, and methyl-paraoxon, respectively. Interestingly, the best mutants are also capable of degrading fensulfothion, which is reported to be an inhibitor for the wild-type enzyme, as well as others that are not substrates of the starting template or previously reported W263 mutants. The broad specificity of these engineered variants makes them promising candidates for the bioremediation of organophosphorus compounds. Analysis of their structures reveals that the increase in activity mainly occurs through the destabilization of the active site loop involved in substrate binding, and it has been observed that the level of disorder correlates with the width of the enzyme specificity spectrum. This finding supports the idea that active site conformational flexibility is essential to the acquisition of broader substrate specificity.
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Affiliation(s)
- Pauline Jacquet
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Julien Hiblot
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
- MPI for Medical Research, Chemical Biology department (EPFL), Heidelberg, Germany
| | - David Daudé
- Gene&GreenTK, IHU Méditerranée Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Céline Bergonzi
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA
| | - Guillaume Gotthard
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Nicholas Armstrong
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Eric Chabrière
- CNRS UMR 7278, IRD198, INSERM U1095, APHM, Institut Hospitalier Universitaire Méditerranée-Infection, Aix-Marseille Université, 19-21 Bd Jean Moulin, 13005, Marseille, France.
| | - Mikael Elias
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics & Biotechnology Institute, St. Paul, MN, 55108, USA.
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Nguyen TTH, Kim SB, Kim NM, Kang C, Chung B, Park JS, Kim D. Production of steviol from steviol glucosides using β-glycosidase from Sulfolobus solfataricus. Enzyme Microb Technol 2016; 93-94:157-165. [PMID: 27702476 DOI: 10.1016/j.enzmictec.2016.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 05/30/2016] [Revised: 08/12/2016] [Accepted: 08/23/2016] [Indexed: 11/15/2022]
Abstract
Steviol is a diterpene isolated from the plant Stevia rebaudiana that has a potential role as an antihyperglycemic agent by stimulating insulin secretion from pancreatic beta cells and also has significant potential to diminish the renal clearance of anionic drugs and their metabolites. In this study, the lacS gene, which encodes a thermostable β-glycosidase (SSbgly) enzyme from the extremely thermoacidophillic archaeon Sulfolobus solfataricus, was cloned and expressed in E. coli Rossetta BL21(DE3)pLyS using lactose as an inducer. Through fermentation, SSbgly was expressed as a 61kDa protein with activity of 24.3U/mg and the OD600 of 23 was reached after 18h induction with 10mM lactose. Purified protein was obtained by Ni-Sepharose chromatography with a yield of 92.3%. SSbgly hydrolyzed steviol glycosides to produce steviol with a yield of 99.2%. The optimum conditions for steviol production were 50U/ml SSbgly and 90mg/ml Ste at 75°C as determined by the response surface method.
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Affiliation(s)
- Thi Thanh Hanh Nguyen
- Institute of Food Industrialization, Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang-gun, Gangwon-do, 25354, South Korea
| | - Seong-Bo Kim
- CJ CheilJedang, Life Ingredient & Material Research Institute, Suwon, 16495, South Korea
| | - Nahyun M Kim
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Choongil Kang
- OTTOGI Corporation, Anyang, Kyunggi, 06177, South Korea
| | | | - Jun-Seong Park
- Skin Research Institute, Amorepacific Corporation R&D Center, Yongin, 17074, South Korea
| | - Doman Kim
- Institute of Food Industrialization, Institutes of Green Bio Science & Technology, Seoul National University, Pyeongchang-gun, Gangwon-do, 25354, South Korea; Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang-gun, Gangwon-do, 25354, South Korea.
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15
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Zhang J, Graham S, Tello A, Liu H, White MF. Multiple nucleic acid cleavage modes in divergent type III CRISPR systems. Nucleic Acids Res 2016; 44:1789-99. [PMID: 26801642 PMCID: PMC4770243 DOI: 10.1093/nar/gkw020] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [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: 10/26/2015] [Revised: 12/14/2015] [Accepted: 01/07/2016] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas is an RNA-guided adaptive immune system that protects bacteria and archaea from invading nucleic acids. Type III systems (Cmr, Csm) have been shown to cleave RNA targets in vitro and some are capable of transcription-dependent DNA targeting. The crenarchaeon Sulfolobus solfataricus has two divergent subtypes of the type III system (Sso-IIID and a Cmr7-containing variant of Sso-IIIB). Here, we report that both the Sso-IIID and Sso-IIIB complexes cleave cognate RNA targets with a ruler mechanism and 6 or 12 nt spacing that relates to the organization of the Cas7 backbone. This backbone-mediated cleavage activity thus appears universal for the type III systems. The Sso-IIIB complex is also known to possess a distinct 'UA' cleavage mode. The predominant activity observed in vitro depends on the relative molar concentration of protein and target RNA. The Sso-IIID complex can cleave plasmid DNA targets in vitro, generating linear DNA products with an activity that is dependent on both the cyclase and HD nuclease domains of the Cas10 subunit, suggesting a role for both nuclease active sites in the degradation of double-stranded DNA targets.
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Affiliation(s)
- Jing Zhang
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - Agnes Tello
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - Huanting Liu
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, Fife KY16 9ST, UK
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16
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McCarthy S, Johnson T, Pavlik BJ, Payne S, Schackwitz W, Martin J, Lipzen A, Keffeler E, Blum P. Expanding the Limits of Thermoacidophily in the Archaeon Sulfolobus solfataricus by Adaptive Evolution. Appl Environ Microbiol 2016; 82:857-67. [PMID: 26590281 PMCID: PMC4725277 DOI: 10.1128/aem.03225-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 11/15/2015] [Indexed: 11/20/2022] Open
Abstract
Extremely thermoacidophilic Crenarchaeota belonging to the order Sulfolobales flourish in hot acidic habitats that are strongly oxidizing. The pH extremes of these habitats, however, often exceed the acid tolerance of type species and strains. Here, adaptive laboratory evolution was used over a 3-year period to test whether such organisms harbor additional thermoacidophilic capacity. Three distinct cell lines derived from a single type species were subjected to high-temperature serial passage while culture acidity was gradually increased. A 178-fold increase in thermoacidophily was achieved after 29 increments of shifted culture pH resulting in growth at pH 0.8 and 80°C. These strains were named super-acid-resistant Crenarchaeota (SARC). Mathematical modeling using growth parameters predicted the limits of acid resistance, while genome resequencing and transcriptome resequencing were conducted for insight into mechanisms responsible for the evolved trait. Among the mutations that were detected, a set of eight nonsynonymous changes may explain the heritability of increased acid resistance despite an unexpected lack of transposition. Four multigene components of the SARC transcriptome implicated oxidative stress as a primary challenge accompanying growth at acid extremes. These components included accelerated membrane biogenesis, induction of the mer operon, and an increased capacity for the generation of energy and reductant.
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Affiliation(s)
- Samuel McCarthy
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Tyler Johnson
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Benjamin J Pavlik
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Sophie Payne
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Wendy Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Joel Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Erica Keffeler
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Paul Blum
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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17
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Shin KC, Choi HY, Seo MJ, Oh DK. Compound K Production from Red Ginseng Extract by β-Glycosidase from Sulfolobus solfataricus Supplemented with α-L-Arabinofuranosidase from Caldicellulosiruptor saccharolyticus. PLoS One 2015; 10:e0145876. [PMID: 26710074 PMCID: PMC4692446 DOI: 10.1371/journal.pone.0145876] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [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: 09/24/2015] [Accepted: 12/09/2015] [Indexed: 11/18/2022] Open
Abstract
Ginsenoside compound K (C-K) is attracting a lot of interest because of its biological and pharmaceutical activities, including hepatoprotective, antitumor, anti-wrinkling, and anti-skin aging activities. C-K has been used as the principal ingredient in skin care products. For the effective application of ginseng extracts to the manufacture of cosmetics, the PPD-type ginsenosides in ginseng extracts should be converted to C-K by enzymatic conversion. For increased yield of C-K from the protopanaxadiol (PPD)-type ginsenosides in red-ginseng extract (RGE), the α-L-arabinofuranoside-hydrolyzing α-L-arabinofuranosidase from Caldicellulosiruptor saccharolyticus (CS-abf) was used along with the β-D-glucopyranoside/α-L-arabinopyranoside-hydrolyzing β-glycosidase from Sulfolobus solfataricus (SS-bgly) because SS-bgly showed very low hydrolytic activity on the α-L-arabinofuranoside linkage in ginsenosides. The optimal reaction conditions for C-K production were as follows: pH 6.0, 80°C, 2 U/mL SS-bgly, 3 U/mL CS-abf, and 7.5 g/L PPD-type ginsenosides in RGE. Under these optimized conditions, SS-bgly supplemented with CS-abf produced 4.2 g/L C-K from 7.5 g/L PPD-type ginsenosides in 12 h without other ginsenosides, with a molar yield of 100% and a productivity of 348 mg/L/h. To the best of our knowledge, this is the highest concentration and productivity of C-K from ginseng extract ever published in literature.
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Affiliation(s)
- Kyung-Chul Shin
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Hye-Yeon Choi
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Min-Ju Seo
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
- * E-mail:
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18
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De Falco M, Catalano F, Rossi M, Ciaramella M, De Felice M. NurA Is Endowed with Endo- and Exonuclease Activities that Are Modulated by HerA: New Insight into Their Role in DNA-End Processing. PLoS One 2015; 10:e0142345. [PMID: 26560692 PMCID: PMC4641729 DOI: 10.1371/journal.pone.0142345] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 09/16/2015] [Accepted: 10/20/2015] [Indexed: 11/18/2022] Open
Abstract
The nuclease NurA and the ATPase HerA are present in all known thermophilic archaea and cooperate with the highly conserved MRE11/RAD50 proteins to facilitate efficient DNA double-strand break end processing during homologous recombinational repair. However, contradictory results have been reported on the exact activities and mutual dependence of these two enzymes. To understand the functional relationship between these two enzymes we deeply characterized Sulfolobus solfataricus NurA and HerA proteins. We found that NurA is endowed with exo- and endonuclease activities on various DNA substrates, including linear (single-stranded and double stranded) as well as circular molecules (single stranded and supercoiled double-stranded). All these activities are not strictly dependent on the presence of HerA, require divalent ions (preferably Mn2+), and are inhibited by the presence of ATP. The endo- and exonculease activities have distinct requirements: whereas the exonuclease activity on linear DNA fragments is stimulated by HerA and depends on the catalytic D58 residue, the endonuclease activity on circular double-stranded DNA is HerA-independent and is not affected by the D58A mutation. On the basis of our results we propose a mechanism of action of NurA/HerA complex during DNA end processing.
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Affiliation(s)
- Mariarosaria De Falco
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
- * E-mail: (M. De Falco); (M. De Felice)
| | - Federico Catalano
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
| | - Mosè Rossi
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
| | - Maria Ciaramella
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
| | - Mariarita De Felice
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, Naples, 80131, Italy
- * E-mail: (M. De Falco); (M. De Felice)
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19
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Sholder G, Creech A, Loechler EL. How Y-Family DNA polymerase IV is more accurate than Dpo4 at dCTP insertion opposite an N2-dG adduct of benzo[a]pyrene. DNA Repair (Amst) 2015; 35:144-53. [PMID: 26523515 DOI: 10.1016/j.dnarep.2015.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/11/2015] [Accepted: 09/11/2015] [Indexed: 12/11/2022]
Abstract
To bypass DNA damage, cells have Y-Family DNA polymerases (DNAPs). One Y-Family-class includes DNAP κ and DNAP IV, which accurately insert dCTP opposite N(2)-dG adducts, including from the carcinogen benzo[a]pyrene (BP). Another class includes DNAP η and DNAP V, which insert accurately opposite UV-damage, but inaccurately opposite BP-N(2)-dG. To investigate structural differences between Y-Family-classes, regions are swapped between DNAP IV (a κ/IV-class-member) and Dpo4 (a η/V-class-member); the kinetic consequences are evaluated via primer-extension studies with a BP-N(2)-dG-containing template. Four key structural elements are revealed. (1) Y-Family DNAPs have discreet non-covalent contacts between their little finger-domain (LF-Domain) and their catalytic core-domain (CC-Domain), which we call "non-covalent bridges" (NCBs). Arg37 and Arg38 in DNAP IV's CC-Domain near the active site form a non-covalent bridge (AS-NCB) by interacting with Glu251 and Asp252, respectively, in DNAP IV's LF-Domain. Without these interactions dATP/dGTP/dTTP misinsertions increase. DNAP IV's AS-NCB suppresses misinsertions better than Dpo4's equivalent AS-NCB. (2) DNAP IV also suppresses dATP/dGTP/dTTP misinsertions via a second non-covalent bridge, which is ∼8Å from the active site (Distal-NCB). Dpo4 has no Distal-NCB, rendering it inferior at dATP/dGTP/dTTP suppression. (3) dCTP insertion is facilitated by the larger minor groove opening near the active site in DNAP IV versus Dpo4, which is sensible given that Watson/Crick-like [dCTP:BP-N(2)-dG] pairing requires the BP-moiety to be in the minor groove. (4) Compared to Dpo4, DNAP IV has a smaller major groove opening, which suppresses dGTP misinsertion, implying BP-N(2)-dG bulk in the major groove during Hoogsteen syn-adduct-dG:dGTP pairing. In summary, DNAP IV has a large minor groove opening to enhance dCTP insertion, a plugged major groove opening to suppress dGTP misinsertion, and two non-covalent bridges (near and distal to the active site) to suppress dATP/dGTP/dTTP misinsertions; collectively these four structural features enhance DNAP IV's dNTP insertion fidelity opposite a BP-N(2)-dG adduct compared to Dpo4.
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Affiliation(s)
- Gabriel Sholder
- Biology Department, Boston University, Boston, MA 02215, USA
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20
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Abstract
Infection of archaea with phylogenetically diverse single viruses, performed in different laboratories, has failed to activate spacer acquisition into host CRISPR loci. The first successful uptake of archaeal de novo spacers was observed on infection of Sulfolobus solfataricus P2 with an environmental virus mixture isolated from Yellowstone National Park (Erdmann and Garrett, Mol Microbiol 85:1044-1056, 2012). Experimental studies of isolated genetic elements from this mixture revealed that SMV1 (S ulfolobus Monocauda Virus 1), a tailed spindle-shaped virus, can induce spacer acquisition in CRISPR loci of Sulfolobus species from a second coinfecting conjugative plasmid or virus (Erdmann and Garrett, Mol Microbiol 85:1044-1056, 2012; Erdmann et al. Mol Microbiol 91:900-917, 2014). Here we describe, firstly, the isolation of archaeal virus mixtures from terrestrial hot springs and the techniques used both to infect laboratory strains with these virus mixtures and to obtain purified virus particles. Secondly, we present the experimental conditions required for activating SMV1-induced spacer acquisition in two different Sulfolobus species.
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Affiliation(s)
- Susanne Erdmann
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen N, Denmark,
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21
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Zaramela LS, Vêncio RZN, ten-Caten F, Baliga NS, Koide T. Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life. PLoS One 2014; 9:e107680. [PMID: 25238539 PMCID: PMC4169567 DOI: 10.1371/journal.pone.0107680] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [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: 03/09/2014] [Accepted: 08/18/2014] [Indexed: 01/06/2023] Open
Abstract
A plethora of non-coding RNAs has been discovered using high-resolution transcriptomics tools, indicating that transcriptional and post-transcriptional regulation is much more complex than previously appreciated. Small RNAs associated with transcription start sites of annotated coding regions (TSSaRNAs) are pervasive in both eukaryotes and bacteria. Here, we provide evidence for existence of TSSaRNAs in several archaeal transcriptomes including: Halobacterium salinarum, Pyrococcus furiosus, Methanococcus maripaludis, and Sulfolobus solfataricus. We validated TSSaRNAs from the model archaeon Halobacterium salinarum NRC-1 by deep sequencing two independent small-RNA enriched (RNA-seq) and a primary-transcript enriched (dRNA-seq) strand-specific libraries. We identified 652 transcripts, of which 179 were shown to be primary transcripts (∼7% of the annotated genome). Distinct growth-associated expression patterns between TSSaRNAs and their cognate genes were observed, indicating a possible role in environmental responses that may result from RNA polymerase with varying pausing rhythms. This work shows that TSSaRNAs are ubiquitous across all domains of life.
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Affiliation(s)
- Livia S. Zaramela
- Department Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Ricardo Z. N. Vêncio
- Department of Computing and Mathematics, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Felipe ten-Caten
- Department Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Tie Koide
- Department Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- * E-mail:
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Abstract
The DNA cutting and joining reactions of HIV-1 integration are catalyzed by integrase (IN), a viral protein that functions as a tetramer bridging the two viral DNA ends (intasome). Two major obstacles for biochemical and structural studies of HIV-1 intasomes are 1) the low efficiency of assembly with oligonucleotide DNA substrates, and 2) the non-specific aggregation of both intasomes and free IN in the reaction mixture. By fusing IN with a small non-specific DNA binding protein, Sulfolobus solfataricus chromosomal protein Sso7d (PDB: 1BNZ), we have engineered a highly soluble and hyperactive IN. Unlike wild-type IN, it efficiently catalyzes intasome assembly and concerted integration with oligonucleotide DNA substrates. The fusion IN protein also functions to integrate viral reverse transcripts during HIV-infection. The hyperactive HIV-1 IN may assist in facilitating future biochemical and structural studies of HIV-1 intasomes. Understanding the mechanistic basis of the Sso7d-IN fusion protein could provide insight into the factors that have hindered biophysical studies of wild-type HIV-1 IN and intasomes.
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Affiliation(s)
- Min Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kellie A. Jurado
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shiqiang Lin
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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23
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Kim S, Lee SB. Characterization ofSulfolobus solfataricus2-Keto-3-deoxy-D-gluconate Kinase in the Modified Entner-Doudoroff Pathway. Biosci Biotechnol Biochem 2014; 70:1308-16. [PMID: 16794308 DOI: 10.1271/bbb.50566] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [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: 11/08/2022]
Abstract
The thermoacidophilic archaeon Sulfolobus solfataricus is known to utilize D-glucose via the nonphosphorylated Entner-Doudoroff (ED) pathway. But, the genome database shows that this microorganism has a gene (kdgK) encoding 2-keto-3-deoxy-D-gluconate (KDG) kinase (KDGK) which phosphorylates KDG to 2-keto-3-deoxy-6-phosphogluconate. Interestingly, kdgK and three other genes in the modified ED pathway are organized as an operon-like structure. In this study, we report confirmation of the catalytic activity of the S. solfataricus KDGK protein. We also found that the kdgK gene was transcribed as polycistronic transcripts. Proteome analysis of cell lysate revealed that all gene products in the kdgK operon were expressed as functional proteins. These results strongly indicate that S. solfataricus metabolizes D-glucose via the 'partially' nonphosphorylated ED pathway. A purified recombinant S. solfataricus KDGK had K(m) and k(cat) values of 0.14 mM and 60.8 s(-1) respectively for KDG, and showed maximal activity at temperatures between 70 and 80 degrees C and pHs between 7.0 and 8.0.
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Affiliation(s)
- Seonghun Kim
- School of Environmental Science and Engineering, Pohang University of Science and Technology, Korea
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Märtens B, Manoharadas S, Hasenöhrl D, Zeichen L, Bläsi U. Back to translation: removal of aIF2 from the 5'-end of mRNAs by translation recovery factor in the crenarchaeon Sulfolobus solfataricus. Nucleic Acids Res 2014; 42:2505-11. [PMID: 24271401 PMCID: PMC3936769 DOI: 10.1093/nar/gkt1169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 07/01/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 11/13/2022] Open
Abstract
The translation initiation factor aIF2 of the crenarchaeon Sulfolobus solfataricus (Sso) recruits initiator tRNA to the ribosome and stabilizes mRNAs by binding via the γ-subunit to their 5'-triphosphate end. It has been hypothesized that the latter occurs predominantly during unfavorable growth conditions, and that aIF2 or aIF2-γ is released on relief of nutrient stress to enable in particular anew translation of leaderless mRNAs. As leaderless mRNAs are prevalent in Sso and aIF2-γ bound to the 5'-end of a leaderless RNA inhibited ribosome binding in vitro, we aimed at elucidating the mechanism underlying aIF2/aIF2-γ recycling from mRNAs. We have identified a protein termed Trf (translation recovery factor) that co-purified with trimeric aIF2 during outgrowth of cells from prolonged stationary phase. Subsequent in vitro studies revealed that Trf triggers the release of trimeric aIF2 from RNA, and that Trf directly interacts with the aIF2-γ subunit. The importance of Trf is further underscored by an impaired protein synthesis during outgrowth from stationary phase in a Sso trf deletion mutant.
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Affiliation(s)
- Birgit Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Salim Manoharadas
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - David Hasenöhrl
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Lukas Zeichen
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
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Comte A, Christen P, Davidson S, Pophillat M, Lorquin J, Auria R, Simon G, Casalot L. Biochemical, transcriptional and translational evidences of the phenol-meta-degradation pathway by the hyperthermophilic Sulfolobus solfataricus 98/2. PLoS One 2013; 8:e82397. [PMID: 24349276 PMCID: PMC3859572 DOI: 10.1371/journal.pone.0082397] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022] Open
Abstract
Phenol is a widespread pollutant and a model molecule to study the biodegradation of monoaromatic compounds. After a first oxidation step leading to catechol in mesophilic and thermophilic microorganisms, two main routes have been identified depending on the cleavage of the aromatic ring: ortho involving a catechol 1,2 dioxygenase (C12D) and meta involving a catechol 2,3 dioxygenase (C23D). Our work aimed at elucidating the phenol-degradation pathway in the hyperthermophilic archaea Sulfolobus solfataricus 98/2. For this purpose, the strain was cultivated in a fermentor under different substrate and oxygenation conditions. Indeed, reducing dissolved-oxygen concentration allowed slowing down phenol catabolism (specific growth and phenol-consumption rates dropped 55% and 39%, respectively) and thus, evidencing intermediate accumulations in the broth. HPLC/Diode Array Detector and LC-MS analyses on culture samples at low dissolved-oxygen concentration (DOC = 0.06 mg x L(-1)) suggested, apart for catechol, the presence of 2-hydroxymuconic acid, 4-oxalocrotonate and 4-hydroxy-2-oxovalerate, three intermediates of the meta route. RT-PCR analysis on oxygenase-coding genes of S. solfataricus 98/2 showed that the gene coding for the C23D was expressed only on phenol. In 2D-DIGE/MALDI-TOF analysis, the C23D was found and identified only on phenol. This set of results allowed us concluding that S. solfataricus 98/2 degrade phenol through the meta route.
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Affiliation(s)
- Alexia Comte
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Pierre Christen
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Sylvain Davidson
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Matthieu Pophillat
- Institut Paoli-Calmettes, Aix Marseille Université, CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille (CRCM), Marseille, France
| | - Jean Lorquin
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Richard Auria
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Gwenola Simon
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
| | - Laurence Casalot
- Aix Marseille Université, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, Marseille, France
- Université du Sud Toulon-Var, CNRS/INSU, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, La Garde, France
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26
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Manica A, Zebec Z, Steinkellner J, Schleper C. Unexpectedly broad target recognition of the CRISPR-mediated virus defence system in the archaeon Sulfolobus solfataricus. Nucleic Acids Res 2013; 41:10509-17. [PMID: 24021627 PMCID: PMC3905844 DOI: 10.1093/nar/gkt767] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [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: 05/19/2013] [Revised: 08/03/2013] [Accepted: 08/05/2013] [Indexed: 12/26/2022] Open
Abstract
The hyperthermophilic archaeon Sulfolobus solfataricus carries an extensive array of clustered regularly interspaced short palindromic repeats (CRISPR) systems able to mediate DNA degradation of invading genetic elements when complementarity to the small CRISPR-derived (cr)RNAs is given. Studying virus defence in vivo with recombinant viral variants, we demonstrate here that an unexpectedly high number of mutations are tolerated between the CRISPR-derived guide RNAs (crRNAs) and their target sequences (protospacer). Up to 15 mismatches in the crRNA still led to ∼50% of DNA degradation, when these mutations were outside the 'seed' region. More than 15 mutations were necessary to fully abolished interference. Different from other CRISPR systems investigated in vivo, mutations outside the protospacer region indicated no need for a protospacer adjacent motif sequence to confer DNA interference. However, complementarity of only 3 nucleotides between the repeat-derived 5' handle of the crRNA and nucleotides adjacent to the protospacer enabled self-recognition, i.e. protection of the host locus. Our findings show commonalities and differences among the various CRISPR-mediated defence systems and suggest that they should not merely be perceived as a 'first-barrier-defence system' but may be considered to have a broader mechanism that allows host cells to cope with viruses keeping them at reduced levels.
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Affiliation(s)
| | | | | | - Christa Schleper
- Department of Genetics in Ecology, University of Vienna, Althanstrasse 14, A-1090 Vienna, Austria
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27
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Hiblot J, Gotthard G, Elias M, Chabriere E. Differential active site loop conformations mediate promiscuous activities in the lactonase SsoPox. PLoS One 2013; 8:e75272. [PMID: 24086491 PMCID: PMC3781021 DOI: 10.1371/journal.pone.0075272] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [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: 05/16/2013] [Accepted: 08/14/2013] [Indexed: 11/19/2022] Open
Abstract
Enzymes are proficient catalysts that enable fast rates of Michaelis-complex formation, the chemical step and products release. These different steps may require different conformational states of the active site that have distinct binding properties. Moreover, the conformational flexibility of the active site mediates alternative, promiscuous functions. Here we focused on the lactonase SsoPox from Sulfolobus solfataricus. SsoPox is a native lactonase endowed with promiscuous phosphotriesterase activity. We identified a position in the active site loop (W263) that governs its flexibility, and thereby affects the substrate specificity of the enzyme. We isolated two different sets of substitutions at position 263 that induce two distinct conformational sampling of the active loop and characterized the structural and kinetic effects of these substitutions. These sets of mutations selectively and distinctly mediate the improvement of the promiscuous phosphotriesterase and oxo-lactonase activities of SsoPox by increasing active-site loop flexibility. These observations corroborate the idea that conformational diversity governs enzymatic promiscuity and is a key feature of protein evolvability.
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Affiliation(s)
- Julien Hiblot
- URMITE UMR CNRS-IRD 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Guillaume Gotthard
- URMITE UMR CNRS-IRD 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
| | - Mikael Elias
- Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel
| | - Eric Chabriere
- URMITE UMR CNRS-IRD 6236, Faculté de Médecine et de Pharmacie, Université de la Méditerranée, Marseille, France
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28
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Fu CW, Wang YP, Fang TY, Lin TH. Interaction between trehalose and MTHase from Sulfolobus solfataricus studied by theoretical computation and site-directed mutagenesis. PLoS One 2013; 8:e68565. [PMID: 23894317 PMCID: PMC3716775 DOI: 10.1371/journal.pone.0068565] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 05/30/2013] [Indexed: 11/18/2022] Open
Abstract
Maltooligosyltrehalose trehalohydrolase (MTHase) catalyzes the release of trehalose by cleaving the α-1,4-glucosidic linkage next to the α-1,1-linked terminal disaccharide of maltooligosyltrehalose. Computer simulation using the hydrogen bond analysis, free energy decomposition, and computational alanine scanning were employed to investigate the interaction between maltooligosyltrehalose and the enzyme. The same residues that were chosen for theoretical investigation were also studied by site-directed mutagenesis and enzyme kinetic analysis. The importance of residues determined either experimentally or computed theoretically were in good accord with each other. It was found that residues Y155, D156, and W218 of subsites -2 and -3 of the enzyme might play an important role in interacting with the ligand. The theoretically constructed structure of the enzyme-ligand complex was further validated through an ab initio quantum chemical calculation using the Gaussian09 package. The activation energy computed from this latter study was very similar to those reported in literatures for the same type of hydrolysis reactions.
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Affiliation(s)
- Chien-wei Fu
- Institute of Molecular Medicine and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Ping Wang
- Department of Food Science and Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
| | - Tsuei-Yun Fang
- Department of Food Science and Center of Excellence for Marine Bioenvironment and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- * E-mail: (THL); (TYF)
| | - Thy-Hou Lin
- Institute of Molecular Medicine and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
- * E-mail: (THL); (TYF)
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29
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Ren Y, She Q, Huang L. Transcriptomic analysis of the SSV2 infection of Sulfolobus solfataricus with and without the integrative plasmid pSSVi. Virology 2013; 441:126-34. [PMID: 23579037 DOI: 10.1016/j.virol.2013.03.012] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 01/25/2013] [Accepted: 03/15/2013] [Indexed: 12/31/2022]
Abstract
The fusellovirus SSV2 and the integrative plasmid pSSVi, which constitute a unique helper-satellite virus system, replicate in Sulfolobus solfataricus P2. In this study, we investigated the interplay among SSV2, pSSVi and their host by transcriptomic analysis. Following infection of S. solfataricus P2, SSV2 activated its promoters in a temporal and distributive fashion, starting from the transcription of ORF305. Expression of several host genes encoding DNA replication and transcription proteins was up-regulated, suggesting that SSV2 depended heavily on the host replication machinery for its replication. SSV2 gene expression appeared to follow a similar pattern in S. solfataricus P2 harboring pSSVi to that in S. solfataricus P2 lacking the plasmid. Several early genes of the virus were transcribed earlier and more efficiently in the presence of pSSVi than in its absence. These results provide valuable clues to the understanding of the three-way interactions among SSV2, pSSVi and the host.
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Affiliation(s)
- Yi Ren
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, PR China
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30
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Ulas T, Riemer SA, Zaparty M, Siebers B, Schomburg D. Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS One 2012; 7:e43401. [PMID: 22952675 PMCID: PMC3432047 DOI: 10.1371/journal.pone.0043401] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [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: 03/22/2012] [Accepted: 07/20/2012] [Indexed: 12/21/2022] Open
Abstract
We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon Sulfolobus solfataricus, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2–4 (optimum 3.5) and a temperature of 75–80°C (optimum 80°C). The genome of Sulfolobus solfataricus P2 contains 2,992,245 bp on a single circular chromosome and encodes 2,977 proteins and a number of RNAs. The network comprises 718 metabolic and 58 transport/exchange reactions and 705 unique metabolites, based on the annotated genome and available biochemical data. Using the model in conjunction with constraint-based methods, we simulated the metabolic fluxes induced by different environmental and genetic conditions. The predictions were compared to experimental measurements and phenotypes of S. solfataricus. Furthermore, the performance of the network for 35 different carbon sources known for S. solfataricus from the literature was simulated. Comparing the growth on different carbon sources revealed that glycerol is the carbon source with the highest biomass flux per imported carbon atom (75% higher than glucose). Experimental data was also used to fit the model to phenotypic observations. In addition to the commonly known heterotrophic growth of S. solfataricus, the crenarchaeon is also able to grow autotrophically using the hydroxypropionate-hydroxybutyrate cycle for bicarbonate fixation. We integrated this pathway into our model and compared bicarbonate fixation with growth on glucose as sole carbon source. Finally, we tested the robustness of the metabolism with respect to gene deletions using the method of Minimization of Metabolic Adjustment (MOMA), which predicted that 18% of all possible single gene deletions would be lethal for the organism.
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Affiliation(s)
- Thomas Ulas
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - S. Alexander Riemer
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Melanie Zaparty
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany
| | - Bettina Siebers
- Faculty of Chemistry, Biofilm Centre, Molecular Enzyme Technology and Biochemistry, University of Duisburg-Essen, Essen, Germany
| | - Dietmar Schomburg
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
- * E-mail:
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31
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Xu N, Li Y, Zhao YT, Guo L, Fang YY, Zhao JH, Wang XJ, Huang L, Guo HS. Identification and characterization of small RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus. PLoS One 2012; 7:e35306. [PMID: 22514725 PMCID: PMC3325985 DOI: 10.1371/journal.pone.0035306] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [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: 12/14/2011] [Accepted: 03/13/2012] [Indexed: 11/18/2022] Open
Abstract
The term RNA silencing (RNA interference, RNAi) describes a set of mechanisms that regulate gene expression in eukaryotes. Small interfering RNAs (siRNA) and microRNAs (miRNAs) are two major types of RNAi-associated small RNAs (smRNAs) found in most eukaryotic organisms. Despite the presence of a plethora of non-coding RNAs longer than 50-nucleotide (nt) in length in various species of Archaea, little is known about smRNAs in archaea that resemble the 20-24-nt long smRNAs found in eukaryotes, which have been implicated in the post-transcriptional control of gene expression. Here, we report the finding of a large number of smRNAs approximatelly 20-nt in length, including phased smRNAs and potential miRNAs, from the hyperthermophilic archaeon Sulfolobus solfataricus p2 (Ssp2) based on deep sequencing. The expression of some of the miRNA candidates in Ssp2 was confirmed. Consistent with the Ssp2 hyperthermophilic properties, we found that higher temperatures more efficiently induced the production of the miRNA candidates in an in vitro system using the putative foldback precursor transcripts incubated with Ssp2 extract. Although we initially predicted putative target genes of some miRNA candidates, further analysis mapped the cleavage sites downstream of the miRNA candidate complementary regions, similar to those involved in plant miRNA-mediated TAS transcript cleavage. We also identified smRNAs from clustered, regularly interspaced, short palindromic repeat (CRISPR) loci, which play important roles in prokaryotic microbial defense systems. Archaea represent a unique life form next to Bacteria and Eukarya, and our results may provide a useful resource for further in-depth study on the regulation and evolution of smRNAs in this special organism.
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Affiliation(s)
- Ning Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ying-Tao Zhao
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Li Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuan-Yuan Fang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Hua Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Xiu-Jie Wang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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32
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Deng L, Kenchappa CS, Peng X, She Q, Garrett RA. Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus. Nucleic Acids Res 2012; 40:2470-80. [PMID: 22139923 PMCID: PMC3315313 DOI: 10.1093/nar/gkr1111] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [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: 09/08/2011] [Revised: 11/04/2011] [Accepted: 11/06/2011] [Indexed: 11/29/2022] Open
Abstract
CRISPR loci are essential components of the adaptive immune system of archaea and bacteria. They consist of long arrays of repeats separated by DNA spacers encoding guide RNAs (crRNA), which target foreign genetic elements. Cbp1 (CRISPR DNA repeat binding protein) binds specifically to the multiple direct repeats of CRISPR loci of members of the acidothermophilic, crenarchaeal order Sulfolobales. cbp1 gene deletion from Sulfolobus islandicus REY15A produced a strong reduction in pre-crRNA yields from CRISPR loci but did not inhibit the foreign DNA targeting capacity of the CRISPR/Cas system. Conversely, overexpression of Cbp1 in S. islandicus generated an increase in pre-crRNA yields while the level of reverse strand transcripts from CRISPR loci remained unchanged. It is proposed that Cbp1 modulates production of longer pre-crRNA transcripts from CRISPR loci. A possible mechanism is that it minimizes interference from potential transcriptional signals carried on spacers deriving from A-T-rich genetic elements and, occasionally, on DNA repeats. Supporting evidence is provided by microarray and northern blotting analyses, and publicly available whole-transcriptome data for S. solfataricus P2.
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Affiliation(s)
| | | | | | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200N Copenhagen K, Denmark
| | - Roger A. Garrett
- Archaea Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200N Copenhagen K, Denmark
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Villafane A, Voskoboynik Y, Ruhl I, Sannino D, Maezato Y, Blum P, Bini E. CopR of Sulfolobus solfataricus represents a novel class of archaeal-specific copper-responsive activators of transcription. Microbiology (Reading) 2011; 157:2808-2817. [PMID: 21757491 DOI: 10.1099/mic.0.051862-0] [Citation(s) in RCA: 27] [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] [Indexed: 11/18/2022]
Abstract
In trace amounts, copper is essential for the function of key enzymes in prokaryotes and eukaryotes. Organisms have developed sophisticated mechanisms to control the cytosolic level of the metal, manage its toxicity and survive in copper-rich environments. Here we show that the Sulfolobus CopR represents a novel class of copper-responsive regulators, unique to the archaeal domain. Furthermore, by disruption of the ORF Sso2652 (copR) of the Sulfolobus solfataricus genome, we demonstrate that the gene encodes a transcriptional activator of the copper-transporting ATPase CopA gene and co-transcribed copT, encoding a putative copper-binding protein. Disruption resulted in a loss of copper tolerance in two copR-knockout mutants, while metals such as zinc, cadmium and chromium did not affect their growth. Copper sensitivity in the mutant was linked to insufficient levels of expression of CopA and CopT. The findings were further supported by time-course inductively coupled plasma optical emission spectrometry measurements, whereby continued accumulation of copper in the S. solfataricus mutant was observed. In contrast, copper accumulation in the wild-type stabilized after reaching approximately 6 pg (µg total protein)(-1). Complementation of the disrupted mutant with a wild-type copy of the copR gene restored the wild-type phenotype with respect to the physiological and transcriptional response to copper. These observations, taken together, lead us to propose that CopR is an activator of copT and copA transcription, and the member of a novel class of copper-responsive regulators.
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Affiliation(s)
- Aramis Villafane
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Yekaterina Voskoboynik
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Ilona Ruhl
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - David Sannino
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Yukari Maezato
- Beadle Center for Genetics, University of Nebraska at Lincoln, Lincoln, NE, USA
| | - Paul Blum
- Beadle Center for Genetics, University of Nebraska at Lincoln, Lincoln, NE, USA
| | - Elisabetta Bini
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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Maezato Y, Daugherty A, Dana K, Soo E, Cooper C, Tachdjian S, Kelly RM, Blum P. VapC6, a ribonucleolytic toxin regulates thermophilicity in the crenarchaeote Sulfolobus solfataricus. RNA 2011; 17:1381-1392. [PMID: 21622901 PMCID: PMC3138573 DOI: 10.1261/rna.2679911] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 04/15/2011] [Indexed: 05/30/2023]
Abstract
The phylum Crenarchaeota includes hyperthermophilic micro-organisms subjected to dynamic thermal conditions. Previous transcriptomic studies of Sulfolobus solfataricus identified vapBC6 as a heat-shock (HS)-inducible member of the Vap toxin-antitoxin gene family. In this study, the inactivation of the vapBC6 operon by targeted gene disruption produced two recessive phenotypes related to fitness, HS sensitivity and a heat-dependent reduction in the rate of growth. In-frame vapBC6 deletion mutants were analyzed to examine the respective roles of each protein. Since vapB6 transcript abundance was elevated in the vapC6 deletion, the VapC6 toxin appears to regulate abundance of its cognate antitoxin. In contrast, vapC6 transcript abundance was reduced in the vapB6 deletion. A putative intergenic terminator may underlie these observations by coordinating vapBC6 expression. As predicted by structural modeling, recombinant VapC6 produced using chaperone cosynthesis exhibited heat-dependent ribonucleolytic activity toward S. solfataricus total RNA. This activity could be blocked by addition of preheated recombinant VapB6. In vivo transcript targets were identified by assessing the relative expression of genes that naturally respond to thermal stress in VapBC6-deficient cells. Preferential increases were observed for dppB-1 and tetR, and preferential decreases were observed for rpoD and eIF2 gamma. Specific VapC6 ribonucleolytic action could also be demonstrated in vitro toward RNAs whose expression increased in the VapBC6-deficient strain during heat shock. These findings provide a biochemical mechanism and identify cellular targets underlying VapBC6-mediated control over microbial growth and survival at temperature extremes.
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Affiliation(s)
- Yukari Maezato
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Amanda Daugherty
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Karl Dana
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Edith Soo
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
| | - Charlotte Cooper
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Sabrina Tachdjian
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, USA
| | - Paul Blum
- Beadle Center for Genetics, School of Biological Sciences, University of Nebraska, Lincoln, Nebraska 68588-0666, USA
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Ng FSW, Wright DM, Seah SYK. Characterization of a phosphotriesterase-like lactonase from Sulfolobus solfataricus and its immobilization for disruption of quorum sensing. Appl Environ Microbiol 2011; 77:1181-6. [PMID: 21183649 PMCID: PMC3067241 DOI: 10.1128/aem.01642-10] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 12/13/2010] [Indexed: 11/20/2022] Open
Abstract
SsoPox, a bifunctional enzyme with organophosphate hydrolase and N-acyl homoserine lactonase activities from the hyperthermophilic archaeon Sulfolobus solfataricus, was overexpressed and purified from recombinant Pseudomonas putida KT2440 with a yield of 9.4 mg of protein per liter of culture. The enzyme has a preference for N-acyl homoserine lactones (AHLs) with acyl chain lengths of at least 8 carbon atoms, mainly due to lower K(m) values for these substrates. The highest specificity constant obtained was for N-3-oxo-decanoyl homoserine lactone (k(cat)/K(m) = 5.5 × 10(3) M(-1)·s(-1)), but SsoPox can also degrade N-butyryl homoserine lactone (C(4)-HSL) and N-oxo-dodecanoyl homoserine lactone (oxo-C(12)-HSL), which are important for quorum sensing in our Pseudomonas aeruginosa model system. When P. aeruginosa PAO1 cultures were grown in the presence of SsoPox-immobilized membranes, the production of C(4)-HSL- and oxo-C(12)-HSL-regulated virulence factors, elastase, protease, and pyocyanin were significantly reduced. This is the first demonstration that immobilized quorum-quenching enzymes can be used to attenuate the production of virulence factors controlled by quorum-sensing signals.
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Affiliation(s)
- Filomena S W Ng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Hasenöhrl D, Konrat R, Bläsi U. Identification of an RNase J ortholog in Sulfolobus solfataricus: implications for 5'-to-3' directional decay and 5'-end protection of mRNA in Crenarchaeota. RNA 2011; 17:99-107. [PMID: 21115637 PMCID: PMC3004070 DOI: 10.1261/rna.2418211] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 10/07/2010] [Indexed: 05/29/2023]
Abstract
In both Bacteria and Eukaryotes, degradation is known to start at the 5' and at the 3' extremities of mRNAs. Until the recent discovery of 5'-to-3' exoribonucleases in hyperthermophilic Euryarchaeota, the exosome was assumed to be the key enzyme in mRNA degradation in Archaea. By means of zymogram assays and bioinformatics, we have identified a 5'-to-3' exoribonuclease activity in the crenarchaeum Sulfolobus solfataricus (Sso), which is affected by the phosphorylation state of the 5'-end of the mRNA. The protein comprises typical signature motifs of the β-CASP family of metallo-β-lactamases and was termed Sso-RNAse J. Thus, our study provides the first evidence for a 5'-to-3' directional mRNA decay pathway in the crenarchaeal clade of Archaea. In Bacteria the 5'-end of mRNAs is often protected by a tri-phosphorylated 5'-terminus and/or by stem-loop structures, while in Eukaryotes the cap-binding complex is responsible for this task. Here, we show that binding of translation initiation factor a/eIF2(γ) to the 5'-end of mRNA counteracts the 5'-to-3' exoribonucleolytic activity of Sso-RNase J in vitro. Hence, 5'-to-3' directional decay and 5'-end protection appear to be conserved features of mRNA turnover in all kingdoms of life.
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Affiliation(s)
- David Hasenöhrl
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, 1030 Vienna, Austria
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Krishna SS, Aravind L, Bakolitsa C, Caruthers J, Carlton D, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Chiu HJ, Clayton T, Deller MC, Duan L, Feuerhelm J, Grant JC, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, McMullan D, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, van den Bedem H, Weekes D, Xu Q, Hodgson KO, Wooley J, Elsliger MA, Deacon AM, Godzik A, Lesley SA, Wilson IA. The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1160-6. [PMID: 20944206 PMCID: PMC2954200 DOI: 10.1107/s1744309110002514] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [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: 10/29/2009] [Accepted: 01/20/2010] [Indexed: 11/30/2022]
Abstract
SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein-protein interactions. Domain architectures, genomic context analysis and functional evidence from certain bacterial representatives of this family suggest that these proteins form a novel fatty-acid-binding component that is involved in the biosynthesis of lipids and polyketide antibiotics and that they possibly function as acyl-CoA-binding proteins. This structure has led to a re-evaluation of the DUF35 family, which has now been split into two entries in the latest Pfam release (v.24.0).
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Affiliation(s)
- S. Sri Krishna
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, California, USA
| | - L. Aravind
- National Institutes of Health, Bethesda, Maryland, USA
| | - Constantina Bakolitsa
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, California, USA
| | - Jonathan Caruthers
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Dennis Carlton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Mitchell D. Miller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Polat Abdubek
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, USA
| | - Tamara Astakhova
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, USA
| | - Herbert L Axelrod
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Hsiu-Ju Chiu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Thomas Clayton
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Marc C. Deller
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Lian Duan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, USA
| | - Julie Feuerhelm
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, USA
| | - Joanna C. Grant
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, USA
| | - Gye Won Han
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Lukasz Jaroszewski
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, California, USA
| | - Kevin K. Jin
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Heath E. Klock
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, USA
| | - Mark W. Knuth
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, USA
| | - Abhinav Kumar
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - David Marciano
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Daniel McMullan
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, USA
| | - Andrew T. Morse
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, USA
| | - Edward Nigoghossian
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, USA
| | - Linda Okach
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, USA
| | - Ron Reyes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Christopher L. Rife
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Henry van den Bedem
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Dana Weekes
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, California, USA
| | - Qingping Xu
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Keith O. Hodgson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Photon Science, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - John Wooley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, USA
| | - Marc-André Elsliger
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
| | - Ashley M. Deacon
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Adam Godzik
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, USA
- Program on Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, California, USA
| | - Scott A. Lesley
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
- Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California, USA
| | - Ian A. Wilson
- Joint Center for Structural Genomics, http://www.jcsg.org, USA
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
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Lu C, Ding F, Ke A. Crystal structure of the S. solfataricus archaeal exosome reveals conformational flexibility in the RNA-binding ring. PLoS One 2010; 5:e8739. [PMID: 20090900 PMCID: PMC2806925 DOI: 10.1371/journal.pone.0008739] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [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: 10/19/2009] [Accepted: 12/18/2009] [Indexed: 11/18/2022] Open
Abstract
Background The exosome complex is an essential RNA 3′-end processing and degradation machinery. In archaeal organisms, the exosome consists of a catalytic ring and an RNA-binding ring, both of which were previously reported to assume three-fold symmetry. Methodology/Principal Findings Here we report an asymmetric 2.9 Å Sulfolobus solfataricus archaeal exosome structure in which the three-fold symmetry is broken due to combined rigid body and thermal motions mainly within the RNA-binding ring. Since increased conformational flexibility was also observed in the RNA-binding ring of the related bacterial PNPase, we speculate that this may reflect an evolutionarily conserved mechanism to accommodate diverse RNA substrates for degradation. Conclusion/Significance This study clearly shows the dynamic structures within the RNA-binding domains, which provides additional insights on mechanism of asymmetric RNA binding and processing.
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Affiliation(s)
- Changrui Lu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Fang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Hasenöhrl D, Fabbretti A, Londei P, Gualerzi CO, Bläsi U. Translation initiation complex formation in the crenarchaeon Sulfolobus solfataricus. RNA 2009; 15:2288-2298. [PMID: 19861425 PMCID: PMC2779686 DOI: 10.1261/rna.1662609] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [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: 03/26/2009] [Accepted: 09/09/2009] [Indexed: 05/28/2023]
Abstract
The function of initiation factors in and the sequence of events during translation initiation have been intensively studied in Bacteria and Eukaryotes, whereas in Archaea knowledge on these functions/processes is limited. By employing chemical probing, we show that translation initiation factor aIF1 of the model crenarchaeon Sulfolobus solfataricus binds to the same area on the ribosome as the bacterial and eukaryal orthologs. Fluorescence energy transfer assays (FRET) showed that aIF1, like its eukaryotic and bacterial orthologs, has a fidelity function in translation initiation complex formation, and that both aIF1 and aIF1A exert a synergistic effect in stimulating ribosomal association of the Met-tRNAi(Met) binding factor a/eIF2. However, as in Eukaryotes their effect on a/eIF2 binding appears to be indirect. Moreover, FRET was used to analyze for the first time the sequence of events toward translation initiation complex formation in an archaeal model system. These studies suggested that a/eIF2-GTP binds first to the ribosome and then recruits Met-tRNAi(Met), which appears to comply with the operational mode of bacterial IF2, and deviates from the shuttle function of the eukaryotic counterpart eIF2. Thus, despite the resemblance of eIF2 and a/eIF2, recruitment of initiator tRNA to the ribosome is mechanistically different in Pro- and Eukaryotes.
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Affiliation(s)
- David Hasenöhrl
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, 1030 Vienna, Austria.
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Maaty WS, Wiedenheft B, Tarlykov P, Schaff N, Heinemann J, Robison-Cox J, Valenzuela J, Dougherty A, Blum P, Lawrence CM, Douglas T, Young MJ, Bothner B. Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress. PLoS One 2009; 4:e6964. [PMID: 19759909 PMCID: PMC2739297 DOI: 10.1371/journal.pone.0006964] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [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: 06/30/2009] [Accepted: 08/06/2009] [Indexed: 11/18/2022] Open
Abstract
To avoid molecular damage of biomolecules due to oxidation, all cells have evolved constitutive and responsive systems to mitigate and repair chemical modifications. Archaea have adapted to some of the most extreme environments known to support life, including highly oxidizing conditions. However, in comparison to bacteria and eukaryotes, relatively little is known about the biology and biochemistry of archaea in response to changing conditions and repair of oxidative damage. In this study transcriptome, proteome, and chemical reactivity analyses of hydrogen peroxide (H(2)O(2)) induced oxidative stress in Sulfolobus solfataricus (P2) were conducted. Microarray analysis of mRNA expression showed that 102 transcripts were regulated by at least 1.5 fold, 30 minutes after exposure to 30 microM H(2)O(2). Parallel proteomic analyses using two-dimensional differential gel electrophoresis (2D-DIGE), monitored more than 800 proteins 30 and 105 minutes after exposure and found that 18 had significant changes in abundance. A recently characterized ferritin-like antioxidant protein, DPSL, was the most highly regulated species of mRNA and protein, in addition to being post-translationally modified. As expected, a number of antioxidant related mRNAs and proteins were differentially regulated. Three of these, DPSL, superoxide dismutase, and peroxiredoxin were shown to interact and likely form a novel supramolecular complex for mitigating oxidative damage. A scheme for the ability of this complex to perform multi-step reactions is presented. Despite the central role played by DPSL, cells maintained a lower level of protection after disruption of the dpsl gene, indicating a level of redundancy in the oxidative stress pathways of S. solfataricus. This work provides the first "omics" scale assessment of the oxidative stress response for an archeal organism and together with a network analysis using data from previous studies on bacteria and eukaryotes reveals evolutionarily conserved pathways where complex and overlapping defense mechanisms protect against oxygen toxicity.
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Affiliation(s)
- Walid S. Maaty
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
| | - Blake Wiedenheft
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Department of Plant Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Pavel Tarlykov
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
| | - Nathan Schaff
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Joshua Heinemann
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
| | - Jim Robison-Cox
- Department of Mathematical Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Jacob Valenzuela
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
| | - Amanda Dougherty
- George Beadle Center for Genetics, University of Nebraska, Lincoln, Nebraska, United States of America
| | - Paul Blum
- George Beadle Center for Genetics, University of Nebraska, Lincoln, Nebraska, United States of America
| | - C. Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
| | - Trevor Douglas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
| | - Mark J. Young
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- Department of Microbiology, Montana State University, Bozeman, Montana, United States of America
- Department of Plant Sciences, Montana State University, Bozeman, Montana, United States of America
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, United States of America
- Thermal Biology Institute, Montana State University, Bozeman, Montana, United States of America
- * E-mail:
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Chu X, Wang L, He Y, Dong Z. [Expression and characterization of chaperonin from Sulfolobus solfataricus P2]. Wei Sheng Wu Xue Bao 2008; 48:1324-1329. [PMID: 19160812] [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: 05/27/2023]
Abstract
OBJECTIVE To elucidate the structure and functional mechanism of beta subunit of chaperonin from the thermoacidophilic archaeon Sulfolobus solfataricus P2. METHODS Molecular cloning of the beta subunit gene of chaperonin from the thermoacidophilic archaeon Sulfolobus solfataricus P2 was performed by using PCR technique. The gene was expressed in BL21 (DE3) of Escherichia coli. After purified and assembled in vitro, the structure of the beta subunit homo-oligomer was observed by transmission electron microscope (TEM). The function of this homo-oligomer as a chaperonin was evaluated. RESULTS The gene encoding beta subunit of chaperonin was amplified by PCR from the genomic DNA of Sulfolobus solfataricus P2 and expressed in BL21 (DE3) of E. coli. In vitro, the purified beta monomer could assemble to a homo-oligomer in the presence of ATP and Mg2+. As observed by transmission electron microscope(TEM), the beta subunit homo-oligomer (beta16mer) showed a double-ring structure, which is typical in group II chaperonins. The optimum temperature for ATPase activity of the beta16mer was 80 degrees C. The beta16mer was able to promote the refolding of denatured GFP and improve the thermostability of xylanase. CONCLUSION According to the prediction and analysis of the chaperonin sequence from thermoacidophilic archaeon Sulfolobus solfataricus P2 genome, we cloned and expressed the beta subunit of chaperonin from P2. This subunit formed a homo-oligomer in vitro and showed a typical structure of group II chaperonins. We found that the beta16mer was able to function correctly when promoting the refolding and improving the thermostability of some other proteins. Our research has laid a foundation for the further study on the molecular mechanism of thermoacidophilic archaeon.
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Affiliation(s)
- Xin Chu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Fröls S, Gordon PMK, Panlilio MA, Duggin IG, Bell SD, Sensen CW, Schleper C. Response of the hyperthermophilic archaeon Sulfolobus solfataricus to UV damage. J Bacteriol 2007; 189:8708-18. [PMID: 17905990 PMCID: PMC2168930 DOI: 10.1128/jb.01016-07] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.5] [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: 11/20/2022] Open
Abstract
In order to characterize the genome-wide transcriptional response of the hyperthermophilic, aerobic crenarchaeote Sulfolobus solfataricus to UV damage, we used high-density DNA microarrays which covered 3,368 genetic features encoded on the host genome, as well as the genes of several extrachromosomal genetic elements. While no significant up-regulation of genes potentially involved in direct DNA damage reversal was observed, a specific transcriptional UV response involving 55 genes could be dissected. Although flow cytometry showed only modest perturbation of the cell cycle, strong modulation of the transcript levels of the Cdc6 replication initiator genes was observed. Up-regulation of an operon encoding Mre11 and Rad50 homologs pointed to induction of recombinational repair. Consistent with this, DNA double-strand breaks were observed between 2 and 8 h after UV treatment, possibly resulting from replication fork collapse at damaged DNA sites. The strong transcriptional induction of genes which potentially encode functions for pilus formation suggested that conjugational activity might lead to enhanced exchange of genetic material. In support of this, a statistical microscopic analysis demonstrated that large cell aggregates formed upon UV exposure. Together, this provided supporting evidence to a link between recombinational repair and conjugation events.
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Affiliation(s)
- Sabrina Fröls
- Center of Geobiology, Dept. Biology, Jahnebakken 5, N-5020 Bergen, Norway
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Mandrich L, Pezzullo M, Rossi M, Manco G. SSoNDelta and SSoNDeltalong: two thermostable esterases from the same ORF in the archaeon Sulfolobus solfataricus? Archaea 2007; 2:109-15. [PMID: 17350931 PMCID: PMC2686388 DOI: 10.1155/2006/748517] [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] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Previously, we reported from the Sulfolobus solfataricus open reading frame (ORF) SSO2517 the cloning, overexpression and characterization of an esterase belonging to the hormone-sensitive lipase (HSL) family and apparently having a deletion at the N-terminus, which we named SSoNDelta. Searching the recently reported Sulfolobus acidocaldarius genome by sequence alignment, using SSO2517 as a query, allowed identity of a putative esterase (ORF SAC1105) sharing high sequence similarity (82%) with SSO2517. This esterase displays an N-terminus and total length similar to other known esterases of the HSL family. Analysis of the upstream DNA sequence of SS02517 revealed the possibility of expressing a longer version of the protein with an extended N-terminus; however, no clear translation signal consistent with a longer protein version was detected. This new version of SSO2517 was cloned, over-expressed, purified and characterized. The resulting protein, named SSoNDeltalong, was 15-fold more active with the substrate p-nitrophenyl hexanoate than SSoNDelta. Furthermore, SSoNDeltalong and SSoNDelta displayed different substrate specificities for triacylglycerols. These results and the phylogenetic relationship between S. solfataricus and S. acidocaldarius suggest a common origin of SSO2517 and SAC1105 from an ancestral gene, followed by divergent evolution. Alternatively, a yet-to-be discovered mechanism of translation that directs the expression of SSoNDeltalong under specific metabolic conditions could be hypothesized.
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Affiliation(s)
- Luigi Mandrich
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Margherita Pezzullo
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Mosè Rossi
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Giuseppe Manco
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
- Corresponding author ()
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Abstract
Glycoside hydrolases form hyperthermophilic archaea are interesting model systems for the study of catalysis at high temperatures and, at the moment, their detailed enzymological characterization is the only approach to define their role in vivo. Family 29 of glycoside hydrolases classification groups alpha-L-fucosidases involved in a variety of biological events in Bacteria and Eukarya. In Archaea the first alpha-L-fucosidase was identified in Sulfolobus solfataricus as interrupted gene expressed by programmed -1 frameshifting. In this review, we describe the identification of the catalytic residues of the archaeal enzyme, by means of the chemical rescue strategy. The intrinsic stability of the hyperthermophilic enzyme allowed the use of this method, which resulted of general applicability for beta and alpha glycoside hydrolases. In addition, the presence in the active site of the archaeal enzyme of a triad of catalytic residues is a rather uncommon feature among the glycoside hydrolases and suggested that in family 29 slightly different catalytic machineries coexist.
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Affiliation(s)
- Beatrice Cobucci-Ponzano
- Institute of Protein Biochemistry, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy.
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45
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Fiorentino G, Ronca R, Cannio R, Rossi M, Bartolucci S. MarR-like transcriptional regulator involved in detoxification of aromatic compounds in Sulfolobus solfataricus. J Bacteriol 2007; 189:7351-60. [PMID: 17675388 PMCID: PMC2168448 DOI: 10.1128/jb.00885-07] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [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: 01/14/2023] Open
Abstract
A DNA binding protein, BldR, was identified in the crenarchaeon Sulfolobus solfataricus as a protein 5- to 10-fold more abundant in cells grown in the presence of toxic aldehydes; it binds to regulatory sequences located upstream of an alcohol dehydrogenase gene (Sso2536). BldR is homologous to bacterial representatives of the MarR (multiple antibiotic resistance) family of transcriptional regulators that mediate response to multiple environmental stresses. Transcriptional analysis revealed that the bldR gene was transcribed in a bicistronic unit composed of the genes encoding the transcriptional regulator (Sso1352) and a putative multidrug transporter (Sso1351) upstream. By homology to bacterial counterparts, the bicistron was named the mar-like operon. The level of mar-like operon expression was found to be increased at least 10-fold in response to chemical stress by aromatic aldehydes. Under the same growth conditions, similar enhanced in vivo levels of Sso2536 gene transcript were also measured. The gene encoding BldR was expressed in E. coli, and the recombinant protein was purified to homogeneity. DNA binding assays demonstrated that the protein is indeed a transcription factor able to recognize site specifically both the Sso2536 and mar-like promoters at sites containing palindromic consensus sequences. Benzaldehyde, the substrate of ADH(Ss), stimulates DNA binding of BldR at both promoters. The role of BldR in the auto-activation as well as in the regulation of the Sso2536 gene, together with results of increased operon and gene expression under conditions of exposure to aromatic aldehydes, indicates a novel coordinate regulatory mechanism in cell defense against stress by aromatic compounds.
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Affiliation(s)
- Gabriella Fiorentino
- Dipartimento di Biologia Strutturale e Funzionale, Università degli Studi di Napoli Federico II, Complesso Universitario Monte S Angelo, Via Cinthia, 80126, Napoli, Italy.
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46
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Jiang PX, Wang J, Feng Y, He ZG. Divergent functions of multiple eukaryote-like Orc1/Cdc6 proteins on modulating the loading of the MCM helicase onto the origins of the hyperthermophilic archaeon Sulfolobus solfataricus P2. Biochem Biophys Res Commun 2007; 361:651-8. [PMID: 17673179 DOI: 10.1016/j.bbrc.2007.07.073] [Citation(s) in RCA: 15] [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] [Received: 07/12/2007] [Accepted: 07/13/2007] [Indexed: 11/29/2022]
Abstract
The Cdc6 protein has been suggested as a loader for the eukaryotic MCM helicase. Archaeal replication machinery represents a core version of that in eukaryotes. In the current work, three eukaryotic Orc1/Cdc6 homologs (SsoCdc6-1, -2, and -3) from crenarchaeon Sulfolobus solfataricus were shown to have totally different effects on the interactions with SsoMCM helicase. SsoCdc6-2 stimulates the binding of the SsoMCM onto the origin DNA, but SsoCdc6-1 and SsoCdc6-3 significantly inhibit the loading activities, and these inhibitive effects can not be reversed by the stimulation of SsoCdc6-2. Using pull-down assays, we showed that three SsoCdc6 proteins interacted physically with the SsoMCM. Furthermore, the C-terminal domains of SsoCdc6 proteins were shown to physically and functionally affect the interactions with SsoMCM. This is the first report on the divergent functions of multiple eukaryote-like Orc1/Cdc6 proteins on regulating the loading of the MCM helicase onto the origins in the archaeon.
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Affiliation(s)
- Pei-Xia Jiang
- National Key Laboratory of Agricultural Microbiology, Center for Proteomics Research, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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47
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Maone E, Di Stefano M, Berardi A, Benelli D, Marzi S, La Teana A, Londei P. Functional analysis of the translation factor aIF2/5B in the thermophilic archaeon Sulfolobus solfataricus. Mol Microbiol 2007; 65:700-13. [PMID: 17608795 PMCID: PMC1976387 DOI: 10.1111/j.1365-2958.2007.05820.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [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] [Indexed: 11/27/2022]
Abstract
The protein IF2/eIF5B is one of the few translation initiation factors shared by all three primary domains of life (bacteria, archaea, eukarya). Despite its phylogenetic conservation, the factor is known to present marked functional divergences in the bacteria and the eukarya. In this work, the function in translation of the archaeal homologue (aIF2/5B) has been analysed in detail for the first time using a variety of in vitro assays. The results revealed that the protein is a ribosome-dependent GTPase which strongly stimulates the binding of initiator tRNA to the ribosomes even in the absence of other factors. In agreement with this finding, aIF2/5B enhances the translation of both leadered and leaderless mRNAs when expressed in a cell-free protein-synthesizing system. Moreover, the degree of functional conservation of the IF2-like factors in the archaeal and bacterial lineages was investigated by analysing the behaviour of 'chimeric' proteins produced by swapping domains between the Sulfolobus solfataricus aIF2/5B factor and the IF2 protein of the thermophilic bacterium Bacillus stearothermophilus. Beside evidencing similarities and differences between the archaeal and bacterial factors, these experiments have provided insight into the common role played by the IF2/5B proteins in all extant cells.
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Affiliation(s)
- Enzo Maone
- Dpt. of Biotecnologie Cellulari ed Ematologia, Università di Roma SapienzaViale Regina Elena 324 Roma, Italy.
| | - Michele Di Stefano
- Istituto di Biochimica, Università Politecnica delle MarcheVia Ranieri Ancona, Italy.
| | - Alessandra Berardi
- Dpt. of Biotecnologie Cellulari ed Ematologia, Università di Roma SapienzaViale Regina Elena 324 Roma, Italy.
| | - Dario Benelli
- DIBIFIM, Università di Bari, Piazzale Giulio CesareBari, Italy.
| | - Stefano Marzi
- Institut for de Biologie Moleculaire et Cellulare CNRS67084 Strasbourg Cedex, France.
| | - Anna La Teana
- Istituto di Biochimica, Università Politecnica delle MarcheVia Ranieri Ancona, Italy.
| | - Paola Londei
- Dpt. of Biotecnologie Cellulari ed Ematologia, Università di Roma SapienzaViale Regina Elena 324 Roma, Italy.
- DIBIFIM, Università di Bari, Piazzale Giulio CesareBari, Italy.
- For correspondence. E-mail ; Tel. (+39) 06 4462891; Fax (+39) 06 4462891
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48
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Elias M, Dupuy J, Merone L, Lecomte C, Rossi M, Masson P, Manco G, Chabriere E. Crystallization and preliminary X-ray diffraction analysis of the hyperthermophilic Sulfolobus solfataricus phosphotriesterase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:553-5. [PMID: 17620708 PMCID: PMC2335143 DOI: 10.1107/s1744309107023512] [Citation(s) in RCA: 14] [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: 03/12/2007] [Accepted: 05/13/2007] [Indexed: 11/11/2022]
Abstract
Organophosphates constitute the largest class of insecticides used worldwide and some of them are potent nerve agents. Consequently, organophosphate-degrading enzymes are of paramount interest as they could be used as bioscavengers and biodecontaminants. Phosphotriesterases (PTEs) are capable of hydrolyzing these toxic compounds with high efficiency. A distant and hyperthermophilic representative of the PTE family was cloned from the archeon Sulfolobus solfataricus MT4, overexpressed in Escherichia coli and crystallized; the crystals diffracted to 2.54 A resolution. Owing to its exceptional thermostability, this PTE may be an excellent candidate for obtaining an efficient organophosphate biodecontaminant. Here, the crystallization conditions and data collection for the hyperthermophilic S. solfataricus PTE are reported.
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Affiliation(s)
- Mikael Elias
- Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS–Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy, France
| | - Jérôme Dupuy
- Laboratoire de Cristallogenèse et Cristallographie des Protéines, Institut de Biologie Structurale J.-P. Ebel, 38027 Grenoble, France
| | - Luigia Merone
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Napoli, Italy
| | - Claude Lecomte
- Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS–Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy, France
| | - Mosè Rossi
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Napoli, Italy
| | - Patrick Masson
- Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées, 38702 La Tronche, France
| | - Giuseppe Manco
- Istituto di Biochimica delle Proteine, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Napoli, Italy
| | - Eric Chabriere
- Laboratoire de Cristallographie et Modélisation des Matériaux Minéraux et Biologiques, CNRS–Université Henri Poincaré, 54506 Vandoeuvre-lès-Nancy, France
- Unité d’Enzymologie, Département de Toxicologie, Centre de Recherches du Service de Santé des Armées, 38702 La Tronche, France
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49
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Berkner S, Grogan D, Albers SV, Lipps G. Small multicopy, non-integrative shuttle vectors based on the plasmid pRN1 for Sulfolobus acidocaldarius and Sulfolobus solfataricus, model organisms of the (cren-)archaea. Nucleic Acids Res 2007; 35:e88. [PMID: 17576673 PMCID: PMC1919505 DOI: 10.1093/nar/gkm449] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [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] [Indexed: 11/14/2022] Open
Abstract
The extreme thermoacidophiles of the genus Sulfolobus are among the best-studied archaea but have lacked small, reliable plasmid vectors, which have proven extremely useful for manipulating and analyzing genes in other microorganisms. Here we report the successful construction of a series of Sulfolobus-Escherichia coli shuttle vectors based on the small multicopy plasmid pRN1 from Sulfolobus islandicus. Selection in suitable uracil auxotrophs is provided through inclusion of pyrEF genes in the plasmid. The shuttle vectors do not integrate into the genome and do not rearrange. The plasmids allow functional overexpression of genes, as could be demonstrated for the beta-glycosidase (lacS) gene of S. solfataricus. In addition, we demonstrate that this beta-glycosidase gene could function as selectable marker in S. solfataricus. The shuttle plasmids differ in their interruption sites within pRN1 and allowed us to delineate functionally important regions of pRN1. The orf56/orf904 operon appears to be essential for pRN1 replication, in contrast interruption of the highly conserved orf80/plrA gene is tolerated. The new vector system promises to facilitate genetic studies of Sulfolobus and to have biotechnological uses, such as the overexpression or optimization of thermophilic enzymes that are not readily performed in mesophilic hosts.
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Affiliation(s)
- Silvia Berkner
- Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany, Department of Biological Sciences, University of Cincinnati, OH 45221-0006, USA and Department of Molecular Microbiology, University of Groningen, 9751 NN Haren, The Netherlands
| | - Dennis Grogan
- Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany, Department of Biological Sciences, University of Cincinnati, OH 45221-0006, USA and Department of Molecular Microbiology, University of Groningen, 9751 NN Haren, The Netherlands
| | - Sonja-Verena Albers
- Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany, Department of Biological Sciences, University of Cincinnati, OH 45221-0006, USA and Department of Molecular Microbiology, University of Groningen, 9751 NN Haren, The Netherlands
| | - Georg Lipps
- Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany, Department of Biological Sciences, University of Cincinnati, OH 45221-0006, USA and Department of Molecular Microbiology, University of Groningen, 9751 NN Haren, The Netherlands
- *To whom correspondence should be addressed: +49 921 552433, Fax: +49 921 552432,
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50
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Ettema TJG, Ahmed H, Geerling ACM, van der Oost J, Siebers B. The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner-Doudoroff pathway. Extremophiles 2007; 12:75-88. [PMID: 17549431 DOI: 10.1007/s00792-007-0082-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Accepted: 03/28/2007] [Indexed: 11/25/2022]
Abstract
Archaea utilize a branched modification of the classical Entner-Doudoroff (ED) pathway for sugar degradation. The semi-phosphorylative branch merges at the level of glyceraldehyde 3-phosphate (GAP) with the lower common shunt of the Emden-Meyerhof-Parnas pathway. In Sulfolobus solfataricus two different GAP converting enzymes-classical phosphorylating GAP dehydrogenase (GAPDH) and the non-phosphorylating GAPDH (GAPN)-were identified. In Sulfolobales the GAPN encoding gene is found adjacent to the ED gene cluster suggesting a function in the regulation of the semi-phosphorylative ED branch. The biochemical characterization of the recombinant GAPN of S. solfataricus revealed that-like the well-characterized GAPN from Thermoproteus tenax-the enzyme of S. solfataricus exhibits allosteric properties. However, both enzymes show some unexpected differences in co-substrate specificity as well as regulatory fine-tuning, which seem to reflect an adaptation to the different lifestyles of both organisms. Phylogenetic analyses and database searches in Archaea indicated a preferred distribution of GAPN (and/or GAP oxidoreductase) in hyperthermophilic Archaea supporting the previously suggested role of GAPN in metabolic thermoadaptation. This work suggests an important role of GAPN in the regulation of carbon degradation via modifications of the EMP and the branched ED pathway in hyperthermophilic Archaea.
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Affiliation(s)
- Thijs J G Ettema
- Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University, Norbyvägen 18C, 752 36 Uppsala, Sweden
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