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Mishra Y, Hall M, Locmelis R, Nam K, Söderberg CAG, Storm P, Chaurasia N, Rai LC, Jansson S, Schröder WP, Sauer UH. Active-site plasticity revealed in the asymmetric dimer of AnPrx6 the 1-Cys peroxiredoxin and molecular chaperone from Anabaena sp. PCC 7210. Sci Rep 2017; 7:17151. [PMID: 29215017 PMCID: PMC5719442 DOI: 10.1038/s41598-017-17044-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 11/16/2017] [Indexed: 12/31/2022] Open
Abstract
Peroxiredoxins (Prxs) are vital regulators of intracellular reactive oxygen species levels in all living organisms. Their activity depends on one or two catalytically active cysteine residues, the peroxidatic Cys (CP) and, if present, the resolving Cys (CR). A detailed catalytic cycle has been derived for typical 2-Cys Prxs, however, little is known about the catalytic cycle of 1-Cys Prxs. We have characterized Prx6 from the cyanobacterium Anabaena sp. strain PCC7120 (AnPrx6) and found that in addition to the expected peroxidase activity, AnPrx6 can act as a molecular chaperone in its dimeric state, contrary to other Prxs. The AnPrx6 crystal structure at 2.3 Å resolution reveals different active site conformations in each monomer of the asymmetric obligate homo-dimer. Molecular dynamic simulations support the observed structural plasticity. A FSH motif, conserved in 1-Cys Prxs, precedes the active site PxxxTxxCp signature and might contribute to the 1-Cys Prx reaction cycle.
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Affiliation(s)
- Yogesh Mishra
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden.,Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden.,Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Michael Hall
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
| | - Roland Locmelis
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
| | - Kwangho Nam
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden.,Computational Life-Science Cluster, CLiC, Umeå University, SE-901 87, Umeå, Sweden.,Department of Chemistry and Biochemistry University of Texas at Arlington, Arlington, TX, 76019-0065, USA
| | | | - Patrik Storm
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden
| | - Neha Chaurasia
- Department of Biotechnology and Bioinformatics, North Eastern Hill University, Shillong, 793022, India
| | - Lal Chand Rai
- Molecular Biology Section, Laboratory of Algal Biology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Stefan Jansson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden
| | - Wolfgang P Schröder
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden.,Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87, Umeå, Sweden
| | - Uwe H Sauer
- Department of Chemistry, Umeå University, SE-901 87, Umeå, Sweden. .,Computational Life-Science Cluster, CLiC, Umeå University, SE-901 87, Umeå, Sweden.
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Lv YJ, Wang X, Ma Q, Bai X, Li BZ, Zhang W, Yuan YJ. Proteomic analysis reveals complex metabolic regulation in Saccharomyces cerevisiae cells against multiple inhibitors stress. Appl Microbiol Biotechnol 2014; 98:2207-21. [PMID: 24442506 DOI: 10.1007/s00253-014-5519-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 12/20/2013] [Accepted: 12/28/2013] [Indexed: 11/24/2022]
Abstract
Toxic compounds including acids, furans, and phenols (AFP) were generated from the pretreatment of lignocellulose. We cultivated Saccharomyces cerevisiae cells in a batch mode, besides the cell culture of original yeast strain in AFP-free medium which was referred as C0, three independent subcultures were cultivated under multiple inhibitors AFP and were referred as C1, C2, and C3 in time sequence. Comparing to C0, the cell density was lowered while the ethanol yield was maintained stably in the three yeast cultures under AFP stress, and the lag phase of C1 was extended while the lag phases of C2 and C3 were not extended. In proteomic analysis, 194 and 215 unique proteins were identified as differently expressed proteins at lag phase and exponential phase, respectively. Specifically, the yeast cells co-regulated protein folding and protein synthesis process to prevent the generation of misfolded proteins and to save cellular energy, they increased the activity of glycolysis, redirected metabolic flux towards phosphate pentose pathway and the biosynthesis of ethanol instead of the biosynthesis of glycerol and acetic acid, and they upregulated several oxidoreductases especially at lag phase and induced programmed cell death at exponential phase. When the yeast cells were cultivated under AFP stress, the new metabolism homeostasis in favor of cellular energy and redox homeostasis was generated in C1, then it was inherited and optimized in C2 and C3, enabling the yeast cells in C2 and C3 to enter the exponential phase in a short period after inoculation, which thus significantly shortened the fermentation time.
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Affiliation(s)
- Ya-Jin Lv
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, 300072, People's Republic of China
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Benesch JLP, Aquilina JA, Baldwin AJ, Rekas A, Stengel F, Lindner RA, Basha E, Devlin GL, Horwitz J, Vierling E, Carver JA, Robinson CV. The quaternary organization and dynamics of the molecular chaperone HSP26 are thermally regulated. ACTA ACUST UNITED AC 2011; 17:1008-17. [PMID: 20851350 DOI: 10.1016/j.chembiol.2010.06.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/21/2010] [Accepted: 06/25/2010] [Indexed: 12/18/2022]
Abstract
The function of ScHSP26 is thermally controlled: the heat shock that causes the destabilization of target proteins leads to its activation as a molecular chaperone. We investigate the structural and dynamical properties of ScHSP26 oligomers through a combination of multiangle light scattering, fluorescence spectroscopy, NMR spectroscopy, and mass spectrometry. We show that ScHSP26 exists as a heterogeneous oligomeric ensemble at room temperature. At heat-shock temperatures, two shifts in equilibria are observed: toward dissociation and to larger oligomers. We examine the quaternary dynamics of these oligomers by investigating the rate of exchange of subunits between them and find that this not only increases with temperature but proceeds via two separate processes. This is consistent with a conformational change of the oligomers at elevated temperatures which regulates the disassembly rates of this thermally activated protein.
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Affiliation(s)
- Justin L P Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford, UK
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Jia B, Lee S, Pham BP, Cho YS, Yang JK, Byeon HS, Kim JC, Cheong GW. An archaeal NADH oxidase causes damage to both proteins and nucleic acids under oxidative stress. Mol Cells 2010; 29:363-71. [PMID: 20213313 DOI: 10.1007/s10059-010-0045-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 12/18/2009] [Accepted: 12/23/2009] [Indexed: 10/19/2022] Open
Abstract
NADH oxidases (NOXs) catalyze the two-electron reduction of oxygen to H2O2 or four-electron reduction of oxygen to H2O. In this report, we show that an NADH oxidase from Thermococcus profundus (NOXtp) displays two forms: a native dimeric protein under physiological conditions and an oxidized hexameric form under oxidative stress. Native NOXtp displays high NADH oxidase activity, and oxidized NOXtp can accelerate the aggregation of partially unfolded proteins. The aggregates formed by NOXtp have characteristics similar to beta-amyloid and Lewy bodies in neurodegenerative diseases, including an increase of beta-sheet content. Oxidized NOXtp can also bind nucleic acids and cause their degradation by oxidizing NADH to produce H2O2. Furthermore, Escherichia coli cells expressing NOXtp are less viable than cells not expressing NOXtp after treatment with H2O2. As NOXtp shares similar features with eukaryotic cell death isozymes and life may have originated from hyperthermophiles, we suggest that NOXtp may be an ancestor of cell death proteins.
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MESH Headings
- Archaeal Proteins/chemistry
- Archaeal Proteins/metabolism
- Archaeal Proteins/ultrastructure
- Blotting, Western
- DNA Damage
- DNA, Archaeal/genetics
- DNA, Archaeal/metabolism
- Electrophoresis, Polyacrylamide Gel
- Escherichia coli/genetics
- Escherichia coli/growth & development
- Hydrogen Peroxide/metabolism
- Hydrogen Peroxide/pharmacology
- Microbial Viability/genetics
- Microscopy, Electron
- Multienzyme Complexes/chemistry
- Multienzyme Complexes/metabolism
- Multienzyme Complexes/ultrastructure
- NADH, NADPH Oxidoreductases/chemistry
- NADH, NADPH Oxidoreductases/metabolism
- NADH, NADPH Oxidoreductases/ultrastructure
- Oxidation-Reduction
- Oxidative Stress
- Protein Conformation/drug effects
- Protein Multimerization
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- Temperature
- Thermococcus/enzymology
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Affiliation(s)
- Baolei Jia
- Division of Applied Life Sciences (Brain Korea 21 Program), Gyeongsang National University, Jinju, 660-701, Korea
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Endoplasmic reticulum associated protein degradation: a chaperone assisted journey to hell. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:694-705. [PMID: 20219571 DOI: 10.1016/j.bbamcr.2010.02.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 02/11/2010] [Accepted: 02/18/2010] [Indexed: 01/16/2023]
Abstract
Recognition and elimination of misfolded proteins are essential cellular processes. More than thirty percent of the cellular proteins are proteins of the secretory pathway. They fold in the lumen or membrane of the endoplasmic reticulum from where they are sorted to their site of action. The folding process, as well as any refolding after cell stress, depends on chaperone activity. In case proteins are unable to acquire their native conformation, chaperones with different substrate specificity and activity guide them to elimination. For most misfolded proteins of the endoplasmic reticulum this requires retro-translocation to the cytosol and polyubiquitylation of the misfolded protein by an endoplasmic reticulum associated machinery. Thereafter ubiquitylated proteins are guided to the proteasome for degradation. This review summarizes our up to date knowledge of chaperone classes and chaperone function in endoplasmic reticulum associated degradation of protein waste.
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Airoldi EM, Huttenhower C, Gresham D, Lu C, Caudy AA, Dunham MJ, Broach JR, Botstein D, Troyanskaya OG. Predicting cellular growth from gene expression signatures. PLoS Comput Biol 2009; 5:e1000257. [PMID: 19119411 PMCID: PMC2599889 DOI: 10.1371/journal.pcbi.1000257] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 11/18/2008] [Indexed: 11/18/2022] Open
Abstract
Maintaining balanced growth in a changing environment is a fundamental systems-level challenge for cellular physiology, particularly in microorganisms. While the complete set of regulatory and functional pathways supporting growth and cellular proliferation are not yet known, portions of them are well understood. In particular, cellular proliferation is governed by mechanisms that are highly conserved from unicellular to multicellular organisms, and the disruption of these processes in metazoans is a major factor in the development of cancer. In this paper, we develop statistical methodology to identify quantitative aspects of the regulatory mechanisms underlying cellular proliferation in Saccharomyces cerevisiae. We find that the expression levels of a small set of genes can be exploited to predict the instantaneous growth rate of any cellular culture with high accuracy. The predictions obtained in this fashion are robust to changing biological conditions, experimental methods, and technological platforms. The proposed model is also effective in predicting growth rates for the related yeast Saccharomyces bayanus and the highly diverged yeast Schizosaccharomyces pombe, suggesting that the underlying regulatory signature is conserved across a wide range of unicellular evolution. We investigate the biological significance of the gene expression signature that the predictions are based upon from multiple perspectives: by perturbing the regulatory network through the Ras/PKA pathway, observing strong upregulation of growth rate even in the absence of appropriate nutrients, and discovering putative transcription factor binding sites, observing enrichment in growth-correlated genes. More broadly, the proposed methodology enables biological insights about growth at an instantaneous time scale, inaccessible by direct experimental methods. Data and tools enabling others to apply our methods are available at http://function.princeton.edu/growthrate.
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Affiliation(s)
- Edoardo M. Airoldi
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory,
Princeton University, Princeton, New Jersey, United States of
America
- Department of Computer Science, Princeton University, Princeton, New
Jersey, United States of America
| | - Curtis Huttenhower
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory,
Princeton University, Princeton, New Jersey, United States of
America
- Department of Computer Science, Princeton University, Princeton, New
Jersey, United States of America
| | - David Gresham
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory,
Princeton University, Princeton, New Jersey, United States of
America
- Department of Molecular Biology, Princeton University, Princeton, New
Jersey, United States of America
| | - Charles Lu
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory,
Princeton University, Princeton, New Jersey, United States of
America
- Department of Molecular Biology, Princeton University, Princeton, New
Jersey, United States of America
| | - Amy A. Caudy
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory,
Princeton University, Princeton, New Jersey, United States of
America
| | - Maitreya J. Dunham
- Department of Genome Sciences, University of Washington, Seattle,
Washington, United States of America
| | - James R. Broach
- Department of Molecular Biology, Princeton University, Princeton, New
Jersey, United States of America
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory,
Princeton University, Princeton, New Jersey, United States of
America
- Department of Molecular Biology, Princeton University, Princeton, New
Jersey, United States of America
- * E-mail: (DB); (OGT)
| | - Olga G. Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory,
Princeton University, Princeton, New Jersey, United States of
America
- Department of Computer Science, Princeton University, Princeton, New
Jersey, United States of America
- * E-mail: (DB); (OGT)
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Luthra A, Mahmood A, Arora A, Ramachandran R. Characterization of Rv3868, an essential hypothetical protein of the ESX-1 secretion system in Mycobacterium tuberculosis. J Biol Chem 2008; 283:36532-41. [PMID: 18974091 DOI: 10.1074/jbc.m807144200] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Rv3868, a conserved hypothetical protein of the ESAT-6 secretion system of Mycobacterium tuberculosis, is essential for the secretion of at least four virulence factors. Each protein chain is approximately 63 kDa and assembles into a hexamer. Limited proteolysis demonstrates that it consists of two domains joined by a linker. The N-terminal domain is a compact, helical domain of approximately 30 kDa and apparently functions to regulate the ATPase activity of the C-terminal domain and the oligomerization. The nucleotide binding site is situated in the C-terminal domain, which exhibits ATP-dependent self-association. It is also the oligomerization domain. Dynamic fluorescence quenching studies demonstrate that the domain is proximal to the C terminus in the apoprotein and exhibits a specific movement upon ATP binding. In silico modeling of the domains suggests that Arg-429 of a neighboring subunit forms a part of the binding site upon oligomerization. Mutational analysis of binding site residues demonstrates that the Arg-429 functions as the important "sensor arginine" in AAA-ATPases. Protein NMR experiments involving CFP-10 and activity assays rule out a general chaperone-like function for Rv3868. On the other hand, ATP-dependent "open-close" movements of the individual domains apparently enable it to interact and transfer energy to co-proteins in the ESX-1 pathway.
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Affiliation(s)
- Amit Luthra
- Molecular and Structural Biology Division, Central Drug Research Institute, P.O. Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow-226001, India
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Chaperone function in organic co-solvents: experimental characterization and modeling of a hyperthermophilic chaperone subunit from Methanocaldococcus jannaschii. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1784:368-78. [PMID: 18154740 DOI: 10.1016/j.bbapap.2007.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2007] [Revised: 10/25/2007] [Accepted: 11/16/2007] [Indexed: 11/21/2022]
Abstract
Molecular chaperones play a central role in maintaining protein structure within a cell. Previously, we determined that the gene encoding a molecular chaperone, a thermosome, from the hyperthermophilic archaeon Methanocaldococcus jannaschii is upregulated upon lethal heat shock. We have recombinantly expressed this thermosome (rTHS) and show here that it is both stable and fully functional in aqueous solutions containing water-miscible organic co-solvents. Based on circular dichroism the secondary structure of rTHS was not affected by one-hour exposures to a variety of co-solvents including 30% v/v acetonitrile (ACN) and 50% methanol (MeOH). By contrast, the secondary structure of a mesophilic homologue, GroEL/GroES (GroE), was substantially disrupted. rTHS reduced the aggregation of ovalbumin and citrate synthase in 30% ACN, assisted refolding of citrate synthase upon solvent-inactivation, and stabilized citrate synthase and glutamate dehydrogenase in the direct presence of co-solvents. Apparent total turnover numbers of these enzymes in denaturing solutions increased by up to 2.5-fold in the presence of rTHS. Mechanistic models are proposed to help ascertain specific conditions that could enhance or limit organic solvent-induced chaperone activity. These models suggest that thermodynamic stability and the reversibility of enzyme unfolding play key roles in the effectiveness of enzyme recovery by rTHS.
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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