. Gfpssra-streptavidine, , p.20

, un système permettant d'accéder à des informations sur le(s) état(s) intermédiaire(s) de dépliement de la protéine substrat GFPssrA. La stratégie envisagée était de bloquer le processus de dépliement par PAN en greffant un module streptavidine à l'extrémité N-terminale ou C-terminale de la GFPssrA, La première partie du chapitre décrit les expériences biochimiques effectuées afin de caractériser l'activité du protéasome PAN-20S avec les constructions GFPssrA_Nter-streptavidine et GFPssrA_Cter-streptavidine dans les conditions d'études nécessaires aux mesures TR-SANS. Les mesures TR-SANS réalisées sur ces mêmes systèmes sont décrites dans la seconde partie de ce chapitre

, Contexte de l'étude 1.1. Stratégie employée dans la littérature

, L'hypothèse de cette étude était que si le processus de dépliement d'un substrat était une conséquence de son transfert au sein de PAN, alors la fixation d'une molécule volumineuse, l'avidine, à la GFPssrA devrait bloquer son transfert et empêcher son dépliement. Pour tester cette hypothèse, les auteurs ont utilisé une stratégie consistant à lier une molécule de biotine, Les travaux présentés dans ce chapitre sont basés sur un article publié en 2001 par Navon & Goldberg 317

A. B. ,

, Une molécule d'avidine peut fixer quatre molécules de biotine, et donc quatre GFPssrA. B & C. Représentation artistique Tous les échantillons souhaités ont néanmoins pu être mesurés au cours de ces deux sessions et les résultats sont présentés dans la partie suivante, Figure, vol.106

, Des mesures TR-SANS ont été réalisées sur la d-GFPssrA_Nter-biotine isolée (figure 116.A), en présence de h-PAN (figure 116.C) et en présence de h-PAN

, Tous les échantillons ont été préparés avec une concentration initiale de 100 mM ATP & 200 mM MgCl2. Les réactions ont été activées lors de leur disposition dans le porte-échantillon à 55°C et suivies pendant 30 minutes avec un point de mesure SANS toutes les minutes et un point de mesure de la fluorescence

, et de la fluorescence à 509 nm (vert) au cours du temps. Dans le tampon à 42% D2O, les signaux provenant de la biotine, streptavidine monovalente, protéine PAN et particule 20S hydrogénées sont masqués. Le R g et I(0) correspondent alors exclusivement au signal de la GFPssrA deutérée et à ses formes dérivées. Les informations à déduire des valeurs R g et de I(0) sont de la même nature que celles décrites dans la partie 2, La figure 116 représente, pour chacun des échantillons, l'évolution de l'intensité à angle nul I(0) (noir), du rayon de giration R g (bleu)

. D-gfpssra_nter-biotine,-h-pan-d-gfpssra_nter-streptavidine,

, On sait que la réaction de dépliement et de dégradation a lieu lors des premières minutes de réaction. De plus, les valeurs initiales du I(0) dans les échantillons de d-GFPssrA_Nter-biotine isolée et en présence de h-PAN (voir tableau 22) indiquent qu'il y a eu une perte importante de la valeur du I(0) au cours des trois premières minutes de réaction, qui a ensuite continué de diminuer progressivement jusqu'à une perte d'environ 75%. La fluorescence diminue quant à elle d'environ 77%. La d-GFPssrA est, Cependant, il est important de noter que les données des trois premières minutes de réaction n'ont pas pu être enregistrées

. La-d-gfpssra_nter-streptavidine-en-présence-de-la-machinerie-protéolytique-complète-hydrogénée, Tout comme la réaction contrôle avec la d-GFPssrA_Nter-biotine, la valeur de I(0) diminue au cours du temps, avec une perte totale de d'environ 55% (voir tableau 22). La fluorescence diminue en parallèle d'environ 79%. On peut donc en conclure qu'environ 69% des d-GFPssrA dénaturées par h-PAN, vol.116

R. Schoenheimer, The dynamic state of body constituents. The dynamic state of body constituents, 1946.

D. H. Wolf and R. Menssen, Mechanisms of cell regulation -proteolysis, the big surprise, FEBS Lett, vol.592, pp.2515-2524, 2018.

D. S. Hogness, M. Cohn, and J. Monod, Studies on the induced synthesis of ?-galactosidase in Escherichia coli: The kinetics and mechanism of sulfur incorporation, Biochimica et Biophysica Acta, vol.16, pp.99-116, 1955.

C. De-duve and . Lysosomes, , vol.60, pp.128-159, 1959.

A. Ciechanover, Proteolysis: from the lysosome to ubiquitin and the proteasome, Nat Rev Mol Cell Biol, vol.6, pp.79-87, 2005.

K. D. Wilkinson, M. K. Urban, and A. L. Haas, Ubiquitin is the ATP-dependent proteolysis factor I of rabbit reticulocytes, J. Biol. Chem, vol.255, pp.7529-7532, 1980.

M. Morange, What history tells us XLI. Ubiquitin and proteolysis, J Biosci, vol.41, pp.325-329, 2016.

A. L. Goldberg, Protein degradation and protection against misfolded or damaged proteins, Nature, vol.426, pp.895-899, 2003.

M. Groll, M. Bochtler, H. Brandstetter, T. Clausen, and R. Huber, Molecular Machines for Protein Degradation, ChemBioChem, vol.6, pp.222-256, 2005.

R. S. Yedidi, P. Wendler, C. Enenkel, and . Aaa-, ATPases in Protein Degradation. Front. Mol. Biosci, vol.4, 2017.

B. Alberts, J. H. Wilson, and T. Hunt, Molecular Biology of the Cell, p.1601, 2008.

J. Demers, P. Fricke, C. Shi, V. Chevelkov, and A. Lange, Structure determination of supra-molecular assemblies by solid-state NMR: Practical considerations, Progress in Nuclear Magnetic Resonance Spectroscopy, vol.109, pp.51-78, 2018.

P. Schanda, Relaxing with liquids and solids -A perspective on biomolecular dynamics, J Magn Reson, vol.306, pp.180-186, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02269125

M. P. Rout and A. Sali, Principles for Integrative Structural Biology Studies, Cell, vol.177, pp.1384-1403, 2019.

E. Nogales, The development of cryo-EM into a mainstream structural biology technique, Nat Methods, vol.13, pp.24-27, 2016.

Y. Cheng, Single-particle cryo-EM-How did it get here and where will it go, Science, vol.361, pp.876-880, 2018.

Y. Cheng, Single-Particle Cryo-EM at Crystallographic Resolution, Cell, vol.161, pp.450-457, 2015.

R. M. Glaeser, How good can cryo-EM become?, Nat Methods, vol.13, pp.28-32, 2016.

N. Coquelle, Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography, Nature Chemistry, vol.10, pp.31-37, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01618533

N. Coquelle, Raster-scanning serial protein crystallography using micro-and nano-focused synchrotron beams, Acta Cryst D, vol.71, pp.1184-1196, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01572740

F. Lehmkühler, Dynamics of soft nanoparticle suspensions at hard X-ray FEL sources below the radiation-damage threshold, IUCrJ, vol.5, pp.801-807, 2018.

Y. Shi, A glimpse of structural biology through X-ray crystallography, Cell, vol.159, pp.995-1014, 2014.

B. Brutscher, NMR Methods for the Study of Instrinsically Disordered Proteins Structure, Dynamics, and Interactions: General Overview and Practical Guidelines. in Intrinsically Disordered Proteins Studied by NMR Spectroscopy, vol.870, pp.49-122, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01233983

E. Delaforge, Investigating the Role of Large-Scale Domain Dynamics in Protein-Protein Interactions, Front Mol Biosci, vol.3, p.54, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01426889

A. Marchanka, C. Kreutz, and T. Carlomagno, Isotope labeling for studying RNA by solid-state NMR spectroscopy, J. Biomol. NMR, vol.71, pp.151-164, 2018.

K. Pervushin, R. Riek, G. Wider, and K. Wuthrich, Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution, Proceedings of the National Academy of Sciences, vol.94, pp.12366-12371, 1997.

R. Riek, K. Pervushin, K. Wüthrich, and C. Trosy, NMR with large molecular and supramolecular structures in solution, Trends in Biochemical Sciences, vol.25, pp.462-468, 2000.

R. Riek, G. Wider, K. Pervushin, and K. Wuthrich, Polarization transfer by cross-correlated relaxation in solution NMR with very large molecules, Proceedings of the National Academy of Sciences, vol.96, pp.4918-4923, 1999.

V. Tugarinov, P. M. Hwang, J. E. Ollerenshaw, and L. E. Kay, Cross-Correlated Relaxation Enhanced 1H?13C NMR Spectroscopy of Methyl Groups in Very High Molecular Weight Proteins and Protein Complexes, J. Am. Chem. Soc, vol.125, pp.10420-10428, 2003.

L. E. Kay, Solution NMR spectroscopy of supra-molecular systems, why bother? A methyl-TROSY view, Journal of Magnetic Resonance, vol.210, pp.159-170, 2011.

C. M. Quinn and T. Polenova, Structural biology of supramolecular assemblies by magic-angle spinning NMR spectroscopy, Quarterly Reviews of Biophysics, vol.50, 2017.

R. W. Martin and K. W. Zilm, Preparation of protein nanocrystals and their characterization by solid state NMR, Journal of Magnetic Resonance, vol.165, pp.162-174, 2003.

I. Bertini, C. Luchinat, G. Parigi, E. Ravera, and . Sednmr, On the Edge between Solution and Solid-State NMR, Acc. Chem. Res, vol.46, pp.2059-2069, 2013.

I. Bertini, Solid-state NMR of proteins sedimented by ultracentrifugation, PNAS, vol.108, pp.10396-10399, 2011.

D. F. Gauto, Integrated NMR and cryo-EM atomic-resolution structure determination of a halfmegadalton enzyme complex, Nat Commun, vol.10, pp.1-12, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02166767

T. Schubeis, T. Le-marchand, L. B. Andreas, and G. Pintacuda, 1H magic-angle spinning NMR evolves as a powerful new tool for membrane proteins, Journal of Magnetic Resonance, vol.287, pp.140-152, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01744878

E. Mahieu and F. Gabel, Biological small-angle neutron scattering: recent results and development, Acta Crystallogr D Struct Biol, vol.74, pp.715-726, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01990364

L. Cerofolini, Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques, Biomolecules, vol.9, p.370, 2019.

A. Appolaire, Pyrococcus horikoshii TET2 Peptidase Assembling Process and Associated Functional Regulation, J. Biol. Chem, vol.288, pp.22542-22554, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01025541

Z. Ibrahim, Time-resolved neutron scattering provides new insight into protein substrate processing by a AAA+ unfoldase, Sci Rep, vol.7, p.40948, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01465686

R. H. Whittaker, New Concepts of Kingdoms of Organisms, Science, vol.163, pp.150-160, 1969.

C. R. Woese and G. E. Fox, Phylogenetic structure of the prokaryotic domain: the primary kingdoms, Proc Natl Acad Sci U S A, vol.74, pp.5088-5090, 1977.

C. R. Woese, O. Kandler, and M. L. Wheelis, Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya, PNAS, vol.87, pp.4576-4579, 1990.

P. Forterre, C. Brochier, and H. Philippe, Evolution of the Archaea. Theoretical Population Biology, vol.61, pp.409-422, 2002.

S. Gribaldo and C. Brochier-armanet, The origin and evolution of Archaea: a state of the art, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.361, pp.1007-1022, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00697930

K. Raymann, C. Brochier-armanet, and S. Gribaldo, The two-domain tree of life is linked to a new root for the Archaea, PNAS, vol.112, pp.6670-6675, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02018983

C. Brochier-armanet, B. Boussau, S. Gribaldo, and P. Forterre, Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota, Nat Rev Microbiol, vol.6, pp.245-252, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00256781

T. Nunoura, Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group, Nucleic Acids Res, vol.39, pp.3204-3223, 2011.

J. G. Elkins, A korarchaeal genome reveals insights into the evolution of the Archaea, Proc Natl Acad Sci U S A, vol.105, pp.8102-8107, 2008.

L. Guy and T. J. Ettema, The archaeal 'TACK' superphylum and the origin of eukaryotes, Trends in Microbiology, vol.19, pp.580-587, 2011.

H. Huber, M. J. Hohn, K. O. Stetter, and R. Rachel, The phylum Nanoarchaeota: Present knowledge and future perspectives of a unique form of life, Research in Microbiology, vol.154, pp.165-171, 2003.

C. Petitjean, P. Deschamps, P. López-garcía, and D. Moreira, Rooting the Domain Archaea by Phylogenomic Analysis Supports the Foundation of the New Kingdom Proteoarchaeota, Genome Biol Evol, vol.7, pp.191-204, 2014.

A. Spang, E. F. Caceres, and T. J. Ettema, Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life, Science, vol.357, p.3883, 2017.

M. A. Kozubal, Geoarchaeota: a new candidate phylum in the Archaea from high-temperature acidic iron mats in Yellowstone National Park, ISME J, vol.7, pp.622-634, 2013.

P. N. Evans, Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genomecentric metagenomics, Science, vol.350, pp.434-438, 2015.

I. Vanwonterghem, Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota, Nat Microbiol, vol.1, pp.1-9, 2016.

C. J. Castelle, Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling, Current Biology, vol.25, pp.690-701, 2015.

C. Rinke, Insights into the phylogeny and coding potential of microbial dark matter, Nature, vol.499, pp.431-437, 2013.

K. Zaremba-niedzwiedzka, Asgard archaea illuminate the origin of eukaryotic cellular complexity, Nature, vol.541, pp.353-358, 2017.

A. Spang, Complex archaea that bridge the gap between prokaryotes and eukaryotes, Nature, vol.521, pp.173-179, 2015.

K. W. Seitz, New Asgard archaea capable of anaerobic hydrocarbon cycling, bioRxiv, vol.527697, 2019.

S. Gribaldo and C. Brochier-armanet, Time for order in microbial systematics, Trends in Microbiology, vol.20, pp.209-210, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00697925

N. Iwabe, K. Kuma, M. Hasegawa, S. Osawa, and T. Miyata, Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes, PNAS, vol.86, pp.9355-9359, 1989.

J. A. Lake, E. Henderson, M. Oakes, and M. W. Clark, Eocytes: a new ribosome structure indicates a kingdom with a close relationship to eukaryotes, PNAS, vol.81, pp.3786-3790, 1984.

M. C. Rivera and J. A. Lake, Evidence that eukaryotes and eocyte prokaryotes are immediate relatives, Science, vol.257, pp.74-76, 1992.

J. J. Kelly, K. Policht, T. Grancharova, and L. S. Hundal, Distinct Responses in Ammonia-Oxidizing Archaea and Bacteria after Addition of Biosolids to an Agricultural Soil, Appl. Environ. Microbiol, vol.77, pp.6551-6558, 2011.

T. A. Williams, P. G. Foster, C. J. Cox, and T. M. Embley, An archaeal origin of eukaryotes supports only two primary domains of life, Nature, vol.504, pp.231-236, 2013.

T. A. Williams and T. M. Embley, Dark Matter" and the Origin of Eukaryotes, Genome Biol Evol, vol.6, pp.474-481, 2014.

E. Lasek-nesselquist and J. P. Gogarten, The effects of model choice and mitigating bias on the ribosomal tree of life, Molecular Phylogenetics and Evolution, vol.69, pp.17-38, 2013.

L. Eme, A. Spang, J. Lombard, C. W. Stairs, and T. J. Ettema, Archaea and the origin of eukaryotes, Nature Reviews Microbiology, vol.15, pp.711-723, 2017.

P. Forterre, The Common Ancestor of Archaea and Eukarya Was Not an Archaeon, Archaea, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00932177

V. D. Cunha, M. Gaia, D. Gadelle, A. Nasir, and P. Forterre, Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes, PLOS Genetics, vol.13, p.1006810, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01570207

V. D. Cunha, M. Gaia, A. Nasir, and P. Forterre, Asgard archaea do not close the debate about the universal tree of life topology, PLOS Genetics, vol.14, p.1007215, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02177609

H. Imachi, Isolation of an archaeon at the prokaryote-eukaryote interface, bioRxiv, vol.726976, 2019.

F. Canganella and J. Wiegel, Extremophiles: from abyssal to terrestrial ecosystems and possibly beyond, Naturwissenschaften, vol.98, pp.253-279, 2011.

L. J. Rothschild and R. L. Mancinelli, Life in extreme environments, Nature, vol.409, pp.1092-1101, 2001.

C. E. Zobell and R. Y. Morita, BAROPHILIC BACTERIA IN SOME DEEP SEA SEDIMENTS1, J Bacteriol, vol.73, pp.563-568, 1957.

C. F. Aguilar, Crystal structure of the ?-glycosidase from the hyperthermophilic archeon Sulfolobus solfataricus: resilience as a key factor in thermostability11Edited by R, Huber. Journal of Molecular Biology, vol.271, pp.789-802, 1997.

G. Antranikian, C. E. Vorgias, and C. Bertoldo, Extreme Environments as a Resource for Microorganisms and Novel Biocatalysts, pp.219-262, 2005.

P. H. Rampelotto, Resistance of Microorganisms to Extreme Environmental Conditions and Its Contribution to, Astrobiology. Sustainability, vol.2, pp.1602-1623, 2010.

S. Leuko, M. J. Raftery, B. P. Burns, M. R. Walter, and B. A. Neilan, Global Protein-Level Responses of Halobacterium salinarum NRC-1 to Prolonged Changes in External Sodium Chloride Concentrations, J. Proteome Res, vol.8, pp.2218-2225, 2009.

M. Kottemann, A. Kish, C. Iloanusi, S. Bjork, and J. Diruggiero, Physiological responses of the halophilic archaeon Halobacterium sp. strain NRC1 to desiccation and gamma irradiation, Extremophiles, vol.9, pp.219-227, 2005.
URL : https://hal.archives-ouvertes.fr/mnhn-02862359

K. Takai and K. Horikoshi, Genetic Diversity of Archaea in Deep-Sea Hydrothermal Vent Environments, Genetics, vol.152, pp.1285-1297, 1999.

D. Daffonchio, Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline, Nature, vol.440, pp.203-207, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00023124

A. Andrei, H. L. Banciu, and A. Oren, Living with salt: metabolic and phylogenetic diversity of archaea inhabiting saline ecosystems, FEMS Microbiol Lett, vol.330, pp.1-9, 2012.

K. O. Stetter, Hyperthermophiles in the history of life, Phil. Trans. R. Soc. B, vol.361, pp.1837-1843, 2006.

K. O. Stetter, Methanothermus fervidus, sp. nov., a novel extremely thermophilic methanogen isolated from an Icelandic hot spring, Zentralblatt für Bakteriologie Mikrobiologie und Hygiene: I. Abt. Originale C: Allgemeine, angewandte und ökologische Mikrobiologie, vol.2, pp.166-178, 1981.

C. Vieille and G. J. Zeikus, Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for, Thermostability. Microbiology and Molecular Biology Reviews, vol.65, pp.1-43, 2001.

L. Achenbach-richter, R. Gupta, K. O. Stetter, and C. R. Woese, Were the original eubacteria thermophiles?, Systematic and Applied Microbiology, vol.9, pp.34-39, 1987.

G. Fiala and K. O. Stetter, Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C, Arch. Microbiol, vol.145, pp.56-61, 1986.

P. López-garcía, F. Rodríguez-valera, C. Pedrós-alió, and D. Moreira, Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton, Nature, vol.409, pp.603-607, 2001.

L. J. Magrum, K. R. Luehrsen, and C. R. Woese, Are extreme halophiles actually "bacteria"?, J Mol Evol, vol.11, pp.1-8, 1978.

M. Ciaramella, A. Napoli, and M. Rossi, Another extreme genome: how to live at pH 0, Trends in Microbiology, vol.13, pp.49-51, 2005.

J. N. Reeve and C. Schleper, Archaea: very diverse, often different but never bad?, Curr Opin Microbiol, vol.14, pp.271-273, 2011.

B. Haegeman, Robust estimation of microbial diversity in theory and in practice, ISME J, vol.7, pp.1092-1101, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00859547

E. F. Delong, Everything in moderation: Archaea as 'non-extremophiles, Current Opinion in Genetics & Development, vol.8, pp.649-654, 1998.

P. Lepage, A metagenomic insight into our gut's microbiome, Gut, vol.62, pp.146-158, 2013.

T. L. Miller, M. J. Wolin, E. C. Macario, and A. J. Macario, Isolation of Methanobrevibacter smithii from human feces, Appl. Environ. Microbiol, vol.43, pp.227-232, 1982.

J. G. Caporaso, Moving pictures of the human microbiome, Genome Biology, vol.12, p.50, 2011.

A. J. Probst, A. K. Auerbach, and C. Moissl-eichinger, Archaea on Human Skin. PLOS ONE, vol.8, p.65388, 2013.

J. G. Ferry, K. A. Kastead, and . Methanogenesis, Archaea, vol.288, issue.314, 2007.

P. S. Adam, G. Borrel, C. Brochier-armanet, and S. Gribaldo, The growing tree of Archaea: new perspectives on their diversity, evolution and ecology, ISME J, vol.11, pp.2407-2425, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-02445405

P. B. Eckburg, P. W. Lepp, and D. A. Relman, Archaea and Their Potential Role in Human Disease, Infection and Immunity, vol.71, pp.591-596, 2003.

N. Gaci, G. Borrel, W. Tottey, P. W. O'toole, and J. Brugère, Archaea and the human gut: New beginning of an old story, World J Gastroenterol, vol.20, pp.16062-16078, 2014.

C. J. Castelle and J. F. Banfield, Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life, Cell, vol.172, pp.1181-1197, 2018.

M. E. Vianna, G. Conrads, B. P. Gomes, and H. P. Horz, T-RFLP-based mcrA gene analysis of methanogenic archaea in association with oral infections and evidence of a novel Methanobrevibacter phylotype, Oral Microbiology and Immunology, vol.24, pp.417-422, 2009.

C. Bang and R. A. Schmitz, Archaea associated with human surfaces: not to be underestimated, FEMS Microbiol Rev, vol.39, pp.631-648, 2015.

B. Dridi, D. Raoult, and M. Drancourt, Archaea as emerging organisms in complex human microbiomes, Anaerobe, vol.17, pp.56-63, 2011.

F. Matarazzo, The domain Archaea in human mucosal surfaces, Clinical Microbiology and Infection, vol.18, pp.834-840, 2012.

E. F. Delong and N. R. Pace, Environmental Diversity of Bacteria and Archaea, Syst Biol, vol.50, pp.470-478, 2001.

J. Hong and J. Cho, Environmental Variables Shaping the Ecological Niche of Thaumarchaeota in Soil: Direct and Indirect Causal Effects, PLOS ONE, vol.10, p.133763, 2015.

W. J. Jones, J. A. Leigh, F. Mayer, C. R. Woese, and R. S. Wolfe, Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent, Arch. Microbiol, vol.136, pp.254-261, 1983.

J. F. Miller, N. N. Shah, C. M. Nelson, J. M. Ludlow, and D. S. Clark, Pressure and Temperature Effects on Growth and Methane Production of the Extreme Thermophile Methanococcus jannaschii, Appl. Environ. Microbiol, vol.54, pp.3039-3042, 1988.

D. E. Graham, N. Kyrpides, I. J. Anderson, R. Overbeek, and W. B. Whitman, Genome of Methanocaldococcus (methanococcus) jannaschii, Methods in Enzymology, vol.330, pp.40-123, 2001.

H. König, R. Rachel, and H. Claus, Proteinaceous Surface Layers of Archaea: Ultrastructure and Biochemistry, Archaea, vol.315, 2007.

L. , S. Joan-&-w, and F. John, Microbiology: An Evolving Science: Third International Student Edition, 2013.

C. J. Bult, Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii, Science, vol.273, pp.1058-1073, 1996.

M. Tehei and G. Zaccai, Adaptation to high temperatures through macromolecular dynamics by neutron scattering: Dynamic basis of thermoadaptation, FEBS Journal, vol.274, pp.4034-4043, 2007.

G. Zaccai, Ecology of Protein Dynamics, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01326144

G. J. Davies, S. J. Gamblin, J. A. Littlechild, and H. C. Watson, The structure of a thermally stable 3-phosphoglycerate kinase and a comparison with its mesophilic equivalent, Proteins: Structure, Function, and Bioinformatics, vol.15, pp.283-289, 1993.

G. Auerbach, Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability, Structure, vol.5, pp.1475-1483, 1997.

Y. Chi, Crystal structure of the ?-glycosidase from the hyperthermophile Thermosphaera aggregans: insights into its activity and thermostability, FEBS Letters, vol.445, pp.375-383, 1999.

J. Hollien and S. Marqusee, Structural distribution of stability in a thermophilic enzyme, PNAS, vol.96, pp.13674-13678, 1999.

M. W. Bauer, L. E. Driskill, and R. M. Kelly, Glycosyl hydrolases from hyperthermophilic microorganisms, Current Opinion in Biotechnology, vol.9, pp.141-145, 1998.

P. Zwickl, S. Fabry, C. Bogedain, A. Haas, and R. Hensel, Glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaebacterium Pyrococcus woesei: characterization of the enzyme, cloning and sequencing of the gene, and expression in Escherichia coli, Journal of Bacteriology, vol.172, pp.4329-4338, 1990.

H. Han, Improvements of thermophilic enzymes: From genetic modifications to applications, Bioresource Technology, vol.279, pp.350-361, 2019.

G. Feller, Protein stability and enzyme activity at extreme biological temperatures, J. Phys.: Condens. Matter, vol.22, p.323101, 2010.

A. Irimia, The 2.9Å Resolution Crystal Structure of Malate Dehydrogenase from Archaeoglobus fulgidus: Mechanisms of Oligomerisation and Thermal Stabilisation, Journal of Molecular Biology, vol.335, pp.343-356, 2004.
URL : https://hal.archives-ouvertes.fr/hal-01955789

M. Karlström, Structure determination, thermal stability and catalytic mechanism of hyperthermostable isocitrate dehydrogenases, 2006.

S. Koutsopoulos, J. Oost, and W. Van-der-&-norde, Temperature-dependent structural and functional features of a hyperthermostable enzyme using elastic neutron scattering, Proteins: Structure, Function, and Bioinformatics, vol.61, pp.377-384, 2005.

P. J. Haney, Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species, PNAS, vol.96, pp.3578-3583, 1999.

H. Hatanaka, R. Tanimura, S. Katoh, and F. Inagaki, Solution structure of ferredoxin from the thermophilic Cyanobacterium Synechococcus elongatus and its thermostability11Edited by, Journal of Molecular Biology, vol.268, pp.922-933, 1997.

G. Wallon, Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus11Edited by A. R. Fersht, Journal of Molecular Biology, vol.266, pp.1016-1031, 1997.

M. K. Chan, S. Mukund, A. Kletzin, M. W. Adams, and D. C. Rees, Structure of a hyperthermophilic tungstopterin enzyme, aldehyde ferredoxin oxidoreductase, Science, vol.267, pp.1463-1469, 1995.

D. W. Rice, Insights into the molecular basis of thermal stability from the structure determination of Pyrococcus furiosus gluatamate dehydrogenase, FEMS Microbiol Rev, vol.18, pp.105-117, 1996.

K. Yip, The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ionpair networks in maintaining enzyme stability at extreme temperatures, Structure, vol.3, pp.1147-1158, 1995.

S. Kumar, B. Ma, C. Tsai, and R. Nussinov, Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers, Proteins: Structure, Function, and Bioinformatics, vol.38, pp.368-383, 2000.

A. Szilágyi and P. Závodszky, Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey, Structure, vol.8, pp.493-504, 2000.

A. H. Elcock, The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins11Edited by B. Honig, Journal of Molecular Biology, vol.284, pp.489-502, 1998.

G. Feller and C. Gerday, Psychrophilic enzymes: hot topics in cold adaptation, Nat Rev Microbiol, vol.1, pp.200-208, 2003.

I. Choi, W. Bang, S. Kim, and Y. G. Yu, Extremely Thermostable Serine-type Protease from Aquifex pyrophilus MOLECULAR CLONING, EXPRESSION, AND CHARACTERIZATION, J. Biol. Chem, vol.274, pp.881-888, 1999.

S. Kumar and R. Nussinov, How do thermophilic proteins deal with heat? CMLS, Cell. Mol. Life Sci, vol.58, pp.1216-1233, 2001.

S. Trivedi, H. S. Gehlot, and S. R. Rao, Protein thermostability in Archaea and Eubacteria, Genetics and Molecular Research, vol.12, 2006.

Y. Tanaka, How Oligomerization Contributes to the Thermostability of an Archaeon Protein PROTEIN l-ISOASPARTYL-O-METHYLTRANSFERASE FROM SULFOLOBUS TOKODAII, J. Biol. Chem, vol.279, pp.32957-32967, 2004.

K. Suhre and J. Claverie, Genomic Correlates of Hyperthermostability, an Update, J. Biol. Chem, vol.278, pp.17198-17202, 2003.

R. Lieph, F. A. Veloso, and D. S. Holmes, Thermophiles like hot T, Trends in Microbiology, vol.14, pp.423-426, 2006.

H. Hashimoto, Hyperthermostable Protein Structure Maintained by Intra and Inter-helix Ion-pairs in Archaeal O6-Methylguanine-DNA Methyltransferase, Journal of Molecular Biology, vol.292, pp.707-716, 1999.

J. Jorda and T. O. Yeates, Widespread Disulfide Bonding in Proteins from Thermophilic Archaea, Archaea, 2011.

M. J. Thompson and D. Eisenberg, Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability1 1Edited by I. B. Honig, Journal of Molecular Biology, vol.290, pp.595-604, 1999.

Y. Yamagata, Entropic Stabilization of the Tryptophan Synthase ?-Subunit from a Hyperthermophile, Pyrococcus furiosus X-RAY ANALYSIS AND CALORIMETRY, J. Biol. Chem, vol.276, pp.11062-11071, 2001.

L. D. Unsworth, J. Oost, and S. Koutsopoulos, Hyperthermophilic enzymes ? stability, activity and implementation strategies for high temperature applications, The FEBS Journal, vol.274, pp.4044-4056, 2007.

E. Ramos, T. Lopez, P. Bosch, M. Asomoza, and R. Gomez, Thermal Stability of Sol-Gel Hydrotalcites, Journal of Sol-Gel Science and Technology, vol.8, pp.437-442, 1997.

H. Santos and M. S. Costa, Compatible solutes of organisms that live in hot saline environments, Environmental Microbiology, vol.4, pp.501-509, 2002.

R. Wirth, Colonization of Black Smokers by Hyperthermophilic Microorganisms, Trends in Microbiology, vol.25, pp.92-99, 2017.

B. B. Boonyaratanakornkit, Transcriptional profiling of the hyperthermophilic methanarchaeon Methanococcus jannaschii in response to lethal heat and non-lethal cold shock, Environmental Microbiology, vol.7, pp.789-797, 2005.

J. Maupin-furlow, Proteasomes and protein conjugation across domains of life, Nat Rev Microbiol, vol.10, pp.100-111, 2012.

B. Franzetti, G. Schoehn, D. Garcia, R. W. Ruigrok, and G. Zaccai, Characterization of the proteasome from the extremely halophilic archaeon Haloarcula marismortui, Archaea, vol.1, pp.53-61, 2002.

G. N. Somero, Proteins and Temperature, Annual Review of Physiology, vol.57, pp.43-68, 1995.

M. Tehei, Adaptation to extreme environments: macromolecular dynamics in bacteria compared in vivo by neutron scattering, EMBO reports, vol.5, pp.66-70, 2004.

A. Habbeche, Purification and biochemical characterization of a detergent-stable keratinase from a newly thermophilic actinomycete Actinomadura keratinilytica strain Cpt29 isolated from poultry compost, Journal of Bioscience and Bioengineering, vol.117, pp.413-421, 2014.

A. A. Kudriaeva and A. A. Belogurov, Proteasome: a Nanomachinery of Creative Destruction, Biochemistry Mosc, vol.84, pp.159-192, 2019.

A. L. Goldberg and J. F. Dice, Intracellular Protein Degradation in Mammalian and Bacterial Cells, Annu. Rev. Biochem, vol.43, pp.835-869, 1974.

A. L. Goldberg, . St, and A. C. John, Intracellular Protein Degradation in Mammalian and Bacterial Cells: Part 2, Annu. Rev. Biochem, vol.45, pp.747-804, 1976.

M. H. Glickman, Getting in and out of the proteasome, Seminars in Cell & Developmental Biology, vol.11, pp.149-158, 2000.

J. Maupin-furlow, H. Wilson, S. Kaczowka, and M. Ou, Proteasomes in the archaea: from structure to function, Frontiers in bioscience : a journal and virtual library, vol.5, pp.837-65, 2000.

R. T. Schimke, R. Ganschow, D. Doyle, and I. M. Arias, Regulation of protein turnover in mammalian tissues, Fed Proc, vol.27, pp.1223-1230, 1968.

A. Ciechanover, Proteolysis: from the lysosome to ubiquitin and the proteasome, Nat Rev Mol Cell Biol, vol.6, pp.79-87, 2005.

M. Y. Sherman and A. L. Goldberg, Cellular defenses against unfolded proteins: a cell biologist thinks about neurodegenerative diseases, Neuron, vol.29, pp.15-32, 2001.

Y. Klemes, J. D. Etlinger, and A. L. Goldberg, Properties of abnormal proteins degraded rapidly in reticulocytes. Intracellular aggregation of the globin molecules prior to hydrolysis, J. Biol. Chem, vol.256, pp.8436-8444, 1981.

F. U. Hartl, Molecular Chaperones in the Cytosol: from Nascent Chain to Folded Protein, Science, vol.295, pp.1852-1858, 2002.

J. Frydman, Folding of Newly Translated Proteins In Vivo: The Role of Molecular Chaperones, Annual Review of Biochemistry, vol.70, pp.603-647, 2001.

J. R. Glover, S. Lindquist, H. Hsp104, and . Hsp40, A Novel Chaperone System that Rescues Previously Aggregated Proteins, Cell, vol.94, pp.73-82, 1998.

J. J. Verplank, S. Lokireddy, M. L. Feltri, A. L. Goldberg, and L. Wrabetz, Impairment of protein degradation and proteasome function in hereditary neuropathies, Glia, vol.66, pp.379-395, 2018.

A. J. Barrett and J. K. Mcdonald, Nomenclature: protease, proteinase and peptidase, Biochem J, vol.237, p.935, 1986.

A. O. Olivares, T. A. Baker, and R. T. Sauer, Mechanistic insights into bacterial AAA+ proteases and protein-remodelling machines, Nat Rev Microbiol, vol.14, pp.33-44, 2016.

E. Kruger, E. Witt, S. Ohlmeier, R. Hanschke, and M. Hecker, The Clp Proteases of Bacillus subtilis Are Directly Involved in Degradation of Misfolded Proteins, Journal of Bacteriology, vol.182, pp.3259-3265, 2000.

M. Hecker, W. Schumann, and U. Völker, Heat-shock and general stress response in Bacillus subtilis, Molecular Microbiology, vol.19, pp.417-428, 1996.

M. C. Duque-magalhães and . La, Biochimie, vol.66, pp.653-662, 1984.

R. R. Kopito, Aggresomes, inclusion bodies and protein aggregation, Trends in Cell Biology, vol.10, pp.524-530, 2000.

A. Ciechanover and P. Brundin, The Ubiquitin Proteasome System in Neurodegenerative Diseases: Sometimes the Chicken, Sometimes the Egg, Neuron, vol.40, pp.427-446, 2003.

M. Schmidt and D. Finley, Regulation of proteasome activity in health and disease, Biochimica et Biophysica Acta (BBA) -Molecular Cell Research, vol.1843, pp.13-25, 2014.

R. T. Sauer, T. A. Baker, and . Proteases, ATP-Fueled Machines of Protein Destruction, Annu. Rev. Biochem, vol.80, pp.587-612, 2011.

K. Tanaka and A. Ichihara, Half-life of proteasomes (multiprotease complexes) in rat liver, Biochemical and Biophysical Research Communications, vol.159, pp.1309-1315, 1989.

M. Schmidt, Sequence information within proteasomal prosequences mediates efficient integration of ?-subunits into the 20 s proteasome complex 11Edited by, Journal of Molecular Biology, vol.288, pp.117-128, 1999.

J. Lowe, Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution, Science, vol.268, pp.533-539, 1995.

E. Seemuller, Proteasome from Thermoplasma acidophilum: a threonine protease, Science, vol.268, pp.579-582, 1995.

E. Seemüller, A. Lupas, and W. Baumeister, Autocatalytic processing of the 20S proteasome, Nature, vol.382, pp.468-470, 1996.

J. Rabl, Mechanism of Gate Opening in the 20S Proteasome by the Proteasomal ATPases, Molecular Cell, vol.30, pp.360-368, 2008.

W. Baumeister, J. Walz, F. Zühl, and E. Seemüller, The Proteasome: Paradigm of a Self-Compartmentalizing Protease, Cell, vol.92, pp.367-380, 1998.

D. Finley, Recognition and Processing of Ubiquitin-Protein Conjugates by the Proteasome, Annual Review of Biochemistry, vol.78, pp.477-513, 2009.

S. Bohn, Structure of the 26S proteasome from Schizosaccharomyces pombe at subnanometer resolution, PNAS, vol.107, pp.20992-20997, 2010.

F. Förster, K. Lasker, S. Nickell, A. Sali, and W. Baumeister, Toward an Integrated Structural Model of the 26S Proteasome, Molecular & Cellular Proteomics, vol.9, pp.1666-1677, 2010.

J. A. Bard, Structure and Function of the 26S Proteasome, Annu. Rev. Biochem, vol.87, pp.697-724, 2018.

J. He, The Structure of the 26S Proteasome Subunit Rpn2 Reveals Its PC Repeat Domain as a Closed Toroid of Two Concentric ?-Helical Rings, Structure, vol.20, pp.513-521, 2012.

Y. Shi, Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome, Science, vol.351, p.9421, 2016.

K. Lasker, Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach, Proceedings of the National Academy of Sciences, vol.109, pp.1380-1387, 2012.

C. Gorbea, D. Taillandier, and M. Rechsteiner, Mapping Subunit Contacts in the Regulatory Complex of the 26 S Proteasome: S2 AND S5b FORM A TETRAMER WITH ATPase SUBUNITS S4 and S7, Journal of Biological Chemistry, vol.275, pp.875-882, 2000.

C. Richmond, C. Gorbea, and M. Rechsteiner, Specific Interactions between ATPase Subunits of the 26 S Protease, J. Biol. Chem, vol.272, pp.13403-13411, 1997.

T. Inobe and R. Genmei, N-Terminal Coiled-Coil Structure of ATPase Subunits of 26S Proteasome Is Crucial for Proteasome Function, PLoS ONE, vol.10, p.134056, 2015.

D. M. Rubin, M. H. Glickman, C. N. Larsen, S. Dhruvakumar, and D. Finley, Active site mutants in the six regulatory particle ATPases reveal multiple roles for ATP in the proteasome, The EMBO Journal, vol.17, pp.4909-4919, 1998.

Y. Zhu, Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome, Nat Commun, vol.9, p.1360, 2018.

E. J. Katz, M. Isasa, and B. Crosas, A new map to understand deubiquitination, Biochem Soc Trans, vol.38, pp.21-28, 2010.

S. M. Nijman, A Genomic and Functional Inventory of Deubiquitinating Enzymes, Cell, vol.123, pp.773-786, 2005.

S. Li and M. Hochstrasser, The Yeast ULP2 (SMT4) Gene Encodes a Novel Protease Specific for the Ubiquitin-Like Smt3 Protein, Molecular and Cellular Biology, vol.20, pp.2367-2377, 2000.

D. Komander and . Mechanism, Specificity and Structure of the Deubiquitinases. in Conjugation and Deconjugation of Ubiquitin Family Modifiers: Subcellular Biochemistry, pp.69-87, 2010.

B. Lee, USP14 deubiquitinates proteasome-bound substrates that are ubiquitinated at multiple sites, Nature, vol.532, pp.398-401, 2016.

J. Hamazaki, A novel proteasome interacting protein recruits the deubiquitinating enzyme UCH37 to 26S proteasomes, The EMBO Journal, vol.25, pp.4524-4536, 2006.

X. Qiu, hRpn13/ADRM1/GP110 is a novel proteasome subunit that binds the deubiquitinating enzyme, UCH37. The EMBO Journal, vol.25, pp.5742-5753, 2006.

K. Husnjak and I. Dikic, Ubiquitin-Binding Proteins: Decoders of Ubiquitin-Mediated Cellular Functions, Annual Review of Biochemistry, vol.81, pp.291-322, 2012.

A. Hershko, Ubiquitin-mediated protein degradation, J. Biol. Chem, vol.263, pp.15237-15240, 1988.

C. M. Pickart and R. E. Cohen, Proteasomes and their kin: proteases in the machine age, Nat Rev Mol Cell Biol, vol.5, pp.177-187, 2004.

M. Scheffner, U. Nuber, and J. M. Huibregtse, Protein ubiquitination involving an E1-E2-E3 enzyme ubiquitin thioester cascade, Nature, vol.373, pp.81-83, 1995.

T. Ravid and M. Hochstrasser, Autoregulation of an E2 enzyme by ubiquitin-chain assembly on its catalytic residue, Nat Cell Biol, vol.9, pp.422-427, 2007.

A. Hershko and A. Ciechanover, The Ubiquitin System. Annual Review of Biochemistry, vol.67, pp.425-479, 1998.

M. S. Hipp, B. Kalveram, S. Raasi, M. Groettrup, and G. Schmidtke, FAT10, a Ubiquitin-Independent Signal for Proteasomal Degradation, Molecular and Cellular Biology, vol.25, pp.3483-3491, 2005.

A. G. Van-der-veen and H. L. Ploegh, Ubiquitin-Like Proteins, Annual Review of Biochemistry, vol.81, pp.323-357, 2012.

M. A. Hoyt and P. Coffino, Ubiquitin-free routes into the proteasome, Cell. Mol. Life Sci, vol.61, pp.1596-1600, 2004.

T. Chen, Clusterin-Mediated Apoptosis Is Regulated by Adenomatous Polyposis Coli and Is p21 Dependent but p53 Independent, Cancer Res, vol.64, pp.7412-7419, 2004.

B. Delabarre and A. T. Brunger, Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains, Nat Struct Mol Biol, vol.10, pp.856-863, 2003.

M. Esaki, A. Johjima-murata, M. T. Islam, and T. Ogura, Biological and Pathological Implications of an Alternative ATP-Powered Proteasomal Assembly With Cdc48 and the 20S Peptidase, Front. Mol. Biosci, vol.5, p.56, 2018.

D. H. Wolf and A. Stolz, The Cdc48 machine in endoplasmic reticulum associated protein degradation, Biochimica et Biophysica Acta (BBA) -Molecular Cell Research, vol.1823, pp.117-124, 2012.

D. Barthelme, R. Jauregui, and R. T. Sauer, An ALS disease mutation in Cdc48/p97 impairs 20S proteasome binding and proteolytic communication: Cdc48 ALS Disease Mutation, Protein Science, vol.24, pp.1521-1527, 2015.

D. Barthelme and R. T. Sauer, Identification of the Cdc48bullet20S Proteasome as an Ancient AAA+ Proteolytic Machine, Science, vol.337, pp.843-846, 2012.

A. Rothballer, N. Tzvetkov, and P. Zwickl, Mutations in p97/VCP induce unfolding activity, FEBS Letters, vol.581, pp.1197-1201, 2007.

A. U. Müller and E. Weber-ban, The Bacterial Proteasome at the Core of Diverse Degradation, Pathways. Front. Mol. Biosci, vol.6, p.23, 2019.

E. Gur, D. Biran, and E. Z. Ron, Regulated proteolysis in Gram-negative bacteria -how and when?, Nat Rev Microbiol, vol.9, pp.839-848, 2011.

C. H. Chung and A. L. Goldberg, The product of the lon (capR) gene in Escherichia coli is the ATPdependent protease, protease La, PNAS, vol.78, pp.4931-4935, 1981.

I. Lee and C. K. Suzuki, Functional mechanics of the ATP-dependent Lon protease-lessons from endogenous protein and synthetic peptide substrates, Biochimica et Biophysica Acta (BBA) -Proteins and Proteomics, vol.1784, pp.727-735, 2008.

F. Striebel, W. Kress, and E. Weber-ban, Controlled destruction: AAA+ ATPases in protein degradation from bacteria to eukaryotes, Current Opinion in Structural Biology, vol.19, pp.209-217, 2009.

R. De-mot, I. Nagy, J. Walz, and W. Baumeister, Proteasomes and other self-compartmentalizing proteases in prokaryotes, Trends in Microbiology, vol.7, pp.88-92, 1999.

M. Unciuleac, P. C. Smith, and S. Shuman, Crystal Structure and Biochemical Characterization of a Mycobacterium smegmatis AAA-Type Nucleoside Triphosphatase Phosphohydrolase (Msm0858), Journal of Bacteriology, vol.198, pp.1521-1533, 2016.

M. Ziemski, Cdc48-like protein of actinobacteria (Cpa) is a novel proteasome interactor in mycobacteria and related organisms, vol.7, p.34055, 2018.

P. Wendler, S. Ciniawsky, M. Kock, and S. Kube, Structure and function of the AAA+ nucleotide binding pocket, Biochimica et Biophysica Acta (BBA) -Molecular Cell Research, vol.1823, pp.2-14, 2012.

K. Ito and Y. Akiyama, Cellular Functions, Mechanism of Action, and Regulation of Ftsh Protease, Annual Review of Microbiology, vol.59, pp.211-231, 2005.

F. Gerdes, T. Tatsuta, and T. Langer, Mitochondrial AAA proteases -Towards a molecular understanding of membrane-bound proteolytic machines, Biochimica et Biophysica Acta (BBA) -Molecular Cell Research, vol.1823, pp.49-55, 2012.

E. Gur, A. Lon, and . Protease, Regulated Proteolysis in Microorganisms, pp.35-51, 2013.

J. B. Jastrab and K. H. Darwin, Bacterial Proteasomes. Annual Review of Microbiology, vol.69, pp.109-127, 2015.

T. Wang, K. H. Darwin, and H. Li, Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation, Nat Struct Mol Biol, vol.17, pp.1352-1357, 2010.

D. Özcelik, Structures of Pup ligase PafA and depupylase Dop from the prokaryotic ubiquitin-like modification pathway, Nat Commun, vol.3, pp.1-10, 2012.

J. M. Flynn, S. B. Neher, Y. Kim, R. T. Sauer, and T. A. Baker, Proteomic Discovery of Cellular Substrates of the ClpXP Protease Reveals Five Classes of ClpX-Recognition Signals, Molecular Cell, vol.11, pp.671-683, 2003.

S. Gottesman, E. Roche, Y. Zhou, and R. T. Sauer, The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system, Genes & Development, vol.12, pp.1338-1347, 1998.

K. C. Keiler, P. R. Waller, and R. T. Sauer, Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA, New Series, vol.271, pp.990-993, 1996.

Y. Komine, M. Kitabatake, T. Yokogawa, K. Nishikawa, and H. Inokuchi, A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli, PNAS, vol.91, pp.9223-9227, 1994.

P. Koodathingal, ATP-dependent Proteases Differ Substantially in Their Ability to Unfold Globular Proteins, J. Biol. Chem, vol.284, pp.18674-18684, 2009.

E. Gur and R. T. Sauer, Recognition of misfolded proteins by Lon, a AAA+ protease, Genes Dev, vol.22, pp.2267-2277, 2008.

J. A. Maupin-furlow, Proteasomes from Structure to Function: Perspectives from Archaea, Current Topics in Developmental Biology, vol.75, pp.125-169, 2006.

S. Bar-nun and M. H. Glickman, Proteasomal AAA-ATPases: Structure and function, Biochimica et Biophysica Acta (BBA) -Molecular Cell Research, vol.1823, pp.67-82, 2012.

D. Forouzan, The Archaeal Proteasome Is Regulated by a Network of AAA ATPases, J. Biol. Chem, vol.287, pp.39254-39262, 2012.

B. Rockel, J. Jakana, W. Chiu, and W. Baumeister, Electron cryo-microscopy of VAT, the archaeal p97/CDC48 homologue from Thermoplasma acidophilum11Edited by D. Rees, Journal of Molecular Biology, vol.317, pp.673-681, 2002.

N. Benaroudj, P. Zwickl, E. Seemüller, W. Baumeister, and A. L. Goldberg, ATP Hydrolysis by the Proteasome Regulatory Complex PAN Serves Multiple Functions in Protein Degradation, Molecular Cell, vol.11, pp.69-78, 2003.

M. A. Humbard and J. A. Maupin-furlow, Prokaryotic Proteasomes: Nanocompartments of Degradation, MMB, vol.23, pp.321-334, 2013.

S. Djuranovic, B. Rockel, A. N. Lupas, and J. Martin, Characterization of AMA, a new AAA protein from Archaeoglobus and methanogenic archaea, Journal of Structural Biology, vol.156, pp.130-138, 2006.

C. J. Reuter, S. J. Kaczowka, and J. A. Maupin-furlow, Differential Regulation of the PanA and PanB Proteasome-Activating Nucleotidase and 20S Proteasomal Proteins of the Haloarchaeon Haloferax volcanii, Journal of Bacteriology, vol.186, pp.7763-7772, 2004.

H. Chamieh, D. Guetta, and B. Franzetti, The two PAN ATPases from Halobacterium display N-terminal heterogeneity and form labile complexes with the 20S proteasome, Biochem. J, vol.411, pp.387-397, 2008.

H. Besche and P. Zwickl, The Thermoplasma acidophilum Lon protease has a Ser-Lys dyad active site, European Journal of Biochemistry, vol.271, pp.4361-4365, 2004.

M. A. Humbard, Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii, Nature, vol.463, pp.54-60, 2010.

H. V. Miranda, E1-and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea, PNAS, vol.108, pp.4417-4422, 2011.

J. A. Maupin-furlow, Archaeal Proteasomes and Sampylation, Regulated Proteolysis in Microorganisms, vol.66, pp.297-327, 2013.

N. L. Hepowit, Archaeal JAB1/MPN/MOV34 metalloenzyme (HvJAMM1) cleaves ubiquitin-like small archaeal modifier proteins (SAMPs) from protein-conjugates, Molecular Microbiology, vol.86, pp.971-987, 2012.

R. S. Anjum, Involvement of a eukaryotic-like ubiquitin-related modifier in the proteasome pathway of the archaeon Sulfolobus acidocaldarius, Nat Commun, vol.6, p.8163, 2015.

N. Benaroudj and A. L. Goldberg, PAN, the proteasome-activating nucleotidase from archaebacteria, is a protein-unfolding molecular chaperone, Nat Cell Biol, vol.2, pp.833-839, 2000.

F. Zhang, Mechanism of Substrate Unfolding and Translocation by the Regulatory Particle of the Proteasome from Methanocaldococcus jannaschii, Molecular Cell, vol.34, pp.485-496, 2009.

A. M. Burroughs, M. Jaffee, L. M. Iyer, and L. Aravind, Anatomy of the E2 ligase fold: Implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation, Journal of Structural Biology, vol.162, pp.205-218, 2008.

A. C. Fuchs, L. Maldoner, M. Wojtynek, M. D. Hartmann, and J. Martin, Rpn11-mediated ubiquitin processing in an ancestral archaeal ubiquitination system, Nat Commun, vol.9, p.2696, 2018.

R. H. James, Functional reconstruction of a eukaryotic-like E1/E2/(RING) E3 ubiquitylation cascade from an uncultured archaeon, Nat Commun, vol.8, pp.1-15, 2017.

B. Alberts, The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists, Cell, vol.92, pp.291-294, 1998.

M. Piccolino, Biological machines: from mills to molecules, Nat Rev Mol Cell Biol, vol.1, pp.149-152, 2000.

L. M. Iyer, D. D. Leipe, E. V. Koonin, and L. Aravind, Evolutionary history and higher order classification of AAA+ ATPases, Journal of Structural Biology, vol.146, pp.11-31, 2004.

T. Ogura and A. J. Wilkinson, AAA+ superfamily ATPases: common structure-diverse function, Genes Cells, vol.6, pp.575-597, 2001.

J. M. Miller and E. J. Enemark, Fundamental Characteristics of AAA+ Protein Family Structure and Function, Archaea, vol.2016, pp.1-12, 2016.

A. F. Neuwald, L. Aravind, J. L. Spouge, and E. V. Koonin, AAA+: A Class of Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly of Protein Complexes, Genome Res, vol.9, pp.27-43, 1999.

P. I. Hanson and S. W. Whiteheart, AAA+ proteins: have engine, will work, Nat Rev Mol Cell Biol, vol.6, pp.519-529, 2005.

J. P. Erzberger and J. M. Berger, EVOLUTIONARY RELATIONSHIPS AND STRUCTURAL MECHANISMS OF AAA+ PROTEINS, Annu. Rev. Biophys. Biomol. Struct, vol.35, pp.93-114, 2006.

G. R. Smith, B. Contreras-moreira, X. Zhang, and P. A. Bates, A link between sequence conservation and domain motion within the AAA+ family, Journal of Structural Biology, vol.146, pp.189-204, 2004.

M. Kessel, Homology in Structural Organization BetweenE. coliClpAP Protease and the Eukaryotic 26 S Proteasome, Journal of Molecular Biology, vol.250, pp.587-594, 1995.

P. Zwickl, An Archaebacterial ATPase, Homologous to ATPases in the Eukaryotic 26 S Proteasome, Activates Protein Breakdown by 20 S Proteasomes, J. Biol. Chem, vol.274, pp.26008-26014, 1999.

H. L. Wilson, M. S. Ou, H. C. Aldrich, and J. Maupin-furlow, Biochemical and Physical Properties of the Methanococcus jannaschii 20S Proteasome and PAN, a Homolog of the ATPase (Rpt) Subunits of the Eucaryal 26S Proteasome, Journal of Bacteriology, vol.182, pp.1680-1692, 2000.

S. Djuranovic, Structure and Activity of the N-Terminal Substrate Recognition Domains in Proteasomal ATPases, Molecular Cell, vol.34, pp.580-590, 2009.

D. Voges, P. Zwickl, and W. Baumeister, The 26S Proteasome: A Molecular Machine Designed for Controlled Proteolysis, Annual Review of Biochemistry, vol.68, pp.1015-1068, 1999.

N. Benaroudj, D. Smith, and A. L. Goldberg, What the Archaeal PAN-Proteasome Complex and Bacterial ATP-Dependent Proteases Can Teach Us About the 26S Proteasome, Protein Degradation Series 215-247, 2007.

A. Forster, The pore of activated 20S proteasomes has an ordered 7-fold symmetric conformation, The EMBO Journal, vol.22, pp.4356-4364, 2003.

D. M. Smith, ATP Binding to PAN or the 26S ATPases Causes Association with the 20S Proteasome, Gate Opening, and Translocation of Unfolded Proteins, Molecular Cell, vol.20, pp.687-698, 2005.

D. M. Smith, S. Chang, S. Park, D. Finley, and Y. Cheng, Docking of the Proteasomal ATPases' Ctermini in the 20S Proteasomes alpha Ring Opens the Gate for Substrate Entry, vol.30, 2008.

D. Barthelme and R. T. Sauer, Bipartite determinants mediate an evolutionarily conserved interaction between Cdc48 and the 20 S peptidase, Proc Natl Acad Sci, vol.110, pp.3327-3332, 2013.

D. Barthelme, J. Z. Chen, J. Grabenstatter, T. A. Baker, and R. T. Sauer, Architecture and assembly of the archaeal Cdc48*20S proteasome, Proceedings of the National Academy of Sciences, vol.111, pp.1687-1694, 2014.

P. Majumder, Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle, Proc Natl Acad Sci U S A, vol.116, pp.534-539, 2019.

Y. Yu, Interactions of PAN's C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome-ATPase interactions, The EMBO Journal, vol.29, pp.692-702, 2010.

N. Koga, T. Kameda, K. Okazaki, and S. Takada, Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations, PNAS, vol.106, pp.18237-18242, 2009.

A. Martin, T. A. Baker, and R. T. Sauer, Diverse Pore Loops of the AAA+ ClpX Machine Mediate Unassisted and Adaptor-Dependent Recognition of ssrA-Tagged Substrates, Molecular Cell, vol.29, pp.441-450, 2008.

A. Matouschek, Protein unfolding -an important process in vivo?, Current Opinion in Structural Biology, vol.13, pp.98-109, 2003.

F. Zhang, Structural Insights into the Regulatory Particle of the Proteasome from Methanocaldococcus jannaschii, Molecular Cell, vol.34, pp.473-484, 2009.

M. E. Matyskiela, G. C. Lander, and A. Martin, Conformational switching of the 26S proteasome enables substrate degradation, Nat Struct Mol Biol, vol.20, pp.781-788, 2013.

K. Nyquist and A. Martin, Marching to the beat of the ring: polypeptide translocation by AAA+ proteases, Trends in Biochemical Sciences, vol.39, pp.53-60, 2014.

A. Schweitzer, Structure of the human 26S proteasome at a resolution of 3.9 Å, Proc Natl Acad Sci, vol.113, pp.7816-7821, 2016.

P. Unverdorben, Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome, PNAS, vol.111, pp.5544-5549, 2014.

P. ?led?, Structure of the 26S proteasome with ATP-?S bound provides insights into the mechanism of nucleotide-dependent substrate translocation, PNAS, vol.110, pp.7264-7269, 2013.

T. Wenzel and W. Baumeister, Conformational constraints in protein degradation by the 20S proteasome, Nat Struct Mol Biol, vol.2, pp.199-204, 1995.

M. Unno, The Structure of the Mammalian 20S Proteasome at 2.75 Å Resolution, Structure, vol.10, pp.609-618, 2002.

M. Bajorek, D. Finley, and M. H. Glickman, Proteasome Disassembly and Downregulation Is Correlated with Viability during Stationary Phase, Current Biology, vol.13, pp.1140-1144, 2003.
URL : https://hal.archives-ouvertes.fr/hal-01608799

T. L. Religa, R. Sprangers, and L. E. Kay, Dynamic Regulation of Archaeal Proteasome Gate Opening As Studied by TROSY NMR, Science, vol.328, pp.98-102, 2010.

B. M. Stadtmueller, C. P. Hill, and . Proteasome-activators, Molecular Cell, vol.41, pp.8-19, 2011.

M. R. Eisele, Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating, Cell Reports, vol.24, 2018.

M. Wehmer, Structural insights into the functional cycle of the ATPase module of the 26S proteasome, Proc Natl Acad Sci, vol.114, pp.1305-1310, 2017.

Z. Ding, High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx, Cell Res, vol.27, pp.373-385, 2017.

A. H. Peña, E. A. Goodall, S. N. Gates, G. C. Lander, and A. Martin, Substrate-engaged 26S proteasome structures reveal mechanisms for ATP-hydrolysis-driven translocation, Science, vol.362, p.725, 2018.

Y. Dong, Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome, Nature, vol.565, pp.49-55, 2019.

F. Beck, Near-atomic resolution structural model of the yeast 26S proteasome, PNAS, vol.109, pp.14870-14875, 2012.

S. N. Gates, Ratchet-like polypeptide translocation mechanism of the AAA+ disaggregase Hsp104, Science, vol.357, pp.273-279, 2017.

M. Su, Mechanism of Vps4 hexamer function revealed by cryo-EM, SCIENCE ADVANCES, vol.8, 2017.

C. Puchades, Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing, Science, vol.358, p.464, 2017.

Y. Kim, A. Snoberger, J. Schupp, and D. M. Smith, ATP binding to neighbouring subunits and intersubunit allosteric coupling underlie proteasomal ATPase function, Nat Commun, vol.6, p.8520, 2015.

J. C. Cordova, Stochastic but Highly Coordinated Protein Unfolding and Translocation by the ClpXP Proteolytic Machine, Cell, vol.158, pp.647-658, 2014.

D. M. Smith, H. Fraga, C. Reis, G. Kafri, and A. L. Goldberg, ATP Binds to Proteasomal ATPases in Pairs with Distinct Functional Effects, Implying an Ordered Reaction Cycle, Cell, vol.144, pp.526-538, 2011.

S. Banerjee, 2.3 A resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition, Science, vol.351, pp.871-875, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01930733

A. Martin, T. A. Baker, and R. T. Sauer, Distinct Static and Dynamic Interactions Control ATPase-Peptidase Communication in a AAA+ Protease, Molecular Cell, vol.27, pp.41-52, 2007.

J. A. Kenniston, T. A. Baker, and R. T. Sauer, Partitioning between unfolding and release of native domains during ClpXP degradation determines substrate selectivity and partial processing, PNAS, vol.102, pp.1390-1395, 2005.

A. Navon and A. L. Goldberg, Proteins Are Unfolded on the Surface of the ATPase Ring before Transport into the Proteasome, Molecular Cell, vol.8, pp.1339-1349, 2001.

M. Aubin-tam, A. O. Olivares, R. T. Sauer, T. A. Baker, and M. J. Lang, Single-Molecule Protein Unfolding and Translocation by an ATP-Fueled Proteolytic Machine, Cell, vol.145, pp.257-267, 2011.

R. A. Maillard, ClpX(P) Generates Mechanical Force to Unfold and Translocate Its Protein Substrates, Cell, vol.145, pp.459-469, 2011.

J. A. Kenniston, T. A. Baker, J. M. Fernandez, and R. T. Sauer, Linkage between ATP Consumption and Mechanical Unfolding during the Protein Processing Reactions of an AAA+ Degradation Machine, Cell, vol.114, pp.511-520, 2003.

C. N. Peterson, I. Levchenko, J. D. Rabinowitz, T. A. Baker, and T. J. Silhavy, RpoS proteolysis is controlled directly by ATP levels in Escherichia coli, Genes Dev, vol.26, pp.548-553, 2012.

A. R. Nager, T. A. Baker, and R. T. Sauer, Stepwise Unfolding of a ? Barrel Protein by the AAA+ ClpXP Protease, Journal of Molecular Biology, vol.413, pp.4-16, 2011.

O. Iosefson, A. R. Nager, T. A. Baker, and R. T. Sauer, Coordinated gripping of substrate by subunits of a AAA+ proteolytic machine, Nature Chemical Biology, vol.11, pp.201-206, 2015.

R. H. Vass and P. Chien, Critical clamp loader processing by an essential AAA+ protease in Caulobacter crescentus, PNAS, vol.110, pp.18138-18143, 2013.

D. I. Svergun, M. H. Koch, P. A. Timmins, and R. P. May, Small angle X-ray and neutron scattering from solutions of biological macromolecules, vol.19, 2013.

C. D. Putnam, M. Hammel, G. L. Hura, and J. A. Tainer, X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution, Q. Rev. Biophys, vol.40, pp.191-285, 2007.

M. Haertlein, Biomolecular deuteration for neutron structural biology and dynamics, Methods in enzymology, vol.566, pp.113-157, 2016.

L. A. Feigin and D. I. Svergun, Structure analysis by small-angle X-ray and neutron scattering, vol.1, 1987.

B. Jacrot, The study of biological structures by neutron scattering from solution. Reports on progress in physics, vol.39, p.911, 1976.

G. Zaccai and B. Jacrot, Small Angle Neutron Scattering, Annual Review of Biophysics and Bioengineering, vol.12, pp.139-157, 1983.
URL : https://hal.archives-ouvertes.fr/hal-02548082

T. Bizien, A Brief Survey of State-of-the-Art BioSAXS, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01461929

C. A. Brosey and J. A. Tainer, Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology, Current Opinion in Structural Biology, vol.58, pp.197-213, 2019.

A. Guinier, G. Fournet, and K. L. Yudowitch, Small-angle scattering of X-rays, 1955.

O. Glatter and O. Kratky, Small angle X-ray scattering, 1982.

E. W. Kaler and H. Brumberger, In Modern Aspects of Small-Angle Scattering. Kluwer Academic, Dordrecht, vol.140, p.329, 1995.

D. S. Sivia, Elementary scattering theory: for X-ray and neutron users, 2011.

C. J. Carlile, Experimental Neutron Scattering: BTM Willis. Carlile, 2013.

B. Jacrot and G. Zaccai, Determination of molecular weight by neutron scattering, Biopolymers: Original Research on Biomolecules, vol.20, pp.2413-2426, 1981.

A. Guinier, La diffraction des rayons X aux très petits angles: application à l'étude de phénomènes ultramicroscopiques, Annales de physique, vol.11, pp.161-237, 1939.

G. Porod, Die Röntgenkleinwinkelstreuung von dichtgepackten kolloiden Systemen, Colloid & Polymer Science, vol.124, pp.83-114, 1951.

O. Glatter, A new method for the evaluation of small-angle scattering data, Journal of Applied Crystallography, vol.10, pp.415-421, 1977.

D. Franke, ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions, J Appl Crystallogr, vol.50, pp.1212-1225, 2017.

P. V. Konarev, V. V. Volkov, A. V. Sokolova, M. H. Koch, and D. I. Svergun, PRIMUS: a Windows PC-based system for small-angle scattering data analysis, Journal of applied crystallography, vol.36, pp.1277-1282, 2003.

D. Franke and D. I. Svergun, DAMMIF, a program for rapid ab-initio shape determination in smallangle scattering, Journal of applied crystallography, vol.42, pp.342-346, 2009.

D. I. Svergun, Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing, Biophysical journal, vol.76, pp.2879-2886, 1999.

D. I. Svergun, Determination of the regularization parameter in indirect-transform methods using perceptual criteria, Journal of applied crystallography, vol.25, pp.495-503, 1992.

D. Svergun, C. Barberato, and M. Koch, CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates, Journal of applied crystallography, vol.28, pp.768-773, 1995.

M. V. Petoukhov and D. I. Svergun, Global rigid body modeling of macromolecular complexes against small-angle scattering data, Biophysical journal, vol.89, pp.1237-1250, 2005.

A. Jordan, SEC-SANS: size exclusion chromatography combined in situ with small-angle neutron scattering, Journal of applied crystallography, vol.49, 2015.

T. A. Harroun, G. D. Wignall, and J. Katsaras, Neutron scattering for biology, Neutron Scattering in Biology 1-18, 2006.

H. B. Stuhrmann, Neutron small-angle scattering of biological macromolecules in solution, Journal of applied crystallography, vol.7, pp.173-178, 1974.

F. W. Studier and B. A. Moffatt, Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes, Journal of molecular biology, vol.189, pp.113-130, 1986.

O. Dunne, Matchout deuterium labelling of proteins for small-angle neutron scattering studies using prokaryotic and eukaryotic expression systems and high cell-density cultures, European Biophysics Journal, vol.46, pp.425-432, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01762233

B. Xu, M. Jahic, and S. Enfors, Modeling of Overflow Metabolism in Batch and Fed-Batch Cultures of Escherichiacoli, Biotechnology progress, vol.15, pp.81-90, 1999.

F. Meilleur, K. L. Weiss, and D. A. Myles, Deuterium labeling for neutron structure-function-dynamics analysis. in Micro and Nano Technologies in Bioanalysis, pp.281-292, 2009.

A. V. Yakhnin, L. M. Vinokurov, A. K. Surin, and Y. B. Alakhov, Green fluorescent protein purification by organic extraction, Protein expression and purification, vol.14, pp.382-386, 1998.

M. Howarth and A. Y. Ting, Monovalent streptavidin expression and purification, Nat. Protoc, 2008.

M. Howarth, A monovalent streptavidin with a single femtomolar biotin binding site, Nat. Methods, vol.3, pp.267-273, 2006.

L. Michaelis and M. L. Menten, The kinetics of the inversion effect, Biochem. Z, vol.49, pp.333-369, 1913.

K. Itaya and M. Ui, A new micromethod for the colorimetric determination of inorganic phosphate, Clinica chimica acta, vol.14, pp.361-366, 1966.

C. L. Penney, A simple micro-assay for inorganic phosphate, Anal. Biochem, vol.75, pp.201-210, 1976.

K. Wilson and J. Walker, Principles and techniques of biochemistry and molecular biology, 2010.

P. Pernot, Upgraded ESRF BM29 beamline for SAXS on macromolecules in solution, Journal of synchrotron radiation, vol.20, pp.660-664, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01572998

C. D. Dewhurst and . Grasp, Graphical Reduction and Analysis SANS Program. ILL Report ILL03DE01T, 2003.

D. Richard, M. Ferrand, and G. J. Kearley, Analysis and visualisation of neutron-scattering data, Journal of Neutron Research, vol.4, pp.33-39, 1996.

B. H. Zimm, The scattering of light and the radial distribution function of high polymer solutions, The Journal of Chemical Physics, vol.16, pp.1093-1099, 1948.

H. Zhao, P. H. Brown, and P. Schuck, On the distribution of protein refractive index increments, Biophys. J, vol.100, pp.2309-2317, 2011.

B. J. Frisken, Revisiting the method of cumulants for the analysis of dynamic light-scattering data, Appl Opt, vol.40, pp.4087-4091, 2001.

W. C. Lau and J. L. Rubinstein, Single particle electron microscopy, Electron Crystallography of Soluble and Membrane Proteins, pp.401-426, 2013.

M. R. Capecchi, Initiation of E. coli proteins, Proc Natl Acad Sci U S A, vol.55, pp.1517-1524, 1966.

D. Panfair, A. Ramamurthy, and A. R. Kusmierczyk, Alpha-ring Independent Assembly of the 20S Proteasome, Sci Rep, vol.5, 2015.

D. Panfair and A. R. Kusmierczyk, Examining Proteasome Assembly with Recombinant Archaeal Proteasomes and Nondenaturing PAGE: The Case for a Combined Approach, J Vis Exp, 2016.

D. M. Smith, N. Benaroudj, and A. Goldberg, Proteasomes and their associated ATPases: A destructive combination, Journal of Structural Biology, vol.156, pp.72-83, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00167551

A. P. Demchenko, Advanced Fluorescence Reporters in Chemistry and Biology I: Fundamentals and Molecular Design, 2010.

R. Berardozzi, Etude photophysique des protéines fluorescentes photoconvertibles utilisées en microscopie de super-résolution, 2016.

S. Dunst and P. Tomancak, Imaging Flies by Fluorescence Microscopy: Principles, Technologies, and Applications, Genetics, vol.211, pp.15-34, 2019.

O. Shimomura, F. H. Johnson, and Y. Saiga, Extraction, Purification and Properties of Aequorin, a Bioluminescent Protein from the Luminous Hydromedusan, Aequorea. Journal of Cellular and Comparative Physiology, vol.59, pp.223-239, 1962.

T. Green and . Protein-|-annual,

M. Chalfie, Y. Tu, G. Euskirchen, W. W. Ward, and D. C. Prasher, Green fluorescent protein as a marker for gene expression, Science, vol.263, pp.802-805, 1994.

G. N. Phillips, Structure and dynamics of green fluorescent protein, Current Opinion in Structural Biology, vol.7, pp.821-827, 1997.

E. Palmer and T. Freeman, Investigation Into the use of C-and N-terminal GFP Fusion Proteins for Subcellular Localization Studies Using Reverse Transfection Microarrays, Comp Funct Genomics, vol.5, pp.342-353, 2004.

K. R. Siemering, R. Golbik, R. Sever, and J. Haseloff, Mutations that suppress the thermosensitivity of green fluorescent protein, Current Biology, vol.6, pp.1653-1663, 1996.

S. H. Bokman and W. W. Ward, Renaturation of Aequorea green-fluorescent protein, Biochemical and Biophysical Research Communications, vol.101, pp.1372-1380, 1981.

F. Yang, L. G. Moss, and G. N. Phillips, The molecular structure of green fluorescent protein, Nat Biotechnol, vol.14, pp.1246-1251, 1996.

W. W. Ward, Energy Transfer Processes in Bioluminescence. in Photochemical and Photobiological Reviews, vol.4, pp.1-57, 1979.

M. W. Forbes and R. A. Jockusch, Deactivation Pathways of an Isolated Green Fluorescent Protein Model Chromophore Studied by Electronic Action Spectroscopy, J. Am. Chem. Soc, vol.131, pp.17038-17039, 2009.

N. M. Webber, K. L. Litvinenko, and S. R. Meech, Radiationless Relaxation in a Synthetic Analogue of the Green Fluorescent Protein Chromophore, J. Phys. Chem. B, vol.105, pp.8036-8039, 2001.

S. Mooney and C. R. , Taking the green fluorescence out of the protein : dynamics of the isolated GFP chromophore anion, Chemical Science, vol.4, pp.921-927, 2013.

E. U. Weber-ban, B. G. Reid, A. D. Miranker, and A. L. Horwich, Global unfolding of a substrate protein by the Hsp100 chaperone ClpA, Nature, vol.401, pp.90-93, 1999.

N. Benaroudj, E. Tarcsa, P. Cascio, and A. L. Goldberg, The unfolding of substrates and ubiquitinindependentprotein degradation by proteasomes, Biochimie, vol.83, pp.311-318, 2001.

G. Gitlin, E. A. Bayer, and M. Wilchek, Studies on the biotin-binding site of avidin. Tryptophan residues involved in the active site, Biochem J, vol.250, pp.291-294, 1988.

P. Zwickl, An Archaebacterial ATPase, Homologous to ATPases in the Eukaryotic 26 S Proteasome, Activates Protein Breakdown by 20 S Proteasomes, J. Biol. Chem, vol.274, pp.26008-26014, 1999.

A. Snoberger, R. T. Anderson, and D. M. Smith, The Proteasomal ATPases Use a Slow but Highly Processive Strategy to Unfold Proteins, Front Mol Biosci, vol.4, 2017.

F. Wold, 1] Affinity labeling-An overview, Methods in Enzymology, vol.46, pp.3-14, 1977.

H. Yaginuma, Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging, Scientific Reports, vol.4, p.6522, 2014.

Y. Kim, A. Snoberger, J. Schupp, and D. M. Smith, ATP binding to neighbouring subunits and intersubunit allosteric coupling underlie proteasomal ATPase function, Nat Commun, vol.6, pp.1-13, 2015.

T. Zemb, P. Lindner, . Neutrons, and . Light, Scattering Methods Applied to Soft Condensed Matter, 2002.

A. H. De-la-peña, E. A. Goodall, S. N. Gates, G. C. Lander, and A. Martin, Substrate-engaged 26 S proteasome structures reveal mechanisms for ATP-hydrolysis-driven translocation, Science, vol.362, p.725, 2018.