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Proteolytic systems of archaea: slicing, dicing, and mincing in the extreme. Emerg Top Life Sci 2018; 2:561-580. [PMID: 32953999 DOI: 10.1042/etls20180025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Archaea are phylogenetically distinct from bacteria, and some of their proteolytic systems reflect this distinction. Here, the current knowledge of archaeal proteolysis is reviewed as it relates to protein metabolism, protein homeostasis, and cellular regulation including targeted proteolysis by proteasomes associated with AAA-ATPase networks and ubiquitin-like modification. Proteases and peptidases that facilitate the recycling of peptides to amino acids as well as membrane-associated and integral membrane proteases are also reviewed.
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Appolaire A, Colombo M, Basbous H, Gabel F, Girard E, Franzetti B. TET peptidases: A family of tetrahedral complexes conserved in prokaryotes. Biochimie 2015; 122:188-96. [PMID: 26546839 DOI: 10.1016/j.biochi.2015.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/02/2015] [Indexed: 11/26/2022]
Abstract
The TET peptidases are large polypeptide destruction machines present among prokaryotes. They form 12-subunits hollow tetrahedral particles, and belong to the family of M42 metallo-peptidases. Structural characterization of various archaeal and bacterial complexes has revealed a unique mechanism of internal compartmentalization and peptide trafficking that distinguishes them from the other oligomeric peptidases. Different versions of the TET complex often co-exist in the cytosol of microorganisms. In depth enzymatic studies have revealed that they are non-processive cobalt-activated aminopeptidases and display contrasting substrate specificities based on the properties of the catalytic chambers. Recent studies have shed light on the assembly mechanism of homo and hetero-dodecameric TET complexes and shown that the activity of TET aminopeptidase towards polypeptides is coupled with its assembly process. These findings suggested a functional regulation based on oligomerization control in vivo. This review describes a current knowledge on M42 TET peptidases biochemistry and discuss their possible physiological roles. This article is a part of the Special Issue entitled: «A potpourri of proteases and inhibitors: from molecular toolboxes to signalling scissors».
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Affiliation(s)
- Alexandre Appolaire
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Matteo Colombo
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Hind Basbous
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Frank Gabel
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - E Girard
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Bruno Franzetti
- CNRS, IBS, F-38027 Grenoble, France; CEA, DSV, IBS, F-38027 Grenoble, France; Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France.
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Slutskaya E, Artemova N, Kleymenov S, Petrova T, Popov V. Heat-induced conformational changes of TET peptidase from crenarchaeon Desulfurococcus kamchatkensis. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015. [PMID: 26219412 DOI: 10.1007/s00249-015-1064-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The effects of heating on the structure and stability of multimeric TET aminopeptidase (APDkam589) were studied by differential scanning calorimetry, tryptophan fluorescence quenching, and dynamic light scattering. Thermally induced structural changes in APDkam589 were found to occur in two phases: local conformational changes, which occur below 70 °C and are not associated with thermal denaturation of the protein, and global structural changes (above 70 °C) induced by irreversible thermal unfolding of the protein accompanied by its spontaneous aggregation. These results may explain the bell-shaped temperature dependence with a maximum at ~70 °C previously observed for enzymatic activity of APDkam589. Interestingly, the thermal unfolding of APDkam589 at about 81.2 °C is accompanied by a so-called blue-shift of about 10 nm-a shift of the Trp fluorescence spectrum toward shorter wavelength. From this point of view, APDkam589 is quite different from most proteins, which are characterized by a long wavelength shift of the spectrum ("red-shift") upon denaturation. The blue-shift of the Trp fluorescence spectrum reflects the changes in the environment of Trp residues, which becomes more hydrophobic upon denaturation. The molecular structure of APDkam589 was determined by X-ray diffraction. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. Therefore, the blue-shift of the Trp fluorescence spectrum can be explained, at least partly, by aggregation of APDkam589, which occurs simultaneously with its thermal denaturation and probably makes the environment of these Trp residues more hydrophobic.
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Affiliation(s)
- Elvira Slutskaya
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation.
| | - Natalia Artemova
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation
| | - Sergey Kleymenov
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation.,N.K. Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova str. 26, Moscow, 119334, Russian Federation
| | - Tatiana Petrova
- Institute of Mathematical Problems of Biology, RAS, Institutskaja str., 4, Pushchino, 142290, Russian Federation
| | - Vladimir Popov
- A.N. Bakh Institute of Biochemistry, Russian Academy of Sciences, Leninsky pr. 33, Moscow, 119071, Russian Federation.,Russian National Research Centre "Kurchatov Institute", Akademika Kurchatova sq. 1, Moscow, 123182, Russian Federation
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Petrova TE, Slutskaya ES, Boyko KM, Sokolova OS, Rakitina TV, Korzhenevskiy DA, Gorbacheva MA, Bezsudnova EY, Popov VO. Structure of the dodecamer of the aminopeptidase APDkam598 from the archaeon Desulfurococcus kamchatkensis. Acta Crystallogr F Struct Biol Commun 2015; 71:277-85. [PMID: 25760701 PMCID: PMC4356302 DOI: 10.1107/s2053230x15000783] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 01/14/2015] [Indexed: 11/10/2022] Open
Abstract
The crystal structure of the aminopeptidase APDkam589 from the thermophilic crenarchaeon Desulfurococcus kamchatkensis was determined at a resolution of 3.0 Å. In the crystal, the monomer of APDkam589 and its symmetry-related monomers are densely packed to form a 12-subunit complex. Single-particle electron-microscopy analysis confirms that APDkam589 is present as a compact dodecamer in solution. The APDkam589 molecule is built similarly to the molecules of the PhTET peptidases, which have the highest sequence identity to APDkam589 among known structures and were isolated from the more thermostable archaeon Pyrococcus horikoshii. A comparison of the interactions of the subunits in APDkam589 with those in PhTET1, PhTET2 and PhTET3 reveals that APDkam589 has a much lower total number of salt bridges, which correlates with the lower thermostability of APDkam589. The monomer of APDkam589 has six Trp residues, five of which are on the external surface of the dodecamer. A superposition of the structure of APDkam589 with those having a high sequence similarity to APDkam589 reveals that, although the positions of Trp45, Trp252 and Trp358 are not conserved in the sequences, the spatial locations of the Trp residues in these models are similar.
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Affiliation(s)
- T. E. Petrova
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
- Institute of Mathematical Problems of Biology, RAS, Institutskaja str. 4, Pushchino 142290, Russian Federation
| | - E. S. Slutskaya
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
| | - K. M. Boyko
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - O. S. Sokolova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/73, Moscow 119991, Russian Federation
| | - T. V. Rakitina
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
- Institute of Bioorganic Chemistry, RAS, Miklukho-Maklaya 16/10, Moscow 117997, Russian Federation
| | - D. A. Korzhenevskiy
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - M. A. Gorbacheva
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
| | - E. Y. Bezsudnova
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
| | - V. O. Popov
- A. N. Bach Institute of Biochemistry, RAS, Leninsky pr. 33, Moscow 119071, Russian Federation
- NRC ‘Kurchatov Institute’, Acad. Kurchatov sq. 1, Moscow 123182, Russian Federation
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