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Izquierdo-Fiallo K, Muñoz-Villagrán C, Orellana O, Sjoberg R, Levicán G. Comparative genomics of the proteostasis network in extreme acidophiles. PLoS One 2023; 18:e0291164. [PMID: 37682893 PMCID: PMC10490939 DOI: 10.1371/journal.pone.0291164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Extreme acidophiles thrive in harsh environments characterized by acidic pH, high concentrations of dissolved metals and high osmolarity. Most of these microorganisms are chemolithoautotrophs that obtain energy from low redox potential sources, such as the oxidation of ferrous ions. Under these conditions, the mechanisms that maintain homeostasis of proteins (proteostasis), as the main organic components of the cells, are of utmost importance. Thus, the analysis of protein chaperones is critical for understanding how these organisms deal with proteostasis under such environmental conditions. In this work, using a bioinformatics approach, we performed a comparative genomic analysis of the genes encoding classical, periplasmic and stress chaperones, and the protease systems. The analysis included 35 genomes from iron- or sulfur-oxidizing autotrophic, heterotrophic, and mixotrophic acidophilic bacteria. The results showed that classical ATP-dependent chaperones, mostly folding chaperones, are widely distributed, although they are sub-represented in some groups. Acidophilic bacteria showed redundancy of genes coding for the ATP-independent holdase chaperones RidA and Hsp20. In addition, a systematically high redundancy of genes encoding periplasmic chaperones like HtrA and YidC was also detected. In the same way, the proteolytic ATPase complexes ClpPX and Lon presented redundancy and broad distribution. The presence of genes that encoded protein variants was noticeable. In addition, genes for chaperones and protease systems were clustered within the genomes, suggesting common regulation of these activities. Finally, some genes were differentially distributed between bacteria as a function of the autotrophic or heterotrophic character of their metabolism. These results suggest that acidophiles possess an abundant and flexible proteostasis network that protects proteins in organisms living in energy-limiting and extreme environmental conditions. Therefore, our results provide a means for understanding the diversity and significance of proteostasis mechanisms in extreme acidophilic bacteria.
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Affiliation(s)
- Katherin Izquierdo-Fiallo
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Claudia Muñoz-Villagrán
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Omar Orellana
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Rachid Sjoberg
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
| | - Gloria Levicán
- Department of Biology, Faculty of Chemistry and Biology, University of Santiago of Chile (USACH), Santiago, Chile
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Nava-Ramírez T, Gutiérrez-Terrazas S, Hansberg W. The Molecular Chaperone Mechanism of the C-Terminal Domain of Large-Size Subunit Catalases. Antioxidants (Basel) 2023; 12:antiox12040839. [PMID: 37107214 PMCID: PMC10135305 DOI: 10.3390/antiox12040839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/11/2023] [Accepted: 03/19/2023] [Indexed: 04/03/2023] Open
Abstract
Large-size subunit catalases (LSCs) have an additional C-terminal domain (CT) that is structurally similar to Hsp31 and DJ-1 proteins, which have molecular chaperone activity. The CT of LSCs derives from a bacterial Hsp31 protein. There are two CT dimers with inverted symmetry in LSCs, one dimer in each pole of the homotetrameric structure. We previously demonstrated the molecular chaperone activity of the CT of LSCs. Like other chaperones, LSCs are abundant proteins that are induced under stress conditions and during cell differentiation in bacteria and fungi. Here, we analyze the mechanism of the CT of LSCs as an unfolding enzyme. The dimeric form of catalase-3 (CAT-3) CT (TDC3) of Neurospora crassa presented the highest activity as compared to its monomeric form. A variant of the CAT-3 CT lacking the last 17 amino acid residues (TDC3Δ17aa), a loop containing hydrophobic and charged amino acid residues only, lost most of its unfolding activity. Substituting charged for hydrophobic residues or vice versa in this C-terminal loop diminished the molecular chaperone activity in all the mutant variants analyzed, indicating that these amino acid residues play a relevant role in its unfolding activity. These data suggest that the general unfolding mechanism of CAT-3 CT involves a dimer with an inverted symmetry, and hydrophobic and charged amino acid residues. Each tetramer has four sites of interaction with partially unfolded or misfolded proteins. LSCs preserve their catalase activity under different stress conditions and, at the same time, function as unfolding enzymes.
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Jimenez-Harrison D, Huseby CJ, Hoffman CN, Sher S, Snyder D, Seal B, Yuan C, Fu H, Wysocki V, Giorgini F, Kuret J. DJ-1 Molecular Chaperone Activity Depresses Tau Aggregation Propensity through Interaction with Monomers. Biochemistry 2023; 62:976-988. [PMID: 36813261 PMCID: PMC9997487 DOI: 10.1021/acs.biochem.2c00581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/19/2023] [Indexed: 02/24/2023]
Abstract
Tau aggregate-bearing lesions are pathological markers and potential mediators of tauopathic neurodegenerative diseases, including Alzheimer's disease. The molecular chaperone DJ-1 colocalizes with tau pathology in these disorders, but it has been unclear what functional link exists between them. In this study, we examined the consequences of tau/DJ-1 interaction as isolated proteins in vitro. When added to full-length 2N4R tau under aggregation-promoting conditions, DJ-1 inhibited both the rate and extent of filament formation in a concentration-dependent manner. Inhibitory activity was low affinity, did not require ATP, and was not affected by substituting oxidation incompetent missense mutation C106A for wild-type DJ-1. In contrast, missense mutations previously linked to familial Parkinson's disease and loss of α-synuclein chaperone activity, M26I and E64D, displayed diminished tau chaperone activity relative to wild-type DJ-1. Although DJ-1 directly bound the isolated microtubule-binding repeat region of tau protein, exposure of preformed tau seeds to DJ-1 did not diminish seeding activity in a biosensor cell model. These data reveal DJ-1 to be a holdase chaperone capable of engaging tau as a client in addition to α-synuclein. Our findings support a role for DJ-1 as part of an endogenous defense against the aggregation of these intrinsically disordered proteins.
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Affiliation(s)
- Daniela Jimenez-Harrison
- Medical
Scientist Training Program, The Ohio State
University, Columbus, Ohio 43210, United States
| | - Carol J. Huseby
- Department
of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, Ohio 43210, United States
| | - Claire N. Hoffman
- Department
of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, Ohio 43210, United States
| | - Steven Sher
- Medical
Scientist Training Program, The Ohio State
University, Columbus, Ohio 43210, United States
| | - Dalton Snyder
- Department
of Chemistry and Biochemistry, The Ohio
State University College of Medicine, Columbus, Ohio 43210, United States
| | - Brayden Seal
- Department
of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, Ohio 43210, United States
| | - Chunhua Yuan
- Campus
Chemical Instrument Center, The Ohio State
University College of Medicine, Columbus, Ohio 43210, United States
| | - Hongjun Fu
- Department
of Neuroscience, The Ohio State University
College of Medicine, Columbus, Ohio 43210, United States
| | - Vicki Wysocki
- Department
of Chemistry and Biochemistry, The Ohio
State University College of Medicine, Columbus, Ohio 43210, United States
| | - Flaviano Giorgini
- Department
of Genetics and Genome Biology, University
of Leicester, Leicester LE1 7RH, United
Kingdom
| | - Jeff Kuret
- Department
of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, Ohio 43210, United States
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Karmakar S, Ghosh T, Sankhla A, Bhattacharjee S, Katiyar V. Insulin biomolecular condensate formed in ionic microenvironment modulates the structural properties of pristine and magnetic cellulosic nanomaterials. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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A novel IONP-decorated two-dimensional [Zn2+]:[Insulin] nanosheet with ordered array of surface channels and cellular uptake potential. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Abstract
The folding of proteins into their native structure is crucial for the functioning of all biological processes. Molecular chaperones are guardians of the proteome that assist in protein folding and prevent the accumulation of aberrant protein conformations that can lead to proteotoxicity. ATP-independent chaperones do not require ATP to regulate their functional cycle. Although these chaperones have been traditionally regarded as passive holdases that merely prevent aggregation, recent work has shown that they can directly affect the folding energy landscape by tuning their affinity to various folding states of the client. This review focuses on emerging paradigms in the mechanism of action of ATP-independent chaperones and on the various modes of regulating client binding and release.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kevin Wu
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, South Korea
| | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA; .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
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Nava Ramírez T, Hansberg W. Características comunes de las chaperonas pequeñas y diméricas. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2020. [DOI: 10.22201/fesz.23958723e.2020.0.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Las chaperonas moleculares constituyen un mecanismo importante para evitar la muerte celular provocada por la agregación de proteínas. Las chaperonas independientes del ATP son un grupo de proteínas de bajo peso molecular que pueden proteger y ayudar a alcanzar la estructura nativa de las proteínas desplegadas o mal plegadas sin necesidad de un gasto energético. Hemos encontrado que el dominio C-terminal de las catalasas de subunidad grande tiene actividad de chaperona. Por ello, en esta revisión analizamos las características más comunes de las chaperonas pequeñas y más estudiadas como: αB-cristalina, Hsp20, Spy, Hsp33 y Hsp31. En particular, se examina la participación de los aminoácidos hidrofóbicos y de los aminoácidos con carga en el reconocimiento de las proteínas sustrato, así como el papel que tiene la forma dimérica y su oligomerización en la actividad de chaperona. En cada una de esas chaperonas revisaremos la estructura de la proteína, su función, localización celular e importancia para la célula.
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