1
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Singh D, Tripathi P, Sharma R, Grover S, Batra JK. Role of a substrate binding pocket in the amino terminal domain of Mycobacterium tuberculosis caseinolytic protease B (ClpB) in its function. J Biomol Struct Dyn 2024; 42:6189-6199. [PMID: 37418201 DOI: 10.1080/07391102.2023.2232032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis when infects the host encounters several stresses within the host, resulting in aggregation of its proteins. To resolve this problem Mtb uses chaperones to either repair the damage or degrade the aggregated proteins. Mtb caseinolytic protein B (ClpB) helps in the prevention of aggregation and also resolubilization of aggregated proteins in bacteria, which is important for the survival of Mtb in the host. To function optimally, ClpB associates with its co-partners DnaK, DnaJ, and GrpE. The role of N-terminal domain (NTD) of Mtb ClpB in its function is not well understood. In this context, we investigated the interaction of three substrate mimicking peptides with the NTD of Mtb ClpB in silico. A substrate binding pocket, within the NTD of ClpB comprising of residues L136, R137, E138, K142, R144, R148, V149, Y158, and Y162 forming an ɑ-helix was thus identified. The residues L136 and R137 of the ɑ-helix were found to be important for the interaction of DnaK to ClpB. Further, nine single alanine recombinant variants of the identified residues were generated. As compared to the wild-type Mtb ClpB all the Mtb ClpB variants generated in this study were found to have reduced ATPase and protein refolding activity indicating the importance of the substrate binding pocket in ClpB function. The study demonstrates that the NTD of Mtb ClpB is important for its substrate interaction activity, and the substrate binding pocket identified in this study plays a crucial role in this interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Digvijay Singh
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | | | - Rahul Sharma
- Department of Molecular Medicine, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Sonam Grover
- Department of Molecular Medicine, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Janendra K Batra
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
- ICMR-National Institute of Pathology, Safdarjung Hospital Complex, New Delhi, India
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2
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Ghosh Dastidar R, Banerjee S, Lal PB, Ghosh Dastidar S. Multifaceted Roles of AFG3L2, a Mitochondrial ATPase in Relation to Neurological Disorders. Mol Neurobiol 2024; 61:3788-3808. [PMID: 38012514 PMCID: PMC11236935 DOI: 10.1007/s12035-023-03768-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
AFG3L2 is a zinc metalloprotease and an ATPase localized in an inner mitochondrial membrane involved in mitochondrial quality control of several nuclear- and mitochondrial-encoded proteins. Mutations in AFG3L2 lead to diseases like slow progressive ataxia, which is a neurological disorder. This review delineates the cellular functions of AFG3L2 and its dysfunction that leads to major clinical outcomes, which include spinocerebellar ataxia type 28, spastic ataxia type 5, and optic atrophy type 12. It summarizes all relevant AFG3L2 mutations associated with the clinical outcomes to understand the detailed mechanisms attributable to its structure-related multifaceted roles in proteostasis and quality control. We face early diagnostic challenges of ataxia and optic neuropathy due to asymptomatic parents and variable clinical manifestations due to heterozygosity/homozygosity of AFG3L2 mutations. This review intends to promote AFG3L2 as a putative prognostic or diagnostic marker.
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Affiliation(s)
- Ranita Ghosh Dastidar
- Department of Biochemistry, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Madhava Nagar, Manipal, 576104, Karnataka, India.
| | - Saradindu Banerjee
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Madhava Nagar, Manipal, 576104, Karnataka, India
| | - Piyush Behari Lal
- Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Madhava Nagar, Manipal, 576104, Karnataka, India.
| | - Somasish Ghosh Dastidar
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Madhava Nagar, Manipal, 576104, Karnataka, India.
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3
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Kunová N, Ondrovičová G, Bauer JA, Krajčovičová V, Pinkas M, Stojkovičová B, Havalová H, Lukáčová V, Kohútová L, Košťan J, Martináková L, Baráth P, Nováček J, Zoll S, Kereϊche S, Kutejová E, Pevala V. Polyphosphate and tyrosine phosphorylation in the N-terminal domain of the human mitochondrial Lon protease disrupts its functions. Sci Rep 2024; 14:9923. [PMID: 38688959 PMCID: PMC11061198 DOI: 10.1038/s41598-024-60030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024] Open
Abstract
Phosphorylation plays a crucial role in the regulation of many fundamental cellular processes. Phosphorylation levels are increased in many cancer cells where they may promote changes in mitochondrial homeostasis. Proteomic studies on various types of cancer identified 17 phosphorylation sites within the human ATP-dependent protease Lon, which degrades misfolded, unassembled and oxidatively damaged proteins in mitochondria. Most of these sites were found in Lon's N-terminal (NTD) and ATPase domains, though little is known about the effects on their function. By combining the biochemical and cryo-electron microscopy studies, we show the effect of Tyr186 and Tyr394 phosphorylations in Lon's NTD, which greatly reduce all Lon activities without affecting its ability to bind substrates or perturbing its tertiary structure. A substantial reduction in Lon's activities is also observed in the presence of polyphosphate, whose amount significantly increases in cancer cells. Our study thus provides an insight into the possible fine-tuning of Lon activities in human diseases, which highlights Lon's importance in maintaining proteostasis in mitochondria.
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Grants
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- 894 Grant No. 1825144Y Grantová Agentura České Republiky
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- StruBioMol, ITMS: 305011X666 Interreg
- UP CIISB (No. CZ.02.1.01/0.0/0.0/18_046/0015974) European Regional Development Fund, European Union
- UP CIISB (No. CZ.02.1.01/0.0/0.0/18_046/0015974) European Regional Development Fund, European Union
- BIOMEDIRES - II. stage, ITMS: 313011W428 European Regional Development Fund
- APVV-15-0375, APVV-19-0298 Agentúra na Podporu Výskumu a Vývoja
- APVV-15-0375, APVV-19-0298 Agentúra na Podporu Výskumu a Vývoja
- 2/0069/23 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
- 2/0069/23 Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
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Affiliation(s)
- Nina Kunová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Gabriela Ondrovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Jacob A Bauer
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Veronika Krajčovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Laboratory of Clinical and Molecular Genetics, National Institute of Children's Diseases, Limbová 1, 833 40, Bratislava, Slovakia
| | - Matyáš Pinkas
- CEITEC, Masaryk University in Brno, Brno, Czech Republic
| | - Barbora Stojkovičová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Henrieta Havalová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | | | - Lenka Kohútová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Július Košťan
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna, Biocenter 5, 1030, Vienna, Austria
| | - Lucia Martináková
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia
| | - Peter Baráth
- Medirex Group Academy, Nitra, Slovakia
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jiří Nováček
- CEITEC, Masaryk University in Brno, Brno, Czech Republic
| | - Sebastian Zoll
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 542/2, 16000, Prague, Czech Republic
| | - Sami Kereϊche
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Namesti 542/2, 16000, Prague, Czech Republic.
| | - Eva Kutejová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
| | - Vladimír Pevala
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51, Bratislava, Slovakia.
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Beardslee PC, Schmitz KR. Toxin-based screening of C-terminal tags in Escherichia coli reveals the exceptional potency of ssrA-like degrons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.576913. [PMID: 38352471 PMCID: PMC10862746 DOI: 10.1101/2024.01.29.576913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
All bacteria possess ATP-dependent proteases that destroy cytosolic proteins. These enzymes help cells mitigate proteotoxic stress, adapt to changing nutrient availability, regulate virulence phenotypes, and transition to pathogenic lifestyles. Moreover, ATP-dependent proteases have emerged as promising antibacterial and antivirulence targets in a variety of pathogens. The physiological roles of these proteases are largely defined by the complement of proteins that they degrade. Substrates are typically recognized in a highly selective manner, often via short unstructured sequences termed degrons. While a few degrons have been identified and rigorously characterized, we lack a systematic understanding of how proteases select valid degrons from the vast complexity of protein sequence space. Here, we describe a novel high-throughput screening approach in Escherichia coli that couples proteolysis of a protein toxin to cell survival. We used this method to screen a combinatorial library of C-terminal pentapeptide sequences for functionality as proteolytic degrons in wild type E. coli, and in strains lacking components of the ClpXP and ClpAP proteases. By examining the competitive enrichment of sequences over time, we found that about one percent of pentapeptide tags lead to toxin proteolysis. Interestingly, the most enriched degrons were ClpXP-dependent and highly similar to the ssrA tag, one of the most extensively characterized degrons in bacteria. Among ssrA-like sequences, we observed that specific upstream residues correlate with successful recognition. The lack of diversity among strongly enriched sequences suggests that ssrA-like tags comprise a uniquely potent class of short C-terminal degron in E. coli. Efficient proteolysis of substrates lacking such degrons likely requires adaptors or multivalent interactions. These findings broaden our understanding of the constraints that shape the bacterial proteolytic landscape. Our screening approach may be broadly applicable to probing aspects of proteolytic substrate selection in other bacterial systems.
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Affiliation(s)
- Patrick C. Beardslee
- Department of Chemistry & Biochemistry, University of Delaware, Newark DE, 19716
| | - Karl R. Schmitz
- Department of Chemistry & Biochemistry, University of Delaware, Newark DE, 19716
- Department of Biological Sciences, University of Delaware, Newark DE, 19716
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5
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Mor-Rashti Z, Levin R, Eichler J, Gur E. The Bacterial Proteasome Inter-domain Is a Selectivity Barrier for Degradation-tag Binding. J Mol Biol 2024; 436:168462. [PMID: 38301806 DOI: 10.1016/j.jmb.2024.168462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/03/2024]
Abstract
Protein degradation, which occurs in all cells, is essential for proper cellular function by regulating many cellular processes, destroying misfolded proteins, and providing protein building blocks under starvation conditions. As proteolysis is a destructive process, it is carried out by tightly regulated enzymes that evolved to interact with their protein substrates in a highly controlled and selective manner. The agents of protein degradation include proteasomes, AAA+ proteolytic machines found in all kingdoms of life. The bacterial proteasome specifically recognizes proteins conjugated to a protein tag termed Pup, with the proteasome regulatory particle, a ring-shaped hexamer termed Mpa in mycobacteria, being responsible for Pup recognition. Once Pup binds Mpa, Pup enters the central pore, where the Mpa AAA+ domain links ATP hydrolysis to the translocation of Pup and its conjugated substrate into a barrel-shaped proteasome core particle, where peptide bond cleavage occurs. As Pup traverses the Mpa pore en route to the AAA+ domain, it passes the inter-domain. Although the inter-domain is conserved in all proteasomes, its role in substrate processing remained unclear. We report here that the Mpa inter-domain promotes Pup binding via electrostatic interactions between conserved charged inter-domain pore loops and charged Pup residues. As such, the inter-domain serves as a gatekeeper that selects for Pup binding, thus facilitating tag interaction with the downstream AAA+ domain. Our findings thus reveal the existence of an additional level of substrate binding regulation in an AAA+ protease.
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Affiliation(s)
- Zohar Mor-Rashti
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Roni Levin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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6
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Mannar D, Ahmed S, Subramaniam S. AAA ATPase protein-protein interactions as therapeutic targets in cancer. Curr Opin Cell Biol 2024; 86:102291. [PMID: 38056141 DOI: 10.1016/j.ceb.2023.102291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023]
Abstract
AAA ATPases are a conserved group of enzymes that couple ATP hydrolysis to diverse activities critical for cellular homeostasis by targeted protein-protein interactions. Some of these interactions are potential therapeutic targets because of their role in cancers which rely on increased AAA ATPase activities for maintenance of genomic stability. Two well-characterized members of this family are p97/VCP and RUVBL ATPases where there is a growing understanding of their structure and function, as well as an emerging landscape of selective inhibitors. Here we highlight recent progress in this field, with particular emphasis on structural advances enabled by cryo-electron microscopy (cryo-EM).
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Affiliation(s)
- Dhiraj Mannar
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sana Ahmed
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Sriram Subramaniam
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Gandeeva Therapeutics, Inc., Burnaby, BC V5C 6N5, Canada.
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7
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Tague N, Coriano-Ortiz C, Sheets MB, Dunlop MJ. Light-inducible protein degradation in E. coli with the LOVdeg tag. eLife 2024; 12:RP87303. [PMID: 38270583 PMCID: PMC10945698 DOI: 10.7554/elife.87303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light-controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system and introduce a powerful new tool for bacterial optogenetics.
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Affiliation(s)
- Nathan Tague
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Cristian Coriano-Ortiz
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Michael B Sheets
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
- Biological Design Center, Boston UniversityBostonUnited States
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8
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Tague N, Coriano-Ortiz C, Sheets MB, Dunlop MJ. Light inducible protein degradation in E. coli with the LOVdeg tag. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530042. [PMID: 36865169 PMCID: PMC9980293 DOI: 10.1101/2023.02.25.530042] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Molecular tools for optogenetic control allow for spatial and temporal regulation of cell behavior. In particular, light controlled protein degradation is a valuable mechanism of regulation because it can be highly modular, used in tandem with other control mechanisms, and maintain functionality throughout growth phases. Here, we engineered LOVdeg, a tag that can be appended to a protein of interest for inducible degradation in Escherichia coli using blue light. We demonstrate the modularity of LOVdeg by using it to tag a range of proteins, including the LacI repressor, CRISPRa activator, and the AcrB efflux pump. Additionally, we demonstrate the utility of pairing the LOVdeg tag with existing optogenetic tools to enhance performance by developing a combined EL222 and LOVdeg system. Finally, we use the LOVdeg tag in a metabolic engineering application to demonstrate post-translational control of metabolism. Together, our results highlight the modularity and functionality of the LOVdeg tag system, and introduce a powerful new tool for bacterial optogenetics.
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9
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Kasal MR, Kotamarthi HC, Johnson MM, Stephens HM, Lang MJ, Sauer RT, Baker TA. Lon degrades stable substrates slowly but with enhanced processivity, redefining the attributes of a successful AAA+ protease. Cell Rep 2023; 42:113061. [PMID: 37660294 PMCID: PMC10695633 DOI: 10.1016/j.celrep.2023.113061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/15/2023] [Accepted: 08/16/2023] [Indexed: 09/05/2023] Open
Abstract
Lon is a widely distributed AAA+ (ATPases associated with diverse cellular activities) protease known for degrading poorly folded and damaged proteins and is often classified as a weak protein unfoldase. Here, using a Lon-degron pair from Mesoplasma florum (MfLon and MfssrA, respectively), we perform ensemble and single-molecule experiments to elucidate the molecular mechanisms underpinning MfLon function. Notably, we find that MfLon unfolds and degrades stably folded substrates and that translocation of these unfolded polypeptides occurs with a ∼6-amino-acid step size. Moreover, the time required to hydrolyze one ATP corresponds to the dwell time between steps, indicating that one step occurs per ATP-hydrolysis-fueled "power stroke." Comparison of MfLon to related AAA+ enzymes now provides strong evidence that HCLR-clade enzymes function using a shared power-stroke mechanism and, surprisingly, that MfLon is more processive than ClpXP and ClpAP. We propose that ample unfoldase strength and substantial processivity are features that contribute to the Lon family's evolutionary success.
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Affiliation(s)
- Meghann R Kasal
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Madeline M Johnson
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Hannah M Stephens
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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10
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Schmitz KR, Handy EL, Compton CL, Gupta S, Bishai WR, Sauer RT, Sello JK. Acyldepsipeptide Antibiotics and a Bioactive Fragment Thereof Differentially Perturb Mycobacterium tuberculosis ClpXP1P2 Activity in Vitro. ACS Chem Biol 2023; 18:724-733. [PMID: 32083462 PMCID: PMC7842861 DOI: 10.1021/acschembio.9b00454] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteolytic complexes in Mycobacterium tuberculosis (Mtb), the deadliest bacterial pathogen, are major foci in tuberculosis drug development programs. The Clp proteases, which are essential for Mtb viability, are high-priority targets. These proteases function through the collaboration of ClpP1P2, a barrel-shaped heteromeric peptidase, with associated ATP-dependent chaperones like ClpX and ClpC1 that recognize and unfold specific substrates in an ATP-dependent fashion. The critical interaction of the peptidase and its unfoldase partners is blocked by the competitive binding of acyldepsipeptide antibiotics (ADEPs) to the interfaces of the ClpP2 subunits. The resulting inhibition of Clp protease activity is lethal to Mtb. Here, we report the surprising discovery that a fragment of the ADEPs retains anti-Mtb activity yet stimulates rather than inhibits the ClpXP1P2-catalyzed degradation of proteins. Our data further suggest that the fragment stabilizes the ClpXP1P2 complex and binds ClpP1P2 in a fashion distinct from that of the intact ADEPs. A structure-activity relationship study of the bioactive fragment defines the pharmacophore and points the way toward the development of new drug leads for the treatment of tuberculosis.
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Affiliation(s)
- Karl R. Schmitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
- Department of Biological Sciences, University of Delaware, Newark, DE
| | - Emma L. Handy
- Department of Chemistry, Brown University, Providence, RI
| | | | - Shashank Gupta
- Department of Chemistry, Brown University, Providence, RI
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Jason K. Sello
- Department of Chemistry, Brown University, Providence, RI
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
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11
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de Campos LJ, Seleem MA, Feng J, Pires de Oliveira KM, de Andrade Dos Santos JV, Hayer S, Clayton JB, Kathi S, Fisher DJ, Ouellette SP, Conda-Sheridan M. Design, Biological Evaluation, and Computer-Aided Analysis of Dihydrothiazepines as Selective Antichlamydial Agents. J Med Chem 2023; 66:2116-2142. [PMID: 36696579 PMCID: PMC10056257 DOI: 10.1021/acs.jmedchem.2c01894] [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] [Indexed: 01/26/2023]
Abstract
Chlamydia trachomatis (CT) causes the most prevalent sexually transmitted bacterial disease in the United States. The lack of drug selectivity is one of the main challenges of the current antichlamydial pharmacotherapy. The metabolic needs of CT are controlled, among others, by cylindrical proteases and their chaperones (e.g., ClpX). It has been shown that dihydrothiazepines can disrupt CT-ClpXP. Based on this precedent, we synthesized a dihydrothiazepine library and characterized its antichlamydial activity using a modified semi-high-throughput screening assay. Then, we demonstrated their ability to inhibit ClpX ATPase activity in vitro, supporting ClpX as a target. Further, our lead compound displayed a promising selectivity profile against CT, acceptable cytotoxicity, no mutagenic potential, and good in vitro stability. A two-dimensional quantitative structure-activity relationship (2D QSAR) model was generated as a support tool in the identification of more potent antichlamydial molecules. This study suggests dihydrothiazepines are a promising starting point for the development of new and selective antichlamydial drugs.
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Affiliation(s)
- Luana Janaína de Campos
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Mohamed A Seleem
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Jiachen Feng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Kelly Mari Pires de Oliveira
- Faculty of Biological and Environmental Science, Federal University of Grande Dourados, Dourados, MS 79804-970, Brazil
| | | | - Shivdeep Hayer
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, United States
| | - Jonathan B Clayton
- Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68182, United States
- Department of Food Science and Technology, University of Nebraska─Lincoln, Lincoln, Nebraska 68588, United States
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
- Nebraska Food for Health Center, University of Nebraska─Lincoln, Lincoln, Nebraska 68508, United States
| | - Sharvath Kathi
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Derek J Fisher
- School of Biological Sciences, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Scot P Ouellette
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Martin Conda-Sheridan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, Nebraska 68198, United States
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12
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Vobruba S, Kadlcik S, Janata J, Kamenik Z. TldD/TldE peptidases and N-deacetylases: A structurally unique yet ubiquitous protein family in the microbial metabolism. Microbiol Res 2022; 265:127186. [PMID: 36155963 DOI: 10.1016/j.micres.2022.127186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
Here we provide a review on TldD/TldE family proteins, summarizing current knowledge and outlining further research perspectives. Despite being widely distributed in bacteria and archaea, TldD/TldE proteins have been escaping attention for a long time until several recent reports pointed to their unique features. Specifically, TldD/TldE generally act as peptidases, though some of them turned out to be N-deacetylases. Biological function of TldD/TldE has been extensively described in bacterial specialized metabolism, in which they participate in the biosynthesis of lincosamide antibiotics (as N-deacetylases), and in the biosynthesis of ribosomally synthesized and post-translationally modified bioactive peptides (as peptidases). These enzymes possess special position in the relevant biosynthesis since they convert non-bioactive intermediates into bioactive metabolites. Further, based on a recent study of Escherichia coli TldD/TldE, these heterodimeric metallopeptidases possess a new protein fold exhibiting several structural features with no precedent in the Protein Data Bank. The most interesting ones are structural elements forming metal-containing active site on the inner surface of the catalytically active subunit TldD, in which substrates bind through β sheet interactions in the sequence-independent manner. It results in relaxed substrate specificity of TldD/TldE, which is counterbalanced by enclosing the active centre within the hollow core of the heterodimer and only appropriate substrates can entry through a narrow channel. Based on the published data, we hypothesize a yet unrecognized central metabolic function of TldD/TldE in the degradation of (partially) unfolded proteins, i.e., in protein quality control.
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Affiliation(s)
- Simon Vobruba
- Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic
| | - Stanislav Kadlcik
- Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic
| | - Jiri Janata
- Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic
| | - Zdenek Kamenik
- Czech Academy of Sciences, Institute of Microbiology, Prague, Czech Republic.
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13
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Dzięgielewska A, Dunislawska A. Mitochondrial Dysfunctions and Potential Molecular Markers in Sport Horses. Int J Mol Sci 2022; 23:ijms23158655. [PMID: 35955789 PMCID: PMC9369138 DOI: 10.3390/ijms23158655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023] Open
Abstract
Mitochondria are an essential part of most eukaryotic cells. The crucial role of these organelles is the production of metabolic energy, which is converted into ATP in oxidative phosphorylation. They are also involved in and constitute apoptosis, the site of many metabolic processes. Some of the factors that negatively affect mitochondria are stress, excessive exercise, disease, and the aging process. Exercise can cause the release of large amounts of free radicals, inflammation, injury, and stress. All of these factors can contribute to mitochondrial dysfunction, which can consistently lead to inflammatory responses, tissue damage, organ dysfunction, and a host of diseases. The functions of the mitochondria and the consequences of their disturbance can be of great importance in the breeding and use of horses. The paper reviews mitochondrial disorders in horses and, based on the literature, indicates genetic markers strongly related to this issue.
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14
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The Development of Single Molecule Force Spectroscopy: From Polymer Biophysics to Molecular Machines. Q Rev Biophys 2022; 55:e9. [PMID: 35916314 DOI: 10.1017/s0033583522000087] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Jadhav P, Chen Y, Butzin N, Buceta J, Urchueguía A. Bacterial degrons in synthetic circuits. Open Biol 2022; 12:220180. [PMID: 35975648 PMCID: PMC9382460 DOI: 10.1098/rsob.220180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial proteases are a promising post-translational regulation strategy in synthetic circuits because they recognize specific amino acid degradation tags (degrons) that can be fine-tuned to modulate the degradation levels of tagged proteins. For this reason, recent efforts have been made in the search for new degrons. Here we review the up-to-date applications of degradation tags for circuit engineering in bacteria. In particular, we pay special attention to the effects of degradation bottlenecks in synthetic oscillators and introduce mathematical approaches to study queueing that enable the quantitative modelling of proteolytic queues.
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Affiliation(s)
- Prajakta Jadhav
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Yanyan Chen
- Program for Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas Butzin
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Javier Buceta
- Institute for Integrative Systems Biology (I2SysBio, CSIC-UV), Paterna, Valencia 46980, Spain
| | - Arantxa Urchueguía
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA.,Institute for Integrative Systems Biology (I2SysBio, CSIC-UV), Paterna, Valencia 46980, Spain
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16
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SmiA is a hybrid priming/scaffolding adaptor for the LonA protease in Bacillus subtilis. J Biol Chem 2022; 298:102045. [PMID: 35595098 PMCID: PMC9204741 DOI: 10.1016/j.jbc.2022.102045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022] Open
Abstract
Regulatory proteolysis targets properly folded clients via a combination of cis-encoded degron sequences and trans-expressed specificity factors called adaptors. SmiA of Bacillus subtilis was identified as the first adaptor protein for the Lon family of proteases, but the mechanism of SmiA-dependent proteolysis is unknown. Here, we develop a fluorescence-based assay to measure the kinetics of SmiA-dependent degradation of its client SwrA and show that SmiA–SwrA interaction and the SwrA degron were both necessary, but not sufficient, for proteolysis. Consistent with a scaffolding adaptor mechanism, we found that stoichiometric excess of SmiA caused substrate-independent inhibition of LonA-dependent turnover. Furthermore, SmiA was strictly required even when SwrA levels were high suggesting that a local increase in substrate concentration mediated by the scaffold was not sufficient for proteolysis. Moreover, SmiA function could not be substituted by thermal denaturation of the substrate, consistent with a priming adaptor mechanism. Taken together, we conclude that SmiA functions via a mechanism that is a hybrid between scaffolding and priming models.
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17
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Hernández R, Chaib De Mares M, Jimenez H, Reyes A, Caro-Quintero A. Functional and Phylogenetic Characterization of Bacteria in Bovine Rumen Using Fractionation of Ruminal Fluid. Front Microbiol 2022; 13:813002. [PMID: 35401437 PMCID: PMC8992543 DOI: 10.3389/fmicb.2022.813002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/01/2022] [Indexed: 01/08/2023] Open
Abstract
Cattle productivity depends on our ability to fully understand and manipulate the fermentation process of plant material that occurs in the bovine rumen, which ultimately leads to the improvement of animal health and increased productivity with a reduction in environmental impact. An essential step in this direction is the phylogenetic and functional characterization of the microbial species composing the ruminal microbiota. To address this challenge, we separated a ruminal fluid sample by size and density using a sucrose density gradient. We used the full sample and the smallest fraction (5%), allowing the enrichment of bacteria, to assemble metagenome-assembled genomes (MAGs). We obtained a total of 16 bacterial genomes, 15 of these enriched in the smallest fraction of the gradient. According to the recently proposed Genome Taxonomy Database (GTDB) taxonomy, these MAGs belong to Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria, and Spirochaetota phyla. Fifteen MAGs were novel at the species level and four at the genus level. The functional characterization of these MAGs suggests differences from what is currently known from the genomic potential of well-characterized members from this complex environment. Species of the phyla Bacteroidota and Spirochaetota show the potential for hydrolysis of complex polysaccharides in the plant cell wall and toward the production of B-complex vitamins and protein degradation in the rumen. Conversely, the MAGs belonging to Firmicutes and Alphaproteobacteria showed a reduction in several metabolic pathways; however, they have genes for lactate fermentation and the presence of hydrolases and esterases related to chitin degradation. Our results demonstrate that the separation of the rumen microbial community by size and density reduced the complexity of the ruminal fluid sample and enriched some poorly characterized ruminal bacteria allowing exploration of their genomic potential and their functional role in the rumen ecosystem.
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Affiliation(s)
- Ruth Hernández
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Maryam Chaib De Mares
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Hugo Jimenez
- Animal Microbiology Laboratory, Agrodiversity Department, Corporación Colombiana de Investigación Agropecuaria - AGROSAVIA, Bogotá, Colombia
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia.,The Edison Family Center for Genome Science and Systems Biology, Washington University School of Medicine, Saint Louis, MO, United States
| | - Alejandro Caro-Quintero
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
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18
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Viola MG, Perdikari TM, Trebino CE, Rahmani N, Mathews KL, Pena CM, Chua XY, Xuan B, LaBreck CJ, Fawzi NL, Camberg JL. An enhancer sequence in the intrinsically disordered region of
FtsZ
promotes polymer‐guided substrate processing by
ClpXP
protease. Protein Sci 2022; 31:e4306. [PMID: 35481648 PMCID: PMC8996474 DOI: 10.1002/pro.4306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/09/2022]
Abstract
The essential bacterial division protein in Escherichia coli, FtsZ, assembles into the FtsZ-ring at midcell and recruits other proteins to the division site to promote septation. A region of the FtsZ amino acid sequence that links the conserved polymerization domain to a C-terminal protein interaction site was predicted to be intrinsically disordered and has been implicated in modulating spacing and architectural arrangements of FtsZ filaments. While the majority of cell division proteins that directly bind to FtsZ engage either the polymerization domain or the C-terminal interaction site, ClpX, the recognition and unfolding component of the bacterial ClpXP proteasome, has a secondary interaction with the predicted intrinsically disordered region (IDR) of FtsZ when FtsZ is polymerized. Here, we use NMR spectroscopy and reconstituted degradation reactions in vitro to demonstrate that this linker region is indeed disordered in solution and, further, that amino acids in the IDR of FtsZ enhance the degradation in polymer-guided interactions.
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Affiliation(s)
- Marissa G. Viola
- Department of Cell and Molecular Biology University of Rhode Island Kingston Rhode Island USA
| | | | - Catherine E. Trebino
- Department of Cell and Molecular Biology University of Rhode Island Kingston Rhode Island USA
| | - Negar Rahmani
- Department of Cell and Molecular Biology University of Rhode Island Kingston Rhode Island USA
| | - Kaylee L. Mathews
- Molecular Biology, Cell Biology, & Biochemistry Graduate Program Brown University Providence Rhode Island USA
| | - Carolina Mejia Pena
- Molecular Biology, Cell Biology, & Biochemistry Graduate Program Brown University Providence Rhode Island USA
| | - Xien Yu Chua
- Department of Molecular Pharmacology, Physiology & Biotechnology Brown University Providence Rhode Island USA
| | - Botai Xuan
- Department of Molecular Pharmacology, Physiology & Biotechnology Brown University Providence Rhode Island USA
| | - Christopher J. LaBreck
- Department of Cell and Molecular Biology University of Rhode Island Kingston Rhode Island USA
| | - Nicolas L. Fawzi
- Department of Molecular Pharmacology, Physiology & Biotechnology Brown University Providence Rhode Island USA
| | - Jodi L. Camberg
- Department of Cell and Molecular Biology University of Rhode Island Kingston Rhode Island USA
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19
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Sauer RT, Fei X, Bell TA, Baker TA. Structure and function of ClpXP, a AAA+ proteolytic machine powered by probabilistic ATP hydrolysis. Crit Rev Biochem Mol Biol 2022; 57:188-204. [PMID: 34923891 PMCID: PMC9871882 DOI: 10.1080/10409238.2021.1979461] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
ClpXP is an archetypical AAA+ protease, consisting of ClpX and ClpP. ClpX is an ATP-dependent protein unfoldase and polypeptide translocase, whereas ClpP is a self-compartmentalized peptidase. ClpXP is currently the only AAA+ protease for which high-resolution structures exist, the molecular basis of recognition for a protein substrate is understood, extensive biochemical and genetic analysis have been performed, and single-molecule optical trapping has allowed direct visualization of the kinetics of substrate unfolding and translocation. In this review, we discuss our current understanding of ClpXP structure and function, evaluate competing sequential and probabilistic mechanisms of ATP hydrolysis, and highlight open questions for future exploration.
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Affiliation(s)
- Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xue Fei
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tristan A. Bell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tania A. Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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20
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Lo HH, Chang HC, Liao CT, Hsiao YM. Expression and function of clpS and clpA in Xanthomonas campestris pv. campestris. Antonie van Leeuwenhoek 2022; 115:589-607. [PMID: 35322326 DOI: 10.1007/s10482-022-01725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
Abstract
ATP-dependent proteases (FtsH, Lon, and Clp family proteins) are ubiquitous in bacteria and play essential roles in numerous regulatory cell processes. Xanthomonas campestris pv. campestris is a Gram-negative pathogen that can cause black rot diseases in crucifers. The genome of X. campestris pv. campestris has several clp genes, namely, clpS, clpA, clpX, clpP, clpQ, and clpY. Among these genes, only clpX and clpP is known to be required for pathogenicity. Here, we focused on two uncharacterized clp genes (clpS and clpA) that encode the adaptor (ClpS) and ATPase subunit (ClpA) of the ClpAP protease complex. Transcriptional analysis revealed that the expression of clpS and clpA was growth phase-dependent and affected by the growth temperature. The inactivation of clpA, but not of clpS, resulted in susceptibility to high temperature and attenuated virulence in the host plant. The altered phenotypes of the clpA mutant could be complemented in trans. Site-directed mutagenesis revealed that K223 and K504 were the amino acid residues critical for ClpA function in heat tolerance. The protein expression profile shown by the clpA mutant in response to heat stress was different from that exhibited by the wild type. In summary, we characterized two clp genes (clpS and clpA) by examining their expression profiles and functions in different processes, including stress tolerance and pathogenicity. We demonstrated that clpS and clpA were expressed in a temperature-dependent manner and that clpA was required for the survival at high temperature and full virulence of X. campestris pv. campestris. This work represents the first time that clpS and clpA were characterized in Xanthomonas.
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Affiliation(s)
- Hsueh-Hsia Lo
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Hsiao-Ching Chang
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Chao-Tsai Liao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan
| | - Yi-Min Hsiao
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, 40601, Taiwan.
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21
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Mabanglo MF, Houry WA. Recent structural insights into the mechanism of ClpP protease regulation by AAA+ chaperones and small molecules. J Biol Chem 2022; 298:101781. [PMID: 35245501 PMCID: PMC9035409 DOI: 10.1016/j.jbc.2022.101781] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/19/2022] Open
Abstract
ClpP is a highly conserved serine protease that is a critical enzyme in maintaining protein homeostasis and is an important drug target in pathogenic bacteria and various cancers. In its functional form, ClpP is a self-compartmentalizing protease composed of two stacked heptameric rings that allow protein degradation to occur within the catalytic chamber. ATPase chaperones such as ClpX and ClpA are hexameric ATPases that form larger complexes with ClpP and are responsible for the selection and unfolding of protein substrates prior to their degradation by ClpP. Although individual structures of ClpP and ATPase chaperones have offered mechanistic insights into their function and regulation, their structures together as a complex have only been recently determined to high resolution. Here, we discuss the cryoelectron microscopy structures of ClpP-ATPase complexes and describe findings previously inaccessible from individual Clp structures, including how a hexameric ATPase and a tetradecameric ClpP protease work together in a functional complex. We then discuss the consensus mechanism for substrate unfolding and translocation derived from these structures, consider alternative mechanisms, and present their strengths and limitations. Finally, new insights into the allosteric control of ClpP gained from studies using small molecules and gain or loss-of-function mutations are explored. Overall, this review aims to underscore the multilayered regulation of ClpP that may present novel ideas for structure-based drug design.
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Affiliation(s)
- Mark F Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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22
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Luo S, Kim C. Current Understanding of Temperature Stress-Responsive Chloroplast FtsH Metalloproteases. Int J Mol Sci 2021; 22:ijms222212106. [PMID: 34829988 PMCID: PMC8622299 DOI: 10.3390/ijms222212106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 12/22/2022] Open
Abstract
Low and high temperatures are life-threatening stress factors, diminishing plant productivity. One of the earliest responses of plants to stress is a rapid burst of reactive oxygen species (ROS) in chloroplasts. Widespread efforts over the past decade shed new light on the chloroplast as an environmental sensor, translating the environmental fluctuation into varying physiological responses by utilizing distinct retrograde (chloroplast-to-nucleus) signals. Recent studies have unveiled that chloroplasts mediate a similar unfolded/misfolded/damaged protein response (cpUPR) as observed in the endoplasmic reticulum and mitochondria. Although observing cpUPR is not surprising since the chloroplast is a prime organelle producing harmful ROS, the intertwined relationship among ROS, protein damage, and chloroplast protein quality controls (cpPQCs) with retrograde signaling has recently been reported. This finding also gives rise to critical attention on chloroplast proteins involved in cpPQCs, ROS detoxifiers, transcription/translation, import of precursor proteins, and assembly/maturation, the deficiency of which compromises chloroplast protein homeostasis (proteostasis). Any perturbation in the protein may require readjustment of proteostasis by transmitting retrograde signal(s) to the nucleus, whose genome encodes most of the chloroplast proteins involved in proteostasis. This review focuses on recent findings on cpUPR and chloroplast-targeted FILAMENTOUS TEMPERATURE-SENSITIVE H proteases involved in cpPQC and retrograde signaling and their impacts on plant responses to temperature stress.
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Affiliation(s)
- Shengji Luo
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chanhong Kim
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
- Correspondence:
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23
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Dong S, Chen H, Zhou Q, Liao N. Protein degradation control and regulation of bacterial survival and pathogenicity: the role of protein degradation systems in bacteria. Mol Biol Rep 2021; 48:7575-7585. [PMID: 34655017 DOI: 10.1007/s11033-021-06744-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Protein degradation systems play crucial roles in all the kingdoms of life. Their natural function is to eliminate proteins that are improperly synthesized, damaged, aggregated, or short-lived, ensuring the timely and accurate regulation of the response to abrupt environmental changes. Thus, proteolysis plays an important role in protein homeostasis, quality control, and the control of regulatory processes, such as adaptation and cell development. Except for the lysosome, ATPases Associated with various cellular Activities (AAA+) ATPase-protease complex is another major protein degradation system in the cell. METHODS AND RESULTS The AAA+ ATPase-protease complex is a giant energy-dependent protease complex found in almost all kinds of cells, including bacteria, archaea and eukarya. Based on sequence analysis of ClpQ (HslV) and 20S proteasome beta subunits, it was found that bacterial ClpQ possess multiple same highly conserved motifs with 20S proteasome beta subunits of archaea and eukaryote. In this review, we also discussed the structure and functional mechanism, protein degradation signals and pathogenic role of proteasome / Clp protease complex in prokaryotes. CONCLUSION Bacterial protein degradation systems play important roles in stress tolerance, protein quality control, DNA protection, transcription and pathogenicity of bacteria. But our current knowledge of the bacterial protease system is incomplete, and further research into the Clp protease complex and associated protein degradation signals will extend our understanding of the metabolism, physiology, reproduction, and pathogenicity of bacteria.
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Affiliation(s)
- Shilei Dong
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, 310013, China
| | - Honghu Chen
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Qingxue Zhou
- Department of Clinical Laboratory, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, 310008, China
| | - Ningbo Liao
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China.
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24
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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25
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Yang T, Zhang T, Zhou X, Wang P, Gan J, Song B, Yang S, Yang CG. Dysregulation of ClpP by Small-Molecule Activators Used Against Xanthomonas oryzae pv. oryzae Infections. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7545-7553. [PMID: 34218658 DOI: 10.1021/acs.jafc.1c01470] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rice bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is considered a destructive plant bacterial disease. The looming crisis of antibiotic resistance necessitates the discovery of antibiotics with new modes of action. Activated caseinolytic protease P (ClpP) can degrade bacterial FtsZ proteins that are essential for cell division; thus, we hypothesized that small-molecule-induced dysregulation of XooClpP may result in degradation of XooFtsZ to treat leaf blight diseases. In this work, we have determined the crystal structures of XooClpP, and its mutant bound with ADEP4, which revealed the action modes of XooClpP assemblies and XooFtsZ degradation by dysregulated XooClpP in the presence of small-molecule activators, such as ONC212 and ADEP4. Additionally, an antibacterial assessment demonstrated that ONC212 displays excellent activity against Xoo and prevents rice bacterial leaf blight in vivo. Thus, these unique antibacterial effects of small-molecule activators of XooClpP represent a potential strategy for the development of agricultural antibiotics by targeting bacterial ClpP.
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Affiliation(s)
- Teng Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tao Zhang
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiang Zhou
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Pengyu Wang
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Gan
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Cai-Guang Yang
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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Suzuki H, Okumura Y, Mikawa Y, Takata M, Yoshimura S, Ohshiro T. Transcriptome and growth efficiency comparisons of recombinant thermophiles that produce thermolabile and thermostable proteins: implications for burden-based selection of thermostable proteins. Extremophiles 2021; 25:403-412. [PMID: 34191121 DOI: 10.1007/s00792-021-01237-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/24/2021] [Indexed: 11/28/2022]
Abstract
Geobacillus kaustophilus is a thermophilic bacterium that grows at temperatures ranging between 42 and 74 °C. Here, we modified this organism to produce the thermolabile protein (PyrFA) or its thermostable variant (PyrFV) and analyzed the transcriptome and growth efficiency profiles of the resultant strains. In the producer of PyrFA, the transcriptome profile was changed to facilitate ATP synthesis from NADH without pooling reduced quinones. This change implies that PyrFA production at elevated temperatures places an energy burden on cells potentially to maintain protein homeostasis. This was consistent with the observation that the PyrFA producer grew slower than the PyrFV producer at > 45 °C and had a lower cellular fitness. Similar growth profiles were also observed in the PyrFA and PyrFV producers derived from another thermophile (Geobacillus thermodenitrificans) but not in those from Escherichia coli at 30 °C. Thus, we suggest that the production of thermolabile proteins impairs host survival at higher temperatures; therefore, thermophiles are under evolutionary selection for thermostable proteins regardless of whether their functions are associated with survival advantages. This hypothesis provides new insights into evolutionary protein selection in thermophiles and suggests an engineering approach to select thermostable protein variants generated via random gene mutagenesis.
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Affiliation(s)
- Hirokazu Suzuki
- Faculty of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan. .,Center for Research On Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan.
| | - Yuta Okumura
- Department of Engineering, Graduate School of Sustainability Science, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Yui Mikawa
- Faculty of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Mao Takata
- Faculty of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Shunsuke Yoshimura
- Department of Engineering, Graduate School of Sustainability Science, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
| | - Takashi Ohshiro
- Faculty of Engineering, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan.,Center for Research On Green Sustainable Chemistry, Tottori University, 4-101 Koyama-Minami, Tottori, 680-8552, Japan
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Koksharova OA, Butenko IO, Pobeguts OV, Safronova NA, Govorun VM. β-N-Methylamino-L-Alanine (BMAA) Causes Severe Stress in Nostoc sp. PCC 7120 Cells under Diazotrophic Conditions: A Proteomic Study. Toxins (Basel) 2021; 13:325. [PMID: 33946501 PMCID: PMC8147232 DOI: 10.3390/toxins13050325] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/07/2021] [Accepted: 04/28/2021] [Indexed: 12/24/2022] Open
Abstract
Non-proteinogenic neurotoxic amino acid β-N-methylamino-L-alanine (BMAA) is synthesized by cyanobacteria, diatoms, and dinoflagellates, and is known to be a causative agent of human neurodegenerative diseases. Different phytoplankton organisms' ability to synthesize BMAA could indicate the importance of this molecule in the interactions between microalgae in nature. We were interested in the following: what kinds of mechanisms underline BMAA's action on cyanobacterial cells in different nitrogen supply conditions. Herein, we present a proteomic analysis of filamentous cyanobacteria Nostoc sp. PCC 7120 cells that underwent BMAA treatment in diazotrophic conditions. In diazotrophic growth conditions, to survive, cyanobacteria can use only biological nitrogen fixation to obtain nitrogen for life. Note that nitrogen fixation is an energy-consuming process. In total, 1567 different proteins of Nostoc sp. PCC 7120 were identified by using LC-MS/MS spectrometry. Among them, 123 proteins belonging to different functional categories were selected-due to their notable expression differences-for further functional analysis and discussion. The presented proteomic data evidences that BMAA treatment leads to very strong (up to 80%) downregulation of α (NifD) and β (NifK) subunits of molybdenum-iron protein, which is known to be a part of nitrogenase. This enzyme is responsible for catalyzing nitrogen fixation. The genes nifD and nifK are under transcriptional control of a global nitrogen regulator NtcA. In this study, we have found that BMAA impacts in a total of 22 proteins that are under the control of NtcA. Moreover, BMAA downregulates 18 proteins that belong to photosystems I or II and light-harvesting complexes; BMAA treatment under diazotrophic conditions also downregulates five subunits of ATP synthase and enzyme NAD(P)H-quinone oxidoreductase. Therefore, we can conclude that the disbalance in energy and metabolite amounts leads to severe intracellular stress that induces the upregulation of stress-activated proteins, such as starvation-inducible DNA-binding protein, four SOS-response enzymes, and DNA repair enzymes, nine stress-response enzymes, and four proteases. The presented data provide new leads into the ecological impact of BMAA on microalgal communities that can be used in future investigations.
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Affiliation(s)
- Olga A. Koksharova
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Leninskie Gory, 1-40, 119991 Moscow, Russia;
- Institute of Molecular Genetics of National Research Center “Kurchatov Institute”, Kurchatov Square, 2, 123182 Moscow, Russia
| | - Ivan O. Butenko
- Scientific-Research Institute of Physical-Chemical Medicine, 119435 Moscow, Russia; (I.O.B.); (O.V.P.); (V.M.G.)
| | - Olga V. Pobeguts
- Scientific-Research Institute of Physical-Chemical Medicine, 119435 Moscow, Russia; (I.O.B.); (O.V.P.); (V.M.G.)
| | - Nina A. Safronova
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Leninskie Gory, 1-40, 119991 Moscow, Russia;
| | - Vadim M. Govorun
- Scientific-Research Institute of Physical-Chemical Medicine, 119435 Moscow, Russia; (I.O.B.); (O.V.P.); (V.M.G.)
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28
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Tzeng SR, Tseng YC, Lin CC, Hsu CY, Huang SJ, Kuo YT, Chang CI. Molecular insights into substrate recognition and discrimination by the N-terminal domain of Lon AAA+ protease. eLife 2021; 10:64056. [PMID: 33929321 PMCID: PMC8087443 DOI: 10.7554/elife.64056] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
The Lon AAA+ protease (LonA) is a ubiquitous ATP-dependent proteolytic machine, which selectively degrades damaged proteins or native proteins carrying exposed motifs (degrons). Here we characterize the structural basis for substrate recognition and discrimination by the N-terminal domain (NTD) of LonA. The results reveal that the six NTDs are attached to the hexameric LonA chamber by flexible linkers such that the formers tumble independently of the latter. Further spectral analyses show that the NTD selectively interacts with unfolded proteins, protein aggregates, and degron-tagged proteins by two hydrophobic patches of its N-lobe, but not intrinsically disordered substrate, α-casein. Moreover, the NTD selectively binds to protein substrates when they are thermally induced to adopt unfolded conformations. Collectively, our findings demonstrate that NTDs enable LonA to perform protein quality control to selectively degrade proteins in damaged states and suggest that substrate discrimination and selective degradation by LonA are mediated by multiple NTD interactions. There are many different types of protein which each have different roles in biology. Most proteins are surrounded by water and are folded so that their water-attracting regions are on the outside and more fat-like regions, which repel water, are on the inside. When a protein becomes damaged or is assembled incorrectly, some of the fat-like regions end up on the outside of the protein and become exposed to water. This can prevent the protein from performing its role and harm the cell instead. LonA proteases are responsible for dismantling and recycling these harmful proteins, as well as proteins that have been labelled for destruction. They do this by unfolding the unwanted protein and transporting it into an enclosed chamber made of six LonA molecules. Once inside the chamber, the target protein is broken down into smaller fragments that can be used to build other structures. LonA proteases contain a region called the N-terminal domain, or NTD for short, which is thought to be responsible for identifying which proteins need degrading. Yet it remained unclear how the NTD recognizes and binds to these target proteins. To answer this question, Tzeng et al. studied the detailed structure of a LonA protease that had been purified from bacteria cells. This revealed that the NTD of LonA contains two water-repelling regions which bind to fat-like segments on the surface of proteins that have become unfolded or tagged for destruction. Further experiments showed that the NTD is bound to the main body of LonA via a ‘flexible linker’. This led Tzeng et al. to propose that the NTD sways around loosely at the end of LonA searching for proteins with exposed water-repelling regions. Once an NTD identifies and attaches to a target, the NTDs of the other LonA molecules then bind to the protein and help insert it into the chamber. Proteases are a vital component of all biological systems. Controlling protein destruction and recycling is a key factor in how cells divide and respond to a changing environment. This study provides new insights into how LonA operates in bacteria, which may apply to proteases more widely. This contributes to our knowledge of fundamental biology and may also be relevant in a range of diseases where protein recycling is defective or inefficient.
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Affiliation(s)
- Shiou-Ru Tzeng
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yin-Chu Tseng
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chien-Chu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-Ying Hsu
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shing-Jong Huang
- Instrumentation Center, National Taiwan University, Taipei, Taiwan
| | - Yi-Ting Kuo
- Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chung-I Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.,Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei, Taiwan
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Dighe SN, van Akker SR, Mathew M, Perera M, Collet TA. Discovery of a Novel Antimicrobial Agent by the Virtual Screening of a Library of Small Molecules. Mol Inform 2021; 40:e2100035. [PMID: 33891375 DOI: 10.1002/minf.202100035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/12/2022]
Abstract
A virtual screening approach based upon a combination of docking and pharmacophore methods was utilized on a library of 1.4 million molecules to identify novel antimicrobial agents, which may potentially act via inhibition of the caseinolytic protease. Using this method, compound 6 was found to be bactericidal against three staphylococcal species (minimum inhibitory concentration (MIC)=4-16 μg/mL). Further, subsequent structural optimization of 6 led to the identification of compound 24, which was shown to be the most potent analog within the series (MIC=4 μg/mL) and outperforming the antibiotic controls for two of the staphylococcal species. The newly discovered antimicrobial agent (24) demonstrated excellent in silico ADME properties and was non-toxic when tested on two human skin cell lines. As such, compound 24 has the potential for use as a lead molecule in the development of a novel class of antimicrobial agents.
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Affiliation(s)
- Satish N Dighe
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Suzannah R van Akker
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Marina Mathew
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Madusha Perera
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Trudi A Collet
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
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30
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Abstract
Degradation of intracellular proteins in Gram-negative bacteria regulates various cellular processes and serves as a quality control mechanism by eliminating damaged proteins. To understand what causes the proteolytic machinery of the cell to degrade some proteins while sparing others, we employed a quantitative pulsed-SILAC (stable isotope labeling with amino acids in cell culture) method followed by mass spectrometry analysis to determine the half-lives for the proteome of exponentially growing Escherichia coli, under standard conditions. We developed a likelihood-based statistical test to find actively degraded proteins and identified dozens of fast-degrading novel proteins. Finally, we used structural, physicochemical, and protein-protein interaction network descriptors to train a machine learning classifier to discriminate fast-degrading proteins from the rest of the proteome, achieving an area under the receiver operating characteristic curve (AUC) of 0.72.IMPORTANCE Bacteria use protein degradation to control proliferation, dispose of misfolded proteins, and adapt to physiological and environmental shifts, but the factors that dictate which proteins are prone to degradation are mostly unknown. In this study, we have used a combined computational-experimental approach to explore protein degradation in E. coli We discovered that the proteome of E. coli is composed of three protein populations that are distinct in terms of stability and functionality, and we show that fast-degrading proteins can be identified using a combination of various protein properties. Our findings expand the understanding of protein degradation in bacteria and have implications for protein engineering. Moreover, as rapidly degraded proteins may play an important role in pathogenesis, our findings may help to identify new potential antibacterial drug targets.
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31
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Kim L, Heo J, Kwon DH, Shin JS, Jang SH, Park ZY, Song HK. Structural basis for the N-degron specificity of ClpS1 from Arabidopsis thaliana. Protein Sci 2020; 30:700-708. [PMID: 33368743 DOI: 10.1002/pro.4018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 12/25/2022]
Abstract
The N-degron pathway determines the half-life of proteins in both prokaryotes and eukaryotes by precisely recognizing the N-terminal residue (N-degron) of substrates. ClpS proteins from bacteria bind to substrates containing hydrophobic N-degrons (Leu, Phe, Tyr, and Trp) and deliver them to the caseinolytic protease system ClpAP. This mechanism is preserved in organelles such as mitochondria and chloroplasts. Bacterial ClpS adaptors bind preferentially to Leu and Phe N-degrons; however, ClpS1 from Arabidopsis thaliana (AtClpS1) shows a difference in that it binds strongly to Phe and Trp N-degrons and only weakly to Leu. This difference in behavior cannot be explained without structural information due to the high sequence homology between bacterial and plant ClpS proteins. Here, we report the structure of AtClpS1 at 2.0 Å resolution in the presence of a bound N-degron. The key determinants for α-amino group recognition are conserved among all ClpS proteins, but the α3-helix of eukaryotic AtClpS1 is significantly shortened, and consequently, a loop forming a pocket for the N-degron is moved slightly outward to enlarge the pocket. In addition, amino acid replacement from Val to Ala causes a reduction in hydrophobic interactions with Leu N-degron. A combination of the fine-tuned hydrophobic residues in the pocket and the basic gatekeeper at the entrance of the pocket controls the N-degron selectivity of the plant ClpS protein.
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Affiliation(s)
- Leehyeon Kim
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Jiwon Heo
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Do Hoon Kwon
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Jin Seok Shin
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Se Hwan Jang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul, South Korea
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32
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Binepal G, Mabanglo MF, Goodreid JD, Leung E, Barghash MM, Wong KS, Lin F, Cossette M, Bansagi J, Song B, Balasco Serrão VH, Pai EF, Batey RA, Gray-Owen SD, Houry WA. Development of Antibiotics That Dysregulate the Neisserial ClpP Protease. ACS Infect Dis 2020; 6:3224-3236. [PMID: 33237740 DOI: 10.1021/acsinfecdis.0c00599] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Evolving antimicrobial resistance has motivated the search for novel targets and alternative therapies. Caseinolytic protease (ClpP) has emerged as an enticing new target since its function is conserved and essential for bacterial fitness, and because its inhibition or dysregulation leads to bacterial cell death. ClpP protease function controls global protein homeostasis and is, therefore, crucial for the maintenance of the bacterial proteome during growth and infection. Previously, acyldepsipeptides (ADEPs) were discovered to dysregulate ClpP, leading to bactericidal activity against both actively growing and dormant Gram-positive pathogens. Unfortunately, these compounds had very low efficacy against Gram-negative bacteria. Hence, we sought to develop non-ADEP ClpP-targeting compounds with activity against Gram-negative species and called these activators of self-compartmentalizing proteases (ACPs). These ACPs bind and dysregulate ClpP in a manner similar to ADEPs, effectively digesting bacteria from the inside out. Here, we performed further ACP derivatization and testing to improve the efficacy and breadth of coverage of selected ACPs against Gram-negative bacteria. We observed that a diverse collection of Neisseria meningitidis and Neisseria gonorrhoeae clinical isolates were exquisitely sensitive to these ACP analogues. Furthermore, based on the ACP-ClpP cocrystal structure solved here, we demonstrate that ACPs could be designed to be species specific. This validates the feasibility of drug-based targeting of ClpP in Gram-negative bacteria.
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Affiliation(s)
- Gursonika Binepal
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Mark F. Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Jordan D. Goodreid
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Marim M. Barghash
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Keith S. Wong
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Funing Lin
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Michele Cossette
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jazmin Bansagi
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Boxi Song
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Vitor Hugo Balasco Serrão
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Emil F. Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Ontario Cancer Institute/Princess Margaret Hospital, Toronto, Ontario M5G 1L7, Canada
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Scott D. Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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33
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Recombinant expression, purification and SAXS analysis of Arabidopsis thaliana ClpC1. Int J Biol Macromol 2020; 167:1273-1280. [PMID: 33189753 DOI: 10.1016/j.ijbiomac.2020.11.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 11/23/2022]
Abstract
Caseinolytic protease-associated chaperones (Clp chaperones) are HSP100 proteins belonging to the family of ATPases having diverse cellular functions, and they occur in various organisms ranging from bacteria to plants and mammals. Most Clp chaperones have a hexameric organization and associate with tetradecameric Clp proteases to recognize and unfold protein substrates that get degraded within the cellular milieu. Vascular plants have a diverse family of Clp chaperones compared to other organisms; wherein, the chloroplasts of Arabidopsis thaliana alone contain four distinct Clp chaperones, such as ClpC1, ClpC2, ClpD, and ClpB3. The paralogs AtClpC1 and AtClpC2 are more than 90% identical, though the extent of functional overlap between the two is not clear. Moreover, in vitro characterization reports are available only for AtClpC2, as AtClpC1 could not be expressed in recombinant form in the past. Herein, using a bacterial expression system, we have successfully expressed and purified AtClpC1 with a short N-terminal truncation, employing a three-step chromatographic purification strategy. We show that AtClpC1 exists as a hexamer in the presence of ATP and MgCl2, as known for other functional Clp chaperones. Further, our SAXS analyses provide a low-resolution envelope structure for the hexameric AtClpC1, which very well fits a ClpC hexamer model.
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34
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Andrianova AG, Kudzhaev AM, Abrikosova VA, Gustchina AE, Smirnov IV, Rotanova TV. Involvement of the N Domain Residues E34, K35, and R38 in the Functionally Active Structure of Escherichia coli Lon Protease. Acta Naturae 2020; 12:86-97. [PMID: 33456980 PMCID: PMC7800598 DOI: 10.32607/actanaturae.11197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/21/2020] [Indexed: 11/20/2022] Open
Abstract
ATP-dependent Lon protease of Escherichia coli (EcLon), which belongs to the superfamily of AAA+ proteins, is a key component of the cellular proteome quality control system. It is responsible for the cleavage of mutant, damaged, and short-lived regulatory proteins that are potentially dangerous for the cell. EcLon functions as a homooligomer whose subunits contain a central characteristic AAA+ module, a C-terminal protease domain, and an N-terminal non-catalytic region composed of the actual N-terminal domain and the inserted α-helical domain. An analysis of the N domain crystal structure suggested a potential involvement of residues E34, K35, and R38 in the formation of stable and active EcLon. We prepared and studied a triple mutant LonEKR in which these residues were replaced with alanine. The introduced substitutions were shown to affect the conformational stability and nucleotide-induced intercenter allosteric interactions, as well as the formation of the proper protein binding site.
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Affiliation(s)
- A. G. Andrianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. M. Kudzhaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - V. A. Abrikosova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. E. Gustchina
- Macromolecular Crystallography Laboratory, NCI-Frederick, P.O. Box B, Frederick, MD 21702, USA
| | - I. V. Smirnov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - T. V. Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
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35
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Deng J, Walther A. ATP-Responsive and ATP-Fueled Self-Assembling Systems and Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2002629. [PMID: 32881127 DOI: 10.1002/adma.202002629] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Adenosine triphosphate (ATP) is a central metabolite that plays an indispensable role in various cellular processes, from energy supply to cell-to-cell signaling. Nature has developed sophisticated strategies to use the energy stored in ATP for many metabolic and non-equilibrium processes, and to sense and bind ATP for biological signaling. The variations in the ATP concentrations from one organelle to another, from extracellular to intracellular environments, and from normal cells to cancer cells are one motivation for designing ATP-triggered and ATP-fueled systems and materials, because they show great potential for applications in biological systems by using ATP as a trigger or chemical fuel. Over the last decade, ATP has been emerging as an attractive co-assembling component for man-made stimuli-responsive as well as for fuel-driven active systems and materials. Herein, current advances and emerging concepts for ATP-triggered and ATP-fueled self-assemblies and materials are discussed, shedding light on applications and highlighting future developments. By bringing together concepts of different domains, that is from supramolecular chemistry to DNA nanoscience, from equilibrium to non-equilibrium self-assembly, and from fundamental sciences to applications, the aim is to cross-fertilize current approaches with the ultimate aim to bring synthetic ATP-dependent systems closer to living systems.
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Affiliation(s)
- Jie Deng
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, Freiburg, 79104, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, Freiburg, 79104, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, Freiburg, 79110, Germany
| | - Andreas Walther
- A3BMS Lab - Active, Adaptive and Autonomous Bioinspired Materials, Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Straße 31, Freiburg, 79104, Germany
- Freiburg Materials Research Center (FMF), University of Freiburg, Stefan-Meier-Str. 21, Freiburg, 79104, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), University of Freiburg, Georges-Köhler-Allee 105, Freiburg, 79110, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Köhler-Allee 105, Freiburg, D-79110, Germany
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36
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Huang M, Zhao Y, Feng L, Zhu L, Zhan L, Chen X. Role of ClpB From Corynebacterium crenatum in Thermal Stress and Arginine Fermentation. Front Microbiol 2020; 11:1660. [PMID: 32765470 PMCID: PMC7380099 DOI: 10.3389/fmicb.2020.01660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/25/2020] [Indexed: 12/04/2022] Open
Abstract
ClpB, an ATP-dependent molecular chaperone, is involved in metabolic pathways and plays important roles in microorganisms under stress conditions. Metabolic pathways and stress resistance are important characteristics of industrially -relevant bacteria during fermentation. Nevertheless, ClpB-related observations have been rarely reported in industrially -relevant microorganisms. Herein, we found a homolog of ClpB from Corynebacterium crenatum. The amino acid sequence of ClpB was analyzed, and the recombinant ClpB protein was purified and characterized. The full function of ClpB requires DnaK as chaperone protein. For this reason, dnaK/clpB deletion mutants and the complemented strains were constructed to investigate the role of ClpB. The results showed that DnaK/ClpB is not essential for the survival of C. crenatum MT under pH and alcohol stresses. The ClpB-deficient or DnaK-deficient C. crenatum mutants showed weakened growth during thermal stress. In addition, the results demonstrated that deletion of the clpB gene affected glucose consumption and L-arginine, L-glutamate, and lactate production during fermentation.
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Affiliation(s)
- Mingzhu Huang
- Department of Life Science, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, Nanchang, China
| | - Yue Zhao
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Lin Feng
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Lingfeng Zhu
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Li Zhan
- Department of Life Science, Jiangxi Normal University, Nanchang, China
| | - Xuelan Chen
- Department of Life Science, Jiangxi Normal University, Nanchang, China.,Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, Nanchang, China
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Torres-Delgado A, Kotamarthi HC, Sauer RT, Baker TA. The Intrinsically Disordered N-terminal Extension of the ClpS Adaptor Reprograms Its Partner AAA+ ClpAP Protease. J Mol Biol 2020; 432:4908-4921. [PMID: 32687854 DOI: 10.1016/j.jmb.2020.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 11/18/2022]
Abstract
Adaptor proteins modulate substrate selection by AAA+ proteases. The ClpS adaptor delivers N-degron substrates to ClpAP but inhibits degradation of substrates bearing ssrA tags or other related degrons. How ClpS inhibits degradation of such substrates is poorly understood. Here, we demonstrate that ClpS impedes recognition of ssrA-tagged substrates by a non-competitive mechanism and also slows subsequent unfolding/translocation of these substrates as well as of N-degron substrates. This suppression of mechanical activity is largely a consequence of the ability of ClpS to repress ATP hydrolysis by ClpA, but several lines of evidence show that ClpS's inhibition of substrate binding and its ATPase repression are separable activities. Using ClpS mutants and ClpS-ClpA chimeras, we establish that engagement of the intrinsically disordered N-terminal extension of ClpS by ClpA is both necessary and sufficient to inhibit multiple steps of ClpAP-catalyzed degradation. These observations reveal how an adaptor can simultaneously modulate the catalytic activity of a AAA+ enzyme, efficiently promote recognition of some substrates, suppress recognition of other substrates, and thereby affect degradation of its menu of substrates in a specific manner. We propose that similar mechanisms are likely to be used by other adaptors to regulate substrate choice and the catalytic activity of molecular machines.
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Affiliation(s)
- Amaris Torres-Delgado
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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38
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Joshi A, Mahmoud SA, Kim SK, Ogdahl JL, Lee VT, Chien P, Yildiz FH. c-di-GMP inhibits LonA-dependent proteolysis of TfoY in Vibrio cholerae. PLoS Genet 2020; 16:e1008897. [PMID: 32589664 PMCID: PMC7371385 DOI: 10.1371/journal.pgen.1008897] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 07/20/2020] [Accepted: 05/30/2020] [Indexed: 02/06/2023] Open
Abstract
The LonA (or Lon) protease is a central post-translational regulator in diverse bacterial species. In Vibrio cholerae, LonA regulates a broad range of behaviors including cell division, biofilm formation, flagellar motility, c-di-GMP levels, the type VI secretion system (T6SS), virulence gene expression, and host colonization. Despite LonA’s role in cellular processes critical for V. cholerae’s aquatic and infectious life cycles, relatively few LonA substrates have been identified. LonA protease substrates were therefore identified through comparison of the proteomes of wild-type and ΔlonA strains following translational inhibition. The most significantly enriched LonA-dependent protein was TfoY, a known regulator of motility and the T6SS in V. cholerae. Experiments showed that TfoY was required for LonA-mediated repression of motility and T6SS-dependent killing. In addition, TfoY was stabilized under high c-di-GMP conditions and biochemical analysis determined direct binding of c-di-GMP to LonA results in inhibition of its protease activity. The work presented here adds to the list of LonA substrates, identifies LonA as a c-di-GMP receptor, demonstrates that c-di-GMP regulates LonA activity and TfoY protein stability, and helps elucidate the mechanisms by which LonA controls important V. cholerae behaviors. This study provides insights into the mechanisms and consequences of LonA-mediated regulated proteolysis in Vibrio cholerae, the causal organism of the acute diarrheal disease cholera that is endemic in more than 47 countries across the globe. Lon is broadly conserved in bacterial systems; uncovering the molecular connection between c-di-GMP signaling and LonA-mediated proteolysis of V. cholerae will provide conceptual frameworks for the development of intervention strategies to combat virulence by bacterial pathogens.
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Affiliation(s)
- Avatar Joshi
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Samar A. Mahmoud
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Soo-Kyoung Kim
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Justyne L. Ogdahl
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Vincent T. Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, California, United States of America
- * E-mail:
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39
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Lon Protease Removes Excess Signal Recognition Particle Protein in Escherichia coli. J Bacteriol 2020; 202:JB.00161-20. [PMID: 32366590 DOI: 10.1128/jb.00161-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Correct targeting of membrane proteins is essential for membrane integrity, cell physiology, and viability. Cotranslational targeting depends on the universally conserved signal recognition particle (SRP), which is a ribonucleoprotein complex comprised of the protein component Ffh and the 4.5S RNA in Escherichia coli About 25 years ago it was reported that Ffh is an unstable protein, but the underlying mechanism has never been explored. Here, we show that Lon is the primary protease responsible for adjusting the cellular Ffh level. When overproduced, Ffh is particularly prone to degradation during transition from exponential to stationary growth and the cellular Ffh amount is lowest in stationary phase. The Ffh protein consists of two domains, the NG domain, responsible for GTP hydrolysis and docking to the membrane receptor FtsY, and the RNA-binding M domain. We find that the NG domain alone is stable, whereas the isolated M domain is degraded. Consistent with the importance of Lon in this process, the M domain confers synthetic lethality to the lon mutant. The Ffh homolog from the model plant Arabidopsis thaliana, which forms a protein-protein complex rather than a protein-RNA complex, is stable, suggesting that the RNA-binding ability residing in the M domain of E. coli Ffh is important for proteolysis. Our results support a model in which excess Ffh not bound to 4.5S RNA is subjected to proteolysis until an appropriate Ffh concentration is reached. The differential proteolysis adjusts Ffh levels to the cellular demand and maintains cotranslational protein transport and membrane integrity.IMPORTANCE Since one-third of all bacterial proteins reside outside the cytoplasm, protein targeting to the appropriate address is an essential process. Cotranslational targeting to the membrane relies on the signal recognition particle (SRP), which is a protein-RNA complex in bacteria. We report that the protein component Ffh is a substrate of the Lon protease. Regulated proteolysis of Ffh provides a simple mechanism to adjust the concentration of the essential protein to the cellular demand. This is important because elevated or depleted SRP levels negatively impact protein targeting and bacterial fitness.
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40
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Ziemski M, Leodolter J, Taylor G, Kerschenmeyer A, Weber-Ban E. Genome-wide interaction screen for Mycobacterium tuberculosis ClpCP protease reveals toxin-antitoxin systems as a major substrate class. FEBS J 2020; 288:111-126. [PMID: 32301575 DOI: 10.1111/febs.15335] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/12/2020] [Accepted: 04/14/2020] [Indexed: 12/30/2022]
Abstract
In Mycobacterium tuberculosis (Mtb), the Clp protease degradation pathway, mediated by the modular ClpCP and ClpXP protease complexes, is essential for growth and presents an attractive drug target. Employing a bacterial adenylate cyclase two-hybrid (BACTH) screening approach that we adapted to screen the proteome of an Mtb ORF library, we identify protein interaction partners of the ClpC1 chaperone on a genome-wide level. Our results demonstrate that bipartite type II toxin-antitoxin (TA) systems represent a major substrate class. Out of the 67 type II TA systems known in Mtb, 25 appear as ClpC1 interaction partners in the BACTH screen, including members of the VapBC, MazEF, and ParDE families, as well as a RelBE member that was identified biochemically. We show that antitoxins of the Vap and Rel families are degraded by ClpCP in vitro. We also demonstrate that ClpCP is responsible for mediating the N-end rule pathway, since the adaptor protein ClpS supports ClpC-dependent degradation of an N-end rule model substrate in vitro.
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Affiliation(s)
- Michal Ziemski
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
| | - Julia Leodolter
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
| | - Gabrielle Taylor
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
| | | | - Eilika Weber-Ban
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
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41
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Fluorescence Methods Applied to the Description of Urea-Dependent YME1L Protease Unfolding. Biomolecules 2020; 10:biom10040656. [PMID: 32340357 PMCID: PMC7226517 DOI: 10.3390/biom10040656] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/25/2022] Open
Abstract
ATP-dependent proteases are ubiquitous across all kingdoms of life and are critical to the maintenance of intracellular protein quality control. The enzymatic function of these enzymes requires structural stability under conditions that may drive instability and/or loss of function in potential protein substrates. Thus, these molecular machines must demonstrate greater stability than their substrates in order to ensure continued function in essential quality control networks. We report here a role for ATP in the stabilization of the inner membrane YME1L protease. Qualitative fluorescence data derived from protein unfolding experiments with urea reveal non-standard protein unfolding behavior that is dependent on [ATP]. Using multiple fluorophore systems, stopped-flow fluorescence experiments demonstrate a depletion of the native YME1L ensemble by urea-dependent unfolding and formation of a non-native conformation. Additional stopped-flow fluorescence experiments based on nucleotide binding and unfoldase activities predict that unfolding yields significant loss of active YME1L hexamers from the starting ensemble. Taken together, these data clearly define the stress limits of an important mitochondrial protease.
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42
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Vassallo A, Palazzotto E, Renzone G, Botta L, Faddetta T, Scaloni A, Puglia AM, Gallo G. The Streptomyces coelicolor Small ORF trpM Stimulates Growth and Morphological Development and Exerts Opposite Effects on Actinorhodin and Calcium-Dependent Antibiotic Production. Front Microbiol 2020; 11:224. [PMID: 32140146 PMCID: PMC7042404 DOI: 10.3389/fmicb.2020.00224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/30/2020] [Indexed: 11/25/2022] Open
Abstract
In actinomycetes, antibiotic production is often associated with a morpho-physiological differentiation program that is regulated by complex molecular and metabolic networks. Many aspects of these regulatory circuits have been already elucidated and many others still deserve further investigations. In this regard, the possible role of many small open reading frames (smORFs) in actinomycete morpho-physiological differentiation is still elusive. In Streptomyces coelicolor, inactivation of the smORF trpM (SCO2038) – whose product modulates L-tryptophan biosynthesis – impairs production of antibiotics and morphological differentiation. Indeed, it was demonstrated that TrpM is able to interact with PepA (SCO2179), a putative cytosol aminopeptidase playing a key role in antibiotic production and sporulation. In this work, a S. coelicolor trpM knock-in (Sco-trpMKI) mutant strain was generated by cloning trpM into overexpressing vector to further investigate the role of trpM in actinomycete growth and morpho-physiological differentiation. Results highlighted that trpM: (i) stimulates growth and actinorhodin (ACT) production; (ii) decreases calcium-dependent antibiotic (CDA) production; (iii) has no effect on undecylprodigiosin production. Metabolic pathways influenced by trpM knock-in were investigated by combining two-difference in gel electrophoresis/nanoliquid chromatography coupled to electrospray linear ion trap tandem mass spectrometry (2D-DIGE/nanoLC-ESI-LIT-MS/MS) and by LC-ESI-MS/MS procedures, respectively. These analyses demonstrated that over-expression of trpM causes an over-representation of factors involved in protein synthesis and nucleotide metabolism as well as a down-representation of proteins involved in central carbon and amino acid metabolism. At the metabolic level, this corresponded to a differential accumulation pattern of different amino acids – including aromatic ones but tryptophan – and central carbon intermediates. PepA was also down-represented in Sco-trpMKI. The latter was produced as recombinant His-tagged protein and was originally proven having the predicted aminopeptidase activity. Altogether, these results highlight the stimulatory effect of trpM in S. coelicolor growth and ACT biosynthesis, which are elicited through the modulation of various metabolic pathways and PepA representation, further confirming the complexity of regulatory networks that control antibiotic production in actinomycetes.
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Affiliation(s)
- Alberto Vassallo
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy.,Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Emilia Palazzotto
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Giovanni Renzone
- Proteomic and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Luigi Botta
- Dipartimento di Ingegneria, Università di Palermo, Palermo, Italy
| | - Teresa Faddetta
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy
| | - Andrea Scaloni
- Proteomic and Mass Spectrometry Laboratory, ISPAAM, National Research Council, Naples, Italy
| | - Anna Maria Puglia
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy
| | - Giuseppe Gallo
- Laboratory of Molecular Microbiology and Biotechnology, STEBICEF Department, University of Palermo, Palermo, Italy
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43
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Steele TE, Glynn SE. Mitochondrial AAA proteases: A stairway to degradation. Mitochondrion 2019; 49:121-127. [PMID: 31377246 DOI: 10.1016/j.mito.2019.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022]
Abstract
Mitochondrial protein quality control requires the action of proteases to remove damaged or unnecessary proteins and perform key regulatory cleavage events. Important components of the quality control network are the mitochondrial AAA proteases, which capture energy from ATP hydrolysis to destabilize and degrade protein substrates on both sides of the inner membrane. Dysfunction of these proteases leads to the breakdown of mitochondrial proteostasis and is linked to the development of severe human diseases. In this review, we will describe recent insights into the structure and motions of the mitochondrial AAA proteases and related enzymes. Together, these studies have revealed the mechanics of ATP-driven protein destruction and significantly advanced our understanding of how these proteases maintain mitochondrial health.
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Affiliation(s)
- Tyler E Steele
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA; Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Steven E Glynn
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA; Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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44
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Abstract
AAA+ proteolytic machines use energy from ATP hydrolysis to degrade damaged, misfolded, or unneeded proteins. Protein degradation occurs within a barrel-shaped self-compartmentalized peptidase. Before protein substrates can enter this peptidase, they must be unfolded and then translocated through the axial pore of an AAA+ ring hexamer. An unstructured region of the protein substrate is initially engaged in the axial pore, and conformational changes in the ring, powered by ATP hydrolysis, generate a mechanical force that pulls on and denatures the substrate. The same conformational changes in the hexameric ring then mediate mechanical translocation of the unfolded polypeptide into the peptidase chamber. For the bacterial ClpXP and ClpAP AAA+ proteases, the mechanical activities of protein unfolding and translocation have been directly visualized by single-molecule optical trapping. These studies in combination with structural and biochemical experiments illuminate many principles that underlie this universal mechanism of ATP-fueled protein unfolding and subsequent destruction.
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Affiliation(s)
- Adrian O Olivares
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Tania A Baker
- Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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Pfiffer V, Sarenko O, Possling A, Hengge R. Genetic dissection of Escherichia coli's master diguanylate cyclase DgcE: Role of the N-terminal MASE1 domain and direct signal input from a GTPase partner system. PLoS Genet 2019; 15:e1008059. [PMID: 31022167 PMCID: PMC6510439 DOI: 10.1371/journal.pgen.1008059] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 05/10/2019] [Accepted: 02/28/2019] [Indexed: 11/18/2022] Open
Abstract
The ubiquitous second messenger c-di-GMP promotes bacterial biofilm formation by playing diverse roles in the underlying regulatory networks. This is reflected in the multiplicity of diguanylate cyclases (DGC) and phosphodiesterases (PDE) that synthesize and degrade c-di-GMP, respectively, in most bacterial species. One of the 12 DGCs of Escherichia coli, DgcE, serves as the top-level trigger for extracellular matrix production during macrocolony biofilm formation. Its multi-domain architecture–a N-terminal membrane-inserted MASE1 domain followed by three PAS, a GGDEF and a degenerate EAL domain–suggested complex signal integration and transmission through DgcE. Genetic dissection of DgcE revealed activating roles for the MASE1 domain and the dimerization-proficient PAS3 region, whereas the inhibitory EALdeg domain counteracts the formation of DgcE oligomers. The MASE1 domain is directly targeted by the GTPase RdcA (YjdA), a dimer or oligomer that together with its partner protein RdcB (YjcZ) activates DgcE, probably by aligning and promoting dimerization of the PAS3 and GGDEF domains. This activation and RdcA/DgcE interaction depend on GTP hydrolysis by RdcA, suggesting GTP as an inhibitor and the pronounced decrease of the cellular GTP pool during entry into stationary phase, which correlates with DgcE-dependent activation of matrix production, as a possible input signal sensed by RdcA. Furthermore, DgcE exhibits rapid, continuous and processive proteolytic turnover that also depends on the relatively disordered transmembrane MASE1 domain. Overall, our study reveals a novel GTP/c-di-GMP-connecting signaling pathway through the multi-domain DGC DgcE with a dual role for the previously uncharacterized MASE1 signaling domain. Biofilms represent a multicellular life form of bacteria, in which large numbers of cells live in communities surrounded and protected by a self-generated extracellular polymeric matrix. As biofilms tolerate antibiotics and host immune systems, they are causally associated with chronic infections. Biofilm formation is generally promoted by the ubiquitous bacterial second messenger c-di-GMP. DgcE, one of the 12 diguanylate cyclases that produce c-di-GMP in E. coli, was previously shown to specifically act as a top level trigger in the regulatory network that drives biofilm matrix production in this bacterium. However, signal input into DgcE itself, which is a large six-domain protein, had remained unknown. Here we demonstrate that DgcE activity is controlled by a novel type of dynamin-like GTPase that directly interacts with the N-terminal membrane-intrinsic MASE1 domain of DgcE. Our finding of a dual function of this MASE1 domain, which is essential for both activation and continuous proteolysis of DgcE, is the first characterization of this widespread bacterial signaling domain. Signal input via the dynamin-like GTPase system suggests that c-di-GMP production by DgcE might be stimulated by the decreasing cellular GTP level during entry into stationary phase, which is precisely the time when biofilm matrix production is turned on.
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Affiliation(s)
- Vanessa Pfiffer
- Institut für Biologie / Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Olga Sarenko
- Institut für Biologie / Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Alexandra Possling
- Institut für Biologie / Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Regine Hengge
- Institut für Biologie / Mikrobiologie, Humboldt-Universität zu Berlin, Berlin, Germany
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46
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Fuchs ACD, Hartmann MD. On the Origins of Symmetry and Modularity in the Proteasome Family. Bioessays 2019; 41:e1800237. [DOI: 10.1002/bies.201800237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/04/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Adrian C. D. Fuchs
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingen Germany
| | - Marcus D. Hartmann
- Department of Protein EvolutionMax Planck Institute for Developmental BiologyTübingen Germany
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47
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Ma X, Wang Y. Anammox bacteria exhibit capacity to withstand long-term starvation stress: A proteomic-based investigation of survival mechanisms. CHEMOSPHERE 2018; 211:952-961. [PMID: 30119026 DOI: 10.1016/j.chemosphere.2018.07.185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/04/2018] [Accepted: 07/30/2018] [Indexed: 06/08/2023]
Abstract
Although anammox bacteria are commonly exposed to long-term starvation during transportation and preservation process, physiological changes in these organisms during long-term starvation are not well understood, nor are the molecular bases of their starvation survival strategies. To reveal survival mechanisms during long-term anaerobic and anoxic starvation (60 days at 20 ± 1 °C), metaproteomic technology was utilized to identify differentially expressed proteins in Candidatus Kuenenia stuttgartiensis. Our results showed that Candidatus Kuenenia stuttgartiensis exhibits a capacity to withstand long-term starvation stress. Although activity decay rates of 0.0129 d-1 and 0.0049 d-1 were observed for anammox sludge in anoxic and anaerobic starvation, the relative abundance of Candidatus Kuenenia stuttgartiensis, the shape of anammox granules, and the fraction of viable cells remained constant under both anaerobic and anoxic starvation conditions. Metaproteomics results illustrated that Candidatus Kuenenia stuttgartiensis maintained stable levels of most intracellular proteins, especially enzymes involved in principal metabolic pathways after 60-d of anaerobic or anoxic starvation, thereby allowing cells to regain metabolic activities once substrates became available. Induction of starvation proteins could be a survival strategy employed by Candidatus Kuenenia stuttgartiensis to resist long-term starvation stresses. During anaerobic starvation, 34 proteins were upregulated, five of which were associated with carbohydrate catabolism and oxidation of organic compounds, thereby increasing potential for utilization of endogenous carbon sources to produce energy. During anoxic starvation, only two proteins were upregulated, which may be attributed to insufficient energy for the synthesis of starvation-induced proteins.
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Affiliation(s)
- Xiao Ma
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Insititue of Pollution Contrl and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, Shanghai Insititue of Pollution Contrl and Ecological Security, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, PR China.
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48
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ClpAP protease is a universal factor that activates the parDE toxin-antitoxin system from a broad host range RK2 plasmid. Sci Rep 2018; 8:15287. [PMID: 30327496 PMCID: PMC6191456 DOI: 10.1038/s41598-018-33726-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/04/2018] [Indexed: 12/12/2022] Open
Abstract
The activity of type II toxin-antitoxin systems (TA), which are responsible for many important features of bacterial cells, is based on the differences between toxin and antitoxin stabilities. The antitoxin lability results from bacterial protease activity. Here, we investigated how particular Escherichia coli cytosolic proteases, namely, Lon, ClpAP, ClpXP, and ClpYQ, affect the stability of both the toxin and antitoxin components of the parDE system from the broad host range plasmid RK2. The results of our in vivo and in vitro experiments show that the ParD antitoxin is degraded by the ClpAP protease, and dsDNA stimulates this process. The ParE toxin is not degraded by any of these proteases and can therefore cause growth inhibition of plasmid-free cells after an unequal plasmid distribution during cell division. We also demonstrate that the ParE toxin interaction with ParD prevents antitoxin proteolysis by ClpAP; however, this interaction does not prevent the ClpAP interaction with ParD. We show that ClpAP protease homologs affect plasmid stability in other bacterial species, indicating that ClpAP is a universal activator of the parDE system and that ParD is a universal substrate for ClpAP.
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49
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Tripathi P, Parijat P, Patel VK, Batra JK. The amino-terminal domain of Mycobacterium tuberculosis ClpB protein plays a crucial role in its substrate disaggregation activity. FEBS Open Bio 2018; 8:1669-1690. [PMID: 30338218 PMCID: PMC6168691 DOI: 10.1002/2211-5463.12509] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/03/2018] [Accepted: 08/08/2018] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is known to persist in extremely hostile environments within host macrophages. The ability to withstand such proteotoxic stress comes from its highly conserved molecular chaperone machinery. ClpB, a unique member of the AAA+ family of chaperones, is responsible for resolving aggregates in Mtb and many other bacterial pathogens. Mtb produces two isoforms of ClpB, a full length and an N-terminally truncated form (ClpB∆N), with the latter arising from an internal translation initiation site. It is not clear why this internal start site is conserved and what role the N-terminal domain (NTD) of Mtb ClpB plays in its function. In the current study, we functionally characterized and compared the two isoforms of Mtb ClpB. We found the NTD to be dispensable for oligomerization, ATPase activity and prevention of aggregation activity of ClpB. Both ClpB and ClpB∆N were found to be capable of resolubilizing protein aggregates. However, the efficiency of ClpB∆N at resolubilizing higher order aggregates was significantly lower than that of ClpB. Further, ClpB∆N exhibited reduced affinity for substrates as compared to ClpB. We also demonstrated that the surface of the NTD of Mtb ClpB has a hydrophobic groove that contains four hydrophobic residues: L97, L101, F140 and V141. These residues act as initial contacts for the substrate and are crucial for stable interaction between ClpB and highly aggregated substrates.
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Affiliation(s)
| | - Priyanka Parijat
- National Institute of ImmunologyNew DelhiIndia
- Present address:
Randall Division of Cell and Molecular BiophysicsKing's College LondonUK
| | | | - Janendra K. Batra
- National Institute of ImmunologyNew DelhiIndia
- Department of BiochemistrySchool of Chemical and Life SciencesJamia HamdardNew DelhiIndia
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He L, Luo D, Yang F, Li C, Zhang X, Deng H, Zhang JR. Multiple domains of bacterial and human Lon proteases define substrate selectivity. Emerg Microbes Infect 2018; 7:149. [PMID: 30120231 PMCID: PMC6098112 DOI: 10.1038/s41426-018-0148-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/16/2018] [Accepted: 06/23/2018] [Indexed: 02/05/2023]
Abstract
The Lon protease selectively degrades abnormal proteins or certain normal proteins in response to environmental and cellular conditions in many prokaryotic and eukaryotic organisms. However, the mechanism(s) behind the substrate selection of normal proteins remains largely unknown. In this study, we identified 10 new substrates of F. tularensis Lon from a total of 21 candidate substrates identified in our previous work, the largest number of novel Lon substrates from a single study. Cross-species degradation of these and other known Lon substrates revealed that human Lon is unable to degrade many bacterial Lon substrates, suggestive of a “organism-adapted” substrate selection mechanism for the natural Lon variants. However, individually replacing the N, A, and P domains of human Lon with the counterparts of bacterial Lon did not enable the human protease to degrade the same bacterial Lon substrates. This result showed that the “organism-adapted” substrate selection depends on multiple domains of the Lon proteases. Further in vitro proteolysis and mass spectrometry analysis revealed a similar substrate cleavage pattern between the bacterial and human Lon variants, which was exemplified by predominant representation of leucine, alanine, and other hydrophobic amino acids at the P(−1) site within the substrates. These observations suggest that the Lon proteases select their substrates at least in part by fine structural matching with the proteins in the same organisms.
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Affiliation(s)
- Lihong He
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China
| | - Dongyang Luo
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Fan Yang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Chunhao Li
- Philip Research Institute for Oral Health, School of Dentistry, Virginia Commonwealth University, Richmond, VA, USA
| | - Xuegong Zhang
- MOE Key Laboratory of Bioinformatics, Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 10084, China
| | - Jing-Ren Zhang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China. .,Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.
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