1
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Omnus DJ, Fink MJ, Kallazhi A, Xandri Zaragoza M, Leppert A, Landreh M, Jonas K. The heat shock protein LarA activates the Lon protease in response to proteotoxic stress. Nat Commun 2023; 14:7636. [PMID: 37993443 PMCID: PMC10665427 DOI: 10.1038/s41467-023-43385-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023] Open
Abstract
The Lon protease is a highly conserved protein degradation machine that has critical regulatory and protein quality control functions in cells from the three domains of life. Here, we report the discovery of a α-proteobacterial heat shock protein, LarA, that functions as a dedicated Lon regulator. We show that LarA accumulates at the onset of proteotoxic stress and allosterically activates Lon-catalysed degradation of a large group of substrates through a five amino acid sequence at its C-terminus. Further, we find that high levels of LarA cause growth inhibition in a Lon-dependent manner and that Lon-mediated degradation of LarA itself ensures low LarA levels in the absence of stress. We suggest that the temporal LarA-dependent activation of Lon helps to meet an increased proteolysis demand in response to protein unfolding stress. Our study defines a regulatory interaction of a conserved protease with a heat shock protein, serving as a paradigm of how protease activity can be tuned under changing environmental conditions.
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Affiliation(s)
- Deike J Omnus
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm, 10691, Sweden
| | - Matthias J Fink
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm, 10691, Sweden
| | - Aswathy Kallazhi
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm, 10691, Sweden
| | - Maria Xandri Zaragoza
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm, 10691, Sweden
| | - Axel Leppert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, 17165, Solna, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solnavägen 9, 17165, Solna, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 751 24, Uppsala, Sweden
| | - Kristina Jonas
- Science for Life Laboratory and Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm, 10691, Sweden.
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2
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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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3
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Son A, Huizar Cabral V, Huang Z, Litberg TJ, Horowitz S. G-quadruplexes rescuing protein folding. Proc Natl Acad Sci U S A 2023; 120:e2216308120. [PMID: 37155907 PMCID: PMC10194009 DOI: 10.1073/pnas.2216308120] [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: 09/23/2022] [Accepted: 04/12/2023] [Indexed: 05/10/2023] Open
Abstract
Maintaining the health of the proteome is a critical cellular task. Recently, we found G-quadruplex (G4) nucleic acids are especially potent at preventing protein aggregation in vitro and could at least indirectly improve the protein folding environment of Escherichia coli. However, the roles of G4s in protein folding were not yet explored. Here, through in vitro protein folding experiments, we discover that G4s can accelerate protein folding by rescuing kinetically trapped intermediates to both native and near-native folded states. Time-course folding experiments in E. coli further demonstrate that these G4s primarily improve protein folding quality in E. coli as opposed to preventing protein aggregation. The ability of a short nucleic acid to rescue protein folding opens up the possibility of nucleic acids and ATP-independent chaperones to play considerable roles in dictating the ultimate folding fate of proteins.
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Affiliation(s)
- Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Veronica Huizar Cabral
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Zijue Huang
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Theodore J. Litberg
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO80208
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4
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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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5
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Menacho-Melgar R, Ye Z, Moreb EA, Yang T, Efromson JP, Decker JS, Wang R, Lynch MD. Scalable, two-stage, autoinduction of recombinant protein expression in E. coli utilizing phosphate depletion. Biotechnol Bioeng 2020; 117:2715-2727. [PMID: 32441815 DOI: 10.1002/bit.27440] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 12/24/2022]
Abstract
We report the scalable production of recombinant proteins in Escherichia coli, reliant on tightly controlled autoinduction, triggered by phosphate depletion in the stationary phase. The method, reliant on engineered strains and plasmids, enables improved protein expression across scales. Expression levels using this approach have reached as high as 55% of the total cellular protein. The initial use of the method in instrumented fed-batch fermentations enables cell densities of ∼30 gCDW/L and protein titers up to 8.1 ± 0.7 g/L (∼270 mg/gCDW). The process has also been adapted to an optimized autoinduction media, enabling routine batch production at culture volumes of 20 μl (384-well plates), 100 μl (96-well plates), 20 ml, and 100 ml. In batch cultures, cell densities routinely reach ∼5-7 gCDW/L, offering protein titers above 2 g/L. The methodology has been validated with a set of diverse heterologous proteins and is of general use for the facile optimization of routine protein expression from high throughput screens to fed-batch fermentation.
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Affiliation(s)
| | - Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Eirik A Moreb
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Tian Yang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - John P Efromson
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - John S Decker
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Ruixin Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
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6
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Wang Y, Wang H, Tran MV, Algar WR, Li H. Yellow fluorescent protein-based label-free tension sensors for monitoring integrin tension. Chem Commun (Camb) 2020; 56:5556-5559. [DOI: 10.1039/d0cc01635g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Yellow fluorescent protein serves as a label-free tension sensor to monitor integrin tension.
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Affiliation(s)
- Yongliang Wang
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - Han Wang
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - Michael V. Tran
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - W. Russ Algar
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
| | - Hongbin Li
- Department of Chemistry
- University of British Columbia
- Vancouver
- Canada
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7
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Yang Y, Gunasekara M, Muhammednazaar S, Li Z, Hong H. Proteolysis mediated by the membrane-integrated ATP-dependent protease FtsH has a unique nonlinear dependence on ATP hydrolysis rates. Protein Sci 2019; 28:1262-1275. [PMID: 31008538 DOI: 10.1002/pro.3629] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/17/2019] [Indexed: 12/16/2022]
Abstract
ATPases associated with diverse cellular activities (AAA+) proteases utilize ATP hydrolysis to actively unfold native or misfolded proteins and translocate them into a protease chamber for degradation. This basic mechanism yields diverse cellular consequences, including the removal of misfolded proteins, control of regulatory circuits, and remodeling of protein conformation. Among various bacterial AAA+ proteases, FtsH is only membrane-integrated and plays a key role in membrane protein quality control. Previously, we have shown that FtsH has substantial unfoldase activity for degrading membrane proteins overcoming a dual energetic burden of substrate unfolding and membrane dislocation. Here, we asked how efficiently FtsH utilizes ATP hydrolysis to degrade membrane proteins. To answer this question, we measured degradation rates of the model membrane substrate GlpG at various ATP hydrolysis rates in the lipid bilayers. We find that the dependence of degradation rates on ATP hydrolysis rates is highly nonlinear: (i) FtsH cannot degrade GlpG until it reaches a threshold ATP hydrolysis rate; (ii) after exceeding the threshold, the degradation rates steeply increase and saturate at the ATP hydrolysis rates far below the maxima. During the steep increase, FtsH efficiently utilizes ATP hydrolysis for degradation, consuming only 40-60% of the total ATP cost measured at the maximal ATP hydrolysis rates. This behavior does not fundamentally change against water-soluble substrates as well as upon addition of the macromolecular crowding agent Ficoll 70. The Hill analysis shows that the nonlinearity stems from coupling of three to five ATP hydrolysis events to degradation, which represents unique cooperativity compared to other AAA+ proteases including ClpXP, HslUV, Lon, and proteasomes.
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Affiliation(s)
- Yiqing Yang
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | - Mihiravi Gunasekara
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | | | - Zhen Li
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, 48824
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8
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Fernández-Fernández ÁD, Van der Hoorn RAL, Gevaert K, Van Breusegem F, Stael S. Caught green-handed: methods for in vivo detection and visualization of protease activity. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2125-2141. [PMID: 30805604 DOI: 10.1093/jxb/erz076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/25/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Proteases are enzymes that cleave peptide bonds of other proteins. Their omnipresence and diverse activities make them important players in protein homeostasis and turnover of the total cell proteome as well as in signal transduction in plant stress responses and development. To understand protease function, it is of paramount importance to assess when and where a specific protease is active. Here, we review the existing methods to detect in vivo protease activity by means of imaging chemical activity-based probes and genetically encoded sensors. We focus on the diverse fluorescent and luminescent sensors at the researcher's disposal and evaluate the potential of imaging techniques to deliver in vivo spatiotemporal detail of protease activity. We predict that in the coming years, revised techniques will help to elucidate plant protease activity and functions and hence expand the current status of the field.
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Affiliation(s)
- Álvaro Daniel Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Simon Stael
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
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9
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Ding B, Martin DW, Rampello AJ, Glynn SE. Dissecting Substrate Specificities of the Mitochondrial AFG3L2 Protease. Biochemistry 2018; 57:4225-4235. [PMID: 29932645 DOI: 10.1021/acs.biochem.8b00565] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. Identifying how AFG3L2 selects substrates from the diverse complement of matrix-localized proteins is essential for understanding mitochondrial protein biogenesis and quality control. Here, we create solubilized forms of AFG3L2 to examine the enzyme's substrate specificity mechanisms. We show that conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form. Moreover, these residues can act as a degron, delivering diverse model proteins to AFG3L2 for degradation. By determining the sequence of degradation products from multiple substrates using mass spectrometry, we construct a peptidase specificity profile that displays constrained product lengths and is dominated by the identity of the residue at the P1' position, with a strong preference for hydrophobic and small polar residues. This specificity profile is validated by examining the cleavage of both fluorogenic reporter peptides and full polypeptide substrates bearing different P1' residues. Together, these results demonstrate that AFG3L2 contains multiple modes of specificity, discriminating between potential substrates by recognizing accessible degron sequences and performing peptide bond cleavage at preferred patterns of residues within the compartmental chamber.
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10
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Yang Y, Guo R, Gaffney K, Kim M, Muhammednazaar S, Tian W, Wang B, Liang J, Hong H. Folding-Degradation Relationship of a Membrane Protein Mediated by the Universally Conserved ATP-Dependent Protease FtsH. J Am Chem Soc 2018. [PMID: 29528632 DOI: 10.1021/jacs.8b00832] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
ATP-dependent protein degradation mediated by AAA+ proteases is one of the major cellular pathways for protein quality control and regulation of functional networks. While a majority of studies of protein degradation have focused on water-soluble proteins, it is not well understood how membrane proteins with abnormal conformation are selectively degraded. The knowledge gap stems from the lack of an in vitro system in which detailed molecular mechanisms can be studied as well as difficulties in studying membrane protein folding in lipid bilayers. To quantitatively define the folding-degradation relationship of membrane proteins, we reconstituted the degradation using the conserved membrane-integrated AAA+ protease FtsH as a model degradation machine and the stable helical-bundle membrane protein GlpG as a model substrate in the lipid bilayer environment. We demonstrate that FtsH possesses a substantial ability to actively unfold GlpG, and the degradation significantly depends on the stability and hydrophobicity near the degradation marker. We find that FtsH hydrolyzes 380-550 ATP molecules to degrade one copy of GlpG. Remarkably, FtsH overcomes the dual-energetic burden of substrate unfolding and membrane dislocation with the ATP cost comparable to that for water-soluble substrates by robust ClpAP/XP proteases. The physical principles elucidated in this study provide general insights into membrane protein degradation mediated by ATP-dependent proteolytic systems.
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Affiliation(s)
| | | | | | | | | | - Wei Tian
- Department of Bioengineering , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - Boshen Wang
- Department of Bioengineering , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
| | - Jie Liang
- Department of Bioengineering , University of Illinois at Chicago , Chicago , Illinois 60607 , United States
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11
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Puri N, Karzai AW. HspQ Functions as a Unique Specificity-Enhancing Factor for the AAA+ Lon Protease. Mol Cell 2017; 66:672-683.e4. [PMID: 28575662 DOI: 10.1016/j.molcel.2017.05.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/24/2017] [Accepted: 05/16/2017] [Indexed: 11/26/2022]
Abstract
The AAA+ Lon protease is conserved from bacteria to humans, performs crucial roles in protein homeostasis, and is implicated in bacterial pathogenesis and human disease. We investigated how Lon selectively degrades specific substrates among a diverse array of potential targets. We report the discovery of HspQ as a new Lon substrate, unique specificity-enhancing factor, and potent allosteric activator. Lon recognizes HspQ via a C-terminal degron, whose precise presentation, in synergy with multipartite contacts with the native core of HspQ, is required for allosteric Lon activation. Productive HspQ-Lon engagement enhances degradation of multiple new and known Lon substrates. Our studies reveal the existence and simultaneous utilization of two distinct substrate recognition sites on Lon, an HspQ binding site and an HspQ-modulated allosteric site. Our investigations unveil an unprecedented regulatory use of an evolutionarily conserved heat shock protein and present a distinctive mechanism for how Lon protease achieves temporally enhanced substrate selectivity.
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Affiliation(s)
- Neha Puri
- Department of Biochemistry and Cell Biology, Center for Infectious Diseases, Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - A Wali Karzai
- Department of Biochemistry and Cell Biology, Center for Infectious Diseases, Graduate Program in Molecular and Cellular Biology, Stony Brook University, Stony Brook, NY 11794, USA.
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12
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Shi H, Rampello AJ, Glynn SE. Engineered AAA+ proteases reveal principles of proteolysis at the mitochondrial inner membrane. Nat Commun 2016; 7:13301. [PMID: 27786171 PMCID: PMC5095350 DOI: 10.1038/ncomms13301] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 09/20/2016] [Indexed: 12/17/2022] Open
Abstract
The human YME1L protease is a membrane-anchored AAA+ enzyme that controls proteostasis at the inner membrane and intermembrane space of mitochondria. Understanding how YME1L recognizes substrates and catalyses ATP-dependent degradation has been hampered by the presence of an insoluble transmembrane anchor that drives hexamerization of the catalytic domains to form the ATPase active sites. Here, we overcome this limitation by replacing the transmembrane domain with a soluble hexameric coiled coil to produce active YME1L hexamers that can be studied in vitro. We use these engineered proteases to reveal principles of substrate processing by YME1L. Degradation by YME1L requires substrates to present an accessible signal sequence and is not initiated simply by substrate unfolding. The protease is also capable of processively unfolding substrate proteins with substantial thermodynamic stabilities. Lastly, we show that YME1L discriminates between degradation signals by amino acid composition, implying the use of sequence-specific signals in mitochondrial proteostasis. Human YME1L is a membrane-anchored AAA+ protease that maintains proteostasis in the mitochondrial inner membrane and intermembrane space. Here the authors probe the substrate-binding and degradation activities of YME1L and suggest the existence of sequence-specific degradation signals in mitochondrial proteostasis.
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Affiliation(s)
- Hui Shi
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA
| | - Anthony J Rampello
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA
| | - Steven E Glynn
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA
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13
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Baytshtok V, Fei X, Grant RA, Baker TA, Sauer RT. A Structurally Dynamic Region of the HslU Intermediate Domain Controls Protein Degradation and ATP Hydrolysis. Structure 2016; 24:1766-1777. [PMID: 27667691 DOI: 10.1016/j.str.2016.08.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/02/2016] [Accepted: 08/06/2016] [Indexed: 11/30/2022]
Abstract
The I domain of HslU sits above the AAA+ ring and forms a funnel-like entry to the axial pore, where protein substrates are engaged, unfolded, and translocated into HslV for degradation. The L199Q I-domain substitution, which was originally reported as a loss-of-function mutation, resides in a segment that appears to adopt multiple conformations as electron density is not observed in HslU and HslUV crystal structures. The L199Q sequence change does not alter the structure of the AAA+ ring or its interactions with HslV but increases I-domain susceptibility to limited endoproteolysis. Notably, the L199Q mutation increases the rate of ATP hydrolysis substantially, results in slower degradation of some proteins but faster degradation of other substrates, and markedly changes the preference of HslUV for initiating degradation at the N or C terminus of model substrates. Thus, a structurally dynamic region of the I domain plays a key role in controlling protein degradation by HslUV.
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Affiliation(s)
- Vladimir Baytshtok
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Xue Fei
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert A Grant
- 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; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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14
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Bhattacharyya S, Renn JP, Yu H, Marko JF, Matouschek A. An assay for 26S proteasome activity based on fluorescence anisotropy measurements of dye-labeled protein substrates. Anal Biochem 2016; 509:50-59. [PMID: 27296635 DOI: 10.1016/j.ab.2016.05.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/13/2016] [Accepted: 05/31/2016] [Indexed: 12/12/2022]
Abstract
The 26S proteasome is the molecular machine at the center of the ubiquitin proteasome system and is responsible for adjusting the concentrations of many cellular proteins. It is a drug target in several human diseases, and assays for the characterization of modulators of its activity are valuable. The 26S proteasome consists of two components: a core particle, which contains the proteolytic sites, and regulatory caps, which contain substrate receptors and substrate processing enzymes, including six ATPases. Current high-throughput assays of proteasome activity use synthetic fluorogenic peptide substrates that report directly on the proteolytic activity of the proteasome, but not on the activities of the proteasome caps that are responsible for protein recognition and unfolding. Here, we describe a simple and robust assay for the activity of the entire 26S proteasome using fluorescence anisotropy to follow the degradation of fluorescently labeled protein substrates. We describe two implementations of the assay in a high-throughput format and show that it meets the expected requirement of ATP hydrolysis and the presence of a canonical degradation signal or degron in the target protein.
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Affiliation(s)
| | - Jonathan P Renn
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Houqing Yu
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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15
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The Protease Locus of Francisella tularensis LVS Is Required for Stress Tolerance and Infection in the Mammalian Host. Infect Immun 2016; 84:1387-1402. [PMID: 26902724 DOI: 10.1128/iai.00076-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 02/12/2016] [Indexed: 02/05/2023] Open
Abstract
Francisella tularensis is the causative agent of tularemia and a category A potential agent of bioterrorism, but the pathogenic mechanisms of F. tularensis are largely unknown. Our previous transposon mutagenesis screen identified 95 lung infectivity-associated F. tularensis genes, including those encoding the Lon and ClpP proteases. The present study validates the importance of Lon and ClpP in intramacrophage growth and infection of the mammalian host by using unmarked deletion mutants of the F. tularensis live vaccine strain (LVS). Further experiments revealed that lon and clpP are also required for F. tularensis tolerance to stressful conditions. A quantitative proteomic comparison between heat-stressed LVS and the isogenic Lon-deficient mutant identified 29 putative Lon substrate proteins. The follow-up protein degradation experiments identified five substrates of the F. tularensis Lon protease (FTL578, FTL663, FTL1217, FTL1228, and FTL1957). FTL578 (ornithine cyclodeaminase), FTL663 (heat shock protein), and FTL1228 (iron-sulfur activator complex subunit SufD) have been previously described as virulence-associated factors in F. tularensis Identification of these Lon substrates has thus provided important clues for further understanding of the F. tularensis stress response and pathogenesis. The high-throughput approach developed in this study can be used for systematic identification of the Lon substrates in other prokaryotic and eukaryotic organisms.
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16
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Martinez-Fonts K, Matouschek A. A Rapid and Versatile Method for Generating Proteins with Defined Ubiquitin Chains. Biochemistry 2016; 55:1898-908. [PMID: 26943792 DOI: 10.1021/acs.biochem.5b01310] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ubiquitin and polyubiquitin chains target proteins for a wide variety of cellular processes. Ubiquitin-mediated targeting is regulated by the lysine through which the ubiquitins are linked as well as the broader ubiquitin landscape on the protein. The mechanisms of this regulation are not fully understood. For example, the canonical proteasome targeting signal is a lysine 48-linked polyubiquitin chain, and the canonical endocytosis signal is a lysine 63-linked polyubiquitin chain. However, lysine 63-linked polyubiquitin chains can also target substrates for degradation. Biochemical studies of ubiquitinated proteins have been limited by the difficulty of building proteins with well-defined polyubiquitin chains. Here we describe an efficient and versatile method for synthesizing ubiquitin chains of defined linkage and length. The synthesized ubiquitin chains are then attached to any protein containing a ubiquitin moiety. These proteins can be used to study ubiquitin targeting in in vitro assays in the tightly controlled manner required for biochemical studies.
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Affiliation(s)
- Kirby Martinez-Fonts
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States.,Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States.,Department of Molecular Biosciences, Northwestern University , Evanston, Illinois 60208, United States
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17
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Wang Z, Li S, Li J, Li J, Rong L, Cheng B, Fan J. Engineering uroporphyrinogen III methyltransferase as a red fluorescent reporter in E. coli. Enzyme Microb Technol 2014; 61-62:1-6. [PMID: 24910329 DOI: 10.1016/j.enzmictec.2014.03.004] [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: 10/10/2013] [Revised: 03/04/2014] [Accepted: 03/06/2014] [Indexed: 11/22/2022]
Abstract
Uroporphyrinogen III methyltransferase (UMT) is a novel reporter owing to the catalytic products in the cells that emit strong red fluorescence under UV light. Here, we engineered the gene encoding the functional barley UMT (bUMT) by error-prone PCR and broadened the application UMT as a red fluorescent reporter in Escherichia coli. A variant, termed mbUMT, was selected and emitted stronger cell fluorescence than the wild type bUMT expressed in different E. coli strains, under different promoters and induction conditions respectively. The constructed mbUMT with a C-terminal ssrA tag was degraded in cells by the protease ClpXP encoded by E. coli chromosome, whereas the bUMT was expressed as active aggregates. Before they are exported to the periplasm, both proteins catalyze the substrate in the cytoplasm and emit cell fluorescence. The results suggested that the evolved bUMT is a better candidate to monitor in vivo degradation by E. coli ClpXP.
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Affiliation(s)
- Zhenzhen Wang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Si Li
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Jing Li
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Jingjing Li
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Liang Rong
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Beijiu Cheng
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China
| | - Jun Fan
- School of Life Science, Anhui Agricultural University, Hefei, Anhui 230036, PR China.
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18
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Nie X, Li M, Lu B, Zhang Y, Lan L, Chen L, Lu J. Down-regulating overexpressed human Lon in cervical cancer suppresses cell proliferation and bioenergetics. PLoS One 2013; 8:e81084. [PMID: 24260536 PMCID: PMC3834287 DOI: 10.1371/journal.pone.0081084] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 10/08/2013] [Indexed: 01/14/2023] Open
Abstract
The human mitochondrial ATP-dependent Lon protease functions in regulating the metabolism and quality control of proteins and mitochondrial DNA (mtDNA). However, the role of Lon in cancer is not well understood. Therefore, this study was undertaken to investigate the importance of Lon in cervical cancer cells from patients and in established cell lines. Microarray analysis from 30 cancer and 10 normal cervical tissues were analyzed by immunohistochemistry for Lon protein levels. The expression of Lon was also examined by immunoblotting 16 fresh cervical cancer tissues and their respective non-tumor cervical tissues. In all cases, Lon expression was significantly elevated in cervical carcinomas as compared to normal tissues. Augmented Lon expression in tissue microarrays did not vary between age, tumor-node-metastasis grades, or lymph node metastasis. Knocking down Lon in HeLa cervical cancer cells by lentivrial transduction resulted in a substantial decrease in both mRNA and protein levels. Such down-regulation of Lon expression significantly blocked HeLa cell proliferation. In addition, knocking down Lon resulted in decreased cellular bioenergetics as determined by measuring aerobic respiration and glycolysis using the Seahorse XF24 extracellular flux analyzer. Together, these data demonstrate that Lon plays a potential role in the oncogenesis of cervical cancer, and may be a useful biomarker and target in the treatment of cervical cancer. Lon; immunohistochemistry; cervical cancer; cell proliferation; cellular bioenergetics.
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Affiliation(s)
- Xiaobo Nie
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China ; Department of Biochemistry and Molecular Biology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, New Jersey, United States of America
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19
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Wohlever ML, Baker TA, Sauer RT. Roles of the N domain of the AAA+ Lon protease in substrate recognition, allosteric regulation and chaperone activity. Mol Microbiol 2013; 91:66-78. [PMID: 24205897 DOI: 10.1111/mmi.12444] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2013] [Indexed: 12/14/2022]
Abstract
Degron binding regulates the activities of the AAA+ Lon protease in addition to targeting proteins for degradation. The sul20 degron from the cell-division inhibitor SulA is shown here to bind to the N domain of Escherichia coli Lon, and the recognition site is identified by cross-linking and scanning for mutations that prevent sul20-peptide binding. These N-domain mutations limit the rates of proteolysis of model sul20-tagged substrates and ATP hydrolysis by an allosteric mechanism. Lon inactivation of SulA in vivo requires binding to the N domain and robust ATP hydrolysis but does not require degradation or translocation into the proteolytic chamber. Lon-mediated relief of proteotoxic stress and protein aggregation in vivo can also occur without degradation but is not dependent on robust ATP hydrolysis. In combination, these results demonstrate that Lon can function as a protease or a chaperone and reveal that some of its ATP-dependent biological activities do not require translocation.
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Affiliation(s)
- Matthew L Wohlever
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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20
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A mutation in the N domain of Escherichia coli lon stabilizes dodecamers and selectively alters degradation of model substrates. J Bacteriol 2013; 195:5622-8. [PMID: 24123818 DOI: 10.1128/jb.00886-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli Lon, an ATP-dependent AAA(+) protease, recognizes and degrades many different substrates, including the RcsA and SulA regulatory proteins. More than a decade ago, the E240K mutation in the N domain of Lon was shown to prevent degradation of RcsA but not SulA in vivo. Here, we characterize the biochemical properties of the E240K mutant in vitro and present evidence that the effects of this mutation are complex. For example, Lon(E240K) exists almost exclusively as a dodecamer, whereas wild-type Lon equilibrates between hexamers and dodecamers. Moreover, Lon(E240K) displays degradation defects in vitro that do not correlate in any simple fashion with degron identity, substrate stability, or dodecamer formation. The Lon sequence segment near residue 240 is known to undergo nucleotide-dependent conformational changes, and our results suggest that this region may be important for coupling substrate binding with allosteric activation of Lon protease and ATPase activity.
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