1
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Zhao X, Gao Y, Gong Q, Zhang K, Li S. Elucidating the Architectural dynamics of MuB filaments in bacteriophage Mu DNA transposition. Nat Commun 2024; 15:6445. [PMID: 39085263 PMCID: PMC11292022 DOI: 10.1038/s41467-024-50722-1] [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: 02/19/2024] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
MuB is a non-specific DNA-binding protein and AAA+ ATPase that significantly influences the DNA transposition process of bacteriophage Mu, especially in target DNA selection for transposition. While studies have established the ATP-dependent formation of MuB filament as pivotal to this process, the high-resolution structure of a full-length MuB protomer and the underlying molecular mechanisms governing its oligomerization remain elusive. Here, we use cryo-EM to obtain a 3.4-Å resolution structure of the ATP(+)-DNA(+)-MuB helical filament, which encapsulates the DNA substrate within its axial channel. The structure categorizes MuB within the initiator clade of the AAA+ protein family and precisely locates the ATP and DNA binding sites. Further investigation into the oligomeric states of MuB show the existence of various forms of the filament. These findings lead to a mechanistic model where MuB forms opposite helical filaments along the DNA, exposing potential target sites on the bare DNA and then recruiting MuA, which stimulates MuB's ATPase activity and disrupts the previously formed helical structure. When this happens, MuB generates larger ring structures and dissociates from the DNA.
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Affiliation(s)
- Xiaolong Zhao
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yongxiang Gao
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qingguo Gong
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Kaiming Zhang
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Shanshan Li
- Department of Urology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Cellular Dynamics, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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2
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Lampe GD, King RT, Halpin-Healy TS, Klompe SE, Hogan MI, Vo PLH, Tang S, Chavez A, Sternberg SH. Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases. Nat Biotechnol 2024; 42:87-98. [PMID: 36991112 PMCID: PMC10620015 DOI: 10.1038/s41587-023-01748-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/13/2023] [Indexed: 03/31/2023]
Abstract
Conventional genome engineering with CRISPR-Cas9 creates double-strand breaks (DSBs) that lead to undesirable byproducts and reduce product purity. Here we report an approach for programmable integration of large DNA sequences in human cells that avoids the generation of DSBs by using Type I-F CRISPR-associated transposases (CASTs). We optimized DNA targeting by the QCascade complex through protein design and developed potent transcriptional activators by exploiting the multi-valent recruitment of the AAA+ ATPase TnsC to genomic sites targeted by QCascade. After initial detection of plasmid-based integration, we screened 15 additional CAST systems from a wide range of bacterial hosts, identified a homolog from Pseudoalteromonas that exhibits improved activity and further increased integration efficiencies. Finally, we discovered that bacterial ClpX enhances genomic integration by multiple orders of magnitude, likely by promoting active disassembly of the post-integration CAST complex, akin to its known role in Mu transposition. Our work highlights the ability to reconstitute complex, multi-component machineries in human cells and establishes a strong foundation to exploit CRISPR-associated transposases for eukaryotic genome engineering.
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Affiliation(s)
- George D Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Rebeca T King
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tyler S Halpin-Healy
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA
| | - Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Marcus I Hogan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Phuc Leo H Vo
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA
- Vertex Pharmaceuticals, Inc., Boston, MA, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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3
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Lampe GD, King RT, Halpin-Healy TS, Klompe SE, Hogan MI, Vo PLH, Tang S, Chavez A, Sternberg SH. Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533036. [PMID: 36993517 PMCID: PMC10055298 DOI: 10.1101/2023.03.17.533036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Traditional genome-editing reagents such as CRISPR-Cas9 achieve targeted DNA modification by introducing double-strand breaks (DSBs), thereby stimulating localized DNA repair by endogenous cellular repair factors. While highly effective at generating heterogenous knockout mutations, this approach suffers from undesirable byproducts and an inability to control product purity. Here we develop a system in human cells for programmable, DSB-free DNA integration using Type I CRISPR-associated transposons (CASTs). To adapt our previously described CAST systems, we optimized DNA targeting by the QCascade complex through a comprehensive assessment of protein design, and we developed potent transcriptional activators by exploiting the multi-valent recruitment of the AAA+ ATPase, TnsC, to genomic sites targeted by QCascade. After initial detection of plasmid-based transposition, we screened 15 homologous CAST systems from a wide range of bacterial hosts, identified a CAST homolog from Pseudoalteromonas that exhibited improved activity, and increased integration efficiencies through parameter optimization. We further discovered that bacterial ClpX enhances genomic integration by multiple orders of magnitude, and we propose that this critical accessory factor functions to drive active disassembly of the post-transposition CAST complex, akin to its demonstrated role in Mu transposition. Our work highlights the ability to functionally reconstitute complex, multi-component machineries in human cells, and establishes a strong foundation to realize the full potential of CRISPR-associated transposons for human genome engineering.
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Affiliation(s)
- George D Lampe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Rebeca T King
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tyler S Halpin-Healy
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Sanne E Klompe
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Marcus I Hogan
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Phuc Leo H Vo
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, USA
| | - Stephen Tang
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alejandro Chavez
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Samuel H Sternberg
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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4
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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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5
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Vos MR, Piraino B, LaBreck CJ, Rahmani N, Trebino CE, Schoenle M, Peti W, Camberg JL, Page R. Degradation of the E. coli antitoxin MqsA by the proteolytic complex ClpXP is regulated by zinc occupancy and oxidation. J Biol Chem 2021; 298:101557. [PMID: 34974059 PMCID: PMC8808172 DOI: 10.1016/j.jbc.2021.101557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 11/19/2022] Open
Abstract
It is well established that the antitoxins of toxin-antitoxin (TA) systems are selectively degraded by bacterial proteases in response to stress. However, how distinct stressors result in the selective degradation of specific antitoxins remains unanswered. MqsRA is a TA system activated by various stresses, including oxidation. Here, we reconstituted the Escherichia coli ClpXP proteolytic machinery in vitro to monitor degradation of MqsRA TA components. We show that the MqsA antitoxin is a ClpXP proteolysis substrate, and that its degradation is regulated by both zinc occupancy in MqsA and MqsR toxin binding. Using NMR chemical shift perturbation mapping, we show that MqsA is targeted directly to ClpXP via the ClpX substrate targeting N-domain, and ClpX mutations that disrupt N-domain binding inhibit ClpXP mediated degradation in vitro. Finally, we discovered that MqsA contains a cryptic N-domain recognition sequence that is accessible only in the absence of zinc and MqsR toxin, both of which stabilize the MqsA fold. This recognition sequence is transplantable and sufficient to target a fusion protein for degradation in vitro and in vivo. Based on these results, we propose a model in which stress selectively targets nascent, zinc-free MqsA, resulting in exposure of the ClpX recognition motif for ClpXP mediated degradation.
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Affiliation(s)
- Margaret R Vos
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, USA; Graduate Program in Molecular Biology and Biochemistry, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Benjamin Piraino
- Department of Cell & Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Christopher J LaBreck
- Department of Cell & Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Negar Rahmani
- Department of Cell & Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Catherine E Trebino
- Department of Cell & Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA
| | - Marta Schoenle
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Jodi L Camberg
- Department of Cell & Molecular Biology, The University of Rhode Island, Kingston, Rhode Island, USA.
| | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut, USA.
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6
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Rasila TS, Pulkkinen E, Kiljunen S, Haapa-Paananen S, Pajunen MI, Salminen A, Paulin L, Vihinen M, Rice PA, Savilahti H. Mu transpososome activity-profiling yields hyperactive MuA variants for highly efficient genetic and genome engineering. Nucleic Acids Res 2019; 46:4649-4661. [PMID: 29294068 PMCID: PMC5961161 DOI: 10.1093/nar/gkx1281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/21/2017] [Indexed: 11/22/2022] Open
Abstract
The phage Mu DNA transposition system provides a versatile species non-specific tool for molecular biology, genetic engineering and genome modification applications. Mu transposition is catalyzed by MuA transposase, with DNA cleavage and integration reactions ultimately attaching the transposon DNA to target DNA. To improve the activity of the Mu DNA transposition machinery, we mutagenized MuA protein and screened for hyperactivity-causing substitutions using an in vivo assay. The individual activity-enhancing substitutions were mapped onto the MuA–DNA complex structure, containing a tetramer of MuA transposase, two Mu end segments and a target DNA. This analysis, combined with the varying effect of the mutations in different assays, implied that the mutations exert their effects in several ways, including optimizing protein–protein and protein–DNA contacts. Based on these insights, we engineered highly hyperactive versions of MuA, by combining several synergistically acting substitutions located in different subdomains of the protein. Purified hyperactive MuA variants are now ready for use as second-generation tools in a variety of Mu-based DNA transposition applications. These variants will also widen the scope of Mu-based gene transfer technologies toward medical applications such as human gene therapy. Moreover, the work provides a platform for further design of custom transposases.
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Affiliation(s)
- Tiina S Rasila
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland.,Institute of Biotechnology, Viikki Biocenter, P. O. Box 56, FI-00014 University of Helsinki, Helsinki, Finland
| | - Elsi Pulkkinen
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland
| | - Saija Kiljunen
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland
| | - Saija Haapa-Paananen
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland
| | - Maria I Pajunen
- Division of Biochemistry and Biotechnology, Department of Biosciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Anu Salminen
- Department of Biochemistry, FI-20014 University of Turku, Turku, Finland
| | - Lars Paulin
- Institute of Biotechnology, Viikki Biocenter, P. O. Box 56, FI-00014 University of Helsinki, Helsinki, Finland
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Harri Savilahti
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland.,Institute of Biotechnology, Viikki Biocenter, P. O. Box 56, FI-00014 University of Helsinki, Helsinki, Finland
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7
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LaBreck CJ, May S, Viola MG, Conti J, Camberg JL. The Protein Chaperone ClpX Targets Native and Non-native Aggregated Substrates for Remodeling, Disassembly, and Degradation with ClpP. Front Mol Biosci 2017; 4:26. [PMID: 28523271 PMCID: PMC5415555 DOI: 10.3389/fmolb.2017.00026] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/07/2017] [Indexed: 01/21/2023] Open
Abstract
ClpX is a member of the Clp/Hsp100 family of ATP-dependent chaperones and partners with ClpP, a compartmentalized protease, to degrade protein substrates bearing specific recognition signals. ClpX targets specific proteins for degradation directly or with substrate-specific adaptor proteins. Native substrates of ClpXP include proteins that form large oligomeric assemblies, such as MuA, FtsZ, and Dps in Escherichia coli. To remodel large oligomeric substrates, ClpX utilizes multivalent targeting strategies and discriminates between assembled and unassembled substrate conformations. Although ClpX and ClpP are known to associate with protein aggregates in E. coli, a potential role for ClpXP in disaggregation remains poorly characterized. Here, we discuss strategies utilized by ClpX to recognize native and non-native protein aggregates and the mechanisms by which ClpX alone, and with ClpP, remodels the conformations of various aggregates. We show that ClpX promotes the disassembly and reactivation of aggregated Gfp-ssrA through specific substrate remodeling. In the presence of ClpP, ClpX promotes disassembly and degradation of aggregated substrates bearing specific ClpX recognition signals, including heat-aggregated Gfp-ssrA, as well as polymeric and heat-aggregated FtsZ, which is a native ClpXP substrate in E. coli. Finally, we show that ClpX is present in insoluble aggregates and prevents the accumulation of thermal FtsZ aggregates in vivo, suggesting that ClpXP participates in the management of aggregates bearing ClpX recognition signals.
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Affiliation(s)
- Christopher J LaBreck
- Department of Cell and Molecular Biology, University of Rhode IslandKingston, RI, USA
| | - Shannon May
- Department of Cell and Molecular Biology, University of Rhode IslandKingston, RI, USA
| | - Marissa G Viola
- Department of Cell and Molecular Biology, University of Rhode IslandKingston, RI, USA
| | - Joseph Conti
- Department of Cell and Molecular Biology, University of Rhode IslandKingston, RI, USA
| | - Jodi L Camberg
- Department of Cell and Molecular Biology, University of Rhode IslandKingston, RI, USA
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8
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Strain-Dependent Recognition of a Unique Degradation Motif by ClpXP in Streptococcus mutans. mSphere 2016; 1:mSphere00287-16. [PMID: 27981232 PMCID: PMC5143411 DOI: 10.1128/msphere.00287-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/09/2016] [Indexed: 01/02/2023] Open
Abstract
Regulated proteolysis in bacteria is an important biological process that maintains protein homeostasis. ClpXP, an intracellular proteolytic complex, is the primary protease that is responsible for protein turnover. While the substrates for ClpXP were identified in Escherichia coli, the substrates for vast majority of bacteria are currently unknown. In this study, we identified a unique substrate for ClpXP-mediated degradation in Streptococcus mutans, a dental pathogen. We also found that a small motif composed of 3 amino acids is sufficient for ClpXP-mediated degradation. Identification of this motif will clearly help us to understand the pathogenesis of this organism and other related pathogens. Streptococcus mutans, a dental pathogen, has a remarkable ability to cope with environmental stresses. Under stress conditions, cytoplasmic proteases play a major role in controlling the stability of regulatory proteins and preventing accumulation of damaged and misfolded proteins. ClpXP, a well-conserved cytoplasmic proteolytic system, is crucial in maintaining cellular homeostasis in bacteria. ClpX is primarily responsible for recognition of substrates and subsequent translocation of unfolded substrates into the ClpP proteolytic compartment for degradation. In Escherichia coli, ClpX recognizes distinct motifs present at the C-terminal end of target proteins. However, recognition sequences for ClpXP in other bacteria, including S. mutans, are not known. In this study, using two-dimensional (2D) polyacrylamide gel electrophoresis (PAGE) analysis, we have identified several putative substrates for S. mutans ClpXP. SsbA, which encodes a small DNA binding protein, is one such substrate that is degraded by ClpXP. By sequential deletions, we found that the last 3 C-terminal amino acids, LPF, are sufficient for ClpXP-mediated degradation. Addition of LPF at the C-terminal end of green fluorescent protein (GFP) rendered the protein completely degradable by ClpXP. Alterations of this tripeptide motif impeded ClpXP-mediated degradation. However, recognition of LPF by ClpXP is highly specific to some S. mutans strains (UA159, UA130, and N3209) since not all S. mutans strains recognize the motif. We speculate that an adaptor protein is involved in either substrate recognition or substrate degradation by ClpXP. Nevertheless, this is the first report of a unique recognition sequence for ClpXP in streptococci. IMPORTANCE Regulated proteolysis in bacteria is an important biological process that maintains protein homeostasis. ClpXP, an intracellular proteolytic complex, is the primary protease that is responsible for protein turnover. While the substrates for ClpXP were identified in Escherichia coli, the substrates for vast majority of bacteria are currently unknown. In this study, we identified a unique substrate for ClpXP-mediated degradation in Streptococcus mutans, a dental pathogen. We also found that a small motif composed of 3 amino acids is sufficient for ClpXP-mediated degradation. Identification of this motif will clearly help us to understand the pathogenesis of this organism and other related pathogens.
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9
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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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10
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Abstract
Transposable phage Mu has played a major role in elucidating the mechanism of movement of mobile DNA elements. The high efficiency of Mu transposition has facilitated a detailed biochemical dissection of the reaction mechanism, as well as of protein and DNA elements that regulate transpososome assembly and function. The deduced phosphotransfer mechanism involves in-line orientation of metal ion-activated hydroxyl groups for nucleophilic attack on reactive diester bonds, a mechanism that appears to be used by all transposable elements examined to date. A crystal structure of the Mu transpososome is available. Mu differs from all other transposable elements in encoding unique adaptations that promote its viral lifestyle. These adaptations include multiple DNA (enhancer, SGS) and protein (MuB, HU, IHF) elements that enable efficient Mu end synapsis, efficient target capture, low target specificity, immunity to transposition near or into itself, and efficient mechanisms for recruiting host repair and replication machineries to resolve transposition intermediates. MuB has multiple functions, including target capture and immunity. The SGS element promotes gyrase-mediated Mu end synapsis, and the enhancer, aided by HU and IHF, participates in directing a unique topological architecture of the Mu synapse. The function of these DNA and protein elements is important during both lysogenic and lytic phases. Enhancer properties have been exploited in the design of mini-Mu vectors for genetic engineering. Mu ends assembled into active transpososomes have been delivered directly into bacterial, yeast, and human genomes, where they integrate efficiently, and may prove useful for gene therapy.
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11
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Oxidization without substrate unfolding triggers proteolysis of the peroxide-sensor, PerR. Proc Natl Acad Sci U S A 2015; 113:E23-31. [PMID: 26677871 DOI: 10.1073/pnas.1522687112] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Peroxide operon regulator (PerR) is a broadly conserved hydrogen peroxide sensor in bacteria, and oxidation of PerR at its regulatory metal-binding site is considered irreversible. Here, we tested whether this oxidation specifically targets PerR for proteolysis. We find that oxidizing conditions stimulate PerR degradation in vivo, and LonA is the principal AAA+ (ATPases associated with diverse cellular activities) protease that degrades PerR. Degradation of PerR by LonA is recapitulated in vitro, and biochemical dissection of this degradation reveals that the presence of regulatory metal and PerR-binding DNA dramatically extends the half-life of the protein. We identified a LonA-recognition site critical for oxidation-controlled PerR turnover. Key residues for LonA-interaction are exposed to solvent in PerR lacking metal, but are buried in the metal-bound form. Furthermore, one residue critical for Lon recognition is also essential for specific DNA-binding by PerR, thus explaining how both the metal and DNA ligands prevent PerR degradation. This ligand-controlled allosteric mechanism for protease recognition provides a compelling explanation for how the oxidation-induced conformational change in PerR triggers degradation. Interestingly, the critical residues recognized by LonA and exposed by oxidation do not function as a degron, because they are not sufficient to convert a nonsubstrate protein into a LonA substrate. Rather, these residues are a conformation-discriminator sequence, which must work together with other residues in PerR to evoke efficient degradation. This mechanism provides a useful example of how other proteins with only mild or localized oxidative damage can be targeted for degradation without the need for extensive oxidation-dependent protein denaturation.
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12
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Ling L, Montaño SP, Sauer RT, Rice PA, Baker TA. Deciphering the Roles of Multicomponent Recognition Signals by the AAA+ Unfoldase ClpX. J Mol Biol 2015; 427:2966-82. [PMID: 25797169 DOI: 10.1016/j.jmb.2015.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/10/2015] [Accepted: 03/10/2015] [Indexed: 10/23/2022]
Abstract
ATP-dependent protein remodeling and unfolding enzymes are key participants in protein metabolism in all cells. How these often-destructive enzymes specifically recognize target protein complexes is poorly understood. Here, we use the well-studied AAA+ unfoldase-substrate pair, Escherichia coli ClpX and MuA transposase, to address how these powerful enzymes recognize target protein complexes. We demonstrate that the final transposition product, which is a DNA-bound tetramer of MuA, is preferentially recognized over the monomeric apo-protein through its multivalent display of ClpX recognition tags. The important peptide tags include one at the C-terminus ("C-tag") that binds the ClpX pore and a second one (enhancement or "E-tag") that binds the ClpX N-terminal domain. We construct a chimeric protein to interrogate subunit-specific contributions of these tags. Efficient remodeling of MuA tetramers requires ClpX to contact a minimum of three tags (one C-tag and two or more E-tags), and that these tags are contributed by different subunits within the tetramer. The individual recognition peptides bind ClpX weakly (KD>70 μM) but impart a high-affinity interaction (KD~1.0 μM) when combined in the MuA tetramer. When the weak C-tag signal is replaced with a stronger recognition tag, the E-tags become unnecessary and ClpX's preference for the complex over MuA monomers is eliminated. Additionally, because the spatial orientation of the tags is predicted to change during the final step of transposition, this recognition strategy suggests how AAA+ unfoldases specifically distinguish the completed "end-stage" form of a particular complex for the ideal biological outcome.
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Affiliation(s)
- Lorraine Ling
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 68-132, Cambridge, MA 02139, USA
| | - Sherwin P Montaño
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, W225, Chicago, IL 60637, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 68-132, Cambridge, MA 02139, USA
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, W225, Chicago, IL 60637, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, 68-132, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA.
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13
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Simons M, Diffin FM, Szczelkun MD. ClpXP protease targets long-lived DNA translocation states of a helicase-like motor to cause restriction alleviation. Nucleic Acids Res 2014; 42:12082-91. [PMID: 25260590 PMCID: PMC4231737 DOI: 10.1093/nar/gku851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We investigated how Escherichia coli ClpXP targets the helicase-nuclease (HsdR) subunit of the bacterial Type I restriction–modification enzyme EcoKI during restriction alleviation (RA). RA is a temporary reduction in endonuclease activity that occurs when Type I enzymes bind unmodified recognition sites on the host genome. These conditions arise upon acquisition of a new system by a naïve host, upon generation of new sites by genome rearrangement/mutation or during homologous recombination between hemimethylated DNA. Using recombinant DNA and proteins in vitro, we demonstrate that ClpXP targets EcoKI HsdR during dsDNA translocation on circular DNA but not on linear DNA. Protein roadblocks did not activate HsdR proteolysis. We suggest that DNA translocation lifetime, which is elevated on circular DNA relative to linear DNA, is important to RA. To identify the ClpX degradation tag (degron) in HsdR, we used bioinformatics and biochemical assays to design N- and C-terminal mutations that were analysed in vitro and in vivo. None of the mutants produced a phenotype consistent with loss of the degron, suggesting an as-yet-unidentified recognition pathway. We note that an EcoKI nuclease mutant still produces cell death in a clpx− strain, consistent with DNA damage induced by unregulated motor activity.
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Affiliation(s)
- Michelle Simons
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Fiona M Diffin
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
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14
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Bustamante CJ, Kaiser CM, Maillard RA, Goldman DH, Wilson CAM. Mechanisms of cellular proteostasis: insights from single-molecule approaches. Annu Rev Biophys 2014; 43:119-40. [PMID: 24895851 DOI: 10.1146/annurev-biophys-051013-022811] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cells employ a variety of strategies to maintain proteome homeostasis. Beginning during protein biogenesis, the translation machinery and a number of molecular chaperones promote correct de novo folding of nascent proteins even before synthesis is complete. Another set of molecular chaperones helps to maintain proteins in their functional, native state. Polypeptides that are no longer needed or pose a threat to the cell, such as misfolded proteins and aggregates, are removed in an efficient and timely fashion by ATP-dependent proteases. In this review, we describe how applications of single-molecule manipulation methods, in particular optical tweezers, are shedding new light on the molecular mechanisms of quality control during the life cycles of proteins.
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15
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Camberg JL, Viola MG, Rea L, Hoskins JR, Wickner S. Location of dual sites in E. coli FtsZ important for degradation by ClpXP; one at the C-terminus and one in the disordered linker. PLoS One 2014; 9:e94964. [PMID: 24722340 PMCID: PMC3983244 DOI: 10.1371/journal.pone.0094964] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/21/2014] [Indexed: 12/15/2022] Open
Abstract
ClpXP is a two-component ATP-dependent protease that unfolds and degrades proteins bearing specific recognition signals. One substrate degraded by Escherichia coli ClpXP is FtsZ, an essential cell division protein. FtsZ forms polymers that assemble into a large ring-like structure, termed the Z-ring, during cell division at the site of constriction. The FtsZ monomer is composed of an N-terminal polymerization domain, an unstructured linker region and a C-terminal conserved region. To better understand substrate selection by ClpXP, we engineered FtsZ mutant proteins containing amino acid substitutions or deletions near the FtsZ C-terminus. We identified two discrete regions of FtsZ important for degradation of both FtsZ monomers and polymers by ClpXP in vitro. One region is located 30 residues away from the C-terminus in the unstructured linker region that connects the polymerization domain to the C-terminal region. The other region is near the FtsZ C-terminus and partially overlaps the recognition sites for several other FtsZ-interacting proteins, including MinC, ZipA and FtsA. Mutation of either region caused the protein to be more stable and mutation of both caused an additive effect, suggesting that both regions are important. We also observed that in vitro MinC inhibits degradation of FtsZ by ClpXP, suggesting that some of the same residues in the C-terminal site that are important for degradation by ClpXP are important for binding MinC.
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Affiliation(s)
- Jodi L. Camberg
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Cell and Molecular Biology, College of Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, United States of America
- * E-mail: (JLC); (SW)
| | - Marissa G. Viola
- Department of Cell and Molecular Biology, College of Environment and Life Sciences, University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Leslie Rea
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Joel R. Hoskins
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sue Wickner
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JLC); (SW)
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16
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Critical clamp loader processing by an essential AAA+ protease in Caulobacter crescentus. Proc Natl Acad Sci U S A 2013; 110:18138-43. [PMID: 24145408 DOI: 10.1073/pnas.1311302110] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromosome replication relies on sliding clamps that are loaded by energy-dependent complexes. In Escherichia coli, the ATP-binding clamp loader subunit DnaX exists as both long (τ) and short (γ) forms generated through programmed translational frameshifting, but the need for both forms is unclear. Here, we show that in Caulobacter crescentus, DnaX isoforms are unexpectedly generated through partial proteolysis by the AAA+ protease casein lytic proteinase (Clp) XP. We find that the normally processive ClpXP protease partially degrades DnaX to produce stable fragments upon encountering a glycine-rich region adjacent to a structured domain. Increasing the sequence complexity of this region prevents partial proteolysis and generates a τ-only form of DnaX in vivo that is unable to support viability on its own. Growth is restored when γ is provided in trans, but these strains are more sensitive to DNA damage compared with strains that can generate γ through proteolysis. Our work reveals an unexpected mode of partial processing by the ClpXP protease to generate DnaX isoforms, demonstrates that both τ and γ forms of DnaX are required for Caulobacter viability, and identifies a role for clamp loader diversity in responding to DNA damage. The conservation of distinct DnaX isoforms throughout bacteria despite fundamentally different mechanisms for producing them suggests there may be a conserved need for alternate clamp loader complexes during DNA damaging conditions.
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17
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Bhat NH, Vass RH, Stoddard PR, Shin DK, Chien P. Identification of ClpP substrates in Caulobacter crescentus reveals a role for regulated proteolysis in bacterial development. Mol Microbiol 2013; 88:1083-92. [PMID: 23647068 DOI: 10.1111/mmi.12241] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2013] [Indexed: 12/01/2022]
Abstract
Energy-dependent proteases ensure the timely removal of unwanted proteins in a highly selective fashion. In Caulobacter crescentus, protein degradation by the ClpXP protease is critical for cell cycle progression; however, only a handful of substrates are currently known. Here, we use a trapping approach to identify putative substrates of the ClpP associated proteases in C. crescentus. Biochemical validation of several of these targets reveals specific protease recognition motifs and suggests a need for ClpXP-specific degradation beyond degradation of known cell cycle regulators. We focus on a particular instance of regulated proteolysis in Caulobacter by exploring the role of ClpXP in degrading the stalk synthesis transcription factor TacA. We show that TacA degradation is controlled during the cell cycle dependent on the ClpXP regulator CpdR and that stabilization of TacA increases degradation of another ClpXP substrate, CtrA, while restoring deficiencies associated with prolific CpdR activity. Together, our work reveals a number of new validated ClpXP substrates, clarifies rules of protease substrate selection, and demonstrates how regulated protein degradation is critical for Caulobacter development and cell cycle progression.
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Affiliation(s)
- Nowsheen H Bhat
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, USA
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18
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Diversity in the origins of proteostasis networks--a driver for protein function in evolution. Nat Rev Mol Cell Biol 2013; 14:237-48. [PMID: 23463216 DOI: 10.1038/nrm3542] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Although the sequence of a protein largely determines its function, proteins can adopt different folding states in response to changes in the environment, some of which may be deleterious to the organism. All organisms--Bacteria, Archaea and Eukarya--have evolved a protein homeostasis, or proteostasis, network comprising chaperones and folding factors, degradation components, signalling pathways and specialized compartmentalized modules that manage protein folding in response to environmental stimuli and variation. Surveying the origins of proteostasis networks reveals that they have co-evolved with the proteome to regulate the physiological state of the cell, reflecting the unique stresses that different cells or organisms experience, and that they have a key role in driving evolution by closely managing the link between the phenotype and the genotype.
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19
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Montaño SP, Pigli YZ, Rice PA. The μ transpososome structure sheds light on DDE recombinase evolution. Nature 2012; 491:413-7. [PMID: 23135398 PMCID: PMC3536463 DOI: 10.1038/nature11602] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Accepted: 09/19/2012] [Indexed: 12/11/2022]
Abstract
Studies of bacteriophage Mu transposition paved the way for understanding retroviral integration and V(D)J recombination as well as many other DNA transposition reactions. Here we report the structure of the Mu transpososome--Mu transposase (MuA) in complex with bacteriophage DNA ends and target DNA--determined from data that extend anisotropically to 5.2 Å, 5.2 Å and 3.7 Å resolution, in conjunction with previously determined structures of individual domains. The highly intertwined structure illustrates why chemical activity depends on formation of the synaptic complex, and reveals that individual domains have different roles when bound to different sites. The structure also provides explanations for the increased stability of the final product complex and for its preferential recognition by the ATP-dependent unfoldase ClpX. Although MuA and many other recombinases share a structurally conserved 'DDE' catalytic domain, comparisons among the limited set of available complex structures indicate that some conserved features, such as catalysis in trans and target DNA bending, arose through convergent evolution because they are important for function.
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Affiliation(s)
- Sherwin P. Montaño
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Ying Z. Pigli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Phoebe A. Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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20
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Abstract
In this issue of Structure, Rood and colleagues report that substrate architecture is a key factor in promoting the complete and processive degradation of the Caulobacter cell cycle regulator PdeA by the protease ClpXP. This investigation highlights the important role that the adaptor protein CpdR serves in regulating presentation of PdeA to ClpXP.
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21
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Rood KL, Clark NE, Stoddard PR, Garman SC, Chien P. Adaptor-dependent degradation of a cell-cycle regulator uses a unique substrate architecture. Structure 2012; 20:1223-32. [PMID: 22682744 DOI: 10.1016/j.str.2012.04.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 03/15/2012] [Accepted: 04/25/2012] [Indexed: 01/31/2023]
Abstract
In Caulobacter crescentus, the ClpXP protease degrades several crucial cell-cycle regulators, including the phosphodiesterase PdeA. Degradation of PdeA requires the response regulator CpdR and signals a morphological transition in concert with initiation of DNA replication. Here, we report the structure of a Per-Arnt-Sim (PAS) domain of PdeA and show that it is necessary for CpdR-dependent degradation in vivo and in vitro. CpdR acts as an adaptor, tethering the amino-terminal PAS domain to ClpXP and promoting recognition of the weak carboxyl-terminal degron of PdeA, a combination that ensures processive proteolysis. We identify sites on the PAS domain needed for CpdR recognition and find that one subunit of the PdeA dimer can be delivered to ClpXP by its partner. Finally, we show that improper stabilization of PdeA in vivo alters cellular behavior. These results introduce an adaptor/substrate pair for ClpXP and reveal broad diversity in adaptor-mediated proteolysis.
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Affiliation(s)
- Keith L Rood
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA
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22
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Jang S, Sandler SJ, Harshey RM. Mu insertions are repaired by the double-strand break repair pathway of Escherichia coli. PLoS Genet 2012; 8:e1002642. [PMID: 22511883 PMCID: PMC3325207 DOI: 10.1371/journal.pgen.1002642] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 02/22/2012] [Indexed: 11/21/2022] Open
Abstract
Mu is both a transposable element and a temperate bacteriophage. During lytic growth, it amplifies its genome by replicative transposition. During infection, it integrates into the Escherichia coli chromosome through a mechanism not requiring extensive DNA replication. In the latter pathway, the transposition intermediate is repaired by transposase-mediated resecting of the 5′ flaps attached to the ends of the incoming Mu genome, followed by filling the remaining 5 bp gaps at each end of the Mu insertion. It is widely assumed that the gaps are repaired by a gap-filling host polymerase. Using the E. coli Keio Collection to screen for mutants defective in recovery of stable Mu insertions, we show in this study that the gaps are repaired by the machinery responsible for the repair of double-strand breaks in E. coli—the replication restart proteins PriA-DnaT and homologous recombination proteins RecABC. We discuss alternate models for recombinational repair of the Mu gaps. Transposon activity shapes genome structure and evolution. The movement of these elements generates target site duplications as a result of staggered cuts in the target made initially by the transposase. For replicative transposons, the single-stranded gaps generated after the initial strand transfer event are filled by target-primed replication. However, the majority of known transposable elements transpose by a non-replicative mechanism. Despite a wealth of information available for the mechanism of transposase action, little is known about how the cell repairs gaps left in the wake of transposition of these majority elements. Phage Mu is unique in using both replicative and non-replicative modes of transposition. Our study finds that during its non-replicative pathway, the gaps created by Mu insertion are repaired by the primary machinery for double-strand break repair in E. coli, not by gap-filling polymerases as previously thought. This first report of specific host processes involved in repair of transposon insertions in bacteria is likely to have a broad significance, given also that double-strand break repair pathways have been implicated in repair of the retroviral and Line retroelement insertions.
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Affiliation(s)
- Sooin Jang
- Section of Molecular Genetics and Microbiology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
| | - Steven J. Sandler
- Department of Microbiology, Morill Science Center, University of Massachusetts at Amherst, Amherst, Massachusetts, United States of America
| | - Rasika M. Harshey
- Section of Molecular Genetics and Microbiology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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23
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Abstract
AAA+ family proteolytic machines (ClpXP, ClpAP, ClpCP, HslUV, Lon, FtsH, PAN/20S, and the 26S proteasome) perform protein quality control and are used in regulatory circuits in all cells. These machines contain a compartmental protease, with active sites sequestered in an interior chamber, and a hexameric ring of AAA+ ATPases. Substrate proteins are tethered to the ring, either directly or via adaptor proteins. An unstructured region of the substrate is engaged in the axial pore of the AAA+ ring, and cycles of ATP binding/hydrolysis drive conformational changes that create pulses of pulling that denature the substrate and translocate the unfolded polypeptide through the pore and into the degradation chamber. Here, we review our current understanding of the molecular mechanisms of substrate recognition, adaptor function, and ATP-fueled unfolding and translocation. The unfolding activities of these and related AAA+ machines can also be used to disassemble or remodel macromolecular complexes and to resolubilize aggregates.
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Affiliation(s)
- Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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24
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ClpXP, an ATP-powered unfolding and protein-degradation machine. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:15-28. [PMID: 21736903 DOI: 10.1016/j.bbamcr.2011.06.007] [Citation(s) in RCA: 323] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Revised: 06/10/2011] [Accepted: 06/15/2011] [Indexed: 11/23/2022]
Abstract
ClpXP is a AAA+ protease that uses the energy of ATP binding and hydrolysis to perform mechanical work during targeted protein degradation within cells. ClpXP consists of hexamers of a AAA+ ATPase (ClpX) and a tetradecameric peptidase (ClpP). Asymmetric ClpX hexamers bind unstructured peptide tags in protein substrates, unfold stable tertiary structure in the substrate, and then translocate the unfolded polypeptide chain into an internal proteolytic compartment in ClpP. Here, we review our present understanding of ClpXP structure and function, as revealed by two decades of biochemical and biophysical studies.
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25
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Application of the bacteriophage Mu-driven system for the integration/amplification of target genes in the chromosomes of engineered Gram-negative bacteria--mini review. Appl Microbiol Biotechnol 2011; 91:857-71. [PMID: 21698377 PMCID: PMC3145075 DOI: 10.1007/s00253-011-3416-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 05/24/2011] [Accepted: 05/24/2011] [Indexed: 11/04/2022]
Abstract
The advantages of phage Mu transposition-based systems for the chromosomal editing of plasmid-less strains are reviewed. The cis and trans requirements for Mu phage-mediated transposition, which include the L/R ends of the Mu DNA, the transposition factors MuA and MuB, and the cis/trans functioning of the E element as an enhancer, are presented. Mini-Mu(LR)/(LER) units are Mu derivatives that lack most of the Mu genes but contain the L/R ends or a properly arranged E element in cis to the L/R ends. The dual-component system, which consists of an integrative plasmid with a mini-Mu and an easily eliminated helper plasmid encoding inducible transposition factors, is described in detail as a tool for the integration/amplification of recombinant DNAs. This chromosomal editing method is based on replicative transposition through the formation of a cointegrate that can be resolved in a recombination-dependent manner. (E-plus)- or (E-minus)-helpers that differ in the presence of the trans-acting E element are used to achieve the proper mini-Mu transposition intensity. The systems that have been developed for the construction of stably maintained mini-Mu multi-integrant strains of Escherichia coli and Methylophilus methylotrophus are described. A novel integration/amplification/fixation strategy is proposed for consecutive independent replicative transpositions of different mini-Mu(LER) units with “excisable” E elements in methylotrophic cells.
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26
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Sundar S, McGinness KE, Baker TA, Sauer RT. Multiple sequence signals direct recognition and degradation of protein substrates by the AAA+ protease HslUV. J Mol Biol 2010; 403:420-9. [PMID: 20837023 DOI: 10.1016/j.jmb.2010.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 09/02/2010] [Accepted: 09/03/2010] [Indexed: 11/25/2022]
Abstract
Proteolysis is important for protein quality control and for the proper regulation of many intracellular processes in prokaryotes and eukaryotes. Discerning substrates from other cellular proteins is a key aspect of proteolytic function. The Escherichia coli HslUV protease is a member of a major family of ATP-dependent AAA+ degradation machines. HslU hexamers recognize and unfold native protein substrates and then translocate the polypeptide into the degradation chamber of the HslV peptidase. Although a wealth of structural information is available for this system, relatively little is known about mechanisms of substrate recognition. Here, we demonstrate that mutations in the unstructured N-terminal and C-terminal sequences of two model substrates alter HslUV recognition and degradation kinetics, including changes in V(max). By introducing N- or C-terminal sequences that serve as recognition sites for specific peptide-binding proteins, we show that blocking either terminus of the substrate interferes with HslUV degradation, with synergistic effects when both termini are obstructed. These results support a model in which one terminus of the substrate is tethered to the protease and the other terminus is engaged by the translocation/unfolding machinery in the HslU pore. Thus, degradation appears to consist of discrete steps, which involve the interaction of different terminal sequence signals in the substrate with different receptor sites in the HslUV protease.
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Affiliation(s)
- Shankar Sundar
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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27
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Chowdhury T, Chien P, Ebrahim S, Sauer RT, Baker TA. Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species. Protein Sci 2010; 19:242-54. [PMID: 20014030 DOI: 10.1002/pro.306] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
ClpXP, an AAA+ protease, plays key roles in protein-quality control and many regulatory processes in bacteria. The N-terminal domain of the ClpX component of ClpXP is involved in recognition of many protein substrates, either directly or by binding the SspB adaptor protein, which delivers specific classes of substrates for degradation. Despite very limited sequence homology between the E. coli and C. crescentus SspB orthologs, each of these adaptors can deliver substrates to the ClpXP enzyme from the other bacterial species. We show that the ClpX N domain recognizes different sequence determinants in the ClpX-binding (XB) peptides of C. crescentus SspBalpha and E. coli SspB. The C. crescentus XB determinants span 10 residues and involve interactions with multiple side chains, whereas the E. coli XB determinants span half as many residues with only a few important side chain contacts. These results demonstrate that the N domain of ClpX functions as a highly versatile platform for peptide recognition, allowing the emergence during evolution of alternative adaptor-binding specificities. Our results also reveal highly conserved residues in the XB peptides of both E. coli SspB and C. crescentus SspBalpha that play no detectable role in ClpX-binding or substrate delivery.
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Affiliation(s)
- Tahmeena Chowdhury
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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28
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Abstract
Phage Mu transposes by two distinct pathways depending on the specific stage of its life cycle. A common strand transfer intermediate is resolved differentially in the two pathways. During lytic growth, the intermediate is resolved by replication of Mu initiated within the flanking target DNA; during integration of infecting Mu, it is resolved without replication, by removal and repair of DNA from a previous host that is still attached to the ends of the incoming Mu genome. We have discovered that the cryptic endonuclease activity reported for the isolated C-terminal domain of the transposase MuA [Wu Z, Chaconas G (1995) A novel DNA binding and nuclease activity in domain III of Mu transposase: Evidence for a catalytic region involved in donor cleavage. EMBO J 14:3835-3843], which is not observed in the full-length protein or in the assembled transpososome in vitro, is required in vivo for removal of the attached host DNA or "5'flap" after the infecting Mu genome has integrated into the E. coli chromosome. Efficient flap removal also requires the host protein ClpX, which is known to interact with the C-terminus of MuA to remodel the transpososome for replication. We hypothesize that ClpX constitutes part of a highly regulated mechanism that unmasks the cryptic nuclease activity of MuA specifically in the repair pathway.
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29
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The AAA+ ClpX machine unfolds a keystone subunit to remodel the Mu transpososome. Proc Natl Acad Sci U S A 2010; 107:2437-42. [PMID: 20133746 DOI: 10.1073/pnas.0910905106] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A hyperstable complex of the tetrameric MuA transposase with recombined DNA must be remodeled to allow subsequent DNA replication. ClpX, a AAA+ enzyme, fulfills this function by unfolding one transpososome subunit. Which MuA subunit is extracted, and how complex destabilization relates to establishment of the correct directionality (left to right) of Mu replication, is not known. Here, using altered-specificity MuA proteins/DNA sites, we demonstrate that transpososome destabilization requires preferential ClpX unfolding of either the catalytic-left or catalytic-right subunits, which make extensive intersubunit contacts in the tetramer. In contrast, ClpX recognizes the other two subunits in the tetramer much less efficiently, and their extraction does not substantially destabilize the complex. Thus, ClpX targets the most stable structural components of the complex. Left-end biased Mu replication is not, however, determined by ClpX's intrinsic subunit preference. The specific targeting of a stabilizing "keystone subunit" within a complex for unfolding is an attractive general mechanism for remodeling by AAA+ enzymes.
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Schmidt R, Bukau B, Mogk A. Principles of general and regulatory proteolysis by AAA+ proteases in Escherichia coli. Res Microbiol 2009; 160:629-36. [PMID: 19781640 DOI: 10.1016/j.resmic.2009.08.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 08/20/2009] [Accepted: 08/21/2009] [Indexed: 11/25/2022]
Abstract
General and regulated proteolysis in bacteria is crucial for cellular homeostasis and relies on high substrate specificity of the executing AAA+ proteases. Here we summarize the various strategies that tightly control substrate degradation from both sides: the generation of accessible degrons and their specific recognition by AAA+ proteases and cognate adaptor proteins.
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Affiliation(s)
- Ronny Schmidt
- Zentrum für Molekulare Biologie Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Universität Heidelberg, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
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Davis JH, Baker TA, Sauer RT. Engineering synthetic adaptors and substrates for controlled ClpXP degradation. J Biol Chem 2009; 284:21848-21855. [PMID: 19549779 DOI: 10.1074/jbc.m109.017624] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Facile control of targeted intracellular protein degradation has many potential uses in basic science and biotechnology. One promising approach to this goal is to redesign adaptor proteins, which can regulate proteolytic specificity by tethering substrates to energy-dependent AAA+ proteases. Using the ClpXP protease, we have probed the minimal biochemical functions required for adaptor function by designing and characterizing variant substrates, adaptors, and ClpX enzymes. We find that substrate tethering mediated by heterologous interaction domains and a small bridging molecule mimics substrate delivery by the wild-type system. These results show that simple tethering is sufficient for synthetic adaptor function. In our engineered system, tethering and proteolysis depend on the presence of the macrolide rapamycin, providing a foundation for engineering highly specific degradation of target proteins in cells. Importantly, this degradation is regulated by a small molecule without the need for new adaptor or enzyme biosynthesis.
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Affiliation(s)
| | - Tania A Baker
- Department of Biology, Cambridge, Massachusetts 02139; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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