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Wen ZT, Ellepola K, Wu H. MecA: A Multifunctional ClpP-Dependent and Independent Regulator in Gram-Positive Bacteria. Mol Microbiol 2025; 123:433-438. [PMID: 40070161 DOI: 10.1111/mmi.15356] [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: 01/06/2025] [Revised: 02/24/2025] [Accepted: 02/28/2025] [Indexed: 03/19/2025]
Abstract
MecA is a broadly conserved adaptor protein in Gram-positive bacteria, mediating the recognition and degradation of specific target proteins by ClpCP protease complexes. MecA binds target proteins, often through recognition of degradation tags or motifs, and delivers them to the ClpC ATPase, which unfolds and translocates the substrates into the ClpP protease barrel for degradation. MecA activity is tightly regulated through interactions with ClpC ATPase and other factors, ensuring precise control over protein degradation and cellular homeostasis. Beyond proteolysis, emerging evidence highlights a ClpP-independent role of MecA in modulating the function of its targets, including key enzymes and transcriptional factors involved in biosynthetic and metabolic pathways. However, the full scope and mechanisms of ClpP-independent MecA regulation remain unclear, warranting further investigation.
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Affiliation(s)
- Zezhang T Wen
- Department of Oral and Craniofacial Biology, School of Dentistry, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
- Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Kassapa Ellepola
- Department of Oral Biology, College of Dentistry, University of Illinois Chicago, Chicago, Illinois, USA
| | - Hui Wu
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, Oregon, USA
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2
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Shu S, Tsutsui Y, Nathawat R, Mi W. Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis. Proc Natl Acad Sci U S A 2024; 121:e2321510121. [PMID: 38635633 PMCID: PMC11046580 DOI: 10.1073/pnas.2321510121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
Levels of lipopolysaccharide (LPS), an essential glycolipid on the surface of most gram-negative bacteria, are tightly controlled-making LPS synthesis a promising target for developing new antibiotics. Escherichia coli adaptor protein LapB (YciM) plays an important role in regulating LPS synthesis by promoting degradation of LpxC, a deacetylase that catalyzes the first committed step in LPS synthesis. Under conditions where LPS is abundant, LapB recruits LpxC to the AAA+ protease FtsH for degradation. LapB achieves this by simultaneously interacting with FtsH through its transmembrane helix and LpxC through its cytoplasmic domain. Here, we describe a cryo-EM structure of the complex formed between LpxC and the cytoplasmic domain of LapB (LapBcyto). The structure reveals how LapB exploits both its tetratricopeptide repeat (TPR) motifs and rubredoxin domain to interact with LpxC. Through both in vitro and in vivo analysis, we show that mutations at the LapBcyto/LpxC interface prevent LpxC degradation. Unexpectedly, binding to LapBcyto also inhibits the enzymatic activity of LpxC through allosteric effects reminiscent of LpxC activation by MurA in Pseudomonas aeruginosa. Our findings argue that LapB regulates LPS synthesis in two steps: In the first step, LapB inhibits the activity of LpxC, and in the second step, it commits LpxC to degradation by FtsH.
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Affiliation(s)
- Sheng Shu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
| | - Yuko Tsutsui
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
- Cancer Biology Institute, Yale University, West Haven, CT06516
| | - Rajkanwar Nathawat
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
| | - Wei Mi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT06520
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520
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3
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Xu W, Gao W, Bu Q, Li Y. Degradation Mechanism of AAA+ Proteases and Regulation of Streptomyces Metabolism. Biomolecules 2022; 12:biom12121848. [PMID: 36551276 PMCID: PMC9775585 DOI: 10.3390/biom12121848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Hundreds of proteins work together in microorganisms to coordinate and control normal activity in cells. Their degradation is not only the last step in the cell's lifespan but also the starting point for its recycling. In recent years, protein degradation has been extensively studied in both eukaryotic and prokaryotic organisms. Understanding the degradation process is essential for revealing the complex regulatory network in microorganisms, as well as further artificial reconstructions and applications. This review will discuss several studies on protein quality-control family members Lon, FtsH, ClpP, the proteasome in Streptomyces, and a few classical model organisms, mainly focusing on their structure, recognition mechanisms, and metabolic influences.
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Affiliation(s)
- Weifeng Xu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Wenli Gao
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qingting Bu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yongquan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
- Correspondence:
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4
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Engineering an SspB-mediated degron for novel controllable protein degradation. Metab Eng 2022; 74:150-159. [DOI: 10.1016/j.ymben.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 09/27/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
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5
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Abstract
Despite having a highly reduced genome, Chlamydia trachomatis undergoes a complex developmental cycle in which the bacteria differentiate between the following two functionally and morphologically distinct forms: the infectious, nonreplicative elementary body (EB) and the noninfectious, replicative reticulate body (RB). The transitions between EBs and RBs are not mediated by division events that redistribute intracellular proteins. Rather, both primary (EB to RB) and secondary (RB to EB) differentiation likely require bulk protein turnover. One system for targeted protein degradation is the trans-translation system for ribosomal rescue, where polypeptides stalled during translation are marked with an SsrA tag encoded by a hybrid tRNA-mRNA, tmRNA. ClpX recognizes the SsrA tag, leading to ClpXP-mediated degradation. We hypothesize that ClpX functions in chlamydial differentiation through targeted protein degradation. We found that mutation of a key residue (R230A) within the specific motif in ClpX associated with the recognition of SsrA-tagged substrates resulted in abrogated secondary differentiation while not reducing chlamydial replication or developmental cycle progression as measured by transcripts. Furthermore, inhibition of trans-translation through chemical and targeted genetic approaches also impeded chlamydial development. Knockdown of tmRNA and subsequent complementation with an allele mutated in the SsrA tag closely phenocopied the overexpression of ClpXR230A, thus suggesting that ClpX recognition of SsrA-tagged substrates plays a critical function in secondary differentiation. Taken together, these data provide mechanistic insight into the requirements for transitions between chlamydial developmental forms. IMPORTANCE Chlamydia trachomatis is the leading cause of bacterial sexually transmitted infections and preventable infectious blindness. This unique organism undergoes developmental transitions between infectious, nondividing forms and noninfectious, dividing forms. Therefore, the chlamydial developmental cycle is an attractive target for Chlamydia-specific antibiotics, which would minimize effects of broad-spectrum antibiotics on the spread of antibiotic resistance in other organisms. However, the lack of knowledge about chlamydial development on a molecular level impedes the identification of specific, druggable targets. This work describes a mechanism through which both the fundamental processes of trans-translation and proteomic turnover by ClpXP contribute to chlamydial differentiation, a critical facet of chlamydial growth and survival. Given the almost universal presence of trans-translation and ClpX in eubacteria, this mechanism may be conserved in developmental cycles of other bacterial species. Additionally, this study expands the fields of trans-translation and Clp proteases by emphasizing the functional diversity of these systems throughout bacterial evolution.
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6
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Crystal structure and biochemical analysis suggest that YjoB ATPase is a putative substrate-specific molecular chaperone. Proc Natl Acad Sci U S A 2022; 119:e2207856119. [PMID: 36191235 PMCID: PMC9565160 DOI: 10.1073/pnas.2207856119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
AAA+ ATPases are ubiquitous proteins associated with most cellular processes, including DNA unwinding and protein unfolding. Their functional and structural properties are typically determined by domains and motifs added to the conserved ATPases domain. Currently, the molecular function and structure of many ATPases remain elusive. Here, we report the crystal structure and biochemical analyses of YjoB, a Bacillus subtilis AAA+ protein. The crystal structure revealed that the YjoB hexamer forms a bucket hat-shaped structure with a porous chamber. Biochemical analyses showed that YjoB prevents the aggregation of vegetative catalase KatA and gluconeogenesis-specific glyceraldehyde-3 phosphate dehydrogenase GapB but not citrate synthase, a conventional substrate. Structural and biochemical analyses further showed that the internal chamber of YjoB is necessary for inhibition of substrate aggregation. Our results suggest that YjoB, conserved in the class Bacilli, is a potential molecular chaperone acting in the starvation/stationary phases of B. subtilis growth.
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Abstract
Optogenetics combines light and genetics to enable precise control of living cells, tissues, and organisms with tailored functions. Optogenetics has the advantages of noninvasiveness, rapid responsiveness, tunable reversibility, and superior spatiotemporal resolution. Following the initial discovery of microbial opsins as light-actuated ion channels, a plethora of naturally occurring or engineered photoreceptors or photosensitive domains that respond to light at varying wavelengths has ushered in the next chapter of optogenetics. Through protein engineering and synthetic biology approaches, genetically-encoded photoswitches can be modularly engineered into protein scaffolds or host cells to control a myriad of biological processes, as well as to enable behavioral control and disease intervention in vivo. Here, we summarize these optogenetic tools on the basis of their fundamental photochemical properties to better inform the chemical basis and design principles. We also highlight exemplary applications of opsin-free optogenetics in dissecting cellular physiology (designated "optophysiology"), and describe the current progress, as well as future trends, in wireless optogenetics, which enables remote interrogation of physiological processes with minimal invasiveness. This review is anticipated to spark novel thoughts on engineering next-generation optogenetic tools and devices that promise to accelerate both basic and translational studies.
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Affiliation(s)
- Peng Tan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States.,Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Lian He
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, United States.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, United States
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas, United States.,Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, Texas, United States
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8
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Cargo competition for a dimerization interface restricts and stabilizes a bacterial protease adaptor. Proc Natl Acad Sci U S A 2021; 118:2010523118. [PMID: 33875581 DOI: 10.1073/pnas.2010523118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial protein degradation is a regulated process aided by protease adaptors that alter specificity of energy-dependent proteases. In Caulobacter crescentus, cell cycle-dependent protein degradation depends on a hierarchy of adaptors, such as the dimeric RcdA adaptor, which binds multiple cargo and delivers substrates to the ClpXP protease. RcdA itself is degraded in the absence of cargo, and how RcdA recognizes its targets is unknown. Here, we show that RcdA dimerization and cargo binding compete for a common interface. Cargo binding separates RcdA dimers, and a monomeric variant of RcdA fails to be degraded, suggesting that RcdA degradation is a result of self-delivery. Based on HDX-MS studies showing that different cargo rely on different regions of the dimerization interface, we generate RcdA variants that are selective for specific cargo and show cellular defects consistent with changes in selectivity. Finally, we show that masking of cargo binding by dimerization also limits substrate delivery to restrain overly prolific degradation. Using the same interface for dimerization and cargo binding offers an ability to limit excess protease adaptors by self-degradation while providing a capacity for binding a range of substrates.
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Polymerase delta-interacting protein 38 (PDIP38) modulates the stability and activity of the mitochondrial AAA+ protease CLPXP. Commun Biol 2020; 3:646. [PMID: 33159171 PMCID: PMC7647994 DOI: 10.1038/s42003-020-01358-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/09/2020] [Indexed: 02/06/2023] Open
Abstract
Over a decade ago Polymerase δ interacting protein of 38 kDa (PDIP38) was proposed to play a role in DNA repair. Since this time, both the physiological function and subcellular location of PDIP38 has remained ambiguous and our present understanding of PDIP38 function has been hampered by a lack of detailed biochemical and structural studies. Here we show, that human PDIP38 is directed to the mitochondrion in a membrane potential dependent manner, where it resides in the matrix compartment, together with its partner protein CLPX. Our structural analysis revealed that PDIP38 is composed of two conserved domains separated by an α/β linker region. The N-terminal (YccV-like) domain of PDIP38 forms an SH3-like β-barrel, which interacts specifically with CLPX, via the adaptor docking loop within the N-terminal Zinc binding domain of CLPX. In contrast, the C-terminal (DUF525) domain forms an immunoglobin-like β-sandwich fold, which contains a highly conserved putative substrate binding pocket. Importantly, PDIP38 modulates the substrate specificity of CLPX and protects CLPX from LONM-mediated degradation, which stabilises the cellular levels of CLPX. Collectively, our findings shed new light on the mechanism and function of mitochondrial PDIP38, demonstrating that PDIP38 is a bona fide adaptor protein for the mitochondrial protease, CLPXP. Strack et al find that Polymerase δ interacting protein 38 (PDIP38) is targeted to the mitochondrial matrix where it colocalises with the mitochondrial AAA + protein CLPXP. PDIP38 modulates the specificity of CLPXP in vitro and alters the stability of CLPX in vitro and in cells. The PDIP38 structure leads the authors to speculate that PDIP38 is a CLPXP adaptor.
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10
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Micevski D, Zeth K, Mulhern TD, Schuenemann VJ, Zammit JE, Truscott KN, Dougan DA. Insight into the RssB-Mediated Recognition and Delivery of σ s to the AAA+ Protease, ClpXP. Biomolecules 2020; 10:E615. [PMID: 32316259 PMCID: PMC7226468 DOI: 10.3390/biom10040615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/18/2020] [Accepted: 04/11/2020] [Indexed: 11/23/2022] Open
Abstract
In Escherichia coli, SigmaS (σS) is the master regulator of the general stress response. The cellular levels of σS are controlled by transcription, translation and protein stability. The turnover of σS, by the AAA+ protease (ClpXP), is tightly regulated by a dedicated adaptor protein, termed RssB (Regulator of Sigma S protein B)-which is an atypical member of the response regulator (RR) family. Currently however, the molecular mechanism of σS recognition and delivery by RssB is only poorly understood. Here we describe the crystal structures of both RssB domains (RssBN and RssBC) and the SAXS analysis of full-length RssB (both free and in complex with σS). Together with our biochemical analysis we propose a model for the recognition and delivery of σS by this essential adaptor protein. Similar to most bacterial RRs, the N-terminal domain of RssB (RssBN) comprises a typical mixed (βα)5-fold. Although phosphorylation of RssBN (at Asp58) is essential for high affinity binding of σS, much of the direct binding to σS occurs via the C-terminal effector domain of RssB (RssBC). In contrast to most RRs the effector domain of RssB forms a β-sandwich fold composed of two sheets surrounded by α-helical protrusions and as such, shares structural homology with serine/threonine phosphatases that exhibit a PPM/PP2C fold. Our biochemical data demonstrate that this domain plays a key role in both substrate interaction and docking to the zinc binding domain (ZBD) of ClpX. We propose that RssB docking to the ZBD of ClpX overlaps with the docking site of another regulator of RssB, the anti-adaptor IraD. Hence, we speculate that docking to ClpX may trigger release of its substrate through activation of a "closed" state (as seen in the RssB-IraD complex), thereby coupling adaptor docking (to ClpX) with substrate release. This competitive docking to RssB would prevent futile interaction of ClpX with the IraD-RssB complex (which lacks a substrate). Finally, substrate recognition by RssB appears to be regulated by a key residue (Arg117) within the α5 helix of the N-terminal domain. Importantly, this residue is not directly involved in σS interaction, as σS binding to the R117A mutant can be restored by phosphorylation. Likewise, R117A retains the ability to interact with and activate ClpX for degradation of σS, both in the presence and absence of acetyl phosphate. Therefore, we propose that this region of RssB (the α5 helix) plays a critical role in driving interaction with σS at a distal site.
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Affiliation(s)
- Dimce Micevski
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Victoria, Australia; (D.M.); (J.E.Z.)
| | - Kornelius Zeth
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, D-72076 Tübingen, Germany; (K.Z.); (V.J.S.)
- Department of Science and Environment, Roskilde University, DK-4000 Roskilde, Denmark
| | - Terrence D. Mulhern
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville 3010, Victoria, Australia;
| | - Verena J. Schuenemann
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, D-72076 Tübingen, Germany; (K.Z.); (V.J.S.)
| | - Jessica E. Zammit
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Victoria, Australia; (D.M.); (J.E.Z.)
| | - Kaye N. Truscott
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Victoria, Australia; (D.M.); (J.E.Z.)
| | - David A. Dougan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Victoria, Australia; (D.M.); (J.E.Z.)
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11
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Feng S, Varshney A, Coto Villa D, Modavi C, Kohler J, Farah F, Zhou S, Ali N, Müller JD, Van Hoven MK, Huang B. Bright split red fluorescent proteins for the visualization of endogenous proteins and synapses. Commun Biol 2019; 2:344. [PMID: 31552297 PMCID: PMC6749000 DOI: 10.1038/s42003-019-0589-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/26/2019] [Indexed: 12/22/2022] Open
Abstract
Self-associating split fluorescent proteins (FPs) are split FPs whose two fragments spontaneously associate to form a functional FP. They have been widely used for labeling proteins, scaffolding protein assembly and detecting cell-cell contacts. Recently developments have expanded the palette of self-associating split FPs beyond the original split GFP1-10/11. However, these new ones have suffered from suboptimal fluorescence signal after complementation. Here, by investigating the complementation process, we have demonstrated two approaches to improve split FPs: assistance through SpyTag/SpyCatcher interaction and directed evolution. The latter has yielded two split sfCherry3 variants with substantially enhanced overall brightness, facilitating the tagging of endogenous proteins by gene editing. Based on sfCherry3, we have further developed a new red-colored trans-synaptic marker called Neuroligin-1 sfCherry3 Linker Across Synaptic Partners (NLG-1 CLASP) for multiplexed visualization of neuronal synapses in living C. elegans, demonstrating its broad applications.
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Affiliation(s)
- Siyu Feng
- The UC Berkeley-UCSF Graduate Program in Bioengineering, San Francisco, CA 94143 USA
| | - Aruna Varshney
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192 USA
| | - Doris Coto Villa
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192 USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, University of California in San Francisco, San Francisco, CA 94143 USA
| | - John Kohler
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 USA
| | - Fatima Farah
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192 USA
| | - Shuqin Zhou
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084 China
- Department of Pharmaceutical Chemistry, University of California in San Francisco, San Francisco, CA 94143 USA
| | - Nebat Ali
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192 USA
| | - Joachim D. Müller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455 USA
| | - Miri K. Van Hoven
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192 USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California in San Francisco, San Francisco, CA 94143 USA
- Department Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143 USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158 USA
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12
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Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx. Structure 2019; 27:923-936.e6. [DOI: 10.1016/j.str.2019.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/31/2019] [Accepted: 03/14/2019] [Indexed: 11/18/2022]
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13
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Bittner LM, Arends J, Narberhaus F. When, how and why? Regulated proteolysis by the essential FtsH protease in Escherichia coli. Biol Chem 2017; 398:625-635. [PMID: 28085670 DOI: 10.1515/hsz-2016-0302] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/09/2017] [Indexed: 11/15/2022]
Abstract
Cellular proteomes are dynamic and adjusted to permanently changing conditions by ATP-fueled proteolytic machineries. Among the five AAA+ proteases in Escherichia coli FtsH is the only essential and membrane-anchored metalloprotease. FtsH is a homohexamer that uses its ATPase domain to unfold and translocate substrates that are subsequently degraded without the need of ATP in the proteolytic chamber of the protease domain. FtsH eliminates misfolded proteins in the context of general quality control and properly folded proteins for regulatory reasons. Recent trapping approaches have revealed a number of novel FtsH substrates. This review summarizes the substrate diversity of FtsH and presents details on the surprisingly diverse recognition principles of three well-characterized substrates: LpxC, the key enzyme of lipopolysaccharide biosynthesis; RpoH, the alternative heat-shock sigma factor and YfgM, a bifunctional membrane protein implicated in periplasmic chaperone functions and cytoplasmic stress adaptation.
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Affiliation(s)
- Lisa-Marie Bittner
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
| | - Jan Arends
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
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14
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Hammond RG, Tan X, Johnson MA. SARS-unique fold in the Rousettus bat coronavirus HKU9. Protein Sci 2017; 26:1726-1737. [PMID: 28580734 PMCID: PMC5563143 DOI: 10.1002/pro.3208] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 12/28/2022]
Abstract
The coronavirus nonstructural protein 3 (nsp3) is a multifunctional protein that comprises multiple structural domains. This protein assists viral polyprotein cleavage, host immune interference, and may play other roles in genome replication or transcription. Here, we report the solution NMR structure of a protein from the “SARS‐unique region” of the bat coronavirus HKU9. The protein contains a frataxin fold or double‐wing motif, which is an α + β fold that is associated with protein/protein interactions, DNA binding, and metal ion binding. High structural similarity to the human severe acute respiratory syndrome (SARS) coronavirus nsp3 is present. A possible functional site that is conserved among some betacoronaviruses has been identified using bioinformatics and biochemical analyses. This structure provides strong experimental support for the recent proposal advanced by us and others that the “SARS‐unique” region is not unique to the human SARS virus, but is conserved among several different phylogenetic groups of coronaviruses and provides essential functions. PDB Code(s): 5UTV
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Affiliation(s)
- Robert G Hammond
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Xuan Tan
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Margaret A Johnson
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, 35294
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15
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Joshi KK, Sutherland M, Chien P. Cargo engagement protects protease adaptors from degradation in a substrate-specific manner. J Biol Chem 2017; 292:10973-10982. [PMID: 28507098 DOI: 10.1074/jbc.m117.786392] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/09/2017] [Indexed: 11/06/2022] Open
Abstract
Protein degradation in bacteria is a highly controlled process involving proteolytic adaptors that regulate protein degradation during cell cycle progression or during stress responses. Many adaptors work as scaffolds that selectively bind cargo and tether substrates to their cognate proteases to promote substrate destruction, whereas others primarily activate the target protease. Because adaptors must bind their cognate protease, all adaptors run the risk of being recognized by the protease as substrates themselves, a process that could limit their effectiveness. Here we use purified proteins in a reconstituted system and in vivo studies to show that adaptors of the ClpXP protease are readily degraded but that cargo binding inhibits this degradation. We found that this principle extends across several adaptor systems, including the hierarchical adaptors that drive the Caulobacter bacterial cell cycle and the quality control adaptor SspB. We also found that the ability of a cargo to protect its adaptor is adaptor substrate-specific, as adaptors with artificial degradation tags were not protected even though cargo binding is unaffected. Our work points to an optimization of inherent adaptor degradation and cargo binding that ensures that robust adaptor activity is maintained when high amounts of substrate must be delivered and that adaptors can be eliminated when their tasks have been completed.
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Affiliation(s)
- Kamal Kishore Joshi
- From the Department of Biochemistry and Molecular Biology and.,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003
| | | | - Peter Chien
- From the Department of Biochemistry and Molecular Biology and .,Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003
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16
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Bittner LM, Arends J, Narberhaus F. Mini review: ATP-dependent proteases in bacteria. Biopolymers 2017; 105:505-17. [PMID: 26971705 DOI: 10.1002/bip.22831] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 02/11/2016] [Accepted: 03/07/2016] [Indexed: 01/22/2023]
Abstract
AAA(+) proteases are universal barrel-like and ATP-fueled machines preventing the accumulation of aberrant proteins and regulating the proteome according to the cellular demand. They are characterized by two separate operating units, the ATPase and peptidase domains. ATP-dependent unfolding and translocation of a substrate into the proteolytic chamber is followed by ATP-independent degradation. This review addresses the structure and function of bacterial AAA(+) proteases with a focus on the ATP-driven mechanisms and the coordinated movements in the complex mainly based on the knowledge of ClpXP. We conclude by discussing strategies how novel protease substrates can be trapped by mutated AAA(+) protease variants. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 505-517, 2016.
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Affiliation(s)
| | - Jan Arends
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
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17
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Joshi KK, Bergé M, Radhakrishnan SK, Viollier PH, Chien P. An Adaptor Hierarchy Regulates Proteolysis during a Bacterial Cell Cycle. Cell 2016; 163:419-31. [PMID: 26451486 DOI: 10.1016/j.cell.2015.09.030] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/01/2015] [Accepted: 09/02/2015] [Indexed: 11/30/2022]
Abstract
Regulated protein degradation is essential. The timed destruction of crucial proteins by the ClpXP protease drives cell-cycle progression in the bacterium Caulobacter crescentus. Although ClpXP is active alone, additional factors are inexplicably required for cell-cycle-dependent proteolysis. Here, we show that these factors constitute an adaptor hierarchy wherein different substrates are destroyed based on the degree of adaptor assembly. The hierarchy builds upon priming of ClpXP by the adaptor CpdR, which promotes degradation of one class of substrates and also recruits the adaptor RcdA to degrade a second class of substrates. Adding the PopA adaptor promotes destruction of a third class of substrates and inhibits degradation of the second class. We dissect RcdA to generate bespoke adaptors, identifying critical substrate elements needed for RcdA recognition and uncovering additional cell-cycle-dependent ClpXP substrates. Our work reveals how hierarchical adaptors and primed proteases orchestrate regulated proteolysis during bacterial cell-cycle progression.
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Affiliation(s)
- Kamal Kishore Joshi
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Matthieu Bergé
- Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), University of Geneva Medical School, Geneva CH-1211, Switzerland
| | - Sunish Kumar Radhakrishnan
- Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), University of Geneva Medical School, Geneva CH-1211, Switzerland
| | - Patrick Henri Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), University of Geneva Medical School, Geneva CH-1211, Switzerland
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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18
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Lau J, Hernandez-Alicea L, Vass RH, Chien P. A Phosphosignaling Adaptor Primes the AAA+ Protease ClpXP to Drive Cell Cycle-Regulated Proteolysis. Mol Cell 2015; 59:104-16. [PMID: 26073542 DOI: 10.1016/j.molcel.2015.05.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 03/31/2015] [Accepted: 05/04/2015] [Indexed: 11/30/2022]
Abstract
The response regulator CpdR couples phosphorylation events in Caulobacter crescentus with the AAA+ protease ClpXP to provide punctuated degradation of crucial substrates involved in cell cycle regulation. CpdR functions like an adaptor to alter substrate choice by ClpXP; however, it remains unclear how CpdR influences its multiple targets. Here we show that, unlike canonical ClpXP adaptors, CpdR alone does not strongly bind its substrate. Instead, CpdR binds the N-terminal domain of ClpX and prepares (primes) the unfoldase for substrate engagement. This priming creates a recruitment interface that docks multiple substrates and additional adaptor components. We show that adaptor-dependent priming of ClpX avoids concentration-dependent inhibition that limits traditional scaffolding adaptors. Phosphosignaling disrupts the adaptor-protease interaction, and mutations in CpdR that impact ClpX binding tune adaptor activity and biological function. Together, these results reveal how a single adaptor can command global changes in proteome composition through priming of a protease.
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Affiliation(s)
- Joanne Lau
- Microbiology Graduate Program, Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA
| | - Lisa Hernandez-Alicea
- Molecular and Cellular Biology Graduate Program, Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA
| | - Robert H Vass
- Molecular and Cellular Biology Graduate Program, Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA
| | - Peter Chien
- Microbiology Graduate Program, Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA; Molecular and Cellular Biology Graduate Program, Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA.
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19
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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: 1.0] [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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20
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Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Proc Natl Acad Sci U S A 2014; 112:112-7. [PMID: 25535392 DOI: 10.1073/pnas.1417910112] [Citation(s) in RCA: 461] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The discovery of light-inducible protein-protein interactions has allowed for the spatial and temporal control of a variety of biological processes. To be effective, a photodimerizer should have several characteristics: it should show a large change in binding affinity upon light stimulation, it should not cross-react with other molecules in the cell, and it should be easily used in a variety of organisms to recruit proteins of interest to each other. To create a switch that meets these criteria we have embedded the bacterial SsrA peptide in the C-terminal helix of a naturally occurring photoswitch, the light-oxygen-voltage 2 (LOV2) domain from Avena sativa. In the dark the SsrA peptide is sterically blocked from binding its natural binding partner, SspB. When activated with blue light, the C-terminal helix of the LOV2 domain undocks from the protein, allowing the SsrA peptide to bind SspB. Without optimization, the switch exhibited a twofold change in binding affinity for SspB with light stimulation. Here, we describe the use of computational protein design, phage display, and high-throughput binding assays to create an improved light inducible dimer (iLID) that changes its affinity for SspB by over 50-fold with light stimulation. A crystal structure of iLID shows a critical interaction between the surface of the LOV2 domain and a phenylalanine engineered to more tightly pin the SsrA peptide against the LOV2 domain in the dark. We demonstrate the functional utility of the switch through light-mediated subcellular localization in mammalian cell culture and reversible control of small GTPase signaling.
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21
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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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22
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Remodeling of a delivery complex allows ClpS-mediated degradation of N-degron substrates. Proc Natl Acad Sci U S A 2014; 111:E3853-9. [PMID: 25187555 DOI: 10.1073/pnas.1414933111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ClpS adaptor collaborates with the AAA+ ClpAP protease to recognize and degrade N-degron substrates. ClpS binds the substrate N-degron and assembles into a high-affinity ClpS-substrate-ClpA complex, but how the N-degron is transferred from ClpS to the axial pore of the AAA+ ClpA unfoldase to initiate degradation is not known. Here we demonstrate that the unstructured N-terminal extension (NTE) of ClpS enters the ClpA processing pore in the active ternary complex. We establish that ClpS promotes delivery only in cis, as demonstrated by mixing ClpS variants with distinct substrate specificity and either active or inactive NTE truncations. Importantly, we find that ClpA engagement of the ClpS NTE is crucial for ClpS-mediated substrate delivery by using ClpS variants carrying "blocking" elements that prevent the NTE from entering the pore. These results support models in which enzymatic activity of ClpA actively remodels ClpS to promote substrate transfer, and highlight how ATPase/motor activities of AAA+ proteases can be critical for substrate selection as well as protein degradation.
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23
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Cell cycle-dependent adaptor complex for ClpXP-mediated proteolysis directly integrates phosphorylation and second messenger signals. Proc Natl Acad Sci U S A 2014; 111:14229-34. [PMID: 25197043 DOI: 10.1073/pnas.1407862111] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cell-division cycle of Caulobacter crescentus depends on periodic activation and deactivation of the essential response regulator CtrA. Although CtrA is critical for transcription during some parts of the cell cycle, its activity must be eliminated before chromosome replication because CtrA also blocks the initiation of DNA replication. CtrA activity is down-regulated both by dephosphorylation and by proteolysis, mediated by the ubiquitous ATP-dependent protease ClpXP. Here we demonstrate that proteins needed for rapid CtrA proteolysis in vivo form a phosphorylation-dependent and cyclic diguanylate (cdG)-dependent adaptor complex that accelerates CtrA degradation in vitro by ClpXP. The adaptor complex includes CpdR, a single-domain response regulator; PopA, a cdG-binding protein; and RcdA, a protein whose activity cannot be predicted. When CpdR is unphosphorylated and when PopA is bound to cdG, they work together with RcdA in an all-or-none manner to reduce the Km of CtrA proteolysis 10-fold. We further identified a set of amino acids in the receiver domain of CtrA that modulate its adaptor-mediated degradation in vitro and in vivo. Complex formation between PopA and CtrA depends on these amino acids, which reside on alpha-helix 1 of the CtrA receiver domain, and on cdG binding by PopA. These results reveal that each accessory factor plays an essential biochemical role in the regulated proteolysis of CtrA and demonstrate, to our knowledge, the first example of a multiprotein, cdG-dependent proteolytic adaptor.
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24
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Nagpal J, Tan JL, Truscott KN, Heras B, Dougan DA. Control of protein function through regulated protein degradation: biotechnological and biomedical applications. J Mol Microbiol Biotechnol 2013; 23:335-44. [PMID: 23920496 DOI: 10.1159/000352043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Targeted protein degradation is crucial for the correct function and maintenance of a cell. In bacteria, this process is largely performed by a handful of ATP-dependent machines, which generally consist of two components - an unfoldase and a peptidase. In some cases, however, substrate recognition by the protease may be regulated by specialized delivery factors (known as adaptor proteins). Our detailed understanding of how these machines are regulated to prevent uncontrolled degradation within a cell has permitted the identification of novel antimicrobials that dysregulate these machines, as well as the development of tunable degradation systems that have applications in biotechnology. Here, we focus on the physiological role of the ClpP peptidase in bacteria, its role as a novel antibiotic target and the use of protein degradation as a biotechnological approach to artificially control the expression levels of a protein of interest.
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Affiliation(s)
- Jyotsna Nagpal
- Department of Biochemistry, La Trobe Institute for Molecular Science LIMS, La Trobe University, Melbourne, Vic., Australia
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25
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Abstract
Bacteria are frequently exposed to changes in environmental conditions, such as fluctuations in temperature, pH or the availability of nutrients. These assaults can be detrimental to cell as they often result in a proteotoxic stress, which can cause the accumulation of unfolded proteins. In order to restore a productive folding environment in the cell, bacteria have evolved a network of proteins, known as the protein quality control (PQC) network, which is composed of both chaperones and AAA+ proteases. These AAA+ proteases form a major part of this PQC network, as they are responsible for the removal of unwanted and damaged proteins. They also play an important role in the turnover of specific regulatory or tagged proteins. In this review, we describe the general features of an AAA+ protease, and using two of the best-characterised AAA+ proteases in Escherichia coli (ClpAP and ClpXP) as a model for all AAA+ proteases, we provide a detailed mechanistic description of how these machines work. Specifically, the review examines the physiological role of these machines, as well as the substrates and the adaptor proteins that modulate their substrate specificity.
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26
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Bonnet M, Stegmann M, Maglica Ž, Stiegeler E, Weber-Ban E, Hennecke H, Mesa S. FixK2, a key regulator inBradyrhizobium japonicum, is a substrate for the protease ClpAP in vitro. FEBS Lett 2012. [DOI: 10.1016/j.febslet.2012.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Lungu OI, Hallett RA, Choi EJ, Aiken MJ, Hahn KM, Kuhlman B. Designing photoswitchable peptides using the AsLOV2 domain. ACTA ACUST UNITED AC 2012; 19:507-17. [PMID: 22520757 DOI: 10.1016/j.chembiol.2012.02.006] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 01/12/2012] [Accepted: 02/01/2012] [Indexed: 10/28/2022]
Abstract
Photocontrol of functional peptides is a powerful tool for spatial and temporal control of cell signaling events. We show that the genetically encoded light-sensitive LOV2 domain of Avena Sativa phototropin 1 (AsLOV2) can be used to reversibly photomodulate the affinity of peptides for their binding partners. Sequence analysis and molecular modeling were used to embed two peptides into the Jα helix of the AsLOV2 domain while maintaining AsLOV2 structure in the dark but allowing for binding to effector proteins when the Jα helix unfolds in the light. Caged versions of the ipaA and SsrA peptides, LOV-ipaA and LOV-SsrA, bind their targets with 49- and 8-fold enhanced affinity in the light, respectively. These switches can be used as general tools for light-dependent colocalization, which we demonstrate with photo-activable gene transcription in yeast.
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Affiliation(s)
- Oana I Lungu
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
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28
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Svetlanov A, Puri N, Mena P, Koller A, Karzai AW. Francisella tularensis tmRNA system mutants are vulnerable to stress, avirulent in mice, and provide effective immune protection. Mol Microbiol 2012; 85:122-41. [PMID: 22571636 PMCID: PMC3395464 DOI: 10.1111/j.1365-2958.2012.08093.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Through targeted inactivation of the ssrA and smpB genes, we establish that the trans-translation process is necessary for normal growth, adaptation to cellular stress and virulence by the bacterial pathogen Francisella tularensis. The mutant bacteria grow slower, have reduced resistance to heat and cold shocks, and are more sensitive to oxidative stress and sublethal concentrations of antibiotics. Modifications of the tmRNA tag and use of higher-resolution mass spectrometry approaches enabled the identification of a large number of native tmRNA substrates. Of particular significance to understanding the mechanism of trans-translation, we report the discovery of an extended tmRNA tag and extensive ladder-like pattern of endogenous protein-tagging events in F. tularensis that are likely to be a universal feature of tmRNA activity in eubacteria. Furthermore, the structural integrity and the proteolytic function of the tmRNA tag are both crucial for normal growth and virulence of F. tularensis. Significantly, trans-translation mutants of F. tularensis are impaired in replication within macrophages and are avirulent in mouse models of tularemia. By exploiting these attenuated phenotypes, we find that the mutant strains provide effective immune protection in mice against lethal intradermal, intraperitoneal and intranasal challenges with the fully virulent parental strain.
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Affiliation(s)
- Anton Svetlanov
- Center for Infectious Diseases and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Neha Puri
- Center for Infectious Diseases and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Patricio Mena
- Center for Infectious Diseases and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
| | - Antonius Koller
- The Proteomic Center, Stony Brook University, Stony Brook, New York, 11794
| | - A. Wali Karzai
- Center for Infectious Diseases and Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, 11794
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29
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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: 1.6] [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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30
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Truscott KN, Bezawork-Geleta A, Dougan DA. Unfolded protein responses in bacteria and mitochondria: a central role for the ClpXP machine. IUBMB Life 2012; 63:955-63. [PMID: 22031494 DOI: 10.1002/iub.526] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In the crowded environment of a cell, the protein quality control machinery, such as molecular chaperones and proteases, maintains a population of folded and hence functional proteins. The accumulation of unfolded proteins in a cell is particularly harmful as it not only reduces the concentration of active proteins but also overburdens the protein quality control machinery, which in turn, can lead to a significant increase in nonproductive folding and protein aggregation. To circumvent this problem, cells use heat shock and unfolded protein stress response pathways, which essentially sense the change to protein homeostasis upregulating protein quality control factors that act to restore the balance. Interestingly, several stress response pathways are proteolytically controlled. In this review, we provide a brief summary of targeted protein degradation by AAA+ proteases and focus on the role of ClpXP proteases, particularly in the signaling pathway of the Escherichia coli extracellular stress response and the mitochondrial unfolded protein response.
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Affiliation(s)
- Kaye N Truscott
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
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31
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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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32
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Román-Hernández G, Hou JY, Grant RA, Sauer RT, Baker TA. The ClpS adaptor mediates staged delivery of N-end rule substrates to the AAA+ ClpAP protease. Mol Cell 2011; 43:217-28. [PMID: 21777811 PMCID: PMC3168947 DOI: 10.1016/j.molcel.2011.06.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 04/10/2011] [Accepted: 06/02/2011] [Indexed: 01/07/2023]
Abstract
The ClpS adaptor delivers N-end rule substrates to ClpAP, an energy-dependent AAA+ protease, for degradation. How ClpS binds specific N-end residues is known in atomic detail and clarified here, but the delivery mechanism is poorly understood. We show that substrate binding is enhanced when ClpS binds hexameric ClpA. Reciprocally, N-end rule substrates increase ClpS affinity for ClpA(6). Enhanced binding requires the N-end residue and a peptide bond of the substrate, as well as multiple aspects of ClpS, including a side chain that contacts the substrate α-amino group and the flexible N-terminal extension (NTE). Finally, enhancement also needs the N domain and AAA+ rings of ClpA, connected by a long linker. The NTE can be engaged by the ClpA translocation pore, but ClpS resists unfolding/degradation. We propose a staged-delivery model that illustrates how intimate contacts between the substrate, adaptor, and protease reprogram specificity and coordinate handoff from the adaptor to the protease.
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Affiliation(s)
| | - Jennifer Y. Hou
- 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
| | - 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
,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
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33
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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: 346] [Impact Index Per Article: 24.7] [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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Abstract
The essential cellular functions of secretion and protein degradation require a molecular machine to unfold and translocate proteins either across a membrane or into a proteolytic complex. Protein translocation is also critical for microbial pathogenesis, namely bacteria can use translocase channels to deliver toxic proteins into a target cell. Anthrax toxin (Atx), a key virulence factor secreted by Bacillus anthracis, provides a robust biophysical model to characterize transmembrane protein translocation. Atx is comprised of three proteins: the translocase component, protective antigen (PA) and two enzyme components, lethal factor (LF) and oedema factor (OF). Atx forms an active holotoxin complex containing a ring-shaped PA oligomer bound to multiple copies of LF and OF. These complexes are endocytosed into mammalian host cells, where PA forms a protein-conducting translocase channel. The proton motive force unfolds and translocates LF and OF through the channel. Recent structure and function studies have shown that LF unfolds during translocation in a force-dependent manner via a series of metastable intermediates. Polypeptide-binding clamps located throughout the PA channel catalyse substrate unfolding and translocation by stabilizing unfolding intermediates through the formation of a series of interactions with various chemical groups and α-helical structure presented by the unfolding polypeptide during translocation.
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Affiliation(s)
- Katie L Thoren
- Departments of Chemistry, University of California, Berkeley, CA 94720, USA
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35
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Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers. Nat Struct Mol Biol 2010; 17:1383-90. [PMID: 21037566 PMCID: PMC3133606 DOI: 10.1038/nsmb.1923] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 09/07/2010] [Indexed: 01/07/2023]
Abstract
The protein transporter anthrax lethal toxin is composed of protective antigen (PA), a transmembrane translocase, and lethal factor (LF), a cytotoxic enzyme. After its assembly into holotoxin complexes, PA forms an oligomeric channel that unfolds LF and translocates it into the host cell. We report the crystal structure of the core of a lethal toxin complex to 3.1-Å resolution; the structure contains a PA octamer bound to four LF PA-binding domains (LF(N)). The first α-helix and β-strand of each LF(N) unfold and dock into a deep amphipathic cleft on the surface of the PA octamer, which we call the α clamp. The α clamp possesses nonspecific polypeptide binding activity and is functionally relevant to efficient holotoxin assembly, PA octamer formation, and LF unfolding and translocation. This structure provides insight into the mechanism of translocation-coupled protein unfolding.
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36
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Ollivierre JN, Fang J, Beuning PJ. The Roles of UmuD in Regulating Mutagenesis. J Nucleic Acids 2010; 2010. [PMID: 20936072 PMCID: PMC2948943 DOI: 10.4061/2010/947680] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2010] [Accepted: 08/01/2010] [Indexed: 11/20/2022] Open
Abstract
All organisms are subject to DNA damage from both endogenous and environmental sources. DNA damage that is not fully repaired can lead to mutations. Mutagenesis is now understood to be an active process, in part facilitated by lower-fidelity DNA polymerases that replicate DNA in an error-prone manner. Y-family DNA polymerases, found throughout all domains of life, are characterized by their lower fidelity on undamaged DNA and their specialized ability to copy damaged DNA. Two E. coli Y-family DNA polymerases are responsible for copying damaged DNA as well as for mutagenesis. These DNA polymerases interact with different forms of UmuD, a dynamic protein that regulates mutagenesis. The UmuD gene products, regulated by the SOS response, exist in two principal forms: UmuD(2), which prevents mutagenesis, and UmuD(2)', which facilitates UV-induced mutagenesis. This paper focuses on the multiple conformations of the UmuD gene products and how their protein interactions regulate mutagenesis.
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Affiliation(s)
- Jaylene N Ollivierre
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, 102 Hurtig Hall, Boston, MA 02115, USA
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37
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Shpanchenko OV, Bugaeva EY, Golovin AV, Dontsova OA. Trans-translation: Findings and hypotheses. Mol Biol 2010. [DOI: 10.1134/s0026893310040011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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38
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Lee ME, Baker TA, Sauer RT. Control of substrate gating and translocation into ClpP by channel residues and ClpX binding. J Mol Biol 2010; 399:707-18. [PMID: 20416323 DOI: 10.1016/j.jmb.2010.04.027] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 04/12/2010] [Accepted: 04/15/2010] [Indexed: 11/25/2022]
Abstract
ClpP is a self-compartmentalized protease, which has very limited degradation activity unless it associates with ClpX to form ClpXP or with ClpA to form ClpAP. Here, we show that ClpX binding stimulates ClpP cleavage of peptides larger than a few amino acids and enhances ClpP active-site modification. Stimulation requires ATP binding but not hydrolysis by ClpX. The magnitude of this enhancement correlates with increasing molecular weight of the molecule entering ClpP. Amino-acid substitutions in the channel loop or helix A of ClpP enhance entry of larger substrates into the free enzyme, eliminate ClpX binding in some cases, and are not further stimulated by ClpX binding in other instances. These results support a model in which the channel residues of free ClpP exclude efficient entry of all but the smallest peptides into the degradation chamber, with ClpX binding serving to relieve these inhibitory interactions. Specific ClpP channel variants also prevent ClpXP translocation of certain amino-acid sequences, suggesting that the wild-type channel plays an important role in facilitating broad translocation specificity. In combination with previous studies, our results indicate that collaboration between ClpP and its partner ATPases opens a gate that functions to exclude larger substrates from isolated ClpP.
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Affiliation(s)
- Mary E Lee
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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39
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Truscott KN, Lowth BR, Strack PR, Dougan DA. Diverse functions of mitochondrial AAA+ proteins: protein activation, disaggregation, and degradation. Biochem Cell Biol 2010; 88:97-108. [PMID: 20130683 DOI: 10.1139/o09-167] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
In eukaryotes, mitochondria are required for the proper function of the cell and as such the maintenance of proteins within this organelle is crucial. One class of proteins, collectively known as the AAA+ (ATPases associated with various cellular activities) superfamily, make a number of important contributions to mitochondrial protein homeostasis. In this organelle, they contribute to the maturation and activation of proteins, general protein quality control, respiratory chain complex assembly, and mitochondrial DNA maintenance and integrity. To achieve such diverse functions this group of ATP-dependent unfoldases utilize the energy from ATP hydrolysis to modulate the structure of proteins via unique domains and (or) associated functional components. In this review, we describe the current status of knowledge regarding the known mitochondrial AAA+ proteins and their role in this organelle.
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Affiliation(s)
- Kaye N Truscott
- La Trobe University, Science Dr., Melbourne, Victoria 3086, Australia
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40
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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: 1.2] [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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41
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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: 1.7] [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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42
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Mutations that alter RcdA surface residues decouple protein localization and CtrA proteolysis in Caulobacter crescentus. J Mol Biol 2009; 394:46-60. [PMID: 19747489 DOI: 10.1016/j.jmb.2009.08.076] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 08/24/2009] [Accepted: 08/27/2009] [Indexed: 11/23/2022]
Abstract
Periodic activation and deactivation of the essential transcriptional regulator CtrA is necessary to drive cell cycle progression in Caulobacter crescentus. At the onset of DNA replication (the G1-S cell cycle transition), CtrA and the AAA+ protease ClpXP colocalize at one cell pole along with three accessory proteins, RcdA, CpdR, and PopA, and CtrA is rapidly degraded. RcdA is required for polar sequestration and regulated proteolysis of CtrA in vivo, but it does not stimulate CtrA degradation by ClpXP in vitro; thus, the function of RcdA is unknown. We determined the 2.9-A-resolution crystal structure of RcdA and generated structure-guided mutations in rcdA. We assayed the ability of each RcdA variant to support CtrA proteolysis and polar protein localization in Caulobacter. Deletion of an intrinsically disordered peptide at the C-terminus of RcdA prevents efficient CtrA degradation and blocks the transient localization of RcdA and CtrA at the cell pole. Surprisingly, substitutions in two groups of highly conserved, charged surface residues disrupt polar RcdA or CtrA localization but do not affect CtrA proteolysis. This is the first report showing that localization of RcdA can be decoupled from its effects on CtrA degradation. In addition, we used epistasis experiments to show that RcdA is still required for regulated CtrA proteolysis when all SsrA-tagged proteins, abundant substrates of ClpXP, are absent from the cell. Our results argue that RcdA stimulates CtrA proteolysis neither by localizing CtrA at the cell pole nor by preventing competition from SsrA-tagged substrates.
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43
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Kress W, Maglica Z, Weber-Ban E. Clp chaperone-proteases: structure and function. Res Microbiol 2009; 160:618-28. [PMID: 19732826 DOI: 10.1016/j.resmic.2009.08.006] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 08/14/2009] [Accepted: 08/14/2009] [Indexed: 11/26/2022]
Abstract
Clp proteases are the most widespread energy-dependent proteases in bacteria. Their two-component architecture of protease core and ATPase rings results in an inventory of several Clp protease complexes that often coexist. Here, we present insights into Clp protease function, from their assembly to substrate recruitment and processing, and how this is coupled to the expense of energy.
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Affiliation(s)
- Wolfgang Kress
- ETH Zurich, Institute of Molecular Biology & Biophysics, Schafmattstrasse 20, 8093 Zurich, Switzerland
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44
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Abstract
Members of the AAA+ protein superfamily contribute to many diverse aspects of protein homeostasis in prokaryotic cells. As a fundamental component of numerous proteolytic machines in bacteria, AAA+ proteins play a crucial part not only in general protein quality control but also in the regulation of developmental programmes, through the controlled turnover of key proteins such as transcription factors. To manage these many, varied tasks, Hsp100/Clp and AAA+ proteases use specific adaptor proteins to enhance or expand the substrate recognition abilities of their cognate protease. Here, we review our current knowledge of the modulation of bacterial AAA+ proteases by these cellular arbitrators.
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45
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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: 1.2] [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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46
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Dunn CD, Tamura Y, Sesaki H, Jensen RE. Mgr3p and Mgr1p are adaptors for the mitochondrial i-AAA protease complex. Mol Biol Cell 2008; 19:5387-97. [PMID: 18843051 DOI: 10.1091/mbc.e08-01-0103] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
By screening yeast knockouts for their dependence upon the mitochondrial genome, we identified Mgr3p, a protein that associates with the i-AAA protease complex in the mitochondrial inner membrane. Mgr3p and Mgr1p, another i-AAA-interacting protein, form a subcomplex that bind to the i-AAA subunit Yme1p. We find that loss of Mgr3p, like the lack of Mgr1p, reduces proteolysis by Yme1p. Mgr3p and Mgr1p can bind substrate even in the absence of Yme1p, and both proteins are needed for maximal binding of an unfolded substrate by the i-AAA complex. We speculate that Mgr3p and Mgr1p function in an adaptor complex that targets substrates to the i-AAA protease for degradation.
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Affiliation(s)
- Cory D Dunn
- Department of Cell Biology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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47
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Wang KH, Oakes ESC, Sauer RT, Baker TA. Tuning the strength of a bacterial N-end rule degradation signal. J Biol Chem 2008; 283:24600-7. [PMID: 18550545 DOI: 10.1074/jbc.m802213200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The N-end rule is a degradation pathway conserved from bacteria to mammals that links a protein's stability in vivo to the identity of its N-terminal residue. In Escherichia coli, the components of this pathway directly responsible for protein degradation are the ClpAP protease and its adaptor ClpS. We recently demonstrated that ClpAP is able to recognize N-end motifs in the absence of ClpS although with significantly reduced substrate affinity. In this study, a systematic sequence analysis reveals new features of N-end rule degradation signals. To achieve specificity, recognition of an N-end motif by the protease-adaptor complex uses both the identity of the N-terminal residue and a free alpha-amino group. Acidic residues near the first residue decrease substrate affinity, demonstrating that the identity of adjacent residues can affect recognition although significant flexibility is tolerated. However, shortening the distance between the N-end residue and the stably folded portion of a protein prevents degradation entirely, indicating that an N-end signal alone is not always sufficient for degradation. Together, these data define in vitro the sequence and structural requirements for the function of bacterial N-end signals.
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Affiliation(s)
- Kevin H Wang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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48
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Martin A, Baker TA, Sauer RT. Diverse pore loops of the AAA+ ClpX machine mediate unassisted and adaptor-dependent recognition of ssrA-tagged substrates. Mol Cell 2008; 29:441-50. [PMID: 18313382 DOI: 10.1016/j.molcel.2008.02.002] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 01/30/2008] [Accepted: 02/06/2008] [Indexed: 10/22/2022]
Abstract
ClpX, an archetypal proteolytic AAA+ unfoldase, must engage the ssrA tags of appropriate substrates prior to ATP-dependent unfolding and translocation of the denatured polypeptide into ClpP for degradation. Here, specificity-transplant and disulfide-crosslinking experiments reveal that the ssrA tag interacts with different loops that form the top, middle, and lower portions of the central channel of the ClpX hexamer. Our results support a two-step binding mechanism, in which the top loop serves as a specificity filter and the remaining loops form a binding site for the peptide tag relatively deep within the pore. Crosslinking experiments suggest a staggered arrangement of pore loops in the hexamer and nucleotide-dependent changes in pore-loop conformations. This mechanism of initial tag binding would allow ATP-dependent conformational changes in one or more pore loops to drive peptide translocation, force unfolding, and mediate threading of the denatured protein through the ClpX pore.
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Affiliation(s)
- Andreas Martin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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49
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Cranz-Mileva S, Imkamp F, Kolygo K, Maglica Z, Kress W, Weber-Ban E. The flexible attachment of the N-domains to the ClpA ring body allows their use on demand. J Mol Biol 2008; 378:412-24. [PMID: 18358489 DOI: 10.1016/j.jmb.2008.02.047] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Revised: 02/14/2008] [Accepted: 02/22/2008] [Indexed: 11/18/2022]
Abstract
ClpA is an Hsp100 chaperone that uses the chemical energy of ATP to remodel various protein substrates to prepare them for degradation. It comprises two AAA+ modules and the N-domain, which is attached N-terminally to the first AAA+ module through a linker. On the basis of cryo-electron microscopic and X-ray crystallographic data it has been suggested that the linker confers mobility to the N-domain. In order to define the role of the N-domain in ClpAP-dependent substrate degradation we have generated a Delta N variant at the protein level by introducing a protease cleavage site. The ClpA molecule generated in this way lacks the N-domain and the associated linker but is impaired only slightly in the processing of substrates that are degraded independently of ClpS. In fact, it shows increased catalytic efficiency in the degradation of ssrA-tagged GFP compared to ClpAwt. The role of the linker attaching the N-domain to the bulk of the molecule was probed by characterizing variants with different lengths of the linker. The degradation efficiency of a ClpS-dependent N-end rule substrate, FRliGFP, is reduced for linkers that are shorter or longer than natural linkers but remains the same for the variant where the linker is replaced by an engineered sequence of equivalent length. These results suggest that the flexible attachment of the N-domains to ClpA allows their recruitment to the pore on demand for certain substrates, while allowing them to move out of the way for substrates binding directly to the pore.
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Affiliation(s)
- Susanne Cranz-Mileva
- Institute of Molecular Biology & Biophysics, ETH Zürich, CH-8093 Zürich, Switzerland
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50
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Inobe T, Matouschek A. Protein targeting to ATP-dependent proteases. Curr Opin Struct Biol 2008; 18:43-51. [PMID: 18276129 DOI: 10.1016/j.sbi.2007.12.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 12/21/2007] [Accepted: 12/26/2007] [Indexed: 11/27/2022]
Abstract
ATP-dependent proteases control diverse cellular processes by degrading specific regulatory proteins. Recent work has shown that protein substrates are specifically transferred to ATP-dependent proteases through different routes. These routes can function in parallel or independently. In all of these targeting mechanisms, it can be useful to separate two steps: substrate binding to the protease and initiation of degradation.
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Affiliation(s)
- Tomonao Inobe
- Department of Biochemistry, Molecular Biology and Cell Biology, 2205 Tech Drive, Hogan 2-100 Northwestern University, Evanston, IL, USA
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