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Yokoyama T, Yamagata Y, Honna S, Mizuno S, Katagiri S, Oi R, Nogi T, Hizukuri Y, Akiyama Y. S2P intramembrane protease RseP degrades small membrane proteins and suppresses the cytotoxicity of intrinsic toxin HokB. mBio 2023; 14:e0108623. [PMID: 37409810 PMCID: PMC10470546 DOI: 10.1128/mbio.01086-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 05/25/2023] [Indexed: 07/07/2023] Open
Abstract
The site2-protease (S2P) family of intramembrane proteases (IMPs) is conserved in all kingdoms of life and cleaves transmembrane proteins within the membrane to regulate and maintain various cellular activities. RseP, an Escherichia coli S2P peptidase, is involved in the regulation of gene expression through the regulated cleavage of the two target membrane proteins (RseA and FecR) and in membrane quality control through the proteolytic elimination of remnant signal peptides. RseP is expected to have additional substrates and to be involved in other cellular processes. Recent studies have shown that cells express small membrane proteins (SMPs; single-spanning membrane proteins of approximately 50-100 amino acid residues) with crucial cellular functions. However, little is known about their metabolism, which affects their functions. This study investigated the possible RseP-catalyzed cleavage of E. coli SMPs based on the apparent similarity of the sizes and structures of SMPs to those of remnant signal peptides. We screened SMPs cleaved by RseP in vivo and in vitro and identified 14 SMPs, including HokB, an endogenous toxin that induces persister formation, as potential substrates. We demonstrated that RseP suppresses the cytotoxicity and biological functions of HokB. The identification of several SMPs as novel potential substrates of RseP provides a clue to a comprehensive understanding of the cellular roles of RseP and other S2P peptidases and highlights a novel aspect of the regulation of SMPs. IMPORTANCE Membrane proteins play an important role in cell activity and survival. Thus, understanding their dynamics, including proteolytic degradation, is crucial. E. coli RseP, an S2P family intramembrane protease, cleaves membrane proteins to regulate gene expression in response to environmental changes and to maintain membrane quality. To identify novel substrates of RseP, we screened small membrane proteins (SMPs), a group of proteins that have recently been shown to have diverse cellular functions, and identified 14 potential substrates. We also showed that RseP suppresses the cytotoxicity of the intrinsic toxin, HokB, an SMP that has been reported to induce persister cell formation, by degrading it. These findings provide new insights into the cellular roles of S2P peptidases and the functional regulation of SMPs.
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Affiliation(s)
- Tatsuhiko Yokoyama
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yutaro Yamagata
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Saisei Honna
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Shinya Mizuno
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Shizuka Katagiri
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Rika Oi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Terukazu Nogi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi-ku, Yokohama, Japan
| | - Yohei Hizukuri
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yoshinori Akiyama
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
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Kupke T, Götz RM, Richter FM, Beck R, Lolicato F, Nickel W, Hopf C, Brügger B. In vivo characterization of the bacterial intramembrane-cleaving protease RseP using the heme binding tag-based assay iCliPSpy. Commun Biol 2023; 6:287. [PMID: 36934128 PMCID: PMC10024687 DOI: 10.1038/s42003-023-04654-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 03/02/2023] [Indexed: 03/20/2023] Open
Abstract
Regulated intramembrane proteolysis (RIP) describes the protease-dependent cleavage of transmembrane proteins within the hydrophobic core of cellular membranes. Intramembrane-cleaving proteases (I-CliPs) that catalyze these reactions are found in all kingdoms of life and are involved in a wide range of cellular processes, including signaling and protein homeostasis. I-CLiPs are multispanning membrane proteins and represent challenging targets in structural and enzyme biology. Here we introduce iCLiPSpy, a simple assay to study I-CLiPs in vivo. To allow easy detection of enzyme activity, we developed a heme-binding reporter based on TNFα that changes color after I-CLiP-mediated proteolysis. Co-expression of the protease and reporter in Escherichia coli (E. coli) results in white or green colonies, depending on the activity of the protease. As a proof of concept, we use this assay to study the bacterial intramembrane-cleaving zinc metalloprotease RseP in vivo. iCLiPSpy expands the methodological repertoire for identifying residues important for substrate binding or activity of I-CLiPs and can in principle be adapted to a screening assay for the identification of inhibitors or activators of I-CLiPs, which is of great interest for proteases being explored as biomedical targets.
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Affiliation(s)
- Thomas Kupke
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
| | - Rabea M Götz
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany
| | - Florian M Richter
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany
| | - Rainer Beck
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Fabio Lolicato
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Walter Nickel
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163, Mannheim, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
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3
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Imaizumi Y, Takanuki K, Miyake T, Takemoto M, Hirata K, Hirose M, Oi R, Kobayashi T, Miyoshi K, Aruga R, Yokoyama T, Katagiri S, Matsuura H, Iwasaki K, Kato T, Kaneko MK, Kato Y, Tajiri M, Akashi S, Nureki O, Hizukuri Y, Akiyama Y, Nogi T. Mechanistic insights into intramembrane proteolysis by E. coli site-2 protease homolog RseP. SCIENCE ADVANCES 2022; 8:eabp9011. [PMID: 36001659 PMCID: PMC9401612 DOI: 10.1126/sciadv.abp9011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/01/2022] [Indexed: 05/31/2023]
Abstract
Site-2 proteases are a conserved family of intramembrane proteases that cleave transmembrane substrates to regulate signal transduction and maintain proteostasis. Here, we elucidated crystal structures of inhibitor-bound forms of bacterial site-2 proteases including Escherichia coli RseP. Structure-based chemical modification and cross-linking experiments indicated that the RseP domains surrounding the active center undergo conformational changes to expose the substrate-binding site, suggesting that RseP has a gating mechanism to regulate substrate entry. Furthermore, mutational analysis suggests that a conserved electrostatic linkage between the transmembrane and peripheral membrane-associated domains mediates the conformational changes. In vivo cleavage assays also support that the substrate transmembrane helix is unwound by strand addition to the intramembrane β sheet of RseP and is clamped by a conserved asparagine residue at the active center for efficient cleavage. This mechanism underlying the substrate binding, i.e., unwinding and clamping, appears common across distinct families of intramembrane proteases that cleave transmembrane segments.
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Affiliation(s)
- Yuki Imaizumi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kazunori Takanuki
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takuya Miyake
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Mizuki Takemoto
- Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kunio Hirata
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Mika Hirose
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Rika Oi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tatsuya Kobayashi
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kenichi Miyoshi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Rie Aruga
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tatsuhiko Yokoyama
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Shizuka Katagiri
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hiroaki Matsuura
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Kenji Iwasaki
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Mika K. Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Sendai, Miyagi 980-8575, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Sendai, Miyagi 980-8575, Japan
- Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Sendai, Miyagi 980-8575, Japan
| | - Michiko Tajiri
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Osamu Nureki
- Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yohei Hizukuri
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshinori Akiyama
- Institute for Life and Medical Sciences, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Terukazu Nogi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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Miyazaki R, Watanabe T, Yoshitani K, Akiyama Y. Edge-strand of BepA interacts with immature LptD on the β-barrel assembly machine to direct it to on- and off-pathways. eLife 2021; 10:70541. [PMID: 34463613 PMCID: PMC8423444 DOI: 10.7554/elife.70541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/26/2021] [Indexed: 01/06/2023] Open
Abstract
The outer membrane (OM) of Gram-negative bacteria functions as a selective permeability barrier. Escherichia coli periplasmic Zn-metallopeptidase BepA contributes to the maintenance of OM integrity through its involvement in the biogenesis and degradation of LptD, a β-barrel protein component of the lipopolysaccharide translocon. BepA either promotes the maturation of LptD when it is on the normal assembly pathway (on-pathway) or degrades it when its assembly is compromised (off-pathway). BepA performs these functions probably on the β‐barrel assembly machinery (BAM) complex. However, how BepA recognizes and directs an immature LptD to different pathways remains unclear. Here, we explored the interactions among BepA, LptD, and the BAM complex. We found that the interaction of the BepA edge-strand located adjacent to the active site with LptD was crucial not only for proteolysis but also, unexpectedly, for assembly promotion of LptD. Site-directed crosslinking analyses indicated that the unstructured N-terminal half of the β-barrel-forming domain of an immature LptD contacts with the BepA edge-strand. Furthermore, the C-terminal region of the β-barrel-forming domain of the BepA-bound LptD intermediate interacted with a ‘seam’ strand of BamA, suggesting that BepA recognized LptD assembling on the BAM complex. Our findings provide important insights into the functional mechanism of BepA.
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Affiliation(s)
- Ryoji Miyazaki
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tetsuro Watanabe
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kohei Yoshitani
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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5
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Tamura-Sakaguchi R, Aruga R, Hirose M, Ekimoto T, Miyake T, Hizukuri Y, Oi R, Kaneko MK, Kato Y, Akiyama Y, Ikeguchi M, Iwasaki K, Nogi T. Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion. Acta Crystallogr D Struct Biol 2021; 77:645-662. [PMID: 33950020 PMCID: PMC8098476 DOI: 10.1107/s2059798321002527] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/08/2021] [Indexed: 11/10/2022] Open
Abstract
Antibody labeling has been conducted extensively for structure determination using both X-ray crystallography and electron microscopy (EM). However, establishing target-specific antibodies is a prerequisite for applying antibody-assisted structural analysis. To expand the applicability of this strategy, an alternative method has been developed to prepare an antibody complex by inserting an exogenous epitope into the target. It has already been demonstrated that the Fab of the NZ-1 monoclonal antibody can form a stable complex with a target containing a PA12 tag as an inserted epitope. Nevertheless, it was also found that complex formation through the inserted PA12 tag inevitably caused structural changes around the insertion site on the target. Here, an attempt was made to improve the tag-insertion method, and it was consequently discovered that an alternate tag (PA14) could replace various loops on the target without inducing large structural changes. Crystallographic analysis demonstrated that the inserted PA14 tag adopts a loop-like conformation with closed ends in the antigen-binding pocket of the NZ-1 Fab. Due to proximity of the termini in the bound conformation, the more optimal PA14 tag had only a minor impact on the target structure. In fact, the PA14 tag could also be inserted into a sterically hindered loop for labeling. Molecular-dynamics simulations also showed a rigid structure for the target regardless of PA14 insertion and complex formation with the NZ-1 Fab. Using this improved labeling technique, negative-stain EM was performed on a bacterial site-2 protease, which enabled an approximation of the domain arrangement based on the docking mode of the NZ-1 Fab.
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Affiliation(s)
| | - Rie Aruga
- Graduate School of Medical Life Science, Yokohama City University, Japan
| | - Mika Hirose
- Institute for Protein Research, Osaka University, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, Japan
| | - Takuya Miyake
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Yohei Hizukuri
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Rika Oi
- Graduate School of Medical Life Science, Yokohama City University, Japan
| | - Mika K. Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Japan
- New Industry Creation Hatchery Center, Tohoku University, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Japan
- RIKEN, Medical Life Sciences Innovation Hub Program, Japan
| | - Kenji Iwasaki
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Japan
| | - Terukazu Nogi
- Graduate School of Medical Life Science, Yokohama City University, Japan
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6
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Yokoyama T, Niinae T, Tsumagari K, Imami K, Ishihama Y, Hizukuri Y, Akiyama Y. The Escherichia coli S2P intramembrane protease RseP regulates ferric citrate uptake by cleaving the sigma factor regulator FecR. J Biol Chem 2021; 296:100673. [PMID: 33865858 PMCID: PMC8144685 DOI: 10.1016/j.jbc.2021.100673] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/08/2021] [Accepted: 04/14/2021] [Indexed: 02/03/2023] Open
Abstract
Escherichia coli RseP, a member of the site-2 protease family of intramembrane proteases, is involved in the activation of the σE extracytoplasmic stress response and elimination of signal peptides from the cytoplasmic membrane. However, whether RseP has additional cellular functions is unclear. In this study, we used mass spectrometry-based quantitative proteomic analysis to search for new substrates that might reveal unknown physiological roles for RseP. Our data showed that the levels of several Fec system proteins encoded by the fecABCDE operon (fec operon) were significantly decreased in an RseP-deficient strain. The Fec system is responsible for the uptake of ferric citrate, and the transcription of the fec operon is controlled by FecI, an alternative sigma factor, and its regulator FecR, a single-pass transmembrane protein. Assays with a fec operon expression reporter demonstrated that the proteolytic activity of RseP is essential for the ferric citrate-dependent upregulation of the fec operon. Analysis using the FecR protein and FecR-derived model proteins showed that FecR undergoes sequential processing at the membrane and that RseP participates in the last step of this sequential processing to generate the N-terminal cytoplasmic fragment of FecR that participates in the transcription of the fec operon with FecI. A shortened FecR construct was not dependent on RseP for activation, confirming this cleavage step is the essential and sufficient role of RseP. Our study unveiled that E. coli RseP performs the intramembrane proteolysis of FecR, a novel physiological role that is essential for regulating iron uptake by the ferric citrate transport system.
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Affiliation(s)
- Tatsuhiko Yokoyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tomoya Niinae
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kazuya Tsumagari
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Koshi Imami
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yohei Hizukuri
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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Dou Y, Rutanhira H, Schormann N, Deivanayagam C, Fletcher HM. PG1659 functions as anti-sigma factor to extracytoplasmic function sigma factor RpoE in Porphyromonas gingivalis W83. Mol Oral Microbiol 2021; 36:80-91. [PMID: 33377315 DOI: 10.1111/omi.12329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022]
Abstract
Anti-sigma factors play a critical role in regulating the expression of sigma factors in response to environmental stress signals. PG1659 is cotranscribed with an upstream gene PG1660 (rpoE), which encodes for a sigma factor that plays an important role in oxidative stress resistance and the virulence regulatory network of P. gingivalis. PG1659, which is annotated as a hypothetical gene, is evaluated in this study. PG1659, composed of 130 amino acids, is predicted to be transmembrane protein with a single calcium (Ca2+ ) binding site. In P. gingivalis FLL358 (ΔPG1659::ermF), the rpoE gene was highly upregulated compared to the wild-type W83 strain. RpoE-induced genes were also upregulated in the PG1659-defective isogenic mutant. Both protein-protein pull-down and bacterial two-hybrid assays revealed that the PG1659 protein could interact with/bind RpoE. The N-terminal domain of PG1659, representing the cytoplasmic fragment of the protein, is critical for interaction with RpoE. In the presence of PG1659, the initiation of transcription by the RpoE sigma factor was inhibited. Taken together, our data suggest that PG1659 is an anti-sigma factor which plays an important regulatory role in the modulation of the sigma factor RpoE in P. gingivalis.
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Affiliation(s)
- Yuetan Dou
- Department of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Hiel Rutanhira
- Department of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Norbert Schormann
- Department of Biochemistry and Molecular Genetics, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Champion Deivanayagam
- Department of Biochemistry and Molecular Genetics, School of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hansel M Fletcher
- Department of Microbiology and Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, USA
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Miyake T, Hizukuri Y, Akiyama Y. Involvement of a Membrane-Bound Amphiphilic Helix in Substrate Discrimination and Binding by an Escherichia coli S2P Peptidase RseP. Front Microbiol 2020; 11:607381. [PMID: 33329500 PMCID: PMC7728848 DOI: 10.3389/fmicb.2020.607381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/05/2020] [Indexed: 11/21/2022] Open
Abstract
Intramembrane proteases (IMPs) are a unique class of proteases that catalyze the proteolysis within the membrane and regulate diverse cellular processes in various organisms. RseP, an Escherichia coli site-2 protease (S2P) family IMP, is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-σE) protein RseA. Extracytoplasmic stresses trigger a sequential cleavage of RseA, in which first DegS cleaves off its periplasmic domain, and RseP catalyzes the second cleavage of RseA. The two tandem-arranged periplasmic PDZ (PDZ tandem) domains of RseP serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP IMP domain. However, RseP’s substrate recognition mechanism is not fully understood. Here, we found that a periplasmic region of RseP, located downstream of the PDZ tandem, contains a segment (named H1) predicted to form an amphiphilic helix. Bacterial S2P homologs with various numbers of PDZ domains have a similar amphiphilic helix in the corresponding region. We demonstrated that the H1 segment forms a partially membrane-embedded amphiphilic helix on the periplasmic surface of the membrane. Systematic and random mutagenesis analyses revealed that the H1 helix is important for the stability and proteolytic function of RseP and that mutations in the H1 segment can affect the PDZ-mediated substrate discrimination. Cross-linking experiments suggested that H1 directly interacts with the DegS-cleaved form of RseA. We propose that H1 acts as an adaptor required for proper arrangement of the PDZ tandem domain to perform its filter function and for substrate positioning for its efficient cleavage.
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Affiliation(s)
- Takuya Miyake
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yohei Hizukuri
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
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9
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Ramírez-Guadiana FH, Rodrigues CDA, Marquis KA, Campo N, Barajas-Ornelas RDC, Brock K, Marks DS, Kruse AC, Rudner DZ. Evidence that regulation of intramembrane proteolysis is mediated by substrate gating during sporulation in Bacillus subtilis. PLoS Genet 2018; 14:e1007753. [PMID: 30403663 PMCID: PMC6242693 DOI: 10.1371/journal.pgen.1007753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 11/19/2018] [Accepted: 10/10/2018] [Indexed: 01/11/2023] Open
Abstract
During the morphological process of sporulation in Bacillus subtilis two adjacent daughter cells (called the mother cell and forespore) follow different programs of gene expression that are linked to each other by signal transduction pathways. At a late stage in development, a signaling pathway emanating from the forespore triggers the proteolytic activation of the mother cell transcription factor σK. Cleavage of pro-σK to its mature and active form is catalyzed by the intramembrane cleaving metalloprotease SpoIVFB (B), a Site-2 Protease (S2P) family member. B is held inactive by two mother-cell membrane proteins SpoIVFA (A) and BofA. Activation of pro-σK processing requires a site-1 signaling protease SpoIVB (IVB) that is secreted from the forespore into the space between the two cells. IVB cleaves the extracellular domain of A but how this cleavage activates intramembrane proteolysis has remained unclear. Structural studies of the Methanocaldococcus jannaschii S2P homolog identified closed (substrate-occluded) and open (substrate-accessible) conformations of the protease, but the biological relevance of these conformations has not been established. Here, using co-immunoprecipitation and fluorescence microscopy, we show that stable association between the membrane-embedded protease and its substrate requires IVB signaling. We further show that the cytoplasmic cystathionine-β-synthase (CBS) domain of the B protease is not critical for this interaction or for pro-σK processing, suggesting the IVB-dependent interaction site is in the membrane protease domain. Finally, we provide evidence that the B protease domain adopts both open and closed conformations in vivo. Collectively, our data support a substrate-gating model in which IVB-dependent cleavage of A on one side of the membrane triggers a conformational change in the membrane-embedded protease from a closed to an open state allowing pro-σK access to the caged interior of the protease. Regulated Intramembrane Proteolysis is a broadly conserved mechanism for transducing information across lipid bilayers. In these signaling pathways a protease on one side of the membrane triggers the activation of a membrane-embedded protease that cleaves its substrate within or adjacent to the cytoplasmic face of the membrane. Site-2 metalloproteases (S2P) are the most commonly used intramembrane cleaving proteases in these pathways but the mechanism by which cleavage on one side of the membrane triggers intramembrane proteolysis remains poorly understood. Here, we provide evidence for a substrate-gating model in which an extracellular signaling protease triggers a conformational change in a S2P family member from a closed to an open conformation allowing its substrate access to the catalytic center of the enzyme.
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Affiliation(s)
| | | | - Kathleen A. Marquis
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA United States of America
| | - Nathalie Campo
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA United States of America
| | | | - Kelly Brock
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Debora S. Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Andrew C. Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - David Z. Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston MA United States of America
- * E-mail:
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10
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Dou Y, Rutanhira H, Chen X, Mishra A, Wang C, Fletcher HM. Role of extracytoplasmic function sigma factor PG1660 (RpoE) in the oxidative stress resistance regulatory network of Porphyromonas gingivalis. Mol Oral Microbiol 2017; 33:89-104. [PMID: 29059500 DOI: 10.1111/omi.12204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2017] [Indexed: 12/27/2022]
Abstract
In Porphyromonas gingivalis, the protein PG1660, composed of 174 amino acids, is annotated as an extracytoplasmic function (ECF) sigma factor (RpoE homologue-σ24). Because PG1660 can modulate several virulence factors and responds to environmental signals in P. gingivalis, its genetic properties were evaluated. PG1660 is co-transcribed with its downstream gene PG1659, and the transcription start site was identified as adenine residue 54-nucleotides upstream of the ATG translation start codon. In addition to binding its own promoter, using the purified rPG1660 and RNAP core enzyme from Escherichia coli with the PG1660 promoter DNA as template, the function of PG1660 as a sigma factor was demonstrated in an in vitro transcription assay. Transcriptome analyses of a P. gingivalis PG1660-defective isogenic mutant revealed that under oxidative stress conditions 176 genes including genes involved in secondary metabolism were downregulated more than two-fold compared with the parental strain. The rPG1660 protein also showed the ability to bind to the promoters of the highly downregulated genes in the PG1660-deficient mutant. As the ECF sigma factor PG0162 has a 29% identity with PG1660 and can modulate its expression, the cross-talk between their regulatory networks was explored. The expression profile of the PG0162PG1660-deficient mutant (P. gingivalis FLL356) revealed that the type IX secretion system genes and several virulence genes were downregulated under hydrogen peroxide stress conditions. Taken together, we have confirmed that PG1660 can function as a sigma factor, and plays an important regulatory role in the oxidative stress and virulence regulatory network of P. gingivalis.
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Affiliation(s)
- Y Dou
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - H Rutanhira
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - X Chen
- Department of Basic Sciences, School of Medicine, Center for Genomics, Loma Linda University, Loma Linda, CA, USA
| | - A Mishra
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - C Wang
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA.,Department of Basic Sciences, School of Medicine, Center for Genomics, Loma Linda University, Loma Linda, CA, USA
| | - H M Fletcher
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA.,Institute of Oral Biology, Kyung Hee University, Seoul, Korea
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11
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Bacillus subtilis Intramembrane Protease RasP Activity in Escherichia coli and In Vitro. J Bacteriol 2017; 199:JB.00381-17. [PMID: 28674070 DOI: 10.1128/jb.00381-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/29/2017] [Indexed: 01/19/2023] Open
Abstract
RasP is a predicted intramembrane metalloprotease of Bacillus subtilis that has been proposed to cleave the stress response anti-sigma factors RsiW and RsiV, the cell division protein FtsL, and remnant signal peptides within their transmembrane segments. To provide evidence for direct effects of RasP on putative substrates, we developed a heterologous coexpression system. Since expression of catalytically inactive RasP E21A inhibited expression of other membrane proteins in Escherichia coli, we added extra transmembrane segments to RasP E21A, which allowed accumulation of most other membrane proteins. A corresponding active version of RasP appeared to promiscuously cleave coexpressed membrane proteins, except those with a large periplasmic domain. However, stable cleavage products were not observed, even in clpP mutant E. coli Fusions of transmembrane segment-containing parts of FtsL and RsiW to E. coli maltose-binding protein (MBP) also resulted in proteins that appeared to be RasP substrates upon coexpression in E. coli, including FtsL with a full-length C-terminal domain (suggesting that prior cleavage by a site 1 protease is unnecessary) and RsiW designed to mimic the PrsW site 1 cleavage product (suggesting that further trimming by extracytoplasmic protease is unnecessary). Purified RasP cleaved His6-MBP-RsiW(73-118) in vitro within the RsiW transmembrane segment based on mass spectrometry analysis, demonstrating that RasP is an intramembrane protease. Surprisingly, purified RasP failed to cleave His6-MBP-FtsL(23-117). We propose that the lack of α-helix-breaking residues in the FtsL transmembrane segment creates a requirement for the membrane environment and/or an additional protein(s) in order for RasP to cleave FtsL.IMPORTANCE Intramembrane proteases govern important signaling pathways in nearly all organisms. In bacteria, they function in stress responses, cell division, pathogenesis, and other processes. Their membrane-associated substrates are typically inferred from genetic studies in the native bacterium. Evidence for direct effects has come sometimes from coexpression of the enzyme and potential substrate in a heterologous host and rarely from biochemical reconstitution of cleavage in vitro We applied these two approaches to the B. subtilis enzyme RasP and its proposed substrates RsiW and FtsL. We discovered potential pitfalls and solutions in heterologous coexpression experiments in E. coli, providing evidence that both substrates are cleaved by RasP in vivo but, surprisingly, that only RsiW was cleaved in vitro, suggesting that FtsL has an additional requirement.
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12
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Akiyama K, Hizukuri Y, Akiyama Y. Involvement of a conserved GFG motif region in substrate binding by RseP, an E
scherichia coli
S2P protease. Mol Microbiol 2017; 104:737-751. [DOI: 10.1111/mmi.13659] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Koichiro Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University; Kyoto 606-8507 Japan
| | - Yohei Hizukuri
- Institute for Frontier Life and Medical Sciences, Kyoto University; Kyoto 606-8507 Japan
| | - Yoshinori Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University; Kyoto 606-8507 Japan
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13
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Hizukuri Y, Akiyama K, Akiyama Y. Biochemical Characterization of Function and Structure of RseP, an Escherichia coli S2P Protease. Methods Enzymol 2016; 584:1-33. [PMID: 28065260 DOI: 10.1016/bs.mie.2016.09.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Intramembrane-cleaving proteases (I-CLiPs) are a group of membrane-associated proteases with a unique feature: they are believed to cleave their substrate within the hydrophobic lipid bilayer, even though peptide bond hydrolysis requires a water molecule. Escherichia coli RseP, which belongs to the S2P zinc metalloprotease family of I-CLiPs, plays an essential role in activation of a cell envelope stress response through cleavage of anti-σE protein RseA, a single-span transmembrane protein. A recent study showed that it also cleaves remnant signal peptides generated upon membrane translocation of secretory proteins. Here, we describe several methods for characterization of the proteolytic functions and structure of RseP mainly in vivo, including a proteolytic activity assay using model substrates, an in vitro analysis of cleavage of signal peptides in a detergent solution and in the membrane vesicles, structural analysis of membrane-embedded RseP based on the thiol modifiability of introduced cysteine residues, and the protein interaction analysis by in vivo cross-linking protocols.
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Affiliation(s)
- Y Hizukuri
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - K Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Y Akiyama
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.
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14
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Moreau PL, Loiseau L. Characterization of acetic acid-detoxifying Escherichia coli evolved under phosphate starvation conditions. Microb Cell Fact 2016; 15:42. [PMID: 26895825 PMCID: PMC4759930 DOI: 10.1186/s12934-016-0441-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 02/07/2016] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND During prolonged incubation of Escherichia coli K-12 in batch culture under aerobic, phosphate (Pi) starvation conditions, excess glucose is converted into acetic acid, which may trigger cell death. Following serial cultures, we isolated five evolved strains in two populations that survived prolonged incubation. METHODS We sequenced the genomes of the ancestral and evolved strains, and determined the effects of the genetic changes, tested alone and in combination, on characteristic phenotypes in pure and in mixed cultures. RESULTS Evolved strains used two main strategies: (1) the constitutive expression of the Trk- and Kdp-dependent K(+) transport systems, and (2) the inactivation of the ArcA global regulator. Both processes helped to maintain a residual activity of the tricarboxylic acid cycle, which decreased the production of acetic acid and eventually allowed its re-consumption. Evolved strains acquired a few additional genetic changes besides the trkH, kdpD and arcA mutations, which might increase the scavenging of organophosphates (phnE (+), lapB, and rseP) and the resistance to oxidative (rsxC) and acetic acid stresses (e14(-)/icd (+)). CONCLUSIONS Evolved strains rapidly acquired mutations (phnE (+) lapB rpoS trkH and phnE (+) rseP kdpD) that were globally beneficial to growth on glucose and organophosphates, but detrimental to long-term viability. The spread of these mutant strains might give the ancestral strain time to accumulate up to five genetic changes (phnE (+) arcA rsxC crfC e14(-)/icd (+)), which allowed growth on glucose and organophosphates, and provided a long-term survival. The latter strain, which expressed several mechanisms of protection against endogenous and exogenous stresses, might provide a platform for producing toxic recombinant proteins and chemicals during prolonged incubation under aerobic, Pi starvation conditions.
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Affiliation(s)
- Patrice L Moreau
- Laboratoire de Chimie Bactérienne, UMR 7283, Aix-Marseille Université, Marseille, France.
- Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Marseille, France.
| | - Laurent Loiseau
- Laboratoire de Chimie Bactérienne, UMR 7283, Aix-Marseille Université, Marseille, France.
- Institut de Microbiologie de la Méditerranée, Centre National de la Recherche Scientifique, Marseille, France.
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15
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Structural biology of intramembrane proteases: mechanistic insights from rhomboid and S2P to γ-secretase. Curr Opin Struct Biol 2016; 37:97-107. [PMID: 26811996 DOI: 10.1016/j.sbi.2015.12.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/14/2015] [Accepted: 12/28/2015] [Indexed: 12/21/2022]
Abstract
Intramembrane proteases catalyze hydrolysis of peptide bond within the lipid bilayer and play a key role in a variety of cellular processes. These membrane-embedded enzymes comprise four major classes: rhomboid serine proteases, site-2 metalloproteases, Rce1-type glutamyl proteases, and aspartyl proteases exemplified by signal peptide peptidase and γ-secretase. In the past several years, three-dimensional structures of representative members of these four classes of intramembrane protease have been reported at atomic resolutions, which reveal distinct protein folds and active site configurations. These structures, together with structure-guided biochemical analyses, shed light on the working mechanisms of water access and substrate entry. In this review, we discuss the shared as well as unique features of these intramembrane proteases, with a focus on presenilin-the catalytic component of γ-secretase.
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16
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Akiyama K, Mizuno S, Hizukuri Y, Mori H, Nogi T, Akiyama Y. Roles of the membrane-reentrant β-hairpin-like loop of RseP protease in selective substrate cleavage. eLife 2015; 4. [PMID: 26447507 PMCID: PMC4597795 DOI: 10.7554/elife.08928] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/10/2015] [Indexed: 11/13/2022] Open
Abstract
Molecular mechanisms underlying substrate recognition and cleavage by Escherichia coli RseP, which belongs to S2P family of intramembrane-cleaving proteases, remain unclear. We examined the function of a conserved region looped into the membrane domain of RseP to form a β-hairpin-like structure near its active site in substrate recognition and cleavage. We observed that mutations disturbing the possible β-strand conformation of the loop impaired RseP proteolytic activity and that some of these mutations resulted in the differential cleavage of different substrates. Co-immunoprecipitation and crosslinking experiments suggest that the loop directly interacts with the transmembrane segments of substrates. Helix-destabilising mutations in the transmembrane segments of substrates suppressed the effect of loop mutations in an allele-specific manner. These results suggest that the loop promotes substrate cleavage by selectively recognising the transmembrane segments of substrates in an extended conformation and by presenting them to the proteolytic active site, which contributes to substrate discrimination.
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Affiliation(s)
| | - Shinya Mizuno
- Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Yohei Hizukuri
- Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Hiroyuki Mori
- Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Terukazu Nogi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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17
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Two stress sensor proteins for the expression of sigmaE regulon: DegS and RseB. J Microbiol 2015; 53:306-10. [PMID: 25935301 DOI: 10.1007/s12275-015-5112-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 12/17/2022]
Abstract
In E. coli, sigmaE-dependent transcription is controlled by regulated-proteolysis of RseA. RseA, which holds sigmaE as an anti-sigma factor, is sequentially digested by DegS, RseP and cytoplasmic proteases to liberate sigmaE in response to dysfunction in outer-membrane biogenesis. Additionally, the sequential proteolysis is regulated by RseB binding to RseA (Fig. 1A). Direct interaction between RseA and RseB inhibits RseA-cleavage by DegS. Both proteolytic activation of DegS and binding disruption of RseB are thus required to initiate sigmaE-stress response. For the induction of sigmaEstress response, DegS and RseB recognize the states of OMP and LPS for outer-membrane biogenesis. DegS is activated by binding of unfolded OMPs and RseB binding to RseA is antagonized by LPS accumulated in periplasm. In this regard, DegS and RseB are proposed to be stress sensor proteins for sigmaE signal transduction. Interestingly, biogenesis of OMP and LPS appears to cross-talk with each other, indicating that dysfunction of either OMP or LPS can initiate RseA proteolysis. This review aims to briefly introduce two stress sensor proteins, DegS and RseB, which regulate sigmaEdependent transcription.
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18
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Hizukuri Y, Oda T, Tabata S, Tamura-Kawakami K, Oi R, Sato M, Takagi J, Akiyama Y, Nogi T. A structure-based model of substrate discrimination by a noncanonical PDZ tandem in the intramembrane-cleaving protease RseP. Structure 2014; 22:326-36. [PMID: 24389025 DOI: 10.1016/j.str.2013.12.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 12/04/2013] [Accepted: 12/04/2013] [Indexed: 11/25/2022]
Abstract
During the extracytoplasmic stress response in Escherichia coli, the intramembrane protease RseP cleaves the anti-σ(E) protein RseA only after the membrane-anchored protease DegS truncates the periplasmic part of RseA that suppresses the action of RseP. Here we analyzed the three-dimensional structure of the two tandemly arranged PSD-95/Dlg/ZO-1 (PDZ) domains (PDZ tandem) present in the periplasmic region of RseP and revealed that the two putative ligand-binding grooves constitute a single pocket-like structure that would lie just above the active center sequestrated within the membrane. Complete removal of the PDZ tandem from RseP led to the intramembrane cleavage of RseA without prior truncation by DegS. Furthermore, mutations expected to destabilize the tertiary structure of the PDZ tandem also caused the deregulation of the sequential cleavage. These observations suggest that the PDZ tandem serves as a size-exclusion filter to accommodate the truncated form of RseA into the active center.
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Affiliation(s)
- Yohei Hizukuri
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Takashi Oda
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Sanae Tabata
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | | | - Rika Oi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Mamoru Sato
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan; RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan
| | - Junichi Takagi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yoshinori Akiyama
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Terukazu Nogi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.
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19
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Kroos L, Akiyama Y. Biochemical and structural insights into intramembrane metalloprotease mechanisms. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2873-85. [PMID: 24099006 DOI: 10.1016/j.bbamem.2013.03.032] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 03/07/2013] [Accepted: 03/27/2013] [Indexed: 01/11/2023]
Abstract
Intramembrane metalloproteases are nearly ubiquitous in living organisms and they function in diverse processes ranging from cholesterol homeostasis and the unfolded protein response in humans to sporulation, stress responses, and virulence of bacteria. Understanding how these enzymes function in membranes is a challenge of fundamental interest with potential applications if modulators can be devised. Progress is described toward a mechanistic understanding, based primarily on molecular genetic and biochemical studies of human S2P and bacterial SpoIVFB and RseP, and on the structure of the membrane domain of an archaeal enzyme. Conserved features of the enzymes appear to include transmembrane helices and loops around the active site zinc ion, which may be near the membrane surface. Extramembrane domains such as PDZ (PSD-95, DLG, ZO-1) or CBS (cystathionine-β-synthase) domains govern substrate access to the active site, but several different mechanisms of access and cleavage site selection can be envisioned, which might differ depending on the substrate and the enzyme. More work is needed to distinguish between these mechanisms, both for enzymes that have been relatively well-studied, and for enzymes lacking PDZ and CBS domains, which have not been studied. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Lee Kroos
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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20
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Schneider JS, Glickman MS. Function of site-2 proteases in bacteria and bacterial pathogens. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2808-14. [PMID: 24099002 DOI: 10.1016/j.bbamem.2013.04.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 04/11/2013] [Accepted: 04/15/2013] [Indexed: 01/02/2023]
Abstract
Site-2 proteases (S2Ps) are a class of intramembrane metalloproteases named after the founding member of this protein family, human S2P, which control cholesterol and fatty acid biosynthesis by cleaving Sterol Regulatory Element Binding Proteins which control cholesterol and fatty acid biosynthesis. S2Ps are widely distributed in bacteria and participate in diverse pathways that control such diverse functions as membrane integrity, sporulation, lipid biosynthesis, pheromone production, virulence, and others. The most common signaling mechanism mediated by S2Ps is the coupled degradation of transmembrane anti-Sigma factors to activate ECF Sigma factor regulons. However, additional signaling mechanisms continue to emerge as more prokaryotic S2Ps are characterized, including direct proteolysis of membrane embedded transcription factors and proteolysis of non-transcriptional membrane proteins or membrane protein remnants. In this review we seek to comprehensively review the functions of S2Ps in bacteria and bacterial pathogens and attempt to organize these proteases into conceptual groups that will spur further study. This article is part of a Special Issue entitled: Intramembrane Proteases.
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Affiliation(s)
- Jessica S Schneider
- Immunology Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave., New York, NY 10065, USA; Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Biomedical Sciences, USA
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21
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Site-2 protease substrate specificity and coupling in trans by a PDZ-substrate adapter protein. Proc Natl Acad Sci U S A 2013; 110:19543-8. [PMID: 24218594 DOI: 10.1073/pnas.1305934110] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Site-2 proteases (S2Ps) are intramembrane metalloproteases that cleave transmembrane substrates in all domains of life. Many S2Ps, including human S2P and Mycobacterium tuberculosis Rip1, have multiple substrates in vivo, which are often transcriptional regulators. However, S2Ps will also cleave transmembrane sequences of nonsubstrate proteins, suggesting additional specificity determinants. Many S2Ps also contain a PDZ domain, the function of which is poorly understood. Here, we identify an M. tuberculosis protein, PDZ-interacting protease regulator 1 (Ppr1), which bridges between the Rip1 PDZ domain and anti-sigma factor M (Anti-SigM), a Rip1 substrate, but not Anti-SigK or Anti-SigL, also Rip1 substrates. In vivo analyses of Ppr1 function indicate that it prevents nonspecific activation of the Rip1 pathway while coupling Rip1 cleavage of Anti-SigM, but not Anti-SigL, to site-1 proteolysis. Our results support a model of S2P substrate specificity in which a substrate-specific adapter protein tethers the S2P to its substrate while holding the protease inactive through its PDZ domain.
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22
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Barchinger SE, Ades SE. Regulated proteolysis: control of the Escherichia coli σ(E)-dependent cell envelope stress response. Subcell Biochem 2013; 66:129-60. [PMID: 23479440 DOI: 10.1007/978-94-007-5940-4_6] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, regulatory proteolysis has emerged as a paradigm for transmembrane signal transduction in all organisms, from bacteria to humans. These conserved proteolytic pathways share a common design that involves the sequential proteolysis of a membrane-bound regulatory protein by two proteases. Proteolysis releases the regulator, which is inactive in its membrane-bound form, into the cytoplasm where it performs its cellular function. One of the best-characterized examples of signal transduction via regulatory proteolysis is the pathway governing the σ(E)-dependent cell envelope stress response in Escherichia coli. In unstressed cells, σ(E) is sequestered at the membrane by the transmembrane anti-sigma factor, RseA. Stresses that compromise the cell envelope and interfere with the proper folding of outer membrane proteins (OMPs) activate the proteolytic pathway. The C-terminal residues of unfolded OMPs bind to the inner membrane protease, DegS, to initiate the proteolytic cascade. DegS removes the periplasmic domain of RseA creating a substrate for the next protease in the pathway, RseP. RseP cleaves RseA in the periplasmic region in a process called regulated intramembrane proteolysis (RIP). The remaining fragment of RseA is released into the cytoplasm and fully degraded by the ATP-dependent protease, ClpXP, with the assistance of the adaptor protein, SspB, thereby freeing σ(E) to reprogram gene expression. A growing body of evidence indicates that the overall proteolytic framework that governs the σ(E) response is used to regulate similar anti-sigma factor/sigma factor pairs throughout the bacterial world and has been adapted to recognize a wide variety of signals and control systems as diverse as envelope stress responses, sporulation, virulence, and iron-siderophore uptake. In this chapter, we review the extensive physiological, biochemical, and structural studies on the σ(E) system that provide remarkable insights into the mechanistic underpinnings of this regulated proteolytic signal transduction pathway. These studies reveal design principles that are applicable to related proteases and regulatory proteolytic pathways in all domains of life.
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Affiliation(s)
- Sarah E Barchinger
- Graduate Program in BMMB, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
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