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Wang K, Wu Y, Wang Y, Yang Z, Zhang Y, Liu Z. The effects of phosphate fertilizer on the growth and reproduction of Pardosa pseudoannulata and its potential mechanisms. Comp Biochem Physiol C Toxicol Pharmacol 2023; 265:109538. [PMID: 36563951 DOI: 10.1016/j.cbpc.2022.109538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/04/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
In fields, the natural enemy spider, Pardosa pseudoannulata, plays important roles in insect pest control. Agrochemicals, such as phosphate fertilizer, disturb the ecosystem and weaken the pest control efficiency of the spider. According to the usual habitat of the spider in soil cracks, the soil-application of phosphate fertilizer was carried out to determine its effects on the growth and reproduction of P. pseudoannulata. Phosphate fertilizer treatment prolonged longevity and increased mortality in subadults. The treatment also negatively affected reproduction of P. pseudoannulata adults even with removing phosphate fertilizer stress before adult emergence, leading to a lower mating rate, fewer eggsacs and eggs per female, and fewer offsprings in the first eggsac. The transcriptomic sequencing analysis revealed the up-regulation of unigenes related to stress resistance and down-regulation of unigenes associated with protein processing and proteasomal degradation in phosphate fertilizer-treated P. pseudoannulata. Decline in proper protein processing by E3 ubiquitin-protein ligase complex and endopeptidase activity might provide a partial explanation for negative effects of phosphate fertilizer on the spider reproduction. The study put a notice on negative effects of phosphate fertilizer on beneficial arthropods, which provide a great potential in the protection of P. pseudoannulata and other predator spider species.
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Affiliation(s)
- Kan Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Yong Wu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Yunchao Wang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Zhiming Yang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Yixi Zhang
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China
| | - Zewen Liu
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Weigang 1, Nanjing 210095, China.
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2
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Brucella abortus Encodes an Active Rhomboid Protease: Proteome Response after Rhomboid Gene Deletion. Microorganisms 2022; 10:microorganisms10010114. [PMID: 35056563 PMCID: PMC8778405 DOI: 10.3390/microorganisms10010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 01/18/2023] Open
Abstract
Rhomboids are intramembrane serine proteases highly conserved in the three domains of life. Their key roles in eukaryotes are well understood but their contribution to bacterial physiology is still poorly characterized. Here we demonstrate that Brucella abortus, the etiological agent of the zoonosis called brucellosis, encodes an active rhomboid protease capable of cleaving model heterologous substrates like Drosophila melanogaster Gurken and Providencia stuartii TatA. To address the impact of rhomboid deletion on B. abortus physiology, the proteomes of mutant and parental strains were compared by shotgun proteomics. About 50% of the B. abortus predicted proteome was identified by quantitative proteomics under two experimental conditions and 108 differentially represented proteins were detected. Membrane associated proteins that showed variations in concentration in the mutant were considered as potential rhomboid targets. This class included nitric oxide reductase subunit C NorC (Q2YJT6) and periplasmic protein LptC involved in LPS transport to the outer membrane (Q2YP16). Differences in secretory proteins were also addressed. Differentially represented proteins included a putative lytic murein transglycosylase (Q2YIT4), nitrous-oxide reductase NosZ (Q2YJW2) and high oxygen affinity Cbb3-type cytochrome c oxidase subunit (Q2YM85). Deletion of rhomboid had no obvious effect in B. abortus virulence. However, rhomboid overexpression had a negative impact on growth under static conditions, suggesting an effect on denitrification enzymes and/or high oxygen affinity cytochrome c oxidase required for growth in low oxygen tension conditions.
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3
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Began J, Cordier B, Březinová J, Delisle J, Hexnerová R, Srb P, Rampírová P, Kožíšek M, Baudet M, Couté Y, Galinier A, Veverka V, Doan T, Strisovsky K. Rhomboid intramembrane protease YqgP licenses bacterial membrane protein quality control as adaptor of FtsH AAA protease. EMBO J 2020; 39:e102935. [PMID: 31930742 PMCID: PMC7231995 DOI: 10.15252/embj.2019102935] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/18/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
Magnesium homeostasis is essential for life and depends on magnesium transporters, whose activity and ion selectivity need to be tightly controlled. Rhomboid intramembrane proteases pervade the prokaryotic kingdom, but their functions are largely elusive. Using proteomics, we find that Bacillus subtilis rhomboid protease YqgP interacts with the membrane‐bound ATP‐dependent processive metalloprotease FtsH and cleaves MgtE, the major high‐affinity magnesium transporter in B. subtilis. MgtE cleavage by YqgP is potentiated in conditions of low magnesium and high manganese or zinc, thereby protecting B. subtilis from Mn2+/Zn2+ toxicity. The N‐terminal cytosolic domain of YqgP binds Mn2+ and Zn2+ ions and facilitates MgtE cleavage. Independently of its intrinsic protease activity, YqgP acts as a substrate adaptor for FtsH, a function that is necessary for degradation of MgtE. YqgP thus unites protease and pseudoprotease function, hinting at the evolutionary origin of rhomboid pseudoproteases such as Derlins that are intimately involved in eukaryotic ER‐associated degradation (ERAD). Conceptually, the YqgP‐FtsH system we describe here is analogous to a primordial form of “ERAD” in bacteria and exemplifies an ancestral function of rhomboid‐superfamily proteins.
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Affiliation(s)
- Jakub Began
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.,Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Baptiste Cordier
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France
| | - Jana Březinová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jordan Delisle
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France
| | - Rozálie Hexnerová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Petra Rampírová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
| | - Mathieu Baudet
- CEA, Inserm, IRIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Yohann Couté
- CEA, Inserm, IRIG-BGE, Univ. Grenoble Alpes, Grenoble, France
| | - Anne Galinier
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic.,Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Thierry Doan
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7283, Aix Marseille Univ, Marseille Cedex 20, France.,Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie de la Méditerranée (IMM), CNRS, UMR 7255, Aix Marseille Univ, Marseille Cedex 20, France
| | - Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czech Republic
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4
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Cho S, Baker RP, Ji M, Urban S. Ten catalytic snapshots of rhomboid intramembrane proteolysis from gate opening to peptide release. Nat Struct Mol Biol 2019; 26:910-918. [PMID: 31570873 PMCID: PMC6858540 DOI: 10.1038/s41594-019-0296-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/09/2019] [Indexed: 12/04/2022]
Abstract
Protein cleavage inside the cell membrane triggers various patho-physiological signaling pathways, but the mechanism of catalysis is poorly understood. We solved ten structures of the Escherichia coli rhomboid protease in a bicelle membrane undergoing time-resolved steps that encompass the entire proteolytic reaction on a transmembrane substrate and an aldehyde inhibitor. Extensive gate opening accompanied substrate, but not inhibitor, binding, revealing that substrates and inhibitors take different paths to the active site. Catalysis unexpectedly commenced with, and was guided through subsequent catalytic steps by, motions of an extracellular loop, with local contributions from active site residues. We even captured the elusive tetrahedral intermediate that is uncleaved but covalently attached to the catalytic serine, around which the substrate was forced to bend dramatically. This unexpectedly stable intermediate indicates rhomboid catalysis uses an unprecedented reaction coordinate that may involve mechanically stressing the peptide bond, and could be selectively targeted by inhibitors.
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Affiliation(s)
- Sangwoo Cho
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rosanna P Baker
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ming Ji
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Siniša Urban
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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5
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Kreutzberger AJB, Ji M, Aaron J, Mihaljević L, Urban S. Rhomboid distorts lipids to break the viscosity-imposed speed limit of membrane diffusion. Science 2019; 363:363/6426/eaao0076. [PMID: 30705155 DOI: 10.1126/science.aao0076] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/30/2018] [Accepted: 12/07/2018] [Indexed: 12/25/2022]
Abstract
Enzymes that cut proteins inside membranes regulate diverse cellular events, including cell signaling, homeostasis, and host-pathogen interactions. Adaptations that enable catalysis in this exceptional environment are poorly understood. We visualized single molecules of multiple rhomboid intramembrane proteases and unrelated proteins in living cells (human and Drosophila) and planar lipid bilayers. Notably, only rhomboid proteins were able to diffuse above the Saffman-Delbrück viscosity limit of the membrane. Hydrophobic mismatch with the irregularly shaped rhomboid fold distorted surrounding lipids and propelled rhomboid diffusion. The rate of substrate processing in living cells scaled with rhomboid diffusivity. Thus, intramembrane proteolysis is naturally diffusion-limited, but cells mitigate this constraint by using the rhomboid fold to overcome the "speed limit" of membrane diffusion.
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Affiliation(s)
- Alex J B Kreutzberger
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Ming Ji
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Jesse Aaron
- Howard Hughes Medical Institute, Advanced Imaging Center, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Ljubica Mihaljević
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Siniša Urban
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Room 507 PCTB, 725 North Wolfe Street, Baltimore, MD 21205, USA. .,Howard Hughes Medical Institute, Advanced Imaging Center, Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA
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6
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Recinto SJ, Paschkowsky S, Munter LM. An alternative processing pathway of APP reveals two distinct cleavage modes for rhomboid protease RHBDL4. Biol Chem 2018; 399:1399-1408. [DOI: 10.1515/hsz-2018-0259] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/28/2018] [Indexed: 02/02/2023]
Abstract
AbstractSince the first genetic description of a rhomboid inDrosophila melanogaster, tremendous efforts have been geared towards elucidating the proteolytic mechanism of this particular class of intramembrane proteases. In particular, mammalian rhomboid proteases sparked our interest and we aimed to investigate the human homologue RHBDL4. In light of our recent finding of the amyloid precursor protein (APP) family as efficient substrates of RHBDL4, we were enticed to further study the specific proteolytic mechanism of this enzyme by comparing cleavage patterns of wild type APP and APP TMS chimeras. Here, we demonstrate that the introduction of positively charged amino acid residues in the TMS redirects the RHBDL4-mediated cleavage of APP from its ectodomain closer towards the TMS, possibly inducing an ER-associated degradation (ERAD) of the substrate. In addition, we concluded that the cytoplasmic tail and proposed palmitoylation sites in the ectodomain of APP are not essential for the RHBDL4-mediated APP processing. In summary, our previously identified APP ectodomain cleavages by RHBDL4 are a subsidiary mechanism to the proposed RHBDL4-mediated ERAD of substrates likely through a single cleavage near or within the TMS.
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7
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Peng XM, Gao S, Deng HT, Cai HX, Zhou Z, Xiang R, Zhang QZ, Li LY. Perturbation of epithelial apicobasal polarity by rhomboid family-1 gene overexpression. FASEB J 2018; 32:5577-5586. [PMID: 29727209 DOI: 10.1096/fj.201800016r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
The human rhomboid family (RHBDF)1 gene is highly expressed in breast cancer under clinical conditions but not in normal mammary gland tissues. Silencing the RHBDF1 gene in breast cancer xenograft tumors leads to inhibition of tumor growth. We show in this study that artificially raising RHBDF1 protein levels in the mammary epithelial cells MCF-10A results in severe perturbations of the ability of the cells to form lumen-containing acini, either in 3-dimensional cell cultures or implanted in mouse mammary fat pads. Knocking down RHBDF1 with short hairpin (sh)RNA leads to restoration of acinus formation. Consistently, RHBDF1 overexpression gives rise to disordered distribution of polarity markers GM130 and laminin-5, which otherwise are located in apical and basal positions, respectively, in the acini. Further investigations reveal that RHBDF1 directly binds to Par6a, a component of a protein complex consisting of partitioning-defective scaffold protein (Par)6, Par3, renin-angiotensin system-related C3 botulinum toxin substrate (Rac)1, and cell-division cycle (Cdc)42, which is structurally critical to the formation of apicobasal polarity. RHBDF1 binding to Par6a results in collapse of the protein complex and thus disruption of polarity formation. Since early stages of breast cancer are characterized by the loss of mammary gland epithelial cell polarity, our findings indicate that perturbations of apicobasal polarity by high levels of RHBDF1 is a significant attribute in the development of breast neoplasia.-Peng, X.-M., Gao, S., Deng, H.-T., Cai, H.-X., Zhou, Z., Xiang, R., Zhang, Q.-Z., Li, L.-Y. Perturbation of epithelial apicobasal polarity by rhomboid family-1 gene overexpression.
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Affiliation(s)
- Xue-Mei Peng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Collaborative Innovation Center for Biotherapy and School of Medicine, Nankai University, Tianjin, China; and
- Department of Immunology, School of Medicine, Shanxi Datong University, Datong, China
| | - Shan Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Collaborative Innovation Center for Biotherapy and School of Medicine, Nankai University, Tianjin, China; and
| | - Hui-Ting Deng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Collaborative Innovation Center for Biotherapy and School of Medicine, Nankai University, Tianjin, China; and
| | - Hong-Xing Cai
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Collaborative Innovation Center for Biotherapy and School of Medicine, Nankai University, Tianjin, China; and
| | - Zhuan Zhou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Collaborative Innovation Center for Biotherapy and School of Medicine, Nankai University, Tianjin, China; and
| | - Rong Xiang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Collaborative Innovation Center for Biotherapy and School of Medicine, Nankai University, Tianjin, China; and
| | - Qiang-Zhe Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Collaborative Innovation Center for Biotherapy and School of Medicine, Nankai University, Tianjin, China; and
| | - Lu-Yuan Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Collaborative Innovation Center for Biotherapy and School of Medicine, Nankai University, Tianjin, China; and
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8
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Costa MI, Cerletti M, Paggi RA, Trötschel C, De Castro RE, Poetsch A, Giménez MI. Haloferax volcanii Proteome Response to Deletion of a Rhomboid Protease Gene. J Proteome Res 2018; 17:961-977. [PMID: 29301397 DOI: 10.1021/acs.jproteome.7b00530] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhomboids are conserved intramembrane serine proteases involved in cell signaling processes. Their role in prokaryotes is scarcely known and remains to be investigated in Archaea. We previously constructed a rhomboid homologue deletion mutant (ΔrhoII) in Haloferax volcanii, which showed reduced motility, increased novobiocin sensitivity, and an N- glycosylation defect. To address the impact of rhoII deletion on H. volcanii physiology, the proteomes of mutant and parental strains were compared by shotgun proteomics. A total of 1847 proteins were identified (45.8% of H. volcanii predicted proteome), from which 103 differed in amount. Additionally, the mutant strain evidenced 99 proteins with altered electrophoretic migration, which suggested differential post-translational processing/modification. Integral membrane proteins that evidenced variations in concentration, electrophoretic migration, or semitryptic cleavage in the mutant were considered as potential RhoII targets. These included a PrsW protease homologue (which was less stable in the mutant strain), a predicted halocyanin, and six integral membrane proteins potentially related to the mutant glycosylation (S-layer glycoprotein, Agl15) and cell adhesion/motility (flagellin1, HVO_1153, PilA1, and PibD) defects. This study investigated for the first time the impact of a rhomboid protease on the whole proteome of an organism.
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Affiliation(s)
- Mariana I Costa
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata, Buenos Aires 7600, Argentina
| | - Micaela Cerletti
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata, Buenos Aires 7600, Argentina
| | - Roberto A Paggi
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata, Buenos Aires 7600, Argentina
| | - Christian Trötschel
- Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum , 44801 Bochum, Germany
| | - Rosana E De Castro
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata, Buenos Aires 7600, Argentina
| | - Ansgar Poetsch
- Plant Biochemistry, Faculty of Biology & Biotechnology, Ruhr University Bochum , 44801 Bochum, Germany.,School of Biomedical and Healthcare Sciences, Plymouth University , Plymouth PL4 8AA, United Kingdom
| | - María I Giménez
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata (UNMdP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Funes 3250 4to nivel, Mar del Plata, Buenos Aires 7600, Argentina
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9
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Shokhen M, Albeck A. How does the exosite of rhomboid protease affect substrate processing and inhibition? Protein Sci 2017; 26:2355-2366. [PMID: 28884847 DOI: 10.1002/pro.3294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/27/2017] [Accepted: 09/03/2017] [Indexed: 12/24/2022]
Abstract
Rhomboid proteases constitute a family of intramembrane serine proteases ubiquitous in all forms of life. They differ in many aspects from their soluble counterparts. We applied molecular dynamics (MD) computational approach to address several challenging issues regarding their catalytic mechanism: How does the exosite of GlpG rhomboid protease control the kinetics efficiency of substrate hydrolysis? What is the mechanism of inhibition by the non-competitive peptidyl aldehyde inhibitors bound to the GlpG rhomboid active site (AS)? What is the underlying mechanism that explains the hypothesis that GlpG rhomboid protease is not adopted for the hydrolysis of short peptides that do not contain a transmembrane domain (TMD)? Two fundamental features of rhomboid catalysis, the enzyme recognition and discrimination of substrates by TMD interactions in the exosite, and the concerted mechanism of non-covalent pre-catalytic complex to covalent tetrahedral complex (TC) conversion, provide answers to these mechanistic questions.
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Affiliation(s)
- Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan, 5290002, Israel
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10
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Harsman A, Schneider A. Mitochondrial protein import in trypanosomes: Expect the unexpected. Traffic 2017; 18:96-109. [PMID: 27976830 DOI: 10.1111/tra.12463] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/01/2016] [Accepted: 12/06/2016] [Indexed: 12/11/2022]
Abstract
Mitochondria have many different functions, the most important one of which is oxidative phosphorylation. They originated from an endosymbiotic event between a bacterium and an archaeal host cell. It was the evolution of a protein import system that marked the boundary between the endosymbiotic ancestor of the mitochondrion and a true organelle that is under the control of the nucleus. In present day mitochondria more than 95% of all proteins are imported from the cytosol in a proces mediated by hetero-oligomeric protein complexes in the outer and inner mitochondrial membranes. In this review we compare mitochondrial protein import in the best studied model system yeast and the parasitic protozoan Trypanosoma brucei. The 2 organisms are phylogenetically only remotely related. Despite the fact that mitochondrial protein import has the same function in both species, only very few subunits of their import machineries are conserved. Moreover, while yeast has 2 inner membrane protein translocases, one specialized for presequence-containing and one for mitochondrial carrier proteins, T. brucei has a single inner membrane translocase only, that mediates import of both types of substrates. The evolutionary implications of these findings are discussed.
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Affiliation(s)
- Anke Harsman
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
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11
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Harsman A, Oeljeklaus S, Wenger C, Huot JL, Warscheid B, Schneider A. The non-canonical mitochondrial inner membrane presequence translocase of trypanosomatids contains two essential rhomboid-like proteins. Nat Commun 2016; 7:13707. [PMID: 27991487 PMCID: PMC5187411 DOI: 10.1038/ncomms13707] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/24/2016] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial protein import is essential for all eukaryotes. Here we show that the early diverging eukaryote Trypanosoma brucei has a non-canonical inner membrane (IM) protein translocation machinery. Besides TbTim17, the single member of the Tim17/22/23 family in trypanosomes, the presequence translocase contains nine subunits that co-purify in reciprocal immunoprecipitations and with a presequence-containing substrate that is trapped in the translocation channel. Two of the newly discovered subunits are rhomboid-like proteins, which are essential for growth and mitochondrial protein import. Rhomboid-like proteins were proposed to form the protein translocation pore of the ER-associated degradation system, suggesting that they may contribute to pore formation in the presequence translocase of T. brucei. Pulldown of import-arrested mitochondrial carrier protein shows that the carrier translocase shares eight subunits with the presequence translocase. This indicates that T. brucei may have a single IM translocase that with compositional variations mediates import of presequence-containing and carrier proteins.
The mitochondrial protein import machinery is crucial for eukaryotes but little is known about its evolutionary origin. Here, the authors characterize the translocase of the inner membrane (TIM) in trypanosomes, showing that it contains two rhomboid-like proteins essential for protein import.
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Affiliation(s)
- Anke Harsman
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Silke Oeljeklaus
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestraße 18, Freiburg 79104, Germany
| | - Christoph Wenger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Jonathan L Huot
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
| | - Bettina Warscheid
- Department of Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestraße 18, Freiburg 79104, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, Freiburg 79104, Germany
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern CH-3012, Switzerland
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Paschkowsky S, Hamzé M, Oestereich F, Munter LM. Alternative Processing of the Amyloid Precursor Protein Family by Rhomboid Protease RHBDL4. J Biol Chem 2016; 291:21903-21912. [PMID: 27563067 DOI: 10.1074/jbc.m116.753582] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 12/13/2022] Open
Abstract
The amyloid precursor protein (APP) is an ubiquitously expressed cell surface protein and a key molecule in the etiology of Alzheimer disease. Amyloidogenic processing of APP through secretases leads to the generation of toxic amyloid β (Aβ) peptides, which are regarded as the molecular cause of the disease. We report here an alternative processing pathway of APP through the mammalian intramembrane rhomboid protease RHBDL4. RHBDL4 efficiently cleaves APP inside the cell, thus bypassing APP from amyloidogenic processing, leading to reduced Aβ levels. RHBDL4 cleaves APP multiple times in the ectodomain, resulting in several N- and C-terminal fragments that are not further degraded by classical APP secretases. Knockdown of endogenous RHBDL4 results in decreased levels of C-terminal fragments derived from endogenous APP. Similarly, we found the APP family members APLP1 and APLP2 to be substrates of RHBDL4. We conclude that RHBDL4-mediated APP processing provides insight into APP and rhomboid physiology and qualifies for further investigations to elaborate its impact on Alzheimer disease pathology.
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Affiliation(s)
| | - Mehdi Hamzé
- From the Department of Pharmacology and Therapeutics and
| | - Felix Oestereich
- From the Department of Pharmacology and Therapeutics and Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3G 0B1, Canada
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13
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Strisovsky K. Rhomboid protease inhibitors: Emerging tools and future therapeutics. Semin Cell Dev Biol 2016; 60:52-62. [PMID: 27567709 DOI: 10.1016/j.semcdb.2016.08.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/16/2016] [Accepted: 08/24/2016] [Indexed: 02/01/2023]
Abstract
Rhomboid-family intramembrane serine proteases are evolutionarily widespread. Their functions in different organisms are gradually being uncovered and already suggest medical relevance for infectious diseases and cancer. In contrast to these advances, selective inhibitors that could serve as efficient tools for investigation of physiological functions of rhomboids, validation of their disease relevance or as templates for drug development are lacking. In this review I extract what is known about rhomboid protease mechanism and specificity, examine the currently used inhibitors, their mechanism of action and limitations, and conclude by proposing routes for future development of rhomboid protease inhibitors.
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Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n. 2, Prague 166 10, Czech Republic.
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14
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Abstract
Here, I take a somewhat personal perspective on signalling control, focusing on the rhomboid-like superfamily of proteins that my group has worked on for almost 20 years. As well as describing some of the key and recent advances, I attempt to draw out signalling themes that emerge. One important message is that the genetic and biochemical perspective on signalling has tended to underplay the importance of cell biology. There is clear evidence that signalling pathways exploit the control of intracellular trafficking, protein quality control and degradation and other cell biological phenomena, as important regulatory opportunities.
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Affiliation(s)
- Matthew Freeman
- Dunn School of Pathology, University of Oxford, OX1 3RE, U.K.
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15
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Functional Implications of Domain Organization Within Prokaryotic Rhomboid Proteases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 883:107-17. [PMID: 26621464 DOI: 10.1007/978-3-319-23603-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Intramembrane proteases are membrane embedded enzymes that cleave transmembrane substrates. This interesting class of enzyme and its water mediated substrate cleavage mechanism occurring within the hydrophobic lipid bilayer has drawn the attention of researchers. Rhomboids are a family of ubiquitous serine intramembrane proteases. Bacterial forms of rhomboid proteases are mainly composed of six transmembrane helices that are preceded by a soluble N-terminal domain. Several crystal structures of the membrane domain of the E. coli rhomboid protease ecGlpG have been solved. Independently, the ecGlpG N-terminal cytoplasmic domain structure was solved using both NMR and protein crystallography. Despite these structures, we still do not know the structure of the full-length protein, nor do we know the functional role of these domains in the cell. This chapter will review the structural and functional roles of the different domains associated with prokaryotic rhomboid proteases. Lastly, we will address questions remaining in the field.
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16
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Strisovsky K. Why cells need intramembrane proteases - a mechanistic perspective. FEBS J 2016; 283:1837-45. [DOI: 10.1111/febs.13638] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/19/2015] [Accepted: 12/24/2015] [Indexed: 01/01/2023]
Affiliation(s)
- Kvido Strisovsky
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; Prague Czech Republic
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17
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Uritsky N, Shokhen M, Albeck A. Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015; 55:1680-4. [DOI: 10.1002/anie.201507772] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Neta Uritsky
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
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18
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Uritsky N, Shokhen M, Albeck A. Stepwise Versus Concerted Mechanisms in General-Base Catalysis by Serine Proteases. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Neta Uritsky
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory; Department of Chemistry; Bar Ilan University; Ramat Gan 5290002 Israel
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19
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Nguyen MTN, Kersavond TV, Verhelst SHL. Chemical Tools for the Study of Intramembrane Proteases. ACS Chem Biol 2015; 10:2423-34. [PMID: 26473325 DOI: 10.1021/acschembio.5b00693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Intramembrane proteases (IMPs) reside inside lipid bilayers and perform peptide hydrolysis in transmembrane or juxtamembrane regions of their substrates. Many IMPs are involved in crucial regulatory pathways and human diseases, including Alzheimer's disease, Parkinson's disease, and diabetes. In the past, chemical tools have been instrumental in the study of soluble proteases, enabling biochemical and biomedical research in complex environments such as tissue lysates or living cells. However, IMPs place special challenges on probe design and applications, and progress has been much slower than for soluble proteases. In this review, we will give an overview of the available chemical tools for IMPs, including activity-based probes, affinity-based probes, and synthetic substrates. We will discuss how these have been used to increase our structural and functional understanding of this fascinating group of enzymes, and how they might be applied to address future questions and challenges.
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Affiliation(s)
- Minh T. N. Nguyen
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Tim Van Kersavond
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Steven H. L. Verhelst
- Leibniz Institute for Analytical Sciences ISAS, e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
- KU Leuven − University of Leuven, Department
of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestr. 49 Box 802, 3000 Leuven, Belgium
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Novick PA, Carmona NM, Trujillo M. Evolutionary dynamics of rhomboid proteases in Streptomycetes. BMC Res Notes 2015; 8:234. [PMID: 26054641 PMCID: PMC4467639 DOI: 10.1186/s13104-015-1205-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/08/2015] [Indexed: 11/13/2022] Open
Abstract
Background Proteolytic enzymes are ubiquitous and active in a myriad of biochemical pathways. One type, the rhomboids are intramembrane serine proteases that release their products extracellularly. These proteases are present in all forms of life and their function is not fully understood, although some evidence suggests they participate in cell signaling. Streptomycetes are prolific soil bacteria with diverse physiological and metabolic properties that respond to signals from other cells and from the environment. In the present study, we investigate the evolutionary dynamics of rhomboids in Streptomycetes, as this can shed light into the possible involvement of rhomboids in the complex lifestyles of these bacteria. Results Analysis of Streptomyces genomes revealed that they harbor up to five divergent putative rhomboid genes (arbitrarily labeled families A–E), two of which are orthologous to rhomboids previously described in Mycobacteria. Characterization of each of these rhomboid families reveals that each group is distinctive, and has its own evolutionary history. Two of the Streptomyces rhomboid families are highly conserved across all analyzed genomes suggesting they are essential. At least one family has been horizontally transferred, while others have been lost in several genomes. Additionally, the transcription of the four rhomboid genes identified in Streptomyces coelicolor, the model organism of this genus, was verified by reverse transcription. Conclusions Using phylogenetic and genomic analysis, this study demonstrates the existence of five distinct families of rhomboid genes in Streptomycetes. Families A and D are present in all nine species analyzed indicating a potentially important role for these genes. The four rhomboids present in S. coelicolor are transcribed suggesting they could participate in cellular metabolism. Future studies are needed to provide insight into the involvement of rhomboids in Streptomyces physiology. We are currently constructing knock out (KO) mutants for each of the rhomboid genes from S. coelicolor and will compare the phenotypes of the KOs to the wild type strain.
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Affiliation(s)
- Peter A Novick
- Biological Sciences and Geology Department, Queensborough Community College, City University of New York, Bayside, NY, USA.
| | - Naydu M Carmona
- Biological Sciences and Geology Department, Queensborough Community College, City University of New York, Bayside, NY, USA.
| | - Monica Trujillo
- Biological Sciences and Geology Department, Queensborough Community College, City University of New York, Bayside, NY, USA.
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21
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Freeman M. The Rhomboid-Like Superfamily: Molecular Mechanisms and Biological Roles. Annu Rev Cell Dev Biol 2014; 30:235-54. [DOI: 10.1146/annurev-cellbio-100913-012944] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Matthew Freeman
- Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom;
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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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23
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Urban S. Mechanisms and cellular functions of intramembrane proteases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2797-800. [PMID: 23831604 DOI: 10.1016/j.bbamem.2013.07.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The turn of the millennium coincided with the branding of a fundamentally different class of enzyme - proteases that reside immersed inside the membrane. This new field was the convergence of completely separate lines of research focused on cholesterol homeostasis, Alzheimer's disease, and developmental genetics. None intended their ultimate path, but soon became a richly-integrated fabric for an entirely new field: regulated intramembrane proteolysis. Our aim in this Special Issue is to focus on the ancient and nearly ubiquitous enzymes that catalyze this unexpected yet important reaction. The pace of progress has been dramatic, resulting in a rapidly-expanding universe of known cellular functions, and a paradigm shift in the biochemical understanding of these once heretical enzymes. More recently, the first therapeutic successes have been attained by targeting an intramembrane protease. We consider these advances and identify oncoming opportunities in four parts: growing spectra of cellular roles, insights into biochemical mechanisms, therapeutic strategies, and newly-emerging topics. Recent studies also expose challenges for the future, including non-linear relationships between substrate identification and physiological functions, and the need for potent and specific, not broad-class, inhibitors.
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Affiliation(s)
- Siniša Urban
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, USA.
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