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Rosenberg A, Luth MR, Winzeler EA, Behnke M, Sibley LD. Evolution of resistance in vitro reveals mechanisms of artemisinin activity in Toxoplasma gondii. Proc Natl Acad Sci U S A 2019; 116:26881-26891. [PMID: 31806760 PMCID: PMC6936365 DOI: 10.1073/pnas.1914732116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Artemisinins are effective against a variety of parasites and provide the first line of treatment for malaria. Laboratory studies have identified several mechanisms for artemisinin resistance in Plasmodium falciparum, including mutations in Kelch13 that are associated with delayed clearance in some clinical isolates, although other mechanisms are likely involved. To explore other potential mechanisms of resistance in parasites, we took advantage of the genetic tractability of Toxoplasma gondii, a related parasite that shows moderate sensitivity to artemisinin. Resistant populations of T. gondii were selected by culture in increasing concentrations and whole-genome sequencing identified several nonconservative point mutations that emerged in the population and were fixed over time. Genome editing using CRISPR/Cas9 was used to introduce point mutations conferring amino acid changes in a serine protease homologous to DegP and a serine/threonine protein kinase of unknown function. Single and double mutations conferred a competitive advantage over wild-type parasites in the presence of drug, despite not changing EC50 values. Additionally, the evolved resistant lines showed dramatic amplification of the mitochondria genome, including genes encoding cytochrome b and cytochrome c oxidase I. Prior studies in yeast and mammalian tumor cells implicate the mitochondrion as a target of artemisinins, and treatment of wild-type parasites with high concentrations of drug decreased mitochondrial membrane potential, a phenotype that was stably altered in the resistant parasites. These findings extend the repertoire of mutations associated with artemisinin resistance and suggest that the mitochondrion may be an important target of inhibition of resistance in T. gondii.
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Affiliation(s)
- Alex Rosenberg
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
| | - Madeline R. Luth
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Michael Behnke
- Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
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2
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Zarzecka U, Harrer A, Zawilak-Pawlik A, Skorko-Glonek J, Backert S. Chaperone activity of serine protease HtrA of Helicobacter pylori as a crucial survival factor under stress conditions. Cell Commun Signal 2019; 17:161. [PMID: 31796064 PMCID: PMC6892219 DOI: 10.1186/s12964-019-0481-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Serine protease HtrA exhibits both proteolytic and chaperone activities, which are involved in cellular protein quality control. Moreover, HtrA is an important virulence factor in many pathogens including Helicobacter pylori, for which the crucial stage of infection is the cleavage of E-cadherin and other cell-to-cell junction proteins. METHODS The in vitro study of H. pylori HtrA (HtrAHp) chaperone activity was carried out using light scattering assays and investigation of lysozyme protein aggregates. We produced H. pylori ∆htrA deletion and HtrAHp point mutants without proteolytic activity in strain N6 and investigated the survival of the bacteria under thermal, osmotic, acidic and general stress conditions as well as the presence of puromycin or metronidazole using serial dilution tests and disk diffusion method. The levels of cellular and secreted proteins were examined using biochemical fraction and Western blotting. We also studied the proteolytic activity of secreted HtrAHp using zymography and the enzymatic digestion of β-casein. Finally, the consequences of E-cadherin cleavage were determined by immunofluorescence microscopy. RESULTS We demonstrate that HtrAHp displays chaperone activity that inhibits the aggregation of lysozyme and is stable under various pH and temperature conditions. Next, we could show that N6 expressing only HtrA chaperone activity grow well under thermal, pH and osmotic stress conditions, and in the presence of puromycin or metronidazole. In contrast, in the absence of the entire htrA gene the bacterium was more sensitive to a number of stresses. Analysing the level of cellular and secreted proteins, we noted that H. pylori lacking the proteolytic activity of HtrA display reduced levels of secreted HtrA. Moreover, we compared the amounts of secreted HtrA from several clinical H. pylori strains and digestion of β-casein. We also demonstrated a significant effect of the HtrAHp variants during infection of human epithelial cells and for E-cadherin cleavage. CONCLUSION Here we identified the chaperone activity of the HtrAHp protein and have proven that this activity is important and sufficient for the survival of H. pylori under multiple stress conditions. We also pinpointed the importance of HtrAHp chaperone activity for E- cadherin degradation and therefore for the virulence of this eminent pathogen.
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Affiliation(s)
- Urszula Zarzecka
- Division of Microbiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany.,Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Aileen Harrer
- Division of Microbiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Joanna Skorko-Glonek
- Department of General and Medical Biochemistry, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Steffen Backert
- Division of Microbiology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany.
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3
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Degp degrades a wide range of substrate proteins in Escherichia coli under stress conditions. Biochem J 2019; 476:3549-3564. [DOI: 10.1042/bcj20190446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 11/17/2022]
Abstract
DegP, a periplasmic dual-functional protease and chaperone in Gram-negative bacteria, is critical for bacterial stress resistance, but the precise underlying mechanisms are not fully understood. Here, we show that the protease function of DegP is critical for Escherichia coli cells to maintain membrane integrity, particularly under heat shock conditions (42°C). Site-directed photo-cross-linking, mass spectrometry and immunoblotting analyses reveal that both periplasmic proteins (e.g. OppA and MalE) and β-barrel outer membrane proteins (OMPs) are DegP-interacting proteins and that OppA is degraded by DegP in vitro and in vivo at 42°C. In addition, OmpA and BamA, chimeric β-barrel OMPs containing a soluble periplasmic domain, are bound to DegP in both unfolded and folded forms, whereas only the unfolded forms are degradable by DegP. The presence of folded OmpA as a substrate of DegP is attributed to its periplasmic domain, which is resistant to DegP degradation and even generally protects pure β-barrel OMPs from degradation in an intra-molecular way. Furthermore, a pair of residues (R262 and V328) in the PDZ domain-1 of DegP play important roles for binding unfolded and folded β-barrel OMPs, with R262 being critical. Our study, together with earlier reports, indicates that DegP plays a critical role in protein quality control in the bacterial periplasm by degrading both periplasmic proteins and β-barrel OMPs under stress conditions and likely also by participating in the folding of chimeric β-barrel OMPs. A working model is proposed to illustrate the finely tuned functions of DegP with respect to different substrate proteins.
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4
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Fu X, Wang Y, Shao H, Ma J, Song X, Zhang M, Chang Z. DegP functions as a critical protease for bacterial acid resistance. FEBS J 2018; 285:3525-3538. [DOI: 10.1111/febs.14627] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 06/03/2018] [Accepted: 08/03/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Xinmiao Fu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
- Engineering Research Center of Industrial Microbiology of Ministry of Education College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Yan Wang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
- Engineering Research Center of Industrial Microbiology of Ministry of Education College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Heqi Shao
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation College of Life Sciences Fujian Normal University Fuzhou City Fujian Province China
| | - Jing Ma
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Xinwen Song
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Meng Zhang
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
| | - Zengyi Chang
- State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China
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5
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Szoradi T, Schaeff K, Garcia-Rivera EM, Itzhak DN, Schmidt RM, Bircham PW, Leiss K, Diaz-Miyar J, Chen VK, Muzzey D, Borner GHH, Schuck S. SHRED Is a Regulatory Cascade that Reprograms Ubr1 Substrate Specificity for Enhanced Protein Quality Control during Stress. Mol Cell 2018; 70:1025-1037.e5. [PMID: 29861160 DOI: 10.1016/j.molcel.2018.04.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 03/12/2018] [Accepted: 04/27/2018] [Indexed: 12/31/2022]
Abstract
When faced with proteotoxic stress, cells mount adaptive responses to eliminate aberrant proteins. Adaptive responses increase the expression of protein folding and degradation factors to enhance the cellular quality control machinery. However, it is unclear whether and how this augmented machinery acquires new activities during stress. Here, we uncover a regulatory cascade in budding yeast that consists of the hydrophilin protein Roq1/Yjl144w, the HtrA-type protease Ynm3/Nma111, and the ubiquitin ligase Ubr1. Various stresses stimulate ROQ1 transcription. The Roq1 protein is cleaved by Ynm3. Cleaved Roq1 interacts with Ubr1, transforming its substrate specificity. Altered substrate recognition by Ubr1 accelerates proteasomal degradation of misfolded as well as native proteins at the endoplasmic reticulum membrane and in the cytosol. We term this pathway stress-induced homeostatically regulated protein degradation (SHRED) and propose that it promotes physiological adaptation by reprogramming a key component of the quality control machinery.
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Affiliation(s)
- Tamas Szoradi
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Katharina Schaeff
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Enrique M Garcia-Rivera
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel N Itzhak
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Rolf M Schmidt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Peter W Bircham
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Kevin Leiss
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Juan Diaz-Miyar
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany
| | - Vivian K Chen
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dale Muzzey
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Sebastian Schuck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and CellNetworks Cluster of Excellence, 69120 Heidelberg, Germany.
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Naufahu J, Elliott B, Markiv A, Dunning-Foreman P, McGrady M, Howard D, Watt P, Mackenzie RWA. High-Intensity Exercise Decreases IP6K1 Muscle Content and Improves Insulin Sensitivity (SI2*) in Glucose-Intolerant Individuals. J Clin Endocrinol Metab 2018; 103:1479-1490. [PMID: 29300979 DOI: 10.1210/jc.2017-02019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/20/2017] [Indexed: 12/13/2022]
Abstract
CONTEXT Insulin resistance (IR) in skeletal muscle contributes to whole body hyperglycemia and the secondary complications associated with type 2 diabetes. Inositol hexakisphosphate kinase-1 (IP6K1) may inhibit insulin-stimulated glucose transport in this tissue type. OBJECTIVE Muscle and plasma IP6K1 were correlated with two-compartment models of glucose control in insulin-resistant hyperinsulinemic individuals. Muscle IP6K1 was also compared after two different exercise trials. DESIGN Nine prediabetic [hemoglobin A1c; 6.1% (0.2%)] patients were recruited to take part in a resting control, a continuous exercise (90% of lactate threshold), and a high-intensity exercise trial (6 30-second sprints). Muscle biopsies were drawn before and after each 60-minute trial. A labeled ([6,62H2]glucose) intravenous glucose tolerance test was performed immediately after the second muscle sample. RESULTS Fasting muscle IP6K1 content did not correlate with insulin sensitivity (SI2*) (P = 0.961). High-intensity exercise reduced IP6K1 muscle protein and messenger RNA expression (P = 0.001). There was no effect on protein IP6K1 content after continuous exercise. Akt308 phosphorylation of was significantly greater after high-intensity exercise. Intermittent exercise reduced hepatic glucose production after the same trial. The same intervention also increased SI2*, and this effect was significantly greater compared with the effect of continuous exercise improvements. Our in vitro experiment demonstrated that the chemical inhibition of IP6K1 increased insulin signaling in C2C12 myotubes. CONCLUSIONS The in vivo and in vitro approaches used in the current study suggest that a decrease in muscle IP6K1 may be linked to whole body increases in SI2*. In addition, high-intensity exercise reduces hepatic glucose production in insulin-resistant individuals.
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Affiliation(s)
- Jane Naufahu
- Faculty of Science and Technology, Department of Life Sciences, University of Westminster, London, United Kingdom
| | - Bradley Elliott
- Faculty of Science and Technology, Department of Life Sciences, University of Westminster, London, United Kingdom
| | - Anatoliy Markiv
- Biosciences Education, King's College London, London, United Kingdom
| | - Petra Dunning-Foreman
- Faculty of Science and Technology, Department of Life Sciences, University of Westminster, London, United Kingdom
| | - Maggie McGrady
- Faculty of Science and Technology, Department of Life Sciences, University of Westminster, London, United Kingdom
| | - David Howard
- Department of Oncology, Charing Cross Hospital, Imperial NHS Trust Hospitals, London, United Kingdom
| | - Peter Watt
- Centre for Sport and Exercise Science and Medicine (SESAME), University of Brighton, Eastbourne, United Kingdom
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7
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Abstract
Fungi are able to switch between different lifestyles in order to adapt to environmental changes. Their ecological strategy is connected to their secretome as fungi obtain nutrients by secreting hydrolytic enzymes to their surrounding and acquiring the digested molecules. We focus on fungal serine proteases (SPs), the phylogenetic distribution of which is barely described so far. In order to collect a complete set of fungal proteases, we searched over 600 fungal proteomes. Obtained results suggest that serine proteases are more ubiquitous than expected. From 54 SP families described in MEROPS Peptidase Database, 21 are present in fungi. Interestingly, 14 of them are also present in Metazoa and Viridiplantae - this suggests that, except one (S64), all fungal SP families evolved before plants and fungi diverged. Most representatives of sequenced eukaryotic lineages encode a set of 13-16 SP families. The number of SPs from each family varies among the analysed taxa. The most abundant are S8 proteases. In order to verify hypotheses linking lifestyle and expansions of particular SP, we performed statistical analyses and revealed previously undescribed associations. Here, we present a comprehensive evolutionary history of fungal SP families in the context of fungal ecology and fungal tree of life.
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8
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Chang Z. The function of the DegP (HtrA) protein: Protease versus chaperone. IUBMB Life 2016; 68:904-907. [PMID: 27670951 DOI: 10.1002/iub.1561] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 09/06/2016] [Indexed: 11/06/2022]
Abstract
The DegP (or HtrA) is a highly conserved family of proteins functioning in all living organisms. It was initially identified as a protease functioning in the periplasmic space of the Gram-negative bacterial cells. It was later reported to also exhibit chaperone activity and thus has been designated as a bifunctional protein. However, recent studies demonstrated that in living cells it more likely functions only as a protease with hardly detectable chaperone activities. In this review, I will summarize the evidences clarifying that DegP more likely only functions as a protease rather than as a chaperone in cells. © 2016 IUBMB Life, 68(11):904-907, 2016.
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Affiliation(s)
- Zengyi Chang
- Center for Protein Science, State Key Laboratory of Protein and Plant Gene Studies, School of Life Sciences, Center for History and Philosophy of Science, Peking University, Beijing, China.
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9
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Golani LK, Wallace-Povirk A, Deis SM, Wong J, Ke J, Gu X, Raghavan S, Wilson MR, Li X, Polin L, de Waal PW, White K, Kushner J, O'Connor C, Hou Z, Xu HE, Melcher K, Dann CE, Matherly LH, Gangjee A. Tumor Targeting with Novel 6-Substituted Pyrrolo [2,3-d] Pyrimidine Antifolates with Heteroatom Bridge Substitutions via Cellular Uptake by Folate Receptor α and the Proton-Coupled Folate Transporter and Inhibition of de Novo Purine Nucleotide Biosynthesis. J Med Chem 2016; 59:7856-76. [PMID: 27458733 DOI: 10.1021/acs.jmedchem.6b00594] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Targeted antifolates with heteroatom replacements of the carbon vicinal to the phenyl ring in 1 by N (4), O (8), or S (9), or with N-substituted formyl (5), acetyl (6), or trifluoroacetyl (7) moieties, were synthesized and tested for selective cellular uptake by folate receptor (FR) α and β or the proton-coupled folate transporter. Results show increased in vitro antiproliferative activity toward engineered Chinese hamster ovary cells expressing FRs by 4-9 over the CH2 analogue 1. Compounds 4-9 inhibited de novo purine biosynthesis and glycinamide ribonucleotide formyltransferase (GARFTase). X-ray crystal structures for 4 with FRα and GARFTase showed that the bound conformations of 4 required flexibility for attachment to both FRα and GARFTase. In mice bearing IGROV1 ovarian tumor xenografts, 4 was highly efficacious. Our results establish that heteroatom substitutions in the 3-atom bridge region of 6-substituted pyrrolo[2,3-d]pyrimidines related to 1 provide targeted antifolates that warrant further evaluation as anticancer agents.
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Affiliation(s)
- Lalit K Golani
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Adrianne Wallace-Povirk
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States
| | - Siobhan M Deis
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Jennifer Wong
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Jiyuan Ke
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Van Andel Research Institute , 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, United States
| | - Xin Gu
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Van Andel Research Institute , 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, United States
| | - Sudhir Raghavan
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Mike R Wilson
- Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Xinxin Li
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Lisa Polin
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States.,Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Parker W de Waal
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Van Andel Research Institute , 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, United States
| | - Kathryn White
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States.,Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Juiwanna Kushner
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States.,Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Carrie O'Connor
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States
| | - Zhanjun Hou
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States.,Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - H Eric Xu
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Van Andel Research Institute , 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, United States.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 201203, People's Republic of China
| | - Karsten Melcher
- Laboratory of Structural Sciences and Laboratory of Structural Biology and Biochemistry, Van Andel Research Institute , 333 Bostwick Avenue NE, Grand Rapids, Michigan 49503, United States
| | - Charles E Dann
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Larry H Matherly
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States.,Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States.,Department of Pharmacology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Aleem Gangjee
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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Sharma D, Soni R, Patel S, Joshi D, Bhatt TK. In-silico studies on DegP protein of Plasmodium falciparum in search of anti-malarials. J Mol Model 2016; 22:201. [PMID: 27491850 DOI: 10.1007/s00894-016-3064-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/03/2016] [Indexed: 10/21/2022]
Abstract
Despite encouraging progress over the past decade, malaria caused by the Plasmodium parasite continues to pose an enormous disease burden and is one of the major global health problems. The extreme challenge in malaria management is the resistance of parasites to traditional monochemotherapies like chloroquine and sulfadoxine-pyrimethamine. No vaccine is yet in sight, and the foregoing effective drugs are also losing ground against the disease due to the resistivity of parasites. New antimalarials with novel mechanisms of action are needed to circumvent existing or emerging drug resistance. DegP protein, secretory in nature has been shown to be involved in regulation of thermo-oxidative stress generated during asexual life cycle of Plasmodium, probably required for survival of parasite in host. Considering the significance of protein, in this study, we have generated a three-dimensional structure of PfDegP followed by validation of the modeled structure using several tools like RAMPAGE, ERRAT, and others. We also performed an in-silico screening of small molecule database against PfDegP using Glide. Furthermore, molecular dynamics simulation of protein and protein-ligand complex was carried out using GROMACS. This study substantiated potential drug-like molecules and provides the scope for development of novel antimalarial drugs.
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Affiliation(s)
- Drista Sharma
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Rajasthan, India, 305801
| | - Rani Soni
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Rajasthan, India, 305801
| | - Sachin Patel
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Rajasthan, India, 305801
| | - Deepti Joshi
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Rajasthan, India, 305801
| | - Tarun Kumar Bhatt
- Department of Biotechnology, Central University of Rajasthan, NH-8, Bandarsindri, Rajasthan, India, 305801.
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11
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HtrA, a Temperature- and Stationary Phase-Activated Protease Involved in Maturation of a Key Microbial Virulence Determinant, Facilitates Borrelia burgdorferi Infection in Mammalian Hosts. Infect Immun 2016; 84:2372-2381. [PMID: 27271745 DOI: 10.1128/iai.00360-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/31/2016] [Indexed: 01/04/2023] Open
Abstract
High-temperature requirement protease A (HtrA) represents a family of serine proteases that play important roles in microbial biology. Unlike the genomes of most organisms, that of Borrelia burgdorferi notably encodes a single HtrA gene product, termed BbHtrA. Previous studies identified a few substrates of BbHtrA; however, their physiological relevance could not be ascertained, as targeted deletion of the gene has not been successful. Here we show that BbhtrA transcripts are induced during spirochete growth either in the stationary phase or at elevated temperature. Successful generation of a BbhtrA deletion mutant and restoration by genetic complementation suggest a nonessential role for this protease in microbial viability; however, its remarkable growth, morphological, and structural defects during cultivation at 37°C confirm a high-temperature requirement for protease activation and function. The BbhtrA-deficient spirochetes were unable to establish infection of mice, as evidenced by assessment of culture, PCR, and serology. We show that transcript abundance as well as proteolytic processing of a borrelial protein required for cell fission and infectivity, BB0323, is impaired in BbhtrA mutants grown at 37°C, which likely contributed to their inability to survive in a mammalian host. Together, these results demonstrate the physiological relevance of a unique temperature-regulated borrelial protease, BbHtrA, which further enlightens our knowledge of intriguing aspects of spirochete biology and infectivity.
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12
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Cheregi O, Wagner R, Funk C. Insights into the Cyanobacterial Deg/HtrA Proteases. FRONTIERS IN PLANT SCIENCE 2016; 7:694. [PMID: 27252714 PMCID: PMC4877387 DOI: 10.3389/fpls.2016.00694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/05/2016] [Indexed: 06/05/2023]
Abstract
Proteins are the main machinery for all living processes in a cell; they provide structural elements, regulate biochemical reactions as enzymes, and are the interface to the outside as receptors and transporters. Like any other machinery proteins have to be assembled correctly and need maintenance after damage, e.g., caused by changes in environmental conditions, genetic mutations, and limitations in the availability of cofactors. Proteases and chaperones help in repair, assembly, and folding of damaged and misfolded protein complexes cost-effective, with low energy investment compared with neo-synthesis. Despite their importance for viability, the specific biological role of most proteases in vivo is largely unknown. Deg/HtrA proteases, a family of serine-type ATP-independent proteases, have been shown in higher plants to be involved in the degradation of the Photosystem II reaction center protein D1. The objective of this review is to highlight the structure and function of their cyanobacterial orthologs. Homology modeling was used to find specific features of the SynDeg/HtrA proteases of Synechocystis sp. PCC 6803. Based on the available data concerning their location and their physiological substrates we conclude that these Deg proteases not only have important housekeeping and chaperone functions within the cell, but also are needed for remodeling the cell exterior.
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Święciło A. Cross-stress resistance in Saccharomyces cerevisiae yeast--new insight into an old phenomenon. Cell Stress Chaperones 2016; 21:187-200. [PMID: 26825800 PMCID: PMC4786536 DOI: 10.1007/s12192-016-0667-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/27/2015] [Accepted: 01/04/2016] [Indexed: 12/20/2022] Open
Abstract
Acquired stress resistance is the result of mild stress causing the acquisition of resistance to severe stress of the same or a different type. The mechanism of "same-stress" resistance (resistance to a second, strong stress after mild primary stress of the same type) probably depends on the activation of defense and repair mechanisms specific for a particular type of stress, while cross-stress resistance (i.e., resistance to a second, strong stress after a different type of mild primary stress) is the effect of activation of both a specific and general stress response program, which in Saccharomyces cerevisiae yeast is known as the environmental stress response (ESR). Advancements in research techniques have made it possible to study the mechanism of cross-stress resistance at various levels of cellular organization: stress signal transduction pathways, regulation of gene expression, and transcription or translation processes. As a result of this type of research, views on the cross-stress protection mechanism have been reconsidered. It was originally thought that cross-stress resistance, irrespective of the nature of the two stresses, was determined by universal mechanisms, i.e., the same mechanisms within the general stress response. They are now believed to be more specific and strictly dependent on the features of the first stress.
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Affiliation(s)
- Agata Święciło
- Faculty of Agrobioengineering, Department of Environmental Microbiology, University of Life Sciences in Lublin, Leszczynskiego 7, 20-069, Lublin, Poland.
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Wang L, Wallace A, Raghavan S, Deis SM, Wilson MR, Yang S, Polin L, White K, Kushner J, Orr S, George C, O'Connor C, Hou Z, Mitchell-Ryan S, Dann CE, Matherly LH, Gangjee A. 6-Substituted Pyrrolo[2,3-d]pyrimidine Thienoyl Regioisomers as Targeted Antifolates for Folate Receptor α and the Proton-Coupled Folate Transporter in Human Tumors. J Med Chem 2015; 58:6938-59. [PMID: 26317331 DOI: 10.1021/acs.jmedchem.5b00801] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
2-Amino-4-oxo-6-substituted-pyrrolo[2,3-d]pyrimidine antifolate thiophene regioisomers of AGF94 (4) with a thienoyl side chain and three-carbon bridge lengths [AGF150 (5) and AGF154 (7)] were synthesized as potential antitumor agents. These analogues inhibited proliferation of Chinese hamster ovary (CHO) sublines expressing folate receptors (FRs) α or β (IC50s < 1 nM) or the proton-coupled folate transporter (PCFT) (IC50 < 7 nM). Compounds 5 and 7 inhibited KB, IGROV1, and SKOV3 human tumor cells at subnanomolar concentrations, reflecting both FRα and PCFT uptake. AGF152 (6) and AGF163 (8), 2,4-diamino-5-substituted-furo[2,3-d]pyrimidine thiophene regioisomers, also inhibited growth of FR-expressing CHO and KB cells. All four analogues inhibited glycinamide ribonucleotide formyltransferase (GARFTase). Crystal structures of human GARFTase complexed with 5 and 7 were reported. In severe combined immunodeficient mice bearing SKOV3 tumors, 7 was efficacious. The selectivity of these compounds for PCFT and for FRα and β over the ubiquitously expressed reduced folate carrier is a paradigm for selective tumor targeting.
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Affiliation(s)
- Lei Wang
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Adrianne Wallace
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States
| | - Sudhir Raghavan
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Siobhan M Deis
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Mike R Wilson
- Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Si Yang
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
| | - Lisa Polin
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States.,Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Kathryn White
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States.,Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Juiwanna Kushner
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States.,Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Steven Orr
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States
| | - Christina George
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States
| | - Carrie O'Connor
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States
| | - Zhanjun Hou
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States.,Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Shermaine Mitchell-Ryan
- Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Charles E Dann
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Larry H Matherly
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute , 110 East Warren Avenue, Detroit, Michigan 48201, United States.,Department of Oncology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States.,Department of Pharmacology, Wayne State University School of Medicine , Detroit, Michigan 48201, United States
| | - Aleem Gangjee
- Division of Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, Duquesne University , 600 Forbes Avenue, Pittsburgh, Pennsylvania 15282, United States
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15
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Bohovych I, Chan SS, Khalimonchuk O. Mitochondrial protein quality control: the mechanisms guarding mitochondrial health. Antioxid Redox Signal 2015; 22:977-94. [PMID: 25546710 PMCID: PMC4390190 DOI: 10.1089/ars.2014.6199] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 12/20/2014] [Indexed: 12/20/2022]
Abstract
SIGNIFICANCE Mitochondria are complex dynamic organelles pivotal for cellular physiology and human health. Failure to maintain mitochondrial health leads to numerous maladies that include late-onset neurodegenerative diseases and cardiovascular disorders. Furthermore, a decline in mitochondrial health is prevalent with aging. A set of evolutionary conserved mechanisms known as mitochondrial quality control (MQC) is involved in recognition and correction of the mitochondrial proteome. RECENT ADVANCES Here, we review current knowledge and latest developments in MQC. We particularly focus on the proteolytic aspect of MQC and its impact on health and aging. CRITICAL ISSUES While our knowledge about MQC is steadily growing, critical gaps remain in the mechanistic understanding of how MQC modules sense damage and preserve mitochondrial welfare, particularly in higher organisms. FUTURE DIRECTIONS Delineating how coordinated action of the MQC modules orchestrates physiological responses on both organellar and cellular levels will further elucidate the current picture of MQC's role and function in health, cellular stress, and degenerative diseases.
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Affiliation(s)
- Iryna Bohovych
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
- Nebraska Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Sherine S.L. Chan
- Department of Drug Discovery and Biomedical Sciences, Medical University of South Carolina, Charleston, South Carolina
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska
- Nebraska Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska
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16
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Saleh AA, Bhadra AK, Roy I. Cytotoxicity of mutant huntingtin fragment in yeast can be modulated by the expression level of wild type huntingtin fragment. ACS Chem Neurosci 2014; 5:205-15. [PMID: 24377263 PMCID: PMC3963126 DOI: 10.1021/cn400171d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/26/2013] [Indexed: 12/23/2022] Open
Abstract
Conflicting reports exist in the literature regarding the role of wild-type huntingtin in determining the toxicity of the aggregated, mutant huntingtin in Huntington's disease (HD). Some studies report the amelioration of toxicity of the mutant protein in the presence of the wild-type protein, while others indicate sequestration of the wild-type protein by mutant huntingtin. Over the years, yeast has been established as a valid model organism to study molecular changes associated with HD, especially at the protein level. We have used an inducible system to express human huntingtin fragments harboring normal (25Q) and pathogenic (103Q) polyglutamine lengths under the control of a galactose promoter in a yeast model of HD. We show that the relative expression level of each allele (wild-type/mutant) decides the cellular phenotype. When the expression level of wild-type huntingtin is high, an increase in the solubility of the mutant protein is observed. Fluorescence-recovery-after-photobleaching (FRAP) studies show that solubility reaches ∼94% in these cells. This leads to reduction in oxidative stress and cytotoxicity, and increases cell viability. In-cell FRET studies show that interaction between these proteins does not require the presence of a mediator. When the expression of wild-type huntingtin is low, it is sequestered into aggregates by the mutant protein. Even under these conditions, cytotoxicity is attenuated. Our findings indicate that the presence of wild-type huntingtin has a beneficial role even when its relative expression level is lower than that of the mutant protein.
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Affiliation(s)
- Aliabbas Ahmedbhai Saleh
- Department of Biotechnology, National Institute
of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ankan Kumar Bhadra
- Department of Biotechnology, National Institute
of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Ipsita Roy
- Department of Biotechnology, National Institute
of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160 062, India
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Sharma S, Jadli M, Singh A, Arora K, Malhotra P. A secretory multifunctional serine protease, DegP of Plasmodium falciparum, plays an important role in thermo-oxidative stress, parasite growth and development. FEBS J 2014; 281:1679-99. [PMID: 24494818 DOI: 10.1111/febs.12732] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/27/2013] [Accepted: 01/23/2014] [Indexed: 12/12/2022]
Abstract
UNLABELLED Plasmodium falciparum heat shock proteins and proteases are known for their indispensable roles in parasite virulence and survival in the host cell. They neutralize various host-derived stress responses that are deleterious for parasite growth and invasion. We report identification and functional characterization of the first DegP from an apicomplexan (P. falciparum). To determine the molecular identity and functions of the parasite-encoded DegP, we complemented the Escherichia coli degP null mutant with a putative PfdegP gene, and the results showed that PfDegP complements the growth defect of the temperature sensitive DegP-deficient mutant and imparts resistance to non-permissive temperatures and oxidative stress. Molecular interaction studies showed that PfDegP exists as a complex with parasite-encoded heat shock protein 70, iron superoxide dismutase and enolase. DegP expression is significantly induced in parasite culture upon heat shock/oxidative stress. Our data suggest that the PfDegP protein may play a role in the growth and development of P. falciparum through its ability to confer protection against thermal/oxidative stress. Antibody against DegP showed anti-plasmodial activity against blood-stage parasites in vitro, suggesting that PfDegP and its associated complex may be a potential focus for new anti-malarial therapies. STRUCTURED DIGITAL ABSTRACT ●PfDegP physically interacts with PfHsp70 and PfEno by anti-bait co-immunoprecipitation (View interaction) ●PfDegP physically interacts with PfEno, PfSod, PfOat, PfHsp70, PfLDH and PfGpi by anti-bait co-immunoprecipitation (View interaction) ●PfHsp-70 and PfDegP co-localize by fluorescence microscopy (View interaction) ●PfDegP physically interacts with PfOat, PfHsp70, PfEno, PfSod, PfGpi and PfLDH by surface plasmon resonance (View interaction) ●PfEno and PfDegP co-localize by fluorescence microscopy (View interaction) ●PfDegP and PfHsp70 co-localize by co-sedimentation through density gradient (View interaction).
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Affiliation(s)
- Shweta Sharma
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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18
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Ge X, Wang R, Ma J, Liu Y, Ezemaduka AN, Chen PR, Fu X, Chang Z. DegP primarily functions as a protease for the biogenesis of β-barrel outer membrane proteins in the Gram-negative bacterium Escherichia coli. FEBS J 2014; 281:1226-40. [PMID: 24373465 DOI: 10.1111/febs.12701] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 12/16/2013] [Accepted: 12/17/2013] [Indexed: 12/31/2022]
Abstract
DegP (also designated as HtrA) and its homologs are found in prokaryotic cells and such eukaryotic organelles as mitochondria and chloroplasts. DegP has been found to be essential for the growth of Gram-negative bacteria under heat shock conditions and arguably considered to possess both protease and chaperone activities. The function of DegP has not been clearly defined. Using genetically incorporated non-natural amino acids as photo-crosslinkers, here we identified the β-barrel outer membrane proteins (OMPs) as the major natural substrates of DegP in Escherichia coli cells. We also demonstrated that DegP primarily functions as a protease, at both low and high temperatures, to eliminate unfolded OMPs, with hardly any appreciable chaperone activity in cells. We also found that the toxic and cell membrane-damaging misfolded OMPs would accumulate in DegP-lacking cells cultured under heat shock conditions. Together, our study defines the primary function of DegP in OMP biogenesis and offers a mechanistic insight into the essentiality of DegP for cell growth under heat shock conditions.
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Affiliation(s)
- Xi Ge
- State Key Laboratory of Protein and Plant Gene Research and School of Life Sciences, Peking University, China
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19
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Nuclear FKBPs, Fpr3 and Fpr4 affect genome-wide genes transcription. Mol Genet Genomics 2013; 289:125-36. [DOI: 10.1007/s00438-013-0794-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 11/18/2013] [Indexed: 10/26/2022]
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20
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Galat A. Functional diversity and pharmacological profiles of the FKBPs and their complexes with small natural ligands. Cell Mol Life Sci 2013; 70:3243-75. [PMID: 23224428 PMCID: PMC11113493 DOI: 10.1007/s00018-012-1206-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 10/24/2012] [Accepted: 10/25/2012] [Indexed: 12/25/2022]
Abstract
From 5 to 12 FK506-binding proteins (FKBPs) are encoded in the genomes of disparate marine organisms, which appeared at the dawn of evolutionary events giving rise to primordial multicellular organisms with elaborated internal body plan. Fifteen FKBPs, several FKBP-like proteins and some splicing variants of them are expressed in humans. Human FKBP12 and some of its paralogues bind to different macrocyclic antibiotics such as FK506 or rapamycin and their derivatives. FKBP12/(macrocyclic antibiotic) complexes induce diverse pharmacological activities such as immunosuppression in humans, anticancerous actions and as sustainers of quiescence in certain organisms. Since the FKBPs bind to various assemblies of proteins and other intracellular components, their complexes with the immunosuppressive drugs may differentially perturb miscellaneous cellular functions. Sequence-structure relationships and pharmacological profiles of diverse FKBPs and their involvement in crucial intracellular signalization pathways and modulation of cryptic intercellular communication networks were discussed.
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Affiliation(s)
- Andrzej Galat
- Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Biologie et de Technologies de Saclay, Service d'Ingénierie Moléculaire des Protéines, Bat. 152, 91191, Gif-sur-Yvette Cedex, France.
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21
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Ghosh A, Cannon JF. Analysis of protein phosphatase-1 and aurora protein kinase suppressors reveals new aspects of regulatory protein function in Saccharomyces cerevisiae. PLoS One 2013; 8:e69133. [PMID: 23894419 PMCID: PMC3718817 DOI: 10.1371/journal.pone.0069133] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 06/01/2013] [Indexed: 01/31/2023] Open
Abstract
Protein phosphatase-1 (PP1) controls many processes in eukaryotic cells. Modulation of mitosis by reversing phosphorylation of proteins phosphorylated by aurora protein kinase is a critical function for PP1. Overexpression of the sole PP1, Glc7, in budding yeast, Saccharomyces cerevisiae, is lethal. This work shows that lethality requires the function of Glc7 regulatory proteins Sds22, Reg2, and phosphorylated Glc8. This finding shows that Glc7 overexpression induced cell death requires a specific subset of the many Glc7-interacting proteins and therefore is likely caused by promiscuous dephosphorylation of a variety of substrates. Additionally, suppression can occur by reducing Glc7 protein levels by high-copy Fpr3 without use of its proline isomerase domain. This divulges a novel function of Fpr3. Most suppressors of GLC7 overexpression also suppress aurora protein kinase, ipl1, temperature-sensitive mutations. However, high-copy mutant SDS22 genes show reciprocal suppression of GLC7 overexpression induced cell death or ipl1 temperature sensitivity. Sds22 binds to many proteins besides Glc7. The N-terminal 25 residues of Sds22 are sufficient to bind, directly or indirectly, to seven proteins studied here including the spindle assembly checkpoint protein, Bub3. These data demonstrate that Sds22 organizes several proteins in addition to Glc7 to perform functions that counteract Ipl1 activity or lead to hyper Glc7 induced cell death. These data also emphasize that Sds22 targets Glc7 to nuclear locations distinct from Ipl1 substrates.
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Affiliation(s)
- Anuprita Ghosh
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
| | - John F. Cannon
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, United States of America
- * E-mail:
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Laskar A, Rodger EJ, Chatterjee A, Mandal C. Modeling and structural analysis of PA clan serine proteases. BMC Res Notes 2012; 5:256. [PMID: 22624962 PMCID: PMC3434108 DOI: 10.1186/1756-0500-5-256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 05/11/2012] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Serine proteases account for over a third of all known proteolytic enzymes; they are involved in a variety of physiological processes and are classified into clans sharing structural homology. The PA clan of endopeptidases is the most abundant and over two thirds of this clan is comprised of the S1 family of serine proteases, which bear the archetypal trypsin fold and have a catalytic triad in the order Histidine, Aspartate, Serine. These proteases have been studied in depth and many three dimensional structures have been experimentally determined. However, these structures mostly consist of bacterial and animal proteases, with a small number of plant and fungal proteases and as yet no structures have been determined for protozoa or archaea. The core structure and active site geometry of these proteases is of interest for many applications. This study investigated the structural properties of different S1 family serine proteases from a diverse range of taxa using molecular modeling techniques. RESULTS Our predicted models from protozoa, archaea, fungi and plants were combined with the experimentally determined structures of 16 S1 family members and used for analysis of the catalytic core. Amino acid sequences were submitted to SWISS-MODEL for homology-based structure prediction or the LOOPP server for threading-based structure prediction. Predicted models were refined using INSIGHT II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Some highly conserved residues potentially contributing to the stability of the structural core were identified. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. CONCLUSIONS Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on S1 family serine proteases. Focusing on the common core containing the catalytic site of the enzyme, this analysis is beneficial for future molecular modeling strategies and structural analysis of serine protease models.
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Affiliation(s)
- Aparna Laskar
- Indian Institute of Chemical Biology (CSIR Unit, Government of India), Kolkata, West Bengal, India.
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PpiA, a surface PPIase of the cyclophilin family in Lactococcus lactis. PLoS One 2012; 7:e33516. [PMID: 22442694 PMCID: PMC3307742 DOI: 10.1371/journal.pone.0033516] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 02/10/2012] [Indexed: 12/05/2022] Open
Abstract
Background Protein folding in the envelope is a crucial limiting step of protein export and secretion. In order to better understand this process in Lactococcus lactis, a lactic acid bacterium, genes encoding putative exported folding factors like Peptidyl Prolyl Isomerases (PPIases) were searched for in lactococcal genomes. Results In L. lactis, a new putative membrane PPIase of the cyclophilin subfamily, PpiA, was identified and characterized. ppiA gene was found to be constitutively expressed under normal and stress (heat shock, H2O2) conditions. Under normal conditions, PpiA protein was synthesized and released from intact cells by an exogenously added protease, showing that it was exposed at the cell surface. No obvious phenotype could be associated to a ppiA mutant strain under several laboratory conditions including stress conditions, except a very low sensitivity to H2O2. Induction of a ppiA copy provided in trans had no effect i) on the thermosensitivity of an mutant strain deficient for the lactococcal surface protease HtrA and ii) on the secretion and stability on four exported proteins (a highly degraded hybrid protein and three heterologous secreted proteins) in an otherwise wild-type strain background. However, a recombinant soluble form of PpiA that had been produced and secreted in L. lactis and purified from a culture supernatant displayed both PPIase and chaperone activities. Conclusions Although L. lactis PpiA, a protein produced and exposed at the cell surface under normal conditions, displayed a very moderate role in vivo, it was found, as a recombinant soluble form, to be endowed with folding activities in vitro.
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Nma111p, the pro-apoptotic HtrA-like nuclear serine protease in Saccharomyces cerevisiae: a short survey. Biochem Soc Trans 2012; 39:1499-501. [PMID: 21936841 DOI: 10.1042/bst0391499] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The baker's yeast, Saccharomyces cerevisiae, is also capable of undergoing programmed cell death or apoptosis, for example in response to viral infection as well as during chronological and replicative aging. Intrinsically, programmed cell death in yeast can be induced by, for example, H2O2, acetic acid or the mating-type pheromone. A number of evolutionarily conserved apoptosis-regulatory proteins have been identified in yeast, one of which is the HtrA (high-temperature requirement A)-like serine protease Nma111p (Nma is nuclear mediator of apoptosis). Nma111p is a nuclear serine protease of the HtrA family, which targets Bir1p, the only known inhibitor-of-apoptosis protein in yeast. Nma111p mediates apoptosis in a serine-protease-dependent manner and exhibits its activity exclusively in the nucleus. How the activity of Nma111p is regulated has remained largely elusive, but some evidence points to a control by phosphorylation. Current knowledge of Nma111p's function in apoptosis will be discussed in the present review.
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25
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A new principle of oligomerization of plant DEG7 protease based on interactions of degenerated protease domains. Biochem J 2011; 435:167-74. [PMID: 21247409 PMCID: PMC3194040 DOI: 10.1042/bj20101613] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Deg/HtrA proteases are a large group of ATP-independent serine endoproteases found in almost every organism. Their usual domain arrangement comprises a trypsin-type protease domain and one or more PDZ domains. All Deg/HtrA proteases form homo-oligomers with trimers as the basic unit, where the active protease domain mediates the interaction between individual monomers. Among the members of the Deg/HtrA protease family, the plant protease DEG7 is unique since it contains two protease domains (one active and one degenerated) and four PDZ domains. In the present study, we investigated the oligomerization behaviour of this unusual protease using yeast two-hybrid analysis in vivo and with recombinant protein in vitro. We show that DEG7 forms trimeric complexes, but in contrast with other known Deg/HtrA proteases, it shows a new principle of oligomerization, where trimerization is based on the interactions between degenerated protease domains. We propose that, during evolution, a duplicated active protease domain degenerated and specialized in protein-protein interaction and complex formation.
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26
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Clausen T, Kaiser M, Huber R, Ehrmann M. HTRA proteases: regulated proteolysis in protein quality control. Nat Rev Mol Cell Biol 2011; 12:152-62. [PMID: 21326199 DOI: 10.1038/nrm3065] [Citation(s) in RCA: 347] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Controlled proteolysis underlies a vast diversity of protective and regulatory processes that are of key importance to cell fate. The unique molecular architecture of the widely conserved high temperature requirement A (HTRA) proteases has evolved to mediate critical aspects of ATP-independent protein quality control. The simple combination of a classic Ser protease domain and a carboxy-terminal peptide-binding domain produces cellular factors of remarkable structural and functional plasticity that allow cells to rapidly respond to the presence of misfolded or mislocalized polypeptides.
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Affiliation(s)
- Tim Clausen
- Research Institute of Molecular Pathology, Dr. Bohrgasse 7, A-1030 Vienna, Austria.
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Signaling mechanisms of apoptosis-like programmed cell death in unicellular eukaryotes. Comp Biochem Physiol B Biochem Mol Biol 2010; 155:341-53. [DOI: 10.1016/j.cbpb.2010.01.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 01/19/2010] [Accepted: 01/23/2010] [Indexed: 11/18/2022]
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Belanger KD, Walter D, Henderson TA, Yelton AL, O'Brien TG, Belanger KG, Geier SJ, Fahrenkrog B. Nuclear localisation is crucial for the proapoptotic activity of the HtrA-like serine protease Nma111p. J Cell Sci 2009; 122:3931-41. [DOI: 10.1242/jcs.056887] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Programmed cell death is induced by the activation of a subset of intracellular proteins in response to specific extra- and intracellular signals. In the yeast Saccharomyces cerevisiae, Nma111p functions as a nuclear serine protease that is necessary for apoptosis under cellular stress conditions, such as elevated temperature or treatment of cells with hydrogen peroxide to induce cell death. We have examined the role of nuclear protein import in the function of Nma111p in apoptosis. Nma111p contains two small clusters of basic residues towards its N-terminus, both of which are necessary for efficient translocation into the nucleus. Nma111p does not shuttle between the nucleus and cytoplasm during either normal growth conditions or under environmental stresses that induce apoptosis. The N-terminal half of Nma111p is sufficient to provide the apoptosis-inducing activity of the protein, and the nuclear-localisation signal (NLS) sequences and catalytic serine 235 are both necessary for this function. We provide compelling evidence that intranuclear Nma111p activity is necessary for apoptosis in yeast.
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Affiliation(s)
- Kenneth D. Belanger
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - David Walter
- M. E. Muller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstr. 70, 4056 Basel, Switzerland
| | - Tracey A. Henderson
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - Allison L. Yelton
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - Travis G. O'Brien
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - Karyn G. Belanger
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - Susan J. Geier
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - Birthe Fahrenkrog
- M. E. Muller Institute for Structural Biology, Biozentrum, University of Basel, Klingelbergstr. 70, 4056 Basel, Switzerland
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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