1
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Bhat SY. Drug targeting of aminopeptidases: importance of deploying a right metal cofactor. Biophys Rev 2024; 16:249-256. [PMID: 38737204 PMCID: PMC11078913 DOI: 10.1007/s12551-024-01192-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 05/05/2022] [Indexed: 05/14/2024] Open
Abstract
Aminopeptidases are metal co-factor-dependent hydrolases releasing N-terminal amino acid residues from peptides. Many of these enzymes, particularly the M24 methionine aminopeptidases (MetAPs), are considered valid drug targets in the fight against many parasitic and non-parasitic diseases. Targeting MetAPs has shown promising results against the malarial parasite, Plasmodium, which is regarded as potential anti-cancer targets. While targeting these essential enzymes represents a potentially promising approach, many challenges are often ignored by scientists when designing drugs or inhibitory scaffolds against the MetAPs. One such aspect is the metal co-factor, with inadequate attention paid to its role in catalysis, folding and remodeling of the catalytic site, and its role in inhibitor binding or potency. Knowing that a metal co-factor is essential for aminopeptidase enzyme activity and active site remodeling, it is intriguing that most computational biologists often ignore the metal ion while screening millions of potential inhibitors to find hits. Ironically, a similar trend is followed by biologists who avoid metal promiscuity of these enzymes while screening inhibitor libraries in vitro which may lead to false positives. This review highlights the importance of considering a physiologically relevant metal co-factor during the drug discovery processes targeting metal-dependent aminopeptidases. Graphical abstract
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2
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Mansouri M, Daware K, Webb CT, McGowan S. Understanding the structure and function of Plasmodium aminopeptidases to facilitate drug discovery. Curr Opin Struct Biol 2023; 82:102693. [PMID: 37657352 DOI: 10.1016/j.sbi.2023.102693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 09/03/2023]
Abstract
Malaria continues to be the most widespread parasitic disease affecting humans globally. As parasites develop drug resistance at an alarming pace, it has become crucial to identify novel drug targets. Over the last decade, the metalloaminopeptidases have gained importance as potential targets for new antimalarials. These enzymes are responsible for removing the N-terminal amino acids from proteins and peptides, and their restricted specificities suggest that many perform unique and essential roles within the malaria parasite. This mini-review focuses on the recent progress in structure and functional data relating to the Plasmodium metalloaminopeptidases that have been validated or shown promise as new antimalarial drug targets.
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Affiliation(s)
- Mahta Mansouri
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia; Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia. https://twitter.com/Mahta__Mansouri
| | - Kajal Daware
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia; Centre to Impact AMR, Monash University, Clayton, 3800, Victoria Australia
| | - Chaille T Webb
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia; Centre to Impact AMR, Monash University, Clayton, 3800, Victoria Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, 3800, Australia; Centre to Impact AMR, Monash University, Clayton, 3800, Victoria Australia.
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3
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Morgan CE, Zhang Z, Miyagi M, Golczak M, Yu EW. Toward structural-omics of the bovine retinal pigment epithelium. Cell Rep 2022; 41:111876. [PMID: 36577381 PMCID: PMC9875382 DOI: 10.1016/j.celrep.2022.111876] [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: 03/31/2022] [Revised: 10/12/2022] [Accepted: 12/02/2022] [Indexed: 12/28/2022] Open
Abstract
The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on determining the structure of a particular biomacromolecule of interest. Here, we report the use of cryoelectron microscopy (cryo-EM) to define the composition of a raw bovine retinal pigment epithelium (RPE) lysate. From this sample, we simultaneously identify and solve cryo-EM structures of seven different RPE enzymes whose functions affect neurotransmitter recycling, iron metabolism, gluconeogenesis, glycolysis, axonal development, and energy homeostasis. Interestingly, dysfunction of these important proteins has been directly linked to several neurodegenerative disorders, including Huntington's disease, amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, and schizophrenia. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
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Affiliation(s)
- Christopher E. Morgan
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Department of Chemistry, Thiel College, Greenville, PA 16125, USA,These authors contributed equally
| | - Zhemin Zhang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,These authors contributed equally
| | - Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Marcin Golczak
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA,Lead contact,Correspondence:
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4
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Shang Z, Guo Q, Zhou X, Yue Y, Zhou K, Tang L, Zhang Z, Fu Z, Liu J, Lin J, Xu B, Zhang M, Hong Y. Characterization of aspartyl aminopeptidase from Schistosoma japonicum. Acta Trop 2022; 232:106519. [PMID: 35584779 DOI: 10.1016/j.actatropica.2022.106519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/04/2022] [Accepted: 05/13/2022] [Indexed: 11/27/2022]
Abstract
The tegument of schistosomes is the interface between the worm and the host environment. Some molecules distributed on the tegument participate in host-parasite interactions. Aspartyl aminopeptidase (AAP), identified on the tegument of Schistosoma japonicum (S. japonicum), facilitate protein turnover by acting in concert with other aminopeptidases. In this study, the gene encoding S. japonicum aspartyl aminopeptidase (SjAAP) was cloned, expressed and characterized. Quantitative real-time PCR analysis showed that SjAAP was expressed in all studied developmental stages. The transcript level was higher in 8, 14, 21, and 28 days old worms than the other detected stages. Moreover, the level of expression in 42-day-old male worms was significantly higher than that in females. The recombinant SjAAP (rSjAAP) was expressed as both supernatant and inclusion bodies in Escherichia coli BL21 cells. The enzymatic activity of rSjAAP was 4.45 U/mg. The Km and Vmax values for H-Asp-pNA hydrolysis were discovered to be 5.93 mM and 0.018 mM·min-1. Immunofluorescence analysis revealed that SjAAP is primarily distributed on the tegument and parenchyma of schistosomes. Western blot showed that rSjAAP possessed good immunogenicity. Although specific antibodies were produced in BALB/c mice vaccinated with rSjAAP emulsified with ISA 206 adjuvant, no significant reduction of worm burden and number of eggs in the liver was observed. Therefore, rSjAAP may not be suitable to act as a potential vaccine candidate against schistosomiasis japonica in mice. However, this study provides some foundation for further exploration of the biological function of this molecule.
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5
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Dy ABC, Langlais PR, Barker NK, Addison KJ, Tanyaratsrisakul S, Boitano S, Christenson SA, Kraft M, Meyers D, Bleecker ER, Li X, Ledford JG. Myeloid-associated differentiation marker is a novel SP-A-associated transmembrane protein whose expression on airway epithelial cells correlates with asthma severity. Sci Rep 2021; 11:23392. [PMID: 34862427 PMCID: PMC8642528 DOI: 10.1038/s41598-021-02869-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/19/2021] [Indexed: 12/15/2022] Open
Abstract
Surfactant protein A (SP-A) is well-known for its protective role in pulmonary immunity. Previous studies from our group have shown that SP-A mediates eosinophil activities, including degranulation and apoptosis. In order to identify potential binding partners on eosinophils for SP-A, eosinophil lysates were subjected to SP-A pull-down and tandem mass spectrometry (MS/MS) analysis. We identified one membrane-bound protein, myeloid-associated differentiation marker (MYADM), as a candidate SP-A binding partner. Blocking MYADM on mouse and human eosinophils ex vivo prevented SP-A from inducing apoptosis; blocking MYADM in vivo led to increased persistence of eosinophilia and airway hyper-responsiveness in an ovalbumin (OVA) allergy model and increased airways resistance and mucus production in a house dust mite (HDM) asthma model. Examination of a subset of participants in the Severe Asthma Research Program (SARP) cohort revealed a significant association between epithelial expression of MYADM in asthma patients and parameters of airway inflammation, including: peripheral blood eosinophilia, exhaled nitric oxide (FeNO) and the number of exacerbations in the past 12 months. Taken together, our studies provide the first evidence of MYADM as a novel SP-A-associated protein that is necessary for SP-A to induce eosinophil apoptosis and we bring to light the potential importance of this previously unrecognized transmembrane protein in patients with asthma.
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Affiliation(s)
- Alane Blythe C Dy
- Clinical Translational Sciences, University of Arizona Health Sciences, Tucson, AZ, 85721, USA
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, 85724, USA
| | - Paul R Langlais
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Natalie K Barker
- Division of Endocrinology, Department of Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Kenneth J Addison
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, 85724, USA
| | | | - Scott Boitano
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, 85724, USA
- Department of Physiology, University of Arizona, Tucson, AZ, 85724, USA
| | - Stephanie A Christenson
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, 94117, USA
| | - Monica Kraft
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, 85724, USA
- Department of Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Deborah Meyers
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, 85724, USA
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Eugene R Bleecker
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, 85724, USA
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Xingnan Li
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, 85724, USA
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Julie G Ledford
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, 85724, USA.
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, 85724, USA.
- , 1230 N Cherry Avenue, BSRL Building, Tucson, AZ, 85719, USA.
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6
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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7
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Yuhara H, Ohtani A, Matano M, Kashiwagi Y, Maehashi K. Molecular characterization of a novel aspartyl aminopeptidase that contributes to the increase in glutamic acid content in chicken meat during cooking. FOOD CHEMISTRY: MOLECULAR SCIENCES 2021; 2:100015. [PMID: 35415631 PMCID: PMC8991601 DOI: 10.1016/j.fochms.2021.100015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 12/29/2020] [Accepted: 02/12/2021] [Indexed: 12/02/2022]
Abstract
Chicken homogenate produced significantly more free glutamic acid than beef while heating. DNPEP protein was detected in chicken meat extract by immunoblotting. Chicken DNPEP gene expression was detected in the breast and thigh muscles by RT-PCR. Recombinant cDNPEP showed high preference for glutamyl residues over aspartyl residues. The contribution of DNPEP to a great increase in glutamate in chicken meat during cooking was expected.
The enzyme involved in the increase in glutamic acid content in chicken meat during cooking was identified and characterized. Chicken homogenate produced significantly more free glutamic acid and exhibited higher glutamyl p-nitroanilide (Glu-pNA) hydrolyzing activity than beef when heat cooked. Amino acid sequencing revealed the presence of aspartyl aminopeptidase (DNPEP) in chicken meat. Using RT-PCR, DNPEP gene expression was detected in chicken breast and thigh muscles, liver, and small intestine, together with various other peptidase genes. Full-length DNPEP cDNA was cloned, and recombinant chicken DNPEP (cDNPEP) was expressed in Escherichia coli. cDNPEP showed five-fold higher activity against Glu-pNA than against aspartyl-pNA, which represents a different substrate specificity than observed for recombinant bovine DNPEP (bDNPEP). The Km values of both DNPEPs with Glu p-NA substrates indicated a higher affinity of cDNPEP for glutamyl residues. This unique substrate specificity of cDNPEP contributes to efficient glutamic acid production in chickens.
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Affiliation(s)
- Hitomi Yuhara
- Department of Fermentation Science and Technology, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Akira Ohtani
- Department of Fermentation Science and Technology, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Mami Matano
- Department of Fermentation Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yutaka Kashiwagi
- Department of Fermentation Science and Technology, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
- Department of Fermentation Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Kenji Maehashi
- Department of Fermentation Science and Technology, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
- Department of Fermentation Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
- Corresponding author at: Department of Fermentation Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
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8
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Wang YY, Zhang J, Liu XM, Li Y, Sui J, Dong MQ, Ye K, Du LL. Molecular and structural mechanisms of ZZ domain-mediated cargo selection by Nbr1. EMBO J 2021; 40:e107497. [PMID: 34169534 DOI: 10.15252/embj.2020107497] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/17/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
In selective autophagy, cargo selectivity is determined by autophagy receptors. However, it remains scarcely understood how autophagy receptors recognize specific protein cargos. In the fission yeast Schizosaccharomyces pombe, a selective autophagy pathway termed Nbr1-mediated vacuolar targeting (NVT) employs Nbr1, an autophagy receptor conserved across eukaryotes including humans, to target cytosolic hydrolases into the vacuole. Here, we identify two new NVT cargos, the mannosidase Ams1 and the aminopeptidase Ape4, that bind competitively to the first ZZ domain of Nbr1 (Nbr1-ZZ1). High-resolution cryo-EM analyses reveal how a single ZZ domain recognizes two distinct protein cargos. Nbr1-ZZ1 not only recognizes the N-termini of cargos via a conserved acidic pocket, similar to other characterized ZZ domains, but also engages additional parts of cargos in a cargo-specific manner. Our findings unveil a single-domain bispecific mechanism of autophagy cargo recognition, elucidate its underlying structural basis, and expand the understanding of ZZ domain-mediated protein-protein interactions.
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Affiliation(s)
- Ying-Ying Wang
- College of Life Sciences, Beijing Normal University, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Jianxiu Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, Beijing, China
| | - Yulu Li
- National Institute of Biological Sciences, Beijing, China
| | - Jianhua Sui
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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9
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Dong Z, Yang S, Lee BH. Bioinformatic mapping of a more precise Aspergillus niger degradome. Sci Rep 2021; 11:693. [PMID: 33436802 PMCID: PMC7804941 DOI: 10.1038/s41598-020-80028-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/15/2020] [Indexed: 11/21/2022] Open
Abstract
Aspergillus niger has the ability to produce a large variety of proteases, which are of particular importance for protein digestion, intracellular protein turnover, cell signaling, flavour development, extracellular matrix remodeling and microbial defense. However, the A. niger degradome (the full repertoire of peptidases encoded by the A. niger genome) available is not accurate and comprehensive. Herein, we have utilized annotations of A. niger proteases in AspGD, JGI, and version 12.2 MEROPS database to compile an index of at least 232 putative proteases that are distributed into the 71 families/subfamilies and 26 clans of the 6 known catalytic classes, which represents ~ 1.64% of the 14,165 putative A. niger protein content. The composition of the A. niger degradome comprises ~ 7.3% aspartic, ~ 2.2% glutamic, ~ 6.0% threonine, ~ 17.7% cysteine, ~ 31.0% serine, and ~ 35.8% metallopeptidases. One hundred and two proteases have been reassigned into the above six classes, while the active sites and/or metal-binding residues of 110 proteases were recharacterized. The probable physiological functions and active site architectures of these peptidases were also investigated. This work provides a more precise overview of the complete degradome of A. niger, which will no doubt constitute a valuable resource and starting point for further experimental studies on the biochemical characterization and physiological roles of these proteases.
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Affiliation(s)
- Zixing Dong
- Henan Provincial Engineering Laboratory of Insect Bio-Reactor and Henan Key Laboratory of Ecological Security for Water Region of Mid-Line of South-To-North, Nanyang Normal University, 1638 Wolong Road, Nanyang, 473061, Henan, People's Republic of China.
| | - Shuangshuang Yang
- College of Physical Education, Nanyang Normal University, Nanyang, 473061, People's Republic of China
| | - Byong H Lee
- Department of Microbiology/Immunology, McGill University, Montreal, QC, Canada
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10
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Pascual Alonso I, Rivera Méndez L, Valdés-Tresanco ME, Bounaadja L, Schmitt M, Arrebola Sánchez Y, Alvarez Lajonchere L, Charli JL, Florent I. Biochemical evidences for M1-, M17- and M18-like aminopeptidases in marine invertebrates from Cuban coastline. Z NATURFORSCH C 2020; 75:397-407. [PMID: 32609656 DOI: 10.1515/znc-2019-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 06/01/2020] [Indexed: 11/15/2022]
Abstract
Metallo-aminopeptidases (mAPs) control many physiological processes. They are classified in different families according to structural similarities. Neutral mAPs catalyze the cleavage of neutral amino acids from the N-terminus of proteins or peptide substrates; they need one or two metallic cofactors in their active site. Information about marine invertebrate's neutral mAPs properties is scarce; available data are mainly derived from genomics and cDNA studies. The goal of this work was to characterize the biochemical properties of the neutral APs activities in eight Cuban marine invertebrate species from the Phyla Mollusca, Porifera, Echinodermata, and Cnidaria. Determination of substrate specificity, optimal pH and effects of inhibitors (1,10-phenanthroline, amastatin, and bestatin) and cobalt on activity led to the identification of distinct neutral AP-like activities, whose biochemical behaviors were similar to those of the M1 and M17 families of mAPs. Additionally, M18-like glutamyl AP activities were detected. Thus, marine invertebrates express biochemical activities likely belonging to various families of metallo-aminopeptidases.
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Affiliation(s)
- Isel Pascual Alonso
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Laura Rivera Méndez
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba
| | - Mario E Valdés-Tresanco
- Center for Protein Studies, Faculty of Biology, University of Havana, Havana, Cuba.,Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Lotfi Bounaadja
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Marjorie Schmitt
- Laboratoire d'Innovation Moléculaire et Applications - Université de Haute-Alsace, Université de Strasbourg, CNRS, LIMA UMR7042, Mulhouse, France
| | | | - Luis Alvarez Lajonchere
- Museum of Natural History Felipe Poey, Faculty of Biology, University of Havana, Havana, Cuba
| | - Jean-Louis Charli
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Mexico
| | - Isabelle Florent
- Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR 7245), Muséum National d'Histoire Naturelle, CNRS, Paris, France
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11
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Rebello KM, Borges JN, Teixeira A, Perales J, Santos CP. Proteomic analysis of Ascocotyle longa (Trematoda: Heterophyidae) metacercariae. Mol Biochem Parasitol 2020; 239:111311. [PMID: 32745491 DOI: 10.1016/j.molbiopara.2020.111311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022]
Abstract
Ascocotyle longa is parasitic trematode with wide distribution throughout America, Europe, Africa, and Middle East. Despite the fact that this fish-borne pathogen has been considered an agent of human heterophyiasis in Brazil, the molecules involved in the host-parasite interaction remain unknown. The present study reports the proteome profile of A. longa metacercariae collected from the fish Mugil liza from Brazil. This infective stage for humans, mammals and birds was analyzed using nLC-MS/MS approach. We identified a large repertoire of proteins, which are mainly involved in energy metabolism and cell structure. Peptidases and immunogenic proteins were also identified, which might play roles in host-parasite interface. Our data provided unprecedented insights into the biology of A. longa and represent a first step to understand the natural host-parasite interaction. Moreover, as the first proteome characterized in this trematode, it will provide an important resource for future studies.
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Affiliation(s)
- Karina M Rebello
- Laboratório de Estudos Integrados em Protozoologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil; Laboratório de Toxinologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
| | - Juliana N Borges
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - André Teixeira
- Laboratório de Toxinologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Jonas Perales
- Laboratório de Toxinologia, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Cláudia P Santos
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
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12
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P1' Residue-Oriented Virtual Screening for Potent and Selective Phosphinic (Dehydro) Dipeptide Inhibitors of Metallo-Aminopeptidases. Biomolecules 2020; 10:biom10040659. [PMID: 32344658 PMCID: PMC7225938 DOI: 10.3390/biom10040659] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 01/01/2023] Open
Abstract
Designing side chain substituents complementary to enzyme binding pockets is of great importance in the construction of potent and selective phosphinic dipeptide inhibitors of metallo-aminopeptidases. Proper structure selection makes inhibitor construction more economic, as the development process typically consists of multiple iterative preparation/bioassay steps. On the basis of these principles, using noncomplex computation and modeling methodologies, we comprehensively screened 900 commercial precursors of the P1′ residues of phosphinic dipeptide and dehydrodipeptide analogs to identify the most promising ligands of 52 metallo-dependent aminopeptidases with known crystal structures. The results revealed several nonproteinogenic residues with an improved energy of binding compared with the best known inhibitors. The data are discussed taking into account the selectivity and stereochemical implications of the enzymes. Using this approach, we were able to identify nontrivial structural elements substituting the recognized phosphinic peptidomimetic scaffold of metallo-aminopeptidase inhibitors.
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13
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Dutoit R, Van Gompel T, Brandt N, Van Elder D, Van Dyck J, Sobott F, Droogmans L. How metal cofactors drive dimer-dodecamer transition of the M42 aminopeptidase TmPep1050 of Thermotoga maritima. J Biol Chem 2019; 294:17777-17789. [PMID: 31611236 DOI: 10.1074/jbc.ra119.009281] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/24/2019] [Indexed: 11/06/2022] Open
Abstract
The M42 aminopeptidases are dinuclear aminopeptidases displaying a peculiar tetrahedron-shaped structure with 12 subunits. Their quaternary structure results from the self-assembly of six dimers controlled by their divalent metal ion cofactors. The oligomeric-state transition remains debated despite the structural characterization of several archaeal M42 aminopeptidases. The main bottleneck is the lack of dimer structures, hindering the understanding of structural changes occurring during the oligomerization process. We present the first dimer structure of an M42 aminopeptidase, TmPep1050 of Thermotoga maritima, along with the dodecamer structure. The comparison of both structures has allowed us to describe how the metal ion cofactors modulate the active-site fold and, subsequently, affect the interaction interface between dimers. A mutational study shows that the M1 site strictly controls dodecamer formation. The dodecamer structure of TmPep1050 also reveals that a part of the dimerization domain delimits the catalytic pocket and could participate in substrate binding.
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Affiliation(s)
- Raphaël Dutoit
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, B6041 Charleroi, Belgium .,Labiris Institut de Recherche, avenue Emile Gryzon 1, B1070 Brussels, Belgium
| | - Tom Van Gompel
- Biomolecular and Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Groenenborgerlaan 171, B2020 Antwerpen, Belgium
| | - Nathalie Brandt
- Labiris Institut de Recherche, avenue Emile Gryzon 1, B1070 Brussels, Belgium
| | - Dany Van Elder
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, B6041 Charleroi, Belgium
| | - Jeroen Van Dyck
- Biomolecular and Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Groenenborgerlaan 171, B2020 Antwerpen, Belgium
| | - Frank Sobott
- Biomolecular and Analytical Mass Spectrometry, Department of Chemistry, Universiteit van Antwerpen, Groenenborgerlaan 171, B2020 Antwerpen, Belgium.,Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT Leeds, United Kingdom
| | - Louis Droogmans
- Laboratory of Microbiology, Department of Molecular Biology, Université Libre de Bruxelles, rue des Professeurs Jeener et Brachet 12, B6041 Charleroi, Belgium
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14
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Geng N, Zhang W, Li Y, Li F. Aspartyl Aminopeptidase Suppresses Proliferation, Invasion, and Stemness of Breast Cancer Cells via Targeting CD44. Anat Rec (Hoboken) 2019; 302:2178-2185. [PMID: 31228326 DOI: 10.1002/ar.24206] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/23/2019] [Accepted: 03/11/2019] [Indexed: 01/01/2023]
Abstract
Although involved in diverse cancer processes, the function of aspartyl aminopeptidase (DNPEP) in breast cancer remains elusive. Here, we reported that DNPEP is significantly downregulated in breast cancer tissues. Overexpression of DNPEP resulted in decreased breast cancer cells proliferation, migration, and invasion, while DNPEP knockdown had the opposite effect. Interestingly, we showed that the reduced DNPEP levels were correlated with the elevated cluster of differentiation 44 (CD44) levels in breast cancer. DNPEP promoted CD44 ubiquitin-proteasome-independent degradation, which is dependent on the hydrolase activity of DNPEP. Ectopic DNPEP expression significantly suppressed the stemness properties of breast cancer cells. These results shed light on the prospect of DNPEP in manipulating breast cancer progression. Anat Rec, 302:2178-2185, 2019. © 2019 American Association for Anatomy.
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Affiliation(s)
- Nanxi Geng
- Department of Cell Biology, China Medical University, Shenyang, China
| | - Wenyu Zhang
- Institute of Translational Medicine, China Medical University, Shenyang, China
| | - Yang Li
- Department of Cell Biology, China Medical University, Shenyang, China
| | - Feng Li
- Department of Cell Biology, China Medical University, Shenyang, China
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15
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Geng N, Li Y, Zhang W, Wang F, Wang X, Jin Z, Xing Y, Li D, Zhang H, Li Y, Li X, Cheng M, Jin F, Li F. A PAK5-DNPEP-USP4 axis dictates breast cancer growth and metastasis. Int J Cancer 2019; 146:1139-1151. [PMID: 31219614 DOI: 10.1002/ijc.32523] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/20/2019] [Accepted: 06/13/2019] [Indexed: 12/30/2022]
Abstract
Although clinically associated with the progression of multiple cancers, the biological function of p21-activated kinase 5 (PAK5) in breast cancer remains largely unknown. Here, we reveal that the PAK5-aspartyl aminopeptidase (DNPEP)-ubiquitin-specific protease 4 (USP4) axis is involved in breast cancer progression. We show that PAK5 interacts with and phosphorylates DNPEP at serine 119. Functionally, we demonstrate that DNPEP overexpression suppresses breast cancer cell proliferation and invasion and restricts breast cancer growth and metastasis in mice. Furthermore, we identify USP4 as a downstream target of the PAK5-DNPEP pathway; DNPEP mediates USP4 downregulation. Importantly, we verify that DNPEP expression is frequently downregulated in breast cancer tissues and is negatively correlated with PAK5 and USP4 expression. PAK5 decreases DNPEP abundance via the ubiquitin-proteasome pathway. Consistently, analyses of clinical breast cancer specimens revealed significantly increased PAK5 and USP4 levels and an association between higher PAK5 and USP4 expression and worse breast cancer patient survival. These findings suggest a pivotal role for PAK5-elicited signaling in breast cancer progression.
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Affiliation(s)
- Nanxi Geng
- Department of Cell Biology, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, China Medical University, Shenyang, Liaoning, China
| | - Yang Li
- Department of Cell Biology, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, China Medical University, Shenyang, Liaoning, China
| | - Wenyu Zhang
- Department of Cell Biology, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, China Medical University, Shenyang, Liaoning, China
| | - Fei Wang
- Department of Cell Biology, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, China Medical University, Shenyang, Liaoning, China
| | - Xu Wang
- Department of Breast Surgery, Department of Surgical Oncology, Research Unit of General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zining Jin
- Department of Breast Surgery, Department of Surgical Oncology, Research Unit of General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yao Xing
- Department of Cell Biology, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, China Medical University, Shenyang, Liaoning, China
| | - Danni Li
- Department of Medical Oncology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Hongyan Zhang
- Department of Cell Biology, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, China Medical University, Shenyang, Liaoning, China
| | - Yanshu Li
- Department of Cell Biology, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, China Medical University, Shenyang, Liaoning, China
| | - Xiaodong Li
- Department of Cell Biology, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, China Medical University, Shenyang, Liaoning, China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning, China
| | - Feng Jin
- Department of Breast Surgery, Department of Surgical Oncology, Research Unit of General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Feng Li
- Department of Cell Biology, Key Laboratory of Cell Biology of Ministry of Public Health, and Key Laboratory of Medical Cell Biology of Ministry of Education, China Medical University, Shenyang, Liaoning, China
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16
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Characterization of a Glycyl-Specific TET Aminopeptidase Complex from Pyrococcus horikoshii. J Bacteriol 2018; 200:JB.00059-18. [PMID: 29866801 DOI: 10.1128/jb.00059-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/29/2018] [Indexed: 01/03/2023] Open
Abstract
The TET peptidases are large self-compartmentalized complexes that form dodecameric particles. These metallopeptidases, members of the M42 family, are widely distributed in prokaryotes. Three different versions of TET complexes, with different substrate specificities, were found to coexist in the cytosol of the hyperthermophilic archaeon Pyrococcus horikoshii In the present work, we identified a novel type of TET complex that we named PhTET4. The recombinant PhTET4 enzyme was found to self-assemble as a tetrahedral edifice similar to other TET complexes. We determined PhTET4 substrate specificity using a broad range of monoacyl chromogenic and fluorogenic compounds. High-performance liquid chromatographic peptide degradation assays were also performed. These experiments demonstrated that PhTET4 is a strict glycyl aminopeptidase, devoid of amidolytic activity toward other types of amino acids. The catalytic efficiency of PhTET4 was studied under various conditions. The protein was found to be a hyperthermophilic alkaline aminopeptidase. Interestingly, unlike other peptidases from the same family, it was activated only by nickel ions.IMPORTANCE We describe here the first known peptidase displaying exclusive activity toward N-terminal glycine residues. This work indicates a specific role for intracellular glycyl peptidases in deep sea hyperthermophilic archaeal metabolism. These observations also provide critical evidence for the use of these archaeal extremozymes for biotechnological applications.
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17
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Ewert J, Glück C, Strasdeit H, Fischer L, Stressler T. Influence of the metal ion on the enzyme activity and kinetics of PepA from Lactobacillus delbrueckii. Enzyme Microb Technol 2018; 110:69-78. [DOI: 10.1016/j.enzmictec.2017.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/13/2017] [Accepted: 10/10/2017] [Indexed: 10/18/2022]
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18
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Park SY, Scranton MA, Stajich JE, Yee A, Walling LL. Chlorophyte aspartyl aminopeptidases: Ancient origins, expanded families, new locations, and secondary functions. PLoS One 2017; 12:e0185492. [PMID: 29023459 PMCID: PMC5638241 DOI: 10.1371/journal.pone.0185492] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/13/2017] [Indexed: 11/19/2022] Open
Abstract
M18 aspartyl aminopeptidases (DAPs) are well characterized in microbes and animals with likely functions in peptide processing and vesicle trafficking. In contrast, there is a dearth of knowledge on plant aminopeptidases with a preference for proteins and peptides with N-terminal acidic residues. During evolution of the Plantae, there was an expansion and diversification of the M18 DAPs. After divergence of the ancestral green algae from red and glaucophyte algae, a duplication yielded the DAP1 and DAP2 lineages. Subsequently DAP1 genes were lost in chlorophyte algae. A duplication of DAP2-related genes occurred early in green plant evolution. DAP2 genes were retained in land plants and picoeukaryotic algae and lost in green algae. In contrast, DAP2-like genes persisted in picoeukaryotic and green algae, while this lineage was lost in land plants. Consistent with this evolutionary path, Arabidopsis thaliana has two DAP gene lineages (AtDAP1 and AtDAP2). Similar to animal and yeast DAPs, AtDAP1 is localized to the cytosol or vacuole; while AtDAP2 harbors an N-terminal transit peptide and is chloroplast localized. His6-DAP1 and His6-DAP2 expressed in Escherichia coli were enzymatically active and dodecameric with masses exceeding 600 kDa. His6-DAP1 and His6-DAP2 preferentially hydrolyzed Asp-p-nitroanilide and Glu-p-nitroanilide. AtDAPs are highly conserved metallopeptidases activated by MnCl2 and inhibited by ZnCl2 and divalent ion chelators. The protease inhibitor PMSF inhibited and DTT stimulated both His6-DAP1 and His6-DAP2 activities suggesting a role for thiols in the AtDAP catalytic mechanism. The enzymes had distinct pH and temperature optima, as well as distinct kinetic parameters. Both enzymes had high catalytic efficiencies (kcat/Km) exceeding 1.0 x 107 M-1 sec-1. Using established molecular chaperone assays, AtDAP1 and AtDAP2 prevented thermal denaturation. AtDAP1 also prevented protein aggregation and promoted protein refolding. Collectively, these data indicate that plant DAPs have a complex evolutionary history and have evolved new biochemical features that may enable their role in vivo.
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Affiliation(s)
- Sang-Youl Park
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, United States of America
| | - Melissa A. Scranton
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, United States of America
| | - Jason E. Stajich
- Department of Plant Pathology and Microbiology, Center for Plant Cell Biology, University of California, Riverside, California, United States of America
| | - Ashley Yee
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, United States of America
| | - Linda L. Walling
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, United States of America
- * E-mail:
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19
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Pessoa TBA, Rezende RP, Marques EDLS, Pirovani CP, Dos Santos TF, Dos Santos Gonçalves AC, Romano CC, Dotivo NC, Freitas ACO, Salay LC, Dias JCT. Metagenomic alkaline protease from mangrove sediment. J Basic Microbiol 2017; 57:962-973. [PMID: 28804942 DOI: 10.1002/jobm.201700159] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 06/29/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022]
Abstract
Functional screening of metagenomic libraries is an important tool for the discovery of new molecules. The metabolic diversity of microorganisms enables survival in harsh environments and is related to the production of enzymes. In this study, we identified a protease-producing clone from a metagenomic library derived from mangrove sediment. The protease was purified by ammonium sulphate precipitation and gel filtration chromatography, with a yield of 77.27% and a specific activity of 8.57 U μg-1 . It had a molecular weight of approximately 70 kDa. MS/MS in ESI-Q-TOF revealed nine peptides similar to a peptidase of Bacillus safensis. The aligned partial sequence showed 47.48% identity and 82.74% similarity to the conserved domains of a glutamyl aminopeptidase from the human gut metagenome and 32.12% total coverage. The protease had an optimal pH of 8.5 and optimal activity at 60°C. At pH 9-12, its activity was greater than 80%. It had moderate thermotolerance and thermostability at temperatures of 40 and 50 °C. The KM and Vmax values were estimated to be 0.92 mg ml-1 , and 13.15 mmol min-1 for azocasein. Substrate specificity analysis showed that PR4A3 was active on gelatin, blood, egg yolk, and milk. These results support the potential use of PR4A3 in biotechnological applications.
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Affiliation(s)
- Tharcilla B A Pessoa
- State University of Feira de Santana, Program in Biotechnology, Feira de Santana, Bahia, Brazil
| | - Rachel P Rezende
- Department of Biological Sciences, State University of Santa Cruz, Ilheus, Bahia, Brazil
| | | | - Carlos P Pirovani
- Department of Biological Sciences, State University of Santa Cruz, Ilheus, Bahia, Brazil
| | | | | | - Carla C Romano
- Department of Biological Sciences, State University of Santa Cruz, Ilheus, Bahia, Brazil
| | - Natielle C Dotivo
- State University of Santa Cruz, Undergraduate in Biomedicine, Ilheus, Bahia, Brazil
| | - Ana C O Freitas
- Department of Biological Sciences, State University of Santa Cruz, Ilheus, Bahia, Brazil
| | - Luiz C Salay
- Department of Exact and Technological Sciences, State University of Santa Cruz, Ilheus, Bahia, Brazil
| | - João C T Dias
- Department of Biological Sciences, State University of Santa Cruz, Ilheus, Bahia, Brazil
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20
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Yamasaki A, Noda NN. Structural Biology of the Cvt Pathway. J Mol Biol 2017; 429:531-542. [PMID: 28077284 DOI: 10.1016/j.jmb.2017.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/31/2016] [Accepted: 01/03/2017] [Indexed: 12/13/2022]
Abstract
Macroautophagy is a degradation process in which autophagosomes are generated to isolate and transport various materials, including damaged organelles and protein aggregates, as cargos to the lysosomes or vacuoles. Bulk autophagy is one of the two types of macroautophagy, which is triggered by starvation and targets non-specific cargos. The second type, that is, selective autophagy, identifies and preferentially degrades specific cargos via receptor recognition. Cytoplasm-to-vacuole targeting (Cvt) is a selective autophagy pathway that specifically transports vacuolar hydrolases into the vacuole in budding yeast cells and has been extensively studied as a model of selective autophagy. In the present review, we focused on the Cvt pathway, especially on the recent structural insights into cargo assembly, receptor recognition, and recruitment mechanisms of the Cvt machinery. Elucidating the Cvt pathway would help in understanding the basic molecular mechanisms of various types of selective autophagy.
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Affiliation(s)
- Akinori Yamasaki
- Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, Tokyo 141-0021, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry (BIKAKEN), Microbial Chemistry Research Foundation, Tokyo 141-0021, Japan.
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21
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Characterization of aspartyl aminopeptidase from Toxoplasma gondii. Sci Rep 2016; 6:34448. [PMID: 27678060 PMCID: PMC5039622 DOI: 10.1038/srep34448] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/13/2016] [Indexed: 12/14/2022] Open
Abstract
Aminopeptidases have emerged as new promising drug targets for the development of novel anti-parasitic drugs. An aspartyl aminopeptidase-like gene has been identified in the Toxoplasma gondii genome (TgAAP), although its function remains unknown. In this study, we characterized TgAAP and performed functional analysis of the gene product. Firstly, we expressed a functional recombinant TgAAP (rTgAAP) protein in Escherichia coli, and found that it required metal ions for activity and showed a substrate preference for N-terminal acidic amino acids Glu and Asp. Then, we evaluated the function and drug target potential of TgAAP using the CRISPR/Cas9 knockout system. Western blotting demonstrated the deletion of TgAAP in the knockout strain. Indirect immunofluorescence analysis showed that TgAAP was localized in the cytoplasm of the wild-type parasite, but was not expressed in the knockout strain. Phenotype analysis revealed that TgAAP knockout inhibited the attachment/invasion, replication, and substrate-specific activity in T. gondii. Finally, the activity of drug CID 23724194, previously described as targeting Plasmodium and malarial parasite AAP, was tested against rTgAAP and the parasite. Overall, TgAAP knockout affected the growth of T. gondii but did not completely abolish parasite replication and growth. Therefore, TgAAP may comprise a useful adjunct drug target of T. gondii.
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22
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Su MY, Peng WH, Ho MR, Su SC, Chang YC, Chen GC, Chang CI. Structure of yeast Ape1 and its role in autophagic vesicle formation. Autophagy 2016. [PMID: 26208681 DOI: 10.1080/15548627.2015.1067363] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In Saccharomyces cerevisiae, a constitutive biosynthetic transport pathway, termed the cytoplasm-to-vacuole targeting (Cvt) pathway, sequesters precursor aminopeptidase I (prApe1) dodecamers in the form of a large complex into a Cvt vesicle using autophagic machinery, targeting it into the vacuole (the yeast lysosome) where it is proteolytically processed into its mature form, Ape1, by removal of an amino-terminal 45-amino acid propeptide. prApe1 is thought to serve as a scaffolding cargo critical for the assembly of the Cvt vesicle by presenting the propeptide to mediate higher-ordered complex formation and autophagic receptor recognition. Here we report the X-ray crystal structure of Ape1 at 2.5 Å resolution and reveal its dodecameric architecture consisting of dimeric and trimeric units, which associate to form a large tetrahedron. The propeptide of prApe1 exhibits concentration-dependent oligomerization and forms a stable tetramer. Structure-based mutagenesis demonstrates that disruption of the inter-subunit interface prevents dodecameric assembly and vacuolar targeting in vivo despite the presence of the propeptide. Furthermore, by examining the vacuolar import of propeptide-fused exogenous protein assemblies with different quaternary structures, we found that 3-dimensional spatial distribution of propeptides presented by a scaffolding cargo is essential for the assembly of the Cvt vesicle for vacuolar delivery. This study describes a molecular framework for understanding the mechanism of Cvt or autophagosomal biogenesis in selective macroautophagy.
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Affiliation(s)
- Ming-Yuan Su
- a Institute of Biological Chemistry; Academia Sinica ; Taipei , Taiwan.,b Institute of Biochemical Sciences; College of Life Science; National Taiwan University ; Taipei , Taiwan
| | - Wen-Hsin Peng
- a Institute of Biological Chemistry; Academia Sinica ; Taipei , Taiwan
| | - Meng-Ru Ho
- a Institute of Biological Chemistry; Academia Sinica ; Taipei , Taiwan
| | - Shih-Chieh Su
- a Institute of Biological Chemistry; Academia Sinica ; Taipei , Taiwan.,b Institute of Biochemical Sciences; College of Life Science; National Taiwan University ; Taipei , Taiwan
| | - Yuan-Chih Chang
- c Institute of Cellular and Organismic Biology; Academia Sinica ; Taipei , Taiwan
| | - Guang-Chao Chen
- a Institute of Biological Chemistry; Academia Sinica ; Taipei , Taiwan.,b Institute of Biochemical Sciences; College of Life Science; National Taiwan University ; Taipei , Taiwan
| | - Chung-I Chang
- a Institute of Biological Chemistry; Academia Sinica ; Taipei , Taiwan.,b Institute of Biochemical Sciences; College of Life Science; National Taiwan University ; Taipei , Taiwan
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23
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Mesquita A, Tábara LC, Martinez-Costa O, Santos-Rodrigo N, Vincent O, Escalante R. Dissecting the function of Atg1 complex in Dictyostelium autophagy reveals a connection with the pentose phosphate pathway enzyme transketolase. Open Biol 2016; 5:rsob.150088. [PMID: 26246495 PMCID: PMC4554924 DOI: 10.1098/rsob.150088] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The network of protein–protein interactions of the Dictyostelium discoideum autophagy pathway was investigated by yeast two-hybrid screening of the conserved autophagic proteins Atg1 and Atg8. These analyses confirmed expected interactions described in other organisms and also identified novel interactors that highlight the complexity of autophagy regulation. The Atg1 kinase complex, an essential regulator of autophagy, was investigated in detail here. The composition of the Atg1 complex in D. discoideum is more similar to mammalian cells than to Saccharomyces cerevisiae as, besides Atg13, it contains Atg101, a protein not conserved in this yeast. We found that Atg101 interacts with Atg13 and genetic disruption of these proteins in Dictyostelium leads to an early block in autophagy, although the severity of the developmental phenotype and the degree of autophagic block is higher in Atg13-deficient cells. We have also identified a protein containing zinc-finger B-box and FNIP motifs that interacts with Atg101. Disruption of this protein increases autophagic flux, suggesting that it functions as a negative regulator of Atg101. We also describe the interaction of Atg1 kinase with the pentose phosphate pathway enzyme transketolase (TKT). We found changes in the activity of endogenous TKT activity in strains lacking or overexpressing Atg1, suggesting the presence of an unsuspected regulatory pathway between autophagy and the pentose phosphate pathway in Dictyostelium that seems to be conserved in mammalian cells.
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Affiliation(s)
- Ana Mesquita
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC/UAM, Madrid, Spain
| | - Luis C Tábara
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC/UAM, Madrid, Spain
| | | | | | - Olivier Vincent
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC/UAM, Madrid, Spain
| | - Ricardo Escalante
- Instituto de Investigaciones Biomédicas Alberto Sols, CSIC/UAM, Madrid, Spain
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24
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Colombo M, Girard E, Franzetti B. Tuned by metals: the TET peptidase activity is controlled by 3 metal binding sites. Sci Rep 2016; 6:20876. [PMID: 26853450 PMCID: PMC4745047 DOI: 10.1038/srep20876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 01/11/2016] [Indexed: 11/09/2022] Open
Abstract
TET aminopeptidases are dodecameric particles shared in the three life domains involved in various biological processes, from carbon source provider in archaea to eye-pressure regulation in humans. Each subunit contains a dinuclear metal site (M1 and M2) responsible for the enzyme catalytic activity. However, the role of each metal ion is still uncharacterized. Noteworthy, while mesophilic TETs are activated by Mn(2+), hyperthermophilic TETs prefers Co(2+). Here, by means of anomalous x-ray crystallography and enzyme kinetics measurements of the TET3 aminopeptidase from the hyperthermophilic organism Pyrococcus furiosus (PfTET3), we show that M2 hosts the catalytic activity of the enzyme, while M1 stabilizes the TET3 quaternary structure and controls the active site flexibility in a temperature dependent manner. A new third metal site (M3) was found in the substrate binding pocket, modulating the PfTET3 substrate preferences. These data show that TET activity is tuned by the molecular interplay among three metal sites.
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Affiliation(s)
- Matteo Colombo
- CNRS, IBS, F-38027 Grenoble, France.,CEA, DSV, IBS, F-38027 Grenoble, France.,Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Eric Girard
- CNRS, IBS, F-38027 Grenoble, France.,CEA, DSV, IBS, F-38027 Grenoble, France.,Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
| | - Bruno Franzetti
- CNRS, IBS, F-38027 Grenoble, France.,CEA, DSV, IBS, F-38027 Grenoble, France.,Univ. Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France
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25
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Appolaire A, Girard E, Colombo M, Durá MA, Moulin M, Härtlein M, Franzetti B, Gabel F. Small-angle neutron scattering reveals the assembly mode and oligomeric architecture of TET, a large, dodecameric aminopeptidase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2983-93. [PMID: 25372688 PMCID: PMC4220976 DOI: 10.1107/s1399004714018446] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 08/13/2014] [Indexed: 01/10/2023]
Abstract
The specific self-association of proteins into oligomeric complexes is a common phenomenon in biological systems to optimize and regulate their function. However, de novo structure determination of these important complexes is often very challenging for atomic-resolution techniques. Furthermore, in the case of homo-oligomeric complexes, or complexes with very similar building blocks, the respective positions of subunits and their assembly pathways are difficult to determine using many structural biology techniques. Here, an elegant and powerful approach based on small-angle neutron scattering is applied, in combination with deuterium labelling and contrast variation, to elucidate the oligomeric organization of the quaternary structure and the assembly pathways of 468 kDa, hetero-oligomeric and symmetric Pyrococcus horikoshii TET2-TET3 aminopeptidase complexes. The results reveal that the topology of the PhTET2 and PhTET3 dimeric building blocks within the complexes is not casual but rather suggests that their quaternary arrangement optimizes the catalytic efficiency towards peptide substrates. This approach bears important potential for the determination of quaternary structures and assembly pathways of large oligomeric and symmetric complexes in biological systems.
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Affiliation(s)
- Alexandre Appolaire
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Eric Girard
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Matteo Colombo
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - M. Asunción Durá
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Martine Moulin
- Life Sciences Group, Institut Laue–Langevin, 38042 Grenoble CEDEX 9, France
| | - Michael Härtlein
- Life Sciences Group, Institut Laue–Langevin, 38042 Grenoble CEDEX 9, France
| | - Bruno Franzetti
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
| | - Frank Gabel
- Université Grenoble Alpes, IBS, 38044 Grenoble, France
- CNRS, IBS, 38044 Grenoble, France
- CEA, IBS, 38044 Grenoble, France
- Large Scale Structures Group, Institut Laue–Langevin, 38042 Grenoble CEDEX 9, France
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26
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Markadieu N, Rios K, Spiller BW, McDonald WH, Welling PA, Delpire E. Short forms of Ste20-related proline/alanine-rich kinase (SPAK) in the kidney are created by aspartyl aminopeptidase (Dnpep)-mediated proteolytic cleavage. J Biol Chem 2014; 289:29273-84. [PMID: 25164821 DOI: 10.1074/jbc.m114.604009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Ste20-related kinase SPAK regulates sodium, potassium, and chloride transport in a variety of tissues. Recently, SPAK fragments, which lack the catalytic domain and are inhibitory to Na(+) transporters, have been detected in kidney. It has been hypothesized that the fragments originate from alternative translation start sites, but their precise origin is unknown. Here, we demonstrate that kidney lysate possesses proteolytic cleavage activity toward SPAK. Ion exchange and size exclusion chromatography combined with mass spectrometry identified the protease as aspartyl aminopeptidase. The presence of the protease was verified in the active fractions, and recombinant aspartyl aminopeptidase recapitulated the cleavage pattern observed with kidney lysate. Identification of the sites of cleavage by mass spectrometry allowed us to test the function of the smaller fragments and demonstrate their inhibitory action toward the Na(+)-K(+)-2Cl(-) cotransporter, NKCC2.
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Affiliation(s)
| | | | | | - W Hayes McDonald
- Biochemistry and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 and
| | - Paul A Welling
- the Department of Physiology, University of Maryland School of Medicine, Baltimore, Maryland 21201
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27
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Chen Y, Tang H, Seibel W, Papoian R, Oh K, Li X, Zhang J, Golczak M, Palczewski K, Kiser PD. Identification and characterization of novel inhibitors of Mammalian aspartyl aminopeptidase. Mol Pharmacol 2014; 86:231-42. [PMID: 24913940 DOI: 10.1124/mol.114.093070] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Aspartyl aminopeptidase (DNPEP) has been implicated in the control of angiotensin signaling and endosome trafficking, but its precise biologic roles remain incompletely defined. We performed a high-throughput screen of ∼25,000 small molecules to identify inhibitors of DNPEP for use as tools to study its biologic functions. Twenty-three confirmed hits inhibited DNPEP-catalyzed hydrolysis of angiotensin II with micromolar potency. A counter screen against glutamyl aminopeptidase (ENPEP), an enzyme with substrate specificity similar to that of DNPEP, identified eight DNPEP-selective inhibitors. Structure-activity relationships and modeling studies revealed structural features common to the identified inhibitors, including a metal-chelating group and a charged or polar moiety that could interact with portions of the enzyme active site. The compounds identified in this study should be valuable tools for elucidating DNPEP physiology.
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Affiliation(s)
- Yuanyuan Chen
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Hong Tang
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - William Seibel
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Ruben Papoian
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Ki Oh
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Xiaoyu Li
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Jianye Zhang
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Marcin Golczak
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
| | - Philip D Kiser
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio (Y.C., K.O., X.L., J.Z., M.G., K.P., P.D.K.); and Drug Discovery Center, College of Medicine, University of Cincinnati, Cincinnati, Ohio (H.T., W.S., R.P.)
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28
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Nguyen DD, Pandian R, Kim D, Ha SC, Yoon HJ, Kim KS, Yun KH, Kim JH, Kim KK. Structural and kinetic bases for the metal preference of the M18 aminopeptidase from Pseudomonas aeruginosa. Biochem Biophys Res Commun 2014; 447:101-7. [PMID: 24704201 DOI: 10.1016/j.bbrc.2014.03.109] [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: 03/20/2014] [Accepted: 03/22/2014] [Indexed: 11/15/2022]
Abstract
The peptidases in clan MH are known as cocatalytic zinc peptidases that have two zinc ions in the active site, but their metal preference has not been rigorously investigated. In this study, the molecular basis for metal preference is provided from the structural and biochemical analyses. Kinetic studies of Pseudomonas aeruginosa aspartyl aminopeptidase (PaAP) which belongs to peptidase family M18 in clan MH revealed that its peptidase activity is dependent on Co(2+) rather than Zn(2+): the kcat (s(-1)) values of PaAP were 0.006, 5.10 and 0.43 in no-metal, Co(2+), and Zn(2+)conditions, respectively. Consistently, addition of low concentrations of Co(2+) to PaAP previously saturated with Zn(2+) greatly enhanced the enzymatic activity, suggesting that Co(2+)may be the physiologically relevant cocatalytic metal ion of PaAP. The crystal structures of PaAP complexes with Co(2+) or Zn(2+) commonly showed two metal ions in the active site coordinated with three conserved residues and a bicarbonate ion in a tetragonal geometry. However, Co(2+)- and Zn(2+)-bound structures showed no noticeable alterations relevant to differential effects of metal species, except the relative orientation of Glu-265, a general base in the active site. The characterization of mutant PaAP revealed that the first metal binding site is primarily responsible for metal preference. Similar to PaAP, Streptococcus pneumonia glutamyl aminopeptidase (SpGP), belonging to aminopeptidase family M42 in clan MH, also showed requirement for Co(2+) for maximum activity. These results proposed that clan MH peptidases might be a cocatalytic cobalt peptidase rather than a zinc-dependent peptidase.
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Affiliation(s)
- Duy Duc Nguyen
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Ramesh Pandian
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Doyoun Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Sung Chul Ha
- Pohang Acceleratory Laboratory, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 157-747, Republic of Korea
| | - Kap Sun Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Kyung Hee Yun
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Jin-Hahn Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea.
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea.
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29
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Appolaire A, Rosenbaum E, Durá MA, Colombo M, Marty V, Savoye MN, Godfroy A, Schoehn G, Girard E, Gabel F, Franzetti B. Pyrococcus horikoshii TET2 peptidase assembling process and associated functional regulation. J Biol Chem 2013; 288:22542-54. [PMID: 23696647 PMCID: PMC3829341 DOI: 10.1074/jbc.m113.450189] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 05/13/2013] [Indexed: 11/06/2022] Open
Abstract
Tetrahedral (TET) aminopeptidases are large polypeptide destruction machines present in prokaryotes and eukaryotes. Here, the rules governing their assembly into hollow 12-subunit tetrahedrons are addressed by using TET2 from Pyrococcus horikoshii (PhTET2) as a model. Point mutations allowed the capture of a stable, catalytically active precursor. Small angle x-ray scattering revealed that it is a dimer whose architecture in solution is identical to that determined by x-ray crystallography within the fully assembled TET particle. Small angle x-ray scattering also showed that the reconstituted PhTET2 dodecameric particle displayed the same quaternary structure and thermal stability as the wild-type complex. The PhTET2 assembly intermediates were characterized by analytical ultracentrifugation, native gel electrophoresis, and electron microscopy. They revealed that PhTET2 assembling is a highly ordered process in which hexamers represent the main intermediate. Peptide degradation assays demonstrated that oligomerization triggers the activity of the TET enzyme toward large polypeptidic substrates. Fractionation experiments in Pyrococcus and Halobacterium cells revealed that, in vivo, the dimeric precursor co-exists together with assembled TET complexes. Taken together, our observations explain the biological significance of TET oligomerization and suggest the existence of a functional regulation of the dimer-dodecamer equilibrium in vivo.
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Affiliation(s)
- Alexandre Appolaire
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Eva Rosenbaum
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - M. Asunción Durá
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Matteo Colombo
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Vincent Marty
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Marjolaine Noirclerc Savoye
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Anne Godfroy
- the Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes, 29280 Plouzané, France
| | - Guy Schoehn
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Eric Girard
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Frank Gabel
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
| | - Bruno Franzetti
- From the Institut de Biologie Structurale, CNRS, UMR5075, F-38027/Commissariat à l'Energie Atomique, F-38054/Université Joseph Fourier, F-38027 Grenoble and
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