1
|
Tong L, Rao J, Yang C, Xu J, Lu Y, Zhang Y, Cang X, Xie S, Mao J, Jiang P. Mutational burden of XPNPEP3 leads to defects in mitochondrial complex I and cilia in NPHPL1. iScience 2023; 26:107446. [PMID: 37599822 PMCID: PMC10432713 DOI: 10.1016/j.isci.2023.107446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/29/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Nephronophthisis-like nephropathy-1 (NPHPL1) is a rare ciliopathy, caused by mutations of XPNPEP3. Despite a well-described monogenic etiology, the pathogenesis of XPNPEP3 associated with mitochondrial and ciliary function remains elusive. Here, we identified novel compound heterozygous mutations in NPHPL1 patients with renal lesion only or with extra bone cysts together. Patient-derived lymphoblasts carrying c.634G>A and c.761G>T together exhibit elevated mitochondrial XPNPEP3 levels via the reduction of mRNA degradation, leading to mitochondrial dysfunction in both urine tubular epithelial cells and lymphoblasts from patient. Mitochondrial XPNPEP3 was co-immunoprecipitated with respiratory chain complex I and was required for the stability and activity of complex I. Deletion of Xpnpep3 in mice resulted in lower activity of complex I, elongated primary cilium, and predisposition to tubular dilation and fibrosis under stress. Our findings provide valuable insights into the mitochondrial functions involved in the pathogenesis of NPHP.
Collapse
Affiliation(s)
- Lingxiao Tong
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Jia Rao
- Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China
| | - Chenxi Yang
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Xu
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Yijun Lu
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuchen Zhang
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaohui Cang
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Shanshan Xie
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
| | - Jianhua Mao
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
- Zhejiang Key Laboratory for Neonatal Diseases, The Children’s Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Pingping Jiang
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, China
- Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
2
|
Lloyd AC, Gregory KS, Isaac RE, Acharya KR. A Molecular Analysis of the Aminopeptidase P-Related Domain of PID-5 from Caenorhabditis elegans. Biomolecules 2023; 13:1132. [PMID: 37509168 PMCID: PMC10377022 DOI: 10.3390/biom13071132] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
A novel protein, PID-5, has been shown to be a requirement for germline immortality and has recently been implicated in RNA-induced epigenetic silencing in the Caenorhabditis elegans embryo. Importantly, it has been shown to contain both an eTudor and aminopeptidase P-related domain. However, the silencing mechanism has not yet been fully characterised. In this study, bioinformatic tools were used to compare pre-existing aminopeptidase P molecular structures to the AlphaFold2-predicted aminopeptidase P-related domain of PID-5 (PID-5 APP-RD). Structural homology, metal composition, inhibitor-bonding interactions, and the potential for dimerisation were critically assessed through computational techniques, including structural superimposition and protein-ligand docking. Results from this research suggest that the metallopeptidase-like domain shares high structural homology with known aminopeptidase P enzymes and possesses the canonical 'pita-bread fold'. However, the absence of conserved metal-coordinating residues indicates that only a single Zn2+ may be bound at the active site. The PID-5 APP-RD may form transient interactions with a known aminopeptidase P inhibitor and may therefore recognise substrates in a comparable way to the known structures. However, loss of key catalytic residues suggests the domain will be inactive. Further evidence suggests that heterodimerisation with C. elegans aminopeptidase P is feasible and therefore PID-5 is predicted to regulate proteolytic cleavage in the silencing pathway. PID-5 may interact with PID-2 to bring aminopeptidase P activity to the Z-granule, where it could influence WAGO-4 activity to ensure the balanced production of 22G-RNA signals for transgenerational silencing. Targeted experiments into APPs implicated in malaria and cancer are required in order to build upon the biological and therapeutic significance of this research.
Collapse
Affiliation(s)
- Anna C. Lloyd
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (A.C.L.); (K.S.G.)
| | - Kyle S. Gregory
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (A.C.L.); (K.S.G.)
| | - R. Elwyn Isaac
- School of Biology, University of Leeds, Leeds LS2 9JT, UK;
| | - K. Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (A.C.L.); (K.S.G.)
| |
Collapse
|
3
|
Guo C, Zhou B, Liu Y, Niu H, Lv L, Li M. Simulation analysis and physiological and biochemical evaluation of Sophora flavescens aboveground against aphids using network pharmacology. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 189:105308. [PMID: 36549815 DOI: 10.1016/j.pestbp.2022.105308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/19/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Pests cause substantial damage to human environments; therefore, studying insecticidal mechanisms is crucial for improving pest control. However, the use of chemical pesticides can cause irreversible secondary damage. In this study, we used network pharmacology to investigate the effect of Sophora flavescens Alt., as a biological pest control agent, on glucose-6-phosphate 1-dehydrogenase, thymidylate synthase, and a translocation protein in aphids. The stability and reliability of target proteins was analyzed using molecular docking and molecular dynamic simulations. Enzyme activity assays validated the feasibility of network pharmacology to obtain actionable targets. We used interdisciplinary integration to study pest control and network pharmacology to identify how Sophora flavescens Alt. resists aphid attacks. The results show that the use of network pharmacology can increase the accuracy and specificity of our predictions for the molecules targeted by insecticides. This approach will facilitate improved, environmentally friendly pest control development in the future.
Collapse
Affiliation(s)
- Chunyan Guo
- College of Pharmacy, Qiqihar Medical University, Qiqihar, China; Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, China
| | - Baochang Zhou
- Inner Mongolia Medical University, Hohhot, China; Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, China
| | - Yibo Liu
- Inner Mongolia Medical University, Hohhot, China; Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, China
| | - Hui Niu
- Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, Baotou Medical College, Baotou, China; Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, China
| | - Lijuan Lv
- Department of Basic Science, Tianjin Agricultural University, Tianjin, China.
| | - Minhui Li
- College of Pharmacy, Qiqihar Medical University, Qiqihar, China; Inner Mongolia Medical University, Hohhot, China; Inner Mongolia Key Laboratory of Characteristic Geoherbs Resources Protection and Utilization, Baotou Medical College, Baotou, China; Inner Mongolia Academy of Chinese and Mongolian Medicine, Hohhot, China.
| |
Collapse
|
4
|
Complex of Proline-Specific Peptidases in the Genome and Gut Transcriptomes of Tenebrionidae Insects and Their Role in Gliadin Hydrolysis. Int J Mol Sci 2022; 24:ijms24010579. [PMID: 36614021 PMCID: PMC9820350 DOI: 10.3390/ijms24010579] [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: 11/30/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022] Open
Abstract
A detailed analysis of the complexes of proline-specific peptidases (PSPs) in the midgut transcriptomes of the larvae of agricultural pests Tenebrio molitor and Tribolium castaneum and in the genome of T. castaneum is presented. Analysis of the T. castaneum genome revealed 13 PSP sequences from the clans of serine and metal-dependent peptidases, of which 11 sequences were also found in the gut transcriptomes of both tenebrionid species' larvae. Studies of the localization of PSPs, evaluation of the expression level of their genes in gut transcriptomes, and prediction of the presence of signal peptides determining secretory pathways made it possible to propose a set of peptidases that can directly participate in the hydrolysis of food proteins in the larvae guts. The discovered digestive PSPs of tenebrionids in combination with the post-glutamine cleaving cysteine cathepsins of these insects effectively hydrolyzed gliadins, which are the natural food substrates of the studied pests. Based on the data obtained, a hypothetical scheme for the complete hydrolysis of immunogenic gliadin peptides by T. molitor and T. castaneum digestive peptidases was proposed. These results show promise regarding the development of a drug based on tenebrionid digestive enzymes for the enzymatic therapy of celiac disease and gluten intolerance.
Collapse
|
5
|
Chatenoud L, Marquet C, Valette F, Scott L, Quan J, Bu CH, Hildebrand S, Moresco EMY, Bach JF, Beutler B. Modulation of autoimmune diabetes by N-ethyl-N-nitrosourea- induced mutations in non-obese diabetic mice. Dis Model Mech 2022; 15:275575. [PMID: 35502705 PMCID: PMC9178510 DOI: 10.1242/dmm.049484] [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: 01/25/2022] [Accepted: 04/21/2022] [Indexed: 11/20/2022] Open
Abstract
Genetic association studies of type 1 diabetes (T1D) in humans, and in congenic non-obese diabetic (NOD) mice harboring DNA segments from T1D-resistant mice, face the challenge of assigning causation to specific gene variants among many within loci that affect disease risk. Here, we created random germline mutations in NOD/NckH mice and used automated meiotic mapping to identify mutations modifying T1D incidence and age of onset. In contrast with association studies in humans or congenic NOD mice, we analyzed a relatively small number of genetic changes in each pedigree, permitting implication of specific mutations as causative. Among 844 mice from 14 pedigrees bearing 594 coding/splicing changes, we identified seven mutations that accelerated T1D development, and five that delayed or suppressed T1D. Eleven mutations affected genes not previously known to influence T1D (Xpnpep1, Herc1, Srrm2, Rapgef1, Ppl, Zfp583, Aldh1l1, Col6a1, Ccdc13, Cd200r1, Atrnl1). A suppressor mutation in Coro1a validated the screen. Mutagenesis coupled with automated meiotic mapping can detect genes in which allelic variation influences T1D susceptibility in NOD mice. Variation of some of the orthologous/paralogous genes may influence T1D susceptibility in humans.
Collapse
Affiliation(s)
- Lucienne Chatenoud
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Cindy Marquet
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Fabrice Valette
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Lindsay Scott
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chun Hui Bu
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jean-François Bach
- Université Paris Cité, Institut Necker Enfants Malades, F-75015 Paris, France.,INSERM UMR-S1151, CNRS UMR-S8253, Institut Necker Enfants Malades, F-75015 Paris, France
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
6
|
Silva N, Castellano-Pozo M, Matsuzaki K, Barroso C, Roman-Trufero M, Craig H, Brooks DR, Isaac RE, Boulton SJ, Martinez-Perez E. Proline-specific aminopeptidase P prevents replication-associated genome instability. PLoS Genet 2022; 18:e1010025. [PMID: 35081133 PMCID: PMC8820600 DOI: 10.1371/journal.pgen.1010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/07/2022] [Accepted: 01/10/2022] [Indexed: 11/19/2022] Open
Abstract
Genotoxic stress during DNA replication constitutes a serious threat to genome integrity and causes human diseases. Defects at different steps of DNA metabolism are known to induce replication stress, but the contribution of other aspects of cellular metabolism is less understood. We show that aminopeptidase P (APP1), a metalloprotease involved in the catabolism of peptides containing proline residues near their N-terminus, prevents replication-associated genome instability. Functional analysis of C. elegans mutants lacking APP-1 demonstrates that germ cells display replication defects including reduced proliferation, cell cycle arrest, and accumulation of mitotic DSBs. Despite these defects, app-1 mutants are competent in repairing DSBs induced by gamma irradiation, as well as SPO-11-dependent DSBs that initiate meiotic recombination. Moreover, in the absence of SPO-11, spontaneous DSBs arising in app-1 mutants are repaired as inter-homologue crossover events during meiosis, confirming that APP-1 is not required for homologous recombination. Thus, APP-1 prevents replication stress without having an apparent role in DSB repair. Depletion of APP1 (XPNPEP1) also causes DSB accumulation in mitotically-proliferating human cells, suggesting that APP1’s role in genome stability is evolutionarily conserved. Our findings uncover an unexpected role for APP1 in genome stability, suggesting functional connections between aminopeptidase-mediated protein catabolism and DNA replication. The accurate duplication of DNA that occurs before cells divide is an essential aspect of the cell cycle that is also crucial for the correct development of multicellular organisms. Mutations that compromise the normal function of the DNA replication machinery can lead to the accumulation of replication-related DNA damage, a known cause of human disease and a common feature of cancer and precancerous cells. Therefore, identifying factors that prevent replication-related DNA damage is highly relevant for human health. In this manuscript, we identify aminopeptidase P, an enzyme involved in the breakdown of proteins containing the amino acid Proline at their N-terminus, as a novel factor that prevents replication-related DNA damage. Analysis of C. elegans nematodes lacking aminopeptidase P reveals that this protein is required for normal fertility and development, and that in its absence proliferating germ cells display DNA replication defects, including cell cycle arrest and accumulation of extensive DNA damage. We also show that removal of aminopeptidase P induces DNA damage in proliferating human cells, suggesting that its role in preventing replication defects is evolutionarily conserved. These findings uncover functional connections between aminopeptidase-mediated protein degradation and DNA replication.
Collapse
Affiliation(s)
- Nicola Silva
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | | | - Consuelo Barroso
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
| | - Monica Roman-Trufero
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
| | - Hannah Craig
- School of Biology, University of Leeds, Leeds, United Kingdom
| | - Darren R. Brooks
- School of Science, Engineering and Environment, University of Salford, Salford, United Kingdom
| | - R. Elwyn Isaac
- School of Biology, University of Leeds, Leeds, United Kingdom
| | | | - Enrique Martinez-Perez
- Medical Research Council London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, United Kingdom
- * E-mail:
| |
Collapse
|
7
|
Abstract
Aminopeptidase P (APPro, E.C 3.4.11.9) cleaves N-terminal amino acids from peptides and proteins where the penultimate residue is proline. This metal-ion-dependent enzyme shares a similar fold, catalytic mechanism, and substrate specificity with methionine aminopeptidase and prolidase. It adopts a canonical pita bread fold that serves as a structural basis for the metal-dependent catalysis and assembles as a tetramer in crystals. Similar to other metalloaminopeptidase, APPro requires metal ions for its maximal enzymatic activity, with manganese being the most preferred cation. Microbial aminopeptidase possesses unique characteristics compared with aminopeptidase from other sources, making it a great industrial enzyme for various applications. This review provides a summary of recent progress in the study of the structure and function of aminopeptidase P and describes its various applications in different industries as well as its significance in the environment.
Collapse
|
8
|
Mills B, Isaac RE, Foster R. Metalloaminopeptidases of the Protozoan Parasite Plasmodium falciparum as Targets for the Discovery of Novel Antimalarial Drugs. J Med Chem 2021; 64:1763-1785. [PMID: 33534577 DOI: 10.1021/acs.jmedchem.0c01721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Malaria poses a significant threat to approximately half of the world's population with an annual death toll close to half a million. The emergence of resistance to front-line antimalarials in the most lethal human parasite species, Plasmodium falciparum (Pf), threatens progress made in malaria control. The prospect of losing the efficacy of antimalarial drugs is driving the search for small molecules with new modes of action. Asexual reproduction of the parasite is critically dependent on the recycling of amino acids through catabolism of hemoglobin (Hb), which makes metalloaminopeptidases (MAPs) attractive targets for the development of new drugs. The Pf genome encodes eight MAPs, some of which have been found to be essential for parasite survival. In this article, we discuss the biological structure and function of each MAP within the Pf genome, along with the drug discovery efforts that have been undertaken to identify novel antimalarial candidates of therapeutic value.
Collapse
Affiliation(s)
- Belinda Mills
- School of Chemistry, University of Leeds, Leeds, U.K., LS2 9JT
| | - R Elwyn Isaac
- School of Biology, University of Leeds, Leeds, U.K., LS2 9JT
| | - Richard Foster
- School of Chemistry, University of Leeds, Leeds, U.K., LS2 9JT
| |
Collapse
|
9
|
Dunaevsky YE, Tereshchenkova VF, Oppert B, Belozersky MA, Filippova IY, Elpidina EN. Human proline specific peptidases: A comprehensive analysis. Biochim Biophys Acta Gen Subj 2020; 1864:129636. [DOI: 10.1016/j.bbagen.2020.129636] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/05/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023]
|
10
|
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.
Collapse
|
11
|
Syrén PO. Enzymatic Hydrolysis of Tertiary Amide Bonds by anti Nucleophilic Attack and Protonation. J Org Chem 2018; 83:13543-13548. [DOI: 10.1021/acs.joc.8b02053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, Department of Fibre and Polymer Technology, and Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden 17165
| |
Collapse
|
12
|
Chang HC, Kung CCH, Chang TT, Jao SC, Hsu YT, Li WS. Investigation of the proton relay system operative in human cystosolic aminopeptidase P. PLoS One 2018; 13:e0190816. [PMID: 29351301 PMCID: PMC5774706 DOI: 10.1371/journal.pone.0190816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/20/2017] [Indexed: 11/19/2022] Open
Abstract
Aminopeptidase P, a metalloprotease, targets Xaa-Proline peptides for cleavage [1-4]. There are two forms of human AMPP, a membrane-bound form (hmAMPP) and a soluble cytosolic form (hcAMPP)[5]. Similar to the angiotensin-I-converting enzyme, AMPP plays an important role in the catabolism of inflammatory and vasoactive peptides, known as kinins. The plasma kinin, bradykinin, was used as the substrate to conduct enzymatic activity analyses and to determine the Michaelis constant (Km) of 174 μM and the catalytic rate constant (kcat) of 10.8 s-1 for hcAMPP. Significant differences were observed in the activities of Y527F and R535A hcAMPP mutants, which displayed a 6-fold and 13.5-fold for decrease in turnover rate, respectively. Guanidine hydrochloride restored the activity of R535A hcAMPP, increasing the kcat/Km 20-fold, yet it had no impact on the activities of the wild-type or Y527F mutant hcAMPPs. Activity restoration by guanidine derivatives followed the order guanidine hydrochloride >> methyl-guanidine > amino-guanidine > N-ethyl-guanidine. Overall, the results indicate the participation of R535 in the hydrogen bond network that forms a proton relay system. The quaternary structure of hcAMPP was determined by using analytical ultracentrifugation (AUC). The results show that alanine replacement of Arg535 destabilizes the hcAMPP dimer and that guanidine hydrochloride restores the native monomer-dimer equilibrium. It is proposed that Arg535 plays an important role in hcAMMP catalysis and in stabilization of the catalytically active dimeric state.
Collapse
Affiliation(s)
| | | | | | - Shu-Chuan Jao
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yu-Ting Hsu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Wen-Shan Li
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan
- * E-mail:
| |
Collapse
|
13
|
Peng CT, Liu L, Li CC, He LH, Li T, Shen YL, Gao C, Wang NY, Xia Y, Zhu YB, Song YJ, Lei Q, Yu LT, Bao R. Structure-Function Relationship of Aminopeptidase P from Pseudomonas aeruginosa. Front Microbiol 2017; 8:2385. [PMID: 29259588 PMCID: PMC5723419 DOI: 10.3389/fmicb.2017.02385] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/20/2017] [Indexed: 02/05/2023] Open
Abstract
PepP is a virulence-associated gene in Pseudomonas aeruginosa, making it an attractive target for anti-P. aeruginosa drug development. The encoded protein, aminopeptidases P (Pa-PepP), is a type of X-prolyl peptidase that possesses diverse biological functions. The crystal structure verified its canonical pita-bread fold and functional tetrameric assembly, and the functional studies measured the influences of different metal ions on the activity. A trimetal manganese cluster was observed at the active site, elucidating the mechanism of inhibition by metal ions. Additionally, a loop extending from the active site appeared to be important for specific large-substrate binding. Based on the structural comparison and bacterial invasion assays, we showed that this non-conserved surface loop was critical for P. aeruginosa virulence. Taken together, these findings can extend our understanding of the catalytic mechanism and virulence-related functions of Pa-PepP and provide a solid foundation for the design of specific inhibitors against pathogenic-bacterial infections.
Collapse
Affiliation(s)
- Cui-Ting Peng
- Pharmaceutical and Biological Engineering Department, School of Chemical Engineering, Sichuan University, Chengdu, China,Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Li Liu
- Pharmaceutical and Biological Engineering Department, School of Chemical Engineering, Sichuan University, Chengdu, China,Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Chang-Cheng Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Li-Hui He
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Tao Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ya-Lin Shen
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Chao Gao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ning-Yu Wang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China,School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Yong Xia
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Yi-Bo Zhu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ying-Jie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Qian Lei
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Luo-Ting Yu
- Pharmaceutical and Biological Engineering Department, School of Chemical Engineering, Sichuan University, Chengdu, China,Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China,*Correspondence: Rui Bao, Luo-Ting Yu,
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China,*Correspondence: Rui Bao, Luo-Ting Yu,
| |
Collapse
|
14
|
Matsushita-Morita M, Tada S, Suzuki S, Hattori R, Kusumoto KI. Enzymatic characterization of a novel Xaa-Pro aminopeptidase XpmA from Aspergillus oryzae expressed in Escherichia coli. J Biosci Bioeng 2017; 124:534-541. [DOI: 10.1016/j.jbiosc.2017.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 06/08/2017] [Accepted: 06/18/2017] [Indexed: 01/08/2023]
|
15
|
Proteome profiling of clear cell renal cell carcinoma in von Hippel-Lindau patients highlights upregulation of Xaa-Pro aminopeptidase-1, an anti-proliferative and anti-migratory exoprotease. Oncotarget 2017; 8:100066-100078. [PMID: 29245961 PMCID: PMC5725003 DOI: 10.18632/oncotarget.21929] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/08/2017] [Indexed: 12/21/2022] Open
Abstract
Patients of the von Hippel-Lindau (VHL) disease frequently develop clear cell renal cell carcinoma (ccRCC). Using archived, formalin-fixed, paraffin-embedded (FFPE) samples, we sought to determine global proteome alterations that distinguish ccRCC tissue from adjacent, non-malignant kidney tissue in VHL-patients. Our quantitative proteomic analysis clearly discriminated tumor and non-malignant tissue. Significantly dysregulated proteins were distinguished using the linear models for microarray data algorithm. In the ccRCC tissue, we noticed a predominant under-representation of proteins involved in the tricarboxylic acid cycle and an increase in proteins involved in glycolysis. This profile possibly represents a proteomic fingerprint of the "Warburg effect", which is a molecular hallmark of ccRCC. Furthermore, we observed an increase in proteins involved in extracellular matrix organization. We also noticed differential expression of many exoproteases in the ccRCC tissue. Of particular note were opposing alterations of Xaa-Pro Aminopeptidases-1 and -2 (XPNPEP-1 and -2): a strong decrease of XPNPEP-2 in ccRCC was accompanied by abundant presence of the related protease XPNPEP-1. In both cases, we corroborated the proteomic results by immunohistochemical analysis of ccRCC and adjacent, non-malignant kidney tissue of VHL patients. To functionally investigate the role of XPNPEP-1 in ccRCC, we performed small-hairpin RNA mediated XPNPEP-1 expression silencing in 786-O ccRCC cells harboring a mutated VHL gene. We found that XPNPEP-1 expression dampens cellular proliferation and migration. These results suggest that XPNPEP-1 is likely an anti-target in ccRCC. Methodologically, our work further validates the robustness of using FFPE material for quantitative proteomics.
Collapse
|
16
|
Are VN, Jamdar SN, Ghosh B, Goyal VD, Kumar A, Neema S, Gadre R, Makde RD. Crystal structure of a novel prolidase from Deinococcus radiodurans identifies new subfamily of bacterial prolidases. Proteins 2017; 85:2239-2251. [PMID: 28929533 DOI: 10.1002/prot.25389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/29/2017] [Accepted: 09/15/2017] [Indexed: 11/10/2022]
Abstract
Xaa-Pro peptidases (XPP) are dinuclear peptidases of MEROPS M24B family that hydrolyze Xaa-Pro iminopeptide bond with a trans-proline at the second position of the peptide substrate. XPPs specific towards dipeptides are called prolidases while those that prefer longer oligopeptides are called aminopeptidases P. Though XPPs are strictly conserved in bacterial and archaeal species, the structural and sequence features that distinguish between prolidases and aminopeptidases P are not always clear. Here, we report 1.4 Å resolution crystal structure of a novel XPP from Deinococcus radiodurans (XPPdr). XPPdr forms a novel dimeric structure via unique dimer stabilization loops of N-terminal domains such that their C-terminal domains are placed far apart from each other. This novel dimerization is also the consequence of a different orientation of N-terminal domain in XPPdr monomer than those in other known prolidases. The enzymatic assays show that it is a prolidase with broad substrate specificity. Our structural, mutational, and molecular dynamics simulation analyses show that the conserved Arg46 of N-terminal domain is important for the dipeptide selectivity. Our BLAST search found XPPdr orthologs with conserved sequence motifs which correspond to unique structural features of XPPdr, thus identify a new subfamily of bacterial prolidases.
Collapse
Affiliation(s)
- Venkata N Are
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India.,School of Biochemistry, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Biplab Ghosh
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Venuka Durani Goyal
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Ashwani Kumar
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sanchit Neema
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Rekha Gadre
- School of Biochemistry, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Ravindra D Makde
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, India
| |
Collapse
|
17
|
Wilk P, Uehlein M, Kalms J, Dobbek H, Mueller U, Weiss MS. Substrate specificity and reaction mechanism of human prolidase. FEBS J 2017; 284:2870-2885. [DOI: 10.1111/febs.14158] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/23/2017] [Accepted: 06/30/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Piotr Wilk
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
- Institut für Biologie, Strukturbiologie/Biochemie; Humboldt-Universität zu Berlin; Germany
| | - Monika Uehlein
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
| | - Jacqueline Kalms
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
| | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie; Humboldt-Universität zu Berlin; Germany
| | - Uwe Mueller
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
| | - Manfred S. Weiss
- Helmholtz-Zentrum Berlin, Macromolecular Crystallography (HZB-MX); Berlin Germany
| |
Collapse
|
18
|
Singh R, Jamdar SN, Goyal VD, Kumar A, Ghosh B, Makde RD. Structure of the human aminopeptidase XPNPEP3 and comparison of its in vitro activity with Icp55 orthologs: Insights into diverse cellular processes. J Biol Chem 2017; 292:10035-10047. [PMID: 28476889 DOI: 10.1074/jbc.m117.783357] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 05/04/2017] [Indexed: 11/06/2022] Open
Abstract
The human aminopeptidase XPNPEP3 is associated with cystic kidney disease and TNF-TNFR2 cellular signaling. Its yeast and plant homolog Icp55 processes several imported mitochondrial matrix proteins leading to their stabilization. However, the molecular basis for the diverse roles of these enzymes in the cell is unknown. Here, we report the crystal structure of human XPNPEP3 with bound apstatin product at 1.65 Å resolution, and we compare its in vitro substrate specificity with those of fungal Icp55 enzymes. In contrast to the suggestions by earlier in vivo studies of mitochondrial processing, we found that these enzymes are genuine Xaa-Pro aminopeptidases, which hydrolyze peptides with proline at the second position (P1'). The mitochondrial processing activity involving cleavage of peptides lacking P1' proline was also detected in the purified enzymes. A wide proline pocket as well as molecular complementarity and capping at the S1 substrate site of XPNPEP3 provide the necessary structural features for processing the mitochondrial substrates. However, this activity was found to be significantly lower as compared with Xaa-Pro aminopeptidase activity. Because of similar activity profiles of Icp55 and XPNPEP3, we propose that XPNPEP3 plays the same mitochondrial role in humans as Icp55 does in yeast. Both Xaa-Pro aminopeptidase and mitochondrial processing activities of XPNPEP3 have implications toward mitochondrial fitness and cystic kidney disease. Furthermore, the presence of both these activities in Icp55 elucidates the unexplained processing of the mitochondrial cysteine desulfurase Nfs1 in yeast. The enzymatic and structural analyses reported here provide a valuable molecular framework for understanding the diverse cellular roles of XPNPEP3.
Collapse
Affiliation(s)
- Rahul Singh
- From the High Pressure and Synchrotron Radiation Physics Division and
| | - Sahayog N Jamdar
- Food Technology Division, Bhabha Atomic Research Centre, 400085 Mumbai, India
| | | | - Ashwani Kumar
- From the High Pressure and Synchrotron Radiation Physics Division and
| | - Biplab Ghosh
- From the High Pressure and Synchrotron Radiation Physics Division and
| | - Ravindra D Makde
- From the High Pressure and Synchrotron Radiation Physics Division and
| |
Collapse
|
19
|
Structure and substrate fingerprint of aminopeptidase P from Plasmodium falciparum. Biochem J 2016; 473:3189-204. [DOI: 10.1042/bcj20160550] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 07/26/2016] [Indexed: 12/18/2022]
Abstract
Malaria is one of the world's most prevalent parasitic diseases, with over 200 million cases annually. Alarmingly, the spread of drug-resistant parasites threatens the effectiveness of current antimalarials and has made the development of novel therapeutic strategies a global health priority. Malaria parasites have a complicated lifecycle, involving an asymptomatic ‘liver stage’ and a symptomatic ‘blood stage’. During the blood stage, the parasites utilise a proteolytic cascade to digest host hemoglobin, which produces free amino acids absolutely necessary for parasite growth and reproduction. The enzymes required for hemoglobin digestion are therefore attractive therapeutic targets. The final step of the cascade is catalyzed by several metalloaminopeptidases, including aminopeptidase P (APP). We developed a novel platform to examine the substrate fingerprint of APP from Plasmodium falciparum (PfAPP) and to show that it can catalyze the removal of any residue immediately prior to a proline. Further, we have determined the crystal structure of PfAPP and present the first examination of the 3D structure of this essential malarial enzyme. Together, these analyses provide insights into potential mechanisms of inhibition that could be used to develop novel antimalarial therapeutics.
Collapse
|
20
|
Iyer S, La-Borde PJ, Payne KAP, Parsons MR, Turner AJ, Isaac RE, Acharya KR. Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site. FEBS Open Bio 2015; 5:292-302. [PMID: 25905034 PMCID: PMC4404410 DOI: 10.1016/j.fob.2015.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/28/2015] [Accepted: 03/30/2015] [Indexed: 01/22/2023] Open
Abstract
Eukaryotic aminopeptidase P1 (APP1), also known as X‐prolyl aminopeptidase (XPNPEP1) in human tissues, is a cytosolic exopeptidase that preferentially removes amino acids from the N‐terminus of peptides possessing a penultimate N‐terminal proline residue. The enzyme has an important role in the catabolism of proline containing peptides since peptide bonds adjacent to the imino acid proline are resistant to cleavage by most peptidases. We show that recombinant and catalytically activeCaenorhabditis elegans APP‐1 is a dimer that uses dinuclear zinc at the active site and, for the first time, we provide structural information for a eukaryotic APP‐1 in complex with the inhibitor, apstatin. Our analysis reveals thatC. elegans APP‐1 shares similar mode of substrate binding and a common catalytic mechanism with other known X‐prolyl aminopeptidases. We present the crystal structure ofC. elegans APP‐1 both in bound and unbound forms. We showC. elegans APP‐1 uses dinuclear zinc at the active site. We confirm thatC. elegans APP‐1 is biological dimer. Our analysis reveals thatC. elegans APP‐1 shares a common catalytic mechanism with other X‐prolyl aminopeptidases.
Collapse
Key Words
- APP1, aminopeptidase P1
- Apstatin
- CCP4, computational collaborative project 4
- Di-nuclear active site
- ICP-AES, inductively coupled plasma atomic emission spectroscopy
- ICP-MS, inductively coupled plasma mass spectrometry
- MAP, methionine aminopeptidase
- NMR, nuclear magnetic resonance
- PCR, polymerase chain reaction
- PEG3350, polyethylene glycol 3350
- Protease inhibitor
- X-prolyl aminopeptidase
- X-ray crystallography
- XPNPEP, X-prolyl aminopeptidase
- Zinc metalloprotease
- rmsd, root mean square deviation
Collapse
Affiliation(s)
- Shalini Iyer
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Penelope J La-Borde
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK ; School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Karl A P Payne
- Faculty of Biological Sciences, Clarendon Way, University of Leeds, Leeds LS2 9JT, UK ; Faculty of Life Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Mark R Parsons
- Faculty of Biological Sciences, Clarendon Way, University of Leeds, Leeds LS2 9JT, UK ; Sevenoaks School, Sevenoaks TN13 1HU, UK
| | - Anthony J Turner
- Faculty of Biological Sciences, Clarendon Way, University of Leeds, Leeds LS2 9JT, UK
| | - R Elwyn Isaac
- Faculty of Biological Sciences, Clarendon Way, University of Leeds, Leeds LS2 9JT, UK
| | - K Ravi Acharya
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| |
Collapse
|
21
|
Breton CV, Siegmund KD, Joubert BR, Wang X, Qui W, Carey V, Nystad W, Håberg SE, Ober C, Nicolae D, Barnes KC, Martinez F, Liu A, Lemanske R, Strunk R, Weiss S, London S, Gilliland F, Raby B. Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation. PLoS One 2014; 9:e99716. [PMID: 24964093 PMCID: PMC4070909 DOI: 10.1371/journal.pone.0099716] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/18/2014] [Indexed: 11/19/2022] Open
Abstract
Background Smoking while pregnant is associated with a myriad of negative health outcomes in the child. Some of the detrimental effects may be due to epigenetic modifications, although few studies have investigated this hypothesis in detail. Objectives To characterize site-specific epigenetic modifications conferred by prenatal smoking exposure within asthmatic children. Methods Using Illumina HumanMethylation27 microarrays, we estimated the degree of methylation at 27,578 distinct DNA sequences located primarily in gene promoters using whole blood DNA samples from the Childhood Asthma Management Program (CAMP) subset of Asthma BRIDGE childhood asthmatics (n = 527) ages 5–12 with prenatal smoking exposure data available. Using beta-regression, we screened loci for differential methylation related to prenatal smoke exposure, adjusting for gender, age and clinical site, and accounting for multiple comparisons by FDR. Results Of 27,578 loci evaluated, 22,131 (80%) passed quality control assessment and were analyzed. Sixty-five children (12%) had a history of prenatal smoke exposure. At an FDR of 0.05, we identified 19 CpG loci significantly associated with prenatal smoke, of which two replicated in two independent populations. Exposure was associated with a 2% increase in mean CpG methylation in FRMD4A (p = 0.01) and Cllorf52 (p = 0.001) compared to no exposure. Four additional genes, XPNPEP1, PPEF2, SMPD3 and CRYGN, were nominally associated in at least one replication group. Conclusions These data suggest that prenatal exposure to tobacco smoke is associated with reproducible epigenetic changes that persist well into childhood. However, the biological significance of these altered loci remains unknown.
Collapse
Affiliation(s)
- Carrie V. Breton
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Bonnie R. Joubert
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Xinhui Wang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Weiliang Qui
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vincent Carey
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | | | - Carole Ober
- University of Chicago, Chicago, Illinois, United States of America
| | - Dan Nicolae
- University of Chicago, Chicago, Illinois, United States of America
| | | | - Fernando Martinez
- Arizona Respiratory Center, University of Arizona, Arizona, United States of America
| | - Andy Liu
- National Jewish Health, Denver, Colorado, United States of America
| | - Robert Lemanske
- University of Wisconsin, Madison, Wisconsin, United States of America
| | - Robert Strunk
- Washington University School of Medicine, St. Louis, Montana, United States of America
| | - Scott Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stephanie London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Frank Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Benjamin Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | | |
Collapse
|
22
|
Besio R, Baratto MC, Gioia R, Monzani E, Nicolis S, Cucca L, Profumo A, Casella L, Basosi R, Tenni R, Rossi A, Forlino A. A Mn(II)–Mn(II) center in human prolidase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:197-204. [DOI: 10.1016/j.bbapap.2012.09.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 09/10/2012] [Accepted: 09/12/2012] [Indexed: 12/20/2022]
|
23
|
Durrenberger PF, Fernando FS, Magliozzi R, Kashefi SN, Bonnert TP, Ferrer I, Seilhean D, Nait-Oumesmar B, Schmitt A, Gebicke-Haerter PJ, Falkai P, Grünblatt E, Palkovits M, Parchi P, Capellari S, Arzberger T, Kretzschmar H, Roncaroli F, Dexter DT, Reynolds R. Selection of novel reference genes for use in the human central nervous system: a BrainNet Europe Study. Acta Neuropathol 2012; 124:893-903. [PMID: 22864814 DOI: 10.1007/s00401-012-1027-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/15/2012] [Accepted: 07/24/2012] [Indexed: 01/17/2023]
Abstract
The use of an appropriate reference gene to ensure accurate normalisation is crucial for the correct quantification of gene expression using qPCR assays and RNA arrays. The main criterion for a gene to qualify as a reference gene is a stable expression across various cell types and experimental settings. Several reference genes are commonly in use but more and more evidence reveals variations in their expression due to the presence of on-going neuropathological disease processes, raising doubts concerning their use. We conducted an analysis of genome-wide changes of gene expression in the human central nervous system (CNS) covering several neurological disorders and regions, including the spinal cord, and were able to identify a number of novel stable reference genes. We tested the stability of expression of eight novel (ATP5E, AARS, GAPVD1, CSNK2B, XPNPEP1, OSBP, NAT5 and DCTN2) and four more commonly used (BECN1, GAPDH, QARS and TUBB) reference genes in a smaller cohort using RT-qPCR. The most stable genes out of the 12 reference genes were tested as normaliser to validate increased levels of a target gene in CNS disease. We found that in human post-mortem tissue the novel reference genes, XPNPEP1 and AARS, were efficient in replicating microarray target gene expression levels and that XPNPEP1 was more efficient as a normaliser than BECN1, which has been shown to change in expression as a consequence of neuronal cell loss. We provide herein one more suitable novel reference gene, XPNPEP1, with no current neuroinflammatory or neurodegenerative associations that can be used for gene quantitative gene expression studies with human CNS post-mortem tissue and also suggest a list of potential other candidates. These data also emphasise the importance of organ/tissue-specific stably expressed genes as reference genes for RNA studies.
Collapse
Affiliation(s)
- Pascal F Durrenberger
- Wolfson Neuroscience Laboratories, Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, London, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Wu S, Liu S, Sim S, Pedersen LG. Weakly Antiferromagentic Coupling Via Superexchange Interaction Between Mn(II)-Mn(II) Atoms: A QM/MM Study of the Active Site of Human Cytosolic X-Propyl Aminopeptidase P. J Phys Chem Lett 2012; 3:2293-2297. [PMID: 23145216 PMCID: PMC3491985 DOI: 10.1021/jz300768g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We investigate the dinuclear manganese, Mn(II)-Mn(II), active site of human cytosolic X-propyl aminopeptidase (XPNPEP1) employing the QM/MM method. The optimized structure supports two manganese atoms at the active site and excludes the possibility of a single Mn(II) atom or other combination of divalent metal ions: Ca(II), Fe(II), Mg(II). A broken symmetry solution verifies an antiferromagnetically coupled state between the Mn(II)-Mn(II) pair, which is the ground state. From the energy difference between the high spin state (HS) and the broken symmetry state (BS), we estimate the exchange coupling constant, J, to be 5.15 cm(-1). Also, we observe multiple bridges (p orbitals) from solvent and two carboxylate linking to the Mn(II)-Mn(II), which leads to the weakly antiferromagnetic interaction of d(5)-d(5) electrons through superexchange coupling.
Collapse
Affiliation(s)
- Sangwook Wu
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-329
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420
| | - Sooyeon Sim
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-329
| | - Lee G. Pedersen
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-329
| |
Collapse
|
25
|
Kaewkiattiyot S, Honsawek S, Vejchapipat P, Chongsrisawat V, Poovorawan Y. Association of X-prolyl aminopeptidase 1 rs17095355 polymorphism with biliary atresia in Thai children. Hepatol Res 2011; 41:1249-52. [PMID: 22118303 DOI: 10.1111/j.1872-034x.2011.00870.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
AIM To investigate XPNPEP1 rs17095355 polymorphism in biliary atresia (BA) patients and to determine whether there is an association between XPNPEP1 gene polymorphism and susceptibility to BA in a Thai population. METHODS A total of 124 cases of BA and 114 controls were genotyped for XPNPEP1 rs17095355 polymorphism. The XPNPEP1 rs17095355 C/T genotype was determined by polymerase chain reaction (PCR) and direct sequencing. Allele and genotype frequencies were established by directed counting from the sequences. RESULTS Genotype distributions for the XPNPEP1 rs17095355 polymorphism tested were in Hardy-Weinberg equilibrium for both control and study groups. There were no significant differences in genotype and allele frequencies of the single nucleotide polymorphism between controls and Thai children with BA. Genotype frequencies of rs17095355 of T/T in BA were higher than those of controls (34.68% and 16.67%, P < 0.002). Also, the T allele frequencies of BA were higher than those of controls (56.85% and 42.98%, P < 0.003). CONCLUSION The association between XPNPEP1 rs17095355 polymorphism and BA has been demonstrated, particularly with the T allele. We hypothesize that the XPNPEP1 rs17095355 polymorphism confers increased susceptibility to the disease.
Collapse
Affiliation(s)
- Sarannut Kaewkiattiyot
- Center of Excellence in Clinical Virology Department of Biochemistry, Faculty of Medicine Department of Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | | | | | | |
Collapse
|
26
|
O'Toole JF, Liu Y, Davis EE, Westlake CJ, Attanasio M, Otto EA, Seelow D, Nurnberg G, Becker C, Nuutinen M, Kärppä M, Ignatius J, Uusimaa J, Pakanen S, Jaakkola E, van den Heuvel LP, Fehrenbach H, Wiggins R, Goyal M, Zhou W, Wolf MTF, Wise E, Helou J, Allen SJ, Murga-Zamalloa CA, Ashraf S, Chaki M, Heeringa S, Chernin G, Hoskins BE, Chaib H, Gleeson J, Kusakabe T, Suzuki T, Isaac RE, Quarmby LM, Tennant B, Fujioka H, Tuominen H, Hassinen I, Lohi H, van Houten JL, Rotig A, Sayer JA, Rolinski B, Freisinger P, Madhavan SM, Herzer M, Madignier F, Prokisch H, Nurnberg P, Jackson PK, Jackson P, Khanna H, Katsanis N, Hildebrandt F. Individuals with mutations in XPNPEP3, which encodes a mitochondrial protein, develop a nephronophthisis-like nephropathy. J Clin Invest 2010; 120:791-802. [PMID: 20179356 DOI: 10.1172/jci40076] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 01/06/2010] [Indexed: 01/06/2023] Open
Abstract
The autosomal recessive kidney disease nephronophthisis (NPHP) constitutes the most frequent genetic cause of terminal renal failure in the first 3 decades of life. Ten causative genes (NPHP1-NPHP9 and NPHP11), whose products localize to the primary cilia-centrosome complex, support the unifying concept that cystic kidney diseases are "ciliopathies". Using genome-wide homozygosity mapping, we report here what we believe to be a new locus (NPHP-like 1 [NPHPL1]) for an NPHP-like nephropathy. In 2 families with an NPHP-like phenotype, we detected homozygous frameshift and splice-site mutations, respectively, in the X-prolyl aminopeptidase 3 (XPNPEP3) gene. In contrast to all known NPHP proteins, XPNPEP3 localizes to mitochondria of renal cells. However, in vivo analyses also revealed a likely cilia-related function; suppression of zebrafish xpnpep3 phenocopied the developmental phenotypes of ciliopathy morphants, and this effect was rescued by human XPNPEP3 that was devoid of a mitochondrial localization signal. Consistent with a role for XPNPEP3 in ciliary function, several ciliary cystogenic proteins were found to be XPNPEP3 substrates, for which resistance to N-terminal proline cleavage resulted in attenuated protein function in vivo in zebrafish. Our data highlight an emerging link between mitochondria and ciliary dysfunction, and suggest that further understanding the enzymatic activity and substrates of XPNPEP3 will illuminate novel cystogenic pathways.
Collapse
Affiliation(s)
- John F O'Toole
- Department of Pediatrics, University of Michigan, Ann Arbor, 48109-5646, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Ragheb D, Bompiani K, Dalal S, Klemba M. Evidence for catalytic roles for Plasmodium falciparum aminopeptidase P in the food vacuole and cytosol. J Biol Chem 2009; 284:24806-15. [PMID: 19574214 DOI: 10.1074/jbc.m109.018424] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The metalloenzyme aminopeptidase P catalyzes the hydrolysis of amino acids from the amino termini of peptides with a prolyl residue in the second position. The human malaria parasite Plasmodium falciparum expresses a homolog of aminopeptidase P during its asexual intraerythrocytic cycle. P. falciparum aminopeptidase P (PfAPP) shares with mammalian cytosolic aminopeptidase P a three-domain, homodimeric organization and is most active with Mn(II) as the cofactor. A distinguishing feature of PfAPP is a 120-amino acid amino-terminal extension that appears to be removed from the mature protein. PfAPP is present in the food vacuole and cytosol of the parasite, a distribution that suggests roles in vacuolar hemoglobin catabolism and cytosolic peptide turnover. To evaluate the plausibility of these putative functions, the stability and kinetic properties of recombinant PfAPP were evaluated at the acidic pH of the food vacuole and at the near-neutral pH of the cytosol. PfAPP exhibited high stability at 37 degrees C in the pH range 5.0-7.5. In contrast, recombinant human cytosolic APP1 was unstable and formed a high molecular weight aggregate at acidic pH. At both acidic and slightly basic pH values, PfAPP efficiently hydrolyzed the amino-terminal X-Pro bond of the nonapeptide bradykinin and of two globin pentapeptides that are potential in vivo substrates. These results provide support for roles for PfAPP in peptide catabolism in both the food vacuole and the cytosol and suggest that PfAPP has evolved a dual distribution in response to the metabolic needs of the intraerythrocytic parasite.
Collapse
Affiliation(s)
- Daniel Ragheb
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | | | | | | |
Collapse
|