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Banerjee S, Gadpayle MP, Samanta S, Dutta P, Das S, Datta R, Maiti S. Role of Macrophage PIST Protein in Regulating Leishmania major Infection. ACS Infect Dis 2024; 10:1414-1428. [PMID: 38556987 DOI: 10.1021/acsinfecdis.4c00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
PDZ protein interacting specifically with Tc10 or PIST is a mammalian trans-Golgi resident protein that regulates subcellular sorting of plasma membrane receptors. PIST has recently emerged as a key player in regulating viral pathogenesis. Nevertheless, the involvement of PIST in parasitic infections remains unexplored. Leishmania parasites infiltrate their host macrophage cells through phagocytosis, where they subsequently multiply within the parasitophorous vacuole (PV). Host cell autophagy has been found to be important in regulating this parasite infection. Since PIST plays a pivotal role in triggering autophagy through the Beclin 1-PI3KC3 pathway, it becomes interesting to identify the status of PIST during Leishmania infection. We found that while macrophage cells are infected with Leishmania major (L. major), the expression of PIST protein remains unaltered; however, it traffics from the Golgi compartment to PV. Further, we identified that in L. major-infected macrophage cells, PIST associates with the autophagy regulatory protein Beclin 1 within the PVs; however, PIST does not interact with LC3. Reduction in PIST protein through siRNA silencing significantly increased parasite burden, whereas overexpression of PIST in macrophages restricted L. major infectivity. Together, our study reports that the macrophage PIST protein is essential in regulating L. major infectivity.
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Affiliation(s)
- Sourav Banerjee
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Mandip Pratham Gadpayle
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Suman Samanta
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Priyanka Dutta
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Swagata Das
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Rupak Datta
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
| | - Sankar Maiti
- Department of Biological Sciences, Indian Institute of Science Education & Research Kolkata (IISER-Kolkata), Mohanpur Campus, Kolkata, West Bengal 741 246, India
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Kusuma WA, Fadli A, Fatriani R, Sofyantoro F, Yudha DS, Lischer K, Nuringtyas TR, Putri WA, Purwestri YA, Swasono RT. Prediction of the interaction between Calloselasma rhodostoma venom-derived peptides and cancer-associated hub proteins: A computational study. Heliyon 2023; 9:e21149. [PMID: 37954374 PMCID: PMC10637925 DOI: 10.1016/j.heliyon.2023.e21149] [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: 03/27/2023] [Revised: 09/04/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
The use of peptide drugs to treat cancer is gaining popularity because of their efficacy, fewer side effects, and several advantages over other properties. Identifying the peptides that interact with cancer proteins is crucial in drug discovery. Several approaches related to predicting peptide-protein interactions have been conducted. However, problems arise due to the high costs of resources and time and the smaller number of studies. This study predicts peptide-protein interactions using Random Forest, XGBoost, and SAE-DNN. Feature extraction is also performed on proteins and peptides using intrinsic disorder, amino acid sequences, physicochemical properties, position-specific assessment matrices, amino acid composition, and dipeptide composition. Results show that all algorithms perform equally well in predicting interactions between peptides derived from venoms and target proteins associated with cancer. However, XGBoost produces the best results with accuracy, precision, and area under the receiver operating characteristic curve of 0.859, 0.663, and 0.697, respectively. The enrichment analysis revealed that peptides from the Calloselasma rhodostoma venom targeted several proteins (ESR1, GOPC, and BRD4) related to cancer.
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Affiliation(s)
- Wisnu Ananta Kusuma
- Department of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia
- Tropical Biopharmaca Research Center, IPB University, Bogor, 16128, Indonesia
| | - Aulia Fadli
- Department of Computer Science, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia
| | - Rizka Fatriani
- Tropical Biopharmaca Research Center, IPB University, Bogor, 16128, Indonesia
| | - Fajar Sofyantoro
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Donan Satria Yudha
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Kenny Lischer
- Faculty of Engineering, University of Indonesia, Jakarta, 16424, Indonesia
| | - Tri Rini Nuringtyas
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | | | - Yekti Asih Purwestri
- Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Respati Tri Swasono
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
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Yue L, Lu Z, Guo T, Liu J, Yang B, Yuan C. Proteome Analysis of Alpine Merino Sheep Skin Reveals New Insights into the Mechanisms Involved in Regulating Wool Fiber Diameter. Int J Mol Sci 2023; 24:15227. [PMID: 37894908 PMCID: PMC10607505 DOI: 10.3390/ijms242015227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023] Open
Abstract
Wool fiber is a textile material that is highly valued based on its diameter, which is crucial in determining its economic value. To analyze the molecular mechanisms regulating wool fiber diameter, we used a Data-independent acquisition-based quantitative proteomics approach to analyze the skin proteome of Alpine Merino sheep with four fiber diameter ranges. From three contrasts of defined groups, we identified 275, 229, and 190 differentially expressed proteins (DEPs). Further analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways revealed that pathways associated with cyclic adenosine monophosphate and peroxisome proliferator-activated receptor signaling are relevant to wool fiber diameter. Using the K-means method, we investigated the DEP expression patterns across wool diameter ranges. Using weighted gene co-expression network analysis, we identified seven key proteins (CIDEA, CRYM, MLX, TPST2, GPD1, GOPC, and CAMK2G) that may be involved in regulating wool fiber diameter. Our findings provide a theoretical foundation for identifying DEPs and pathways associated with wool fiber diameter in Alpine Merino sheep to enable a better understanding of the molecular mechanisms underlying the genetic regulation of wool fiber quality.
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Affiliation(s)
- Lin Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou 730050, China
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Group I Metabotropic Glutamate Receptors and Interacting Partners: An Update. Int J Mol Sci 2022; 23:ijms23020840. [PMID: 35055030 PMCID: PMC8778124 DOI: 10.3390/ijms23020840] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/21/2022] Open
Abstract
Group I metabotropic glutamate (mGlu) receptors (mGlu1/5 subtypes) are G protein-coupled receptors and are broadly expressed in the mammalian brain. These receptors play key roles in the modulation of normal glutamatergic transmission and synaptic plasticity, and abnormal mGlu1/5 signaling is linked to the pathogenesis and symptomatology of various mental and neurological disorders. Group I mGlu receptors are noticeably regulated via a mechanism involving dynamic protein-protein interactions. Several synaptic protein kinases were recently found to directly bind to the intracellular domains of mGlu1/5 receptors and phosphorylate the receptors at distinct amino acid residues. A variety of scaffolding and adaptor proteins also interact with mGlu1/5. Constitutive or activity-dependent interactions between mGlu1/5 and their interacting partners modulate trafficking, anchoring, and expression of the receptors. The mGlu1/5-associated proteins also finetune the efficacy of mGlu1/5 postreceptor signaling and mGlu1/5-mediated synaptic plasticity. This review analyzes the data from recent studies and provides an update on the biochemical and physiological properties of a set of proteins or molecules that interact with and thus regulate mGlu1/5 receptors.
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