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Ganzerla MD, Indolfo NDC, Oliveira LCM, Doratioto TR, Avelino TM, de Azevedo RJ, Tofani LB, Terra MF, Elias GB, de Sousa IL, Alborguetti MR, Rocco SA, Arroteia KF, Figueira ACM. Unveiling the intricacies of BPA and BPS: comprehensive insights into its toxic effects using a cutting-edge microphysiological system. Toxicol In Vitro 2024; 98:105849. [PMID: 38772494 DOI: 10.1016/j.tiv.2024.105849] [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] [Received: 02/20/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/23/2024]
Abstract
Concerns over Bisphenol A (BPA) and its substitute, Bisphenol S (BPS), have led to innovative exploration due to potential adverse health effects. BPS, replacing BPA in some regions to avoid toxic impacts, remains insufficiently studied. Besides this, the organ-on-a-chip technology emerges as a transformative solution in drug discovery and chemiclas toxicity testing, minimizing costs and aligning with ethical standards by reducing reliance on animal models, by integrating diverse tissues and dynamic cell environments enhances precision in predicting organ function. Here, we employ a 3-organ-on-a-chip microfluidic device with skin, intestine, and liver cultures to assess the effects of BPA and BPS via topical and oral administration. Our evaluation focused on gene markers associated with carcinogenicity, systemic toxicity, and endocrine disruption. BPA exhibited expected absorption profiles, causing liver injury and genetic modulation in related pathways. BPS, a safer alternative, induced adverse effects on gene expression, particularly in topical absorption, with distinct absorption patterns. Our findings underscore the urgency of addressing BPA and BPS toxicity concerns, highlighting the crucial role of organ-on-a-chip technology in understanding associated health risks. The study promotes the organ-on-a-chip methodology as a valuable tool for safe drug development and disease treatments, offering a novel liver toxicity screening alternative to traditional animal tests. This contributes to advancing comprehension of the biological effects of these compounds, fostering improved safety assessments in human health.
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Kommer DC, Stamatiou K, Vagnarelli P. Cell Cycle-Specific Protein Phosphatase 1 (PP1) Substrates Identification Using Genetically Modified Cell Lines. Methods Mol Biol 2024; 2740:37-61. [PMID: 38393468 DOI: 10.1007/978-1-0716-3557-5_3] [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: 02/25/2024]
Abstract
The identification of protein phosphatase 1 (PP1) holoenzyme substrates has proven to be a challenging task. PP1 can form different holoenzyme complexes with a variety of regulatory subunits, and many of those are cell cycle regulated. Although several methods have been used to identify PP1 substrates, their cell cycle specificity is still an unmet need. Here, we present a new strategy to investigate PP1 substrates throughout the cell cycle using clustered regularly interspersed short palindromic repeats (CRISPR)-Cas9 genome editing and generate cell lines with endogenously tagged PP1 regulatory subunit (regulatory interactor of protein phosphatase one, RIPPO). RIPPOs are tagged with the auxin-inducible degron (AID) or ascorbate peroxidase 2 (APEX2) modules, and PP1 substrate identification is conducted by SILAC proteomic-based approaches. Proteins in close proximity to RIPPOs are first identified through mass spectrometry (MS) analyses using the APEX2 system; then a list of differentially phosphorylated proteins upon RIPPOs rapid degradation (achieved via the AID system) is compiled via SILAC phospho-mass spectrometry. The "in silico" overlap between the two proteomes will be enriched for PP1 putative substrates. Several methods including fluorescence resonance energy transfer (FRET), proximity ligation assays (PLA), and in vitro assays can be used as substrate validations approaches.
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Affiliation(s)
- Dorothee C Kommer
- College of Health, Medicine and Life Science, Brunel University London, London, UK
| | | | - Paola Vagnarelli
- College of Health, Medicine and Life Science, Brunel University London, London, UK.
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Yang BT, Zhao T, Li HJ, Liang ZL, Cong W, Kang YH. Lc-pPG-612-OmpU-CTB: A promising oral vaccine for protecting Carassius auratus against Vibrio mimicus infection. FISH & SHELLFISH IMMUNOLOGY 2023; 140:108973. [PMID: 37481101 DOI: 10.1016/j.fsi.2023.108973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 07/24/2023]
Abstract
Vibrio mimicus (V. mimicus) is known to cause severe bacterial diseases with high mortality rates in fish, resulting in significant economic losses in the global aquaculture industry. Therefore, the objective of this study was to develop a safe and effective vaccine for protecting Carassius auratus (C. auratus) against V. mimicus infection. Recombinant Lactobacillus casei (L. casei) strains, Lc-pPG-612-OmpU and Lc-pPG-612-OmpU-CTB (surface-displayed), were constructed using a L. casei strain (ATCC 393) as an antigen delivery carrier and the cholera toxin B subunit (CTB) as an adjuvant. The two recombinant strains of L. casei were administered to C. auratus via oral immunization, and the protective efficacy of the oral vaccines was assessed. The results demonstrated that oral immunization with the two strains significantly increased the levels of nonspecific immune indicators in C. auratus, including alkaline phosphatase (AKP), lysozyme (LYS), acid phosphatase (ACP), complement 3 (C3), complement 4 (C4), lectin, and superoxide dismutase (SOD). Moreover, the experiment groups exhibited significant increases in specific immunoglobulin M (IgM) antibodies against OmpU, as well as the transcription of immune-related genes (ie., IL-1β, TNF-α, IL-10, and TGF-β), when compared to the control groups. Following infection of C. auratus with V. mimicus, the mortality rate of the recombinant L. casei-treated fish was observed to be lower compared to the control group. This finding suggests that recombinant L. casei demonstrates effective protection against V. mimicus infection in C. auratus. Furthermore, the addition of the immune adjuvant CTB was found to induce a more robust adaptive and innate immune response in C. auratus, resulting in reduced mortality after infection with V. mimicus.
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Affiliation(s)
- Bin-Tong Yang
- Marine College, Shandong University, Weihai, 264209, China; Shandong Fu Han Ocean Sci-Tech Co., Ltd, Haiyang, 265100, China
| | - Tong Zhao
- Marine College, Shandong University, Weihai, 264209, China
| | - Hong-Jin Li
- Marine College, Shandong University, Weihai, 264209, China
| | - Zhen-Lin Liang
- Marine College, Shandong University, Weihai, 264209, China
| | - Wei Cong
- Marine College, Shandong University, Weihai, 264209, China
| | - Yuan-Huan Kang
- Marine College, Shandong University, Weihai, 264209, China; Shandong Key Laboratory of Animal Microecological Preparation, Tai'an, 271000, China.
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Patel S, Bhatt AM, Bhansali P, Setty SRG. Pseudophosphatase STYXL1 depletion enhances glucocerebrosidase trafficking to lysosomes via ER stress. Traffic 2023; 24:254-269. [PMID: 37198709 DOI: 10.1111/tra.12886] [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: 12/07/2022] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/19/2023]
Abstract
Pseudophosphatases are catalytically inactive but share sequence and structural similarities with classical phosphatases. STYXL1 is a pseudophosphatase that belongs to the family of dual-specificity phosphatases and is known to regulate stress granule formation, neurite formation and apoptosis in different cell types. However, the role of STYXL1 in regulating cellular trafficking or the lysosome function has not been elucidated. Here, we show that the knockdown of STYXL1 enhances the trafficking of β-glucocerebrosidase (β-GC) and its lysosomal activity in HeLa cells. Importantly, the STYXL1-depleted cells display enhanced distribution of endoplasmic reticulum (ER), late endosome and lysosome compartments. Further, knockdown of STYXL1 causes the nuclear translocation of unfolded protein response (UPR) and lysosomal biogenesis transcription factors. However, the upregulated β-GC activity in the lysosomes is independent of TFEB/TFE3 nuclear localization in STYXL1 knockdown cells. The treatment of STYXL1 knockdown cells with 4-PBA (ER stress attenuator) significantly reduces the β-GC activity equivalent to control cells but not additive with thapsigargin, an ER stress activator. Additionally, STYXL1-depleted cells show the enhanced contact of lysosomes with ER, possibly via increased UPR. The depletion of STYXL1 in human primary fibroblasts derived from Gaucher patients showed moderately enhanced lysosomal enzyme activity. Overall, these studies illustrated the unique role of pseudophosphatase STYXL1 in modulating the lysosome function both in normal and lysosome-storage disorder cell types. Thus, designing small molecules against STYXL1 possibly can restore the lysosome activity by enhancing ER stress in Gaucher disease.
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Affiliation(s)
- Saloni Patel
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Anshul Milap Bhatt
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Priyanka Bhansali
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Subba Rao Gangi Setty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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5
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Leng K, Rose IVL, Kim H, Xia W, Romero-Fernandez W, Rooney B, Koontz M, Li E, Ao Y, Wang S, Krawczyk M, Tcw J, Goate A, Zhang Y, Ullian EM, Sofroniew MV, Fancy SPJ, Schrag MS, Lippmann ES, Kampmann M. CRISPRi screens in human iPSC-derived astrocytes elucidate regulators of distinct inflammatory reactive states. Nat Neurosci 2022; 25:1528-1542. [PMID: 36303069 PMCID: PMC9633461 DOI: 10.1038/s41593-022-01180-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 09/07/2022] [Indexed: 01/30/2023]
Abstract
Astrocytes become reactive in response to insults to the central nervous system by adopting context-specific cellular signatures and outputs, but a systematic understanding of the underlying molecular mechanisms is lacking. In this study, we developed CRISPR interference screening in human induced pluripotent stem cell-derived astrocytes coupled to single-cell transcriptomics to systematically interrogate cytokine-induced inflammatory astrocyte reactivity. We found that autocrine-paracrine IL-6 and interferon signaling downstream of canonical NF-κB activation drove two distinct inflammatory reactive signatures, one promoted by STAT3 and the other inhibited by STAT3. These signatures overlapped with those observed in other experimental contexts, including mouse models, and their markers were upregulated in human brains in Alzheimer's disease and hypoxic-ischemic encephalopathy. Furthermore, we validated that markers of these signatures were regulated by STAT3 in vivo using a mouse model of neuroinflammation. These results and the platform that we established have the potential to guide the development of therapeutics to selectively modulate different aspects of inflammatory astrocyte reactivity.
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Affiliation(s)
- Kun Leng
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Hyosung Kim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Wenlong Xia
- Departments of Neurology and Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Brendan Rooney
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Mark Koontz
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Emmy Li
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Yan Ao
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shinong Wang
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mitchell Krawczyk
- Interdepartmental PhD Program in Neuroscience, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julia Tcw
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Nash Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison Goate
- Nash Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ye Zhang
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Erik M Ullian
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Michael V Sofroniew
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Stephen P J Fancy
- Departments of Neurology and Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew S Schrag
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Ethan S Lippmann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, USA.
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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Kawaguchi M, Furuse Y, Ieda N, Nakagawa H. Development of Nucleoside Diphosphate-Bearing Fragile Histidine Triad-Imaging Fluorescence Probes with Well-Tuned Hydrophobicity for Intracellular Delivery. ACS Sens 2022; 7:2732-2742. [PMID: 35981239 DOI: 10.1021/acssensors.2c01273] [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] [Indexed: 01/31/2023]
Abstract
Fluorescence-guided cancer surgery can dramatically improve recurrence rates and postoperative quality of life of patients by accurately distinguishing the boundary between normal and cancer tissues during surgery, thereby minimizing excision of normal tissue. One promising target in early stage cancer is fragile histidine triad (FHIT), a cancer suppressor protein with dinucleoside triphosphate hydrolase activity. In this study, we have developed fluorescence probes containing a nucleoside diphosphate moiety, which dramatically improves the reactivity and specificity for FHIT, and a moderately lipophilic ester moiety to increase the membrane permeability. The ester moiety is cleaved by ubiquitous intracellular esterases, and then, FHIT in the cells specifically cleaves nucleoside monophosphate. The remaining phosphate moiety is rapidly cleaved by ubiquitous intracellular phosphatases to release the fluorescent dye. We confirmed that this probe can detect FHIT activity in living cells. A comprehensive evaluation of the effects of various ester moieties revealed that probes with CLogP = 5-7 showed good membrane permeability and were good substrates of the target enzyme; these findings may be helpful in the rational design of other multiple phosphate-containing probes targeting intracellular enzymes.
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Affiliation(s)
- Mitsuyasu Kawaguchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Yuri Furuse
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Naoya Ieda
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
| | - Hidehiko Nakagawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, Aichi 467-8603, Japan
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Kim CL, Lim SB, Kim K, Jeong HS, Mo JS. Phosphorylation analysis of the Hippo-YAP pathway using Phos-tag. J Proteomics 2022; 261:104582. [DOI: 10.1016/j.jprot.2022.104582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 03/22/2022] [Accepted: 03/31/2022] [Indexed: 10/18/2022]
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Alves SR, da Cruz e Silva C, Martins I, Henriques AG, da Cruz e Silva OA. A Bioinformatics Approach Toward Unravelling the Synaptic Molecular Crosstalk Between Alzheimer’s Disease and Diabetes. J Alzheimers Dis 2022; 86:1917-1933. [PMID: 35253743 PMCID: PMC9108712 DOI: 10.3233/jad-215059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Background: Increasing evidence links impaired brain insulin signaling and insulin resistance to the development of Alzheimer’s disease (AD). Objective: This evidence prompted a search for molecular players common to AD and diabetes mellitus (DM). Methods: The work incorporated studies based on a primary care-based cohort (pcb-Cohort) and a bioinformatics analysis to identify central nodes, that are key players in AD and insulin signaling (IS) pathways. The interactome for each of these key proteins was retrieved and network maps were developed for AD and IS. Synaptic enrichment was performed to reveal synaptic common hubs. Results: Cohort analysis showed that individuals with DM exhibited a correlation with poor performance in the Mini-Mental State Examination (MMSE) cognitive test. Additionally, APOE ɛ2 allele carriers appear to potentially be relatively more protected against both DM and cognitive deficits. Ten clusters were identified in this network and 32 key synaptic proteins were common to AD and IS. Given the relevance of signaling pathways, another network was constructed focusing on protein kinases and protein phosphatases, and the top 6 kinase nodes (LRRK2, GSK3B, AKT1, EGFR, MAPK1, and FYN) were further analyzed. Conclusion: This allowed the elaboration of signaling cascades directly impacting AβPP and tau, whereby distinct signaling pathway play a major role and strengthen an AD-IS link at a molecular level.
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Affiliation(s)
- Steven R. Alves
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | | | - Ilka Martins
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Ana Gabriela Henriques
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Odete A.B. da Cruz e Silva
- Department of Medical Sciences, Neurosciences and Signalling Group, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
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Zhang C, Zhou X, Wang X, Ge J, Cai B. Elaeagnus angustifolia can improve salt-alkali soil and the health level of soil: Emphasizing the driving role of core microbial communities. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 305:114401. [PMID: 34974219 DOI: 10.1016/j.jenvman.2021.114401] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/23/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
Saline-alkali environments are widely distributed in China and significantly hinder the development of agriculture. This study characterizes the long-term effects of planting Elaeagnus angustifolia (E. angustifolia) on the physical and chemical properties, enzyme activities and microbial community characteristics of saline-alkali soil in the Songnen Plain (1, 2 and 3 years). The results showed that planting E. angustifolia reduced soil pH and electrical conductivity (EC) and increased soil total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (Nni), total potassium (TK), dissolved organic C (DOC), dissolved organic matter (DOM) and available potassium (AK) content and catalase, urease, polyphenol oxidase, phosphatase, sucrase and cellulase enzyme activities, and the results peaked in the 3 year. High-throughput sequencing showed that the bacterial abundance and diversity were as follows (from high to low) y3 > y2 > y1 > CK. E. angustifolia resulted in an increase in the relative abundance of the dominant bacteria. Proteobacteria and Pseudomonas were the major phylum and genus, respectively. Redundancy analysis showed that changes in the soil microbial community significantly affect the physical and chemical properties of the soil, with Proteobacteria members being the key microorganisms that reduce soil salinity. Network analysis showed that Pseudomonas (Proteobacteria) participated in the synthesis of key soil enzymes. 16S rRNA sequencing predicted that the expression of genes related to carbon (rbcL, acsA, acsB, Pcc and accA) and nitrogen (amoA/B, nxrA, hao, gdh, ureC and nosZ) transformation increased, and Pseudomonas members were key regulators of carbon and nitrogen dynamics. In conclusion, the planting of E. angustifolia could improve the physical and chemical properties of the soil by releasing root exudates into the soil and increasing the diversity and richness of soil microbial communities to improve saline-alkali soil, providing a theoretical basis for improving saline-alkali soil and promoting the sustainable development of modern agriculture.
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Affiliation(s)
- Chi Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Xiaohang Zhou
- College of Basic Medicine, Mudanjiang Medical University, Mudanjiang, 157000, China
| | - Xiaoyu Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, 150080, China
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, 150080, China.
| | - Baiyan Cai
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, 150500, China; Key Laboratory of Microbiology, College of Heilongjiang Province, School of Life Sciences, Heilongjiang University, Harbin, 150080, China.
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10
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Boni C, Laudanna C, Sorio C. A Comprehensive Review of Receptor-Type Tyrosine-Protein Phosphatase Gamma (PTPRG) Role in Health and Non-Neoplastic Disease. Biomolecules 2022; 12:84. [PMID: 35053232 PMCID: PMC8773835 DOI: 10.3390/biom12010084] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/30/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023] Open
Abstract
Protein tyrosine phosphatase receptor gamma (PTPRG) is known to interact with and regulate several tyrosine kinases, exerting a tumor suppressor role in several type of cancers. Its wide expression in human tissues compared to the other component of group 5 of receptor phosphatases, PTPRZ expressed as a chondroitin sulfate proteoglycan in the central nervous system, has raised interest in its role as a possible regulatory switch of cell signaling processes. Indeed, a carbonic anhydrase-like domain (CAH) and a fibronectin type III domain are present in the N-terminal portion and were found to be associated with its role as [HCO3-] sensor in vascular and renal tissues and a possible interaction domain for cell adhesion, respectively. Studies on PTPRG ligands revealed the contactins family (CNTN) as possible interactors. Furthermore, the correlation of PTPRG phosphatase with inflammatory processes in different normal tissues, including cancer, and the increasing amount of its soluble form (sPTPRG) in plasma, suggest a possible role as inflammatory marker. PTPRG has important roles in human diseases; for example, neuropsychiatric and behavioral disorders and various types of cancer such as colon, ovary, lung, breast, central nervous system, and inflammatory disorders. In this review, we sum up our knowledge regarding the latest discoveries in order to appreciate PTPRG function in the various tissues and diseases, along with an interactome map of its relationship with a group of validated molecular interactors.
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Affiliation(s)
| | | | - Claudio Sorio
- Department of Medicine, General Pathology Division, University of Verona, 37134 Verona, Italy; (C.B.); (C.L.)
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11
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Cornejo F, Cortés BI, Findlay GM, Cancino GI. LAR Receptor Tyrosine Phosphatase Family in Healthy and Diseased Brain. Front Cell Dev Biol 2021; 9:659951. [PMID: 34966732 PMCID: PMC8711739 DOI: 10.3389/fcell.2021.659951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 11/17/2021] [Indexed: 11/23/2022] Open
Abstract
Protein phosphatases are major regulators of signal transduction and they are involved in key cellular mechanisms such as proliferation, differentiation, and cell survival. Here we focus on one class of protein phosphatases, the type IIA Receptor-type Protein Tyrosine Phosphatases (RPTPs), or LAR-RPTP subfamily. In the last decade, LAR-RPTPs have been demonstrated to have great importance in neurobiology, from neurodevelopment to brain disorders. In vertebrates, the LAR-RPTP subfamily is composed of three members: PTPRF (LAR), PTPRD (PTPδ) and PTPRS (PTPσ), and all participate in several brain functions. In this review we describe the structure and proteolytic processing of the LAR-RPTP subfamily, their alternative splicing and enzymatic regulation. Also, we review the role of the LAR-RPTP subfamily in neural function such as dendrite and axon growth and guidance, synapse formation and differentiation, their participation in synaptic activity, and in brain development, discussing controversial findings and commenting on the most recent studies in the field. Finally, we discuss the clinical outcomes of LAR-RPTP mutations, which are associated with several brain disorders.
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Affiliation(s)
- Francisca Cornejo
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Bastián I Cortés
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Greg M Findlay
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Gonzalo I Cancino
- Center for Integrative Biology, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.,Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
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Haapalainen AM, Daddali R, Hallman M, Rämet M. Human CPPED1 belongs to calcineurin-like metallophosphoesterase superfamily and dephosphorylates PI3K-AKT pathway component PAK4. J Cell Mol Med 2021; 25:6304-6317. [PMID: 34009729 PMCID: PMC8366450 DOI: 10.1111/jcmm.16607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 12/20/2022] Open
Abstract
Protein kinases and phosphatases regulate cellular processes by reversible phosphorylation and dephosphorylation events. CPPED1 is a recently identified serine/threonine protein phosphatase that dephosphorylates AKT1 of the PI3K-AKT signalling pathway. We previously showed that CPPED1 levels are down-regulated in the human placenta during spontaneous term birth. In this study, based on sequence comparisons, we propose that CPPED1 is a member of the class III phosphodiesterase (PDE) subfamily within the calcineurin-like metallophosphoesterase (MPE) superfamily rather than a member of the phosphoprotein phosphatase (PPP) or metal-dependent protein phosphatase (PPM) protein families. We used a human proteome microarray to identify 36 proteins that putatively interact with CPPED1. Of these, GRB2, PAK4 and PIK3R2 are known to regulate the PI3K-AKT pathway. We further confirmed CPPED1 interactions with PAK4 and PIK3R2 by coimmunoprecipitation analyses. We characterized the effect of CPPED1 on phosphorylation of PAK4 and PIK3R2 in vitro by mass spectrometry. CPPED1 dephosphorylated specific serine residues in PAK4, while phosphorylation levels in PIK3R2 remained unchanged. Our findings indicate that CPPED1 may regulate PI3K-AKT pathway activity at multiple levels. Higher CPPED1 levels may inhibit PI3K-AKT pathway maintaining pregnancy. Consequences of decreased CPPED1 expression during labour remain to be elucidated.
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Affiliation(s)
- Antti M. Haapalainen
- PEDEGO Research Unit and Medical Research Center OuluUniversity of OuluOuluFinland
- Department of Children and AdolescentsOulu University HospitalOuluFinland
| | - Ravindra Daddali
- PEDEGO Research Unit and Medical Research Center OuluUniversity of OuluOuluFinland
- Department of Children and AdolescentsOulu University HospitalOuluFinland
| | - Mikko Hallman
- PEDEGO Research Unit and Medical Research Center OuluUniversity of OuluOuluFinland
- Department of Children and AdolescentsOulu University HospitalOuluFinland
| | - Mika Rämet
- PEDEGO Research Unit and Medical Research Center OuluUniversity of OuluOuluFinland
- Department of Children and AdolescentsOulu University HospitalOuluFinland
- Faculty of Medicine and Health TechnologyTampere UniversityTampereFinland
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13
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Xue Y, Bai H, Peng B, Fang B, Baell J, Li L, Huang W, Voelcker NH. Stimulus-cleavable chemistry in the field of controlled drug delivery. Chem Soc Rev 2021; 50:4872-4931. [DOI: 10.1039/d0cs01061h] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review comprehensively summarises stimulus-cleavable linkers from various research areas and their cleavage mechanisms, thus provides an insightful guideline to extend their potential applications to controlled drug release from nanomaterials.
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Affiliation(s)
- Yufei Xue
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Bin Fang
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Jonathan Baell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Clayton
- Victoria 3168
- Australia
| | - Lin Li
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Wei Huang
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
| | - Nicolas Hans Voelcker
- Frontiers Science Center for Flexible Electronics
- Xi’an Institute of Flexible Electronics (IFE) and Xi’an Institute of Biomedical Materials & Engineering
- Northwestern Polytechnical University
- 127 West Youyi Road
- Xi'an 710072
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14
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Hekman RM, Hume AJ, Goel RK, Abo KM, Huang J, Blum BC, Werder RB, Suder EL, Paul I, Phanse S, Youssef A, Alysandratos KD, Padhorny D, Ojha S, Mora-Martin A, Kretov D, Ash PEA, Verma M, Zhao J, Patten JJ, Villacorta-Martin C, Bolzan D, Perea-Resa C, Bullitt E, Hinds A, Tilston-Lunel A, Varelas X, Farhangmehr S, Braunschweig U, Kwan JH, McComb M, Basu A, Saeed M, Perissi V, Burks EJ, Layne MD, Connor JH, Davey R, Cheng JX, Wolozin BL, Blencowe BJ, Wuchty S, Lyons SM, Kozakov D, Cifuentes D, Blower M, Kotton DN, Wilson AA, Mühlberger E, Emili A. Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2. Mol Cell 2020; 80:1104-1122.e9. [PMID: 33259812 PMCID: PMC7674017 DOI: 10.1016/j.molcel.2020.11.028] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/16/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022]
Abstract
Human transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative pathogen of the COVID-19 pandemic, exerts a massive health and socioeconomic crisis. The virus infects alveolar epithelial type 2 cells (AT2s), leading to lung injury and impaired gas exchange, but the mechanisms driving infection and pathology are unclear. We performed a quantitative phosphoproteomic survey of induced pluripotent stem cell-derived AT2s (iAT2s) infected with SARS-CoV-2 at air-liquid interface (ALI). Time course analysis revealed rapid remodeling of diverse host systems, including signaling, RNA processing, translation, metabolism, nuclear integrity, protein trafficking, and cytoskeletal-microtubule organization, leading to cell cycle arrest, genotoxic stress, and innate immunity. Comparison to analogous data from transformed cell lines revealed respiratory-specific processes hijacked by SARS-CoV-2, highlighting potential novel therapeutic avenues that were validated by a high hit rate in a targeted small molecule screen in our iAT2 ALI system.
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Affiliation(s)
- Ryan M Hekman
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Adam J Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Raghuveera Kumar Goel
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Kristine M Abo
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin C Blum
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Ellen L Suder
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Indranil Paul
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Sadhna Phanse
- Center for Network Systems Biology, Boston University, Boston, MA, USA
| | - Ahmed Youssef
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA
| | - Konstantinos D Alysandratos
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Sandeep Ojha
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | | | - Dmitry Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Peter E A Ash
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Mamta Verma
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Jian Zhao
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - J J Patten
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
| | - Dante Bolzan
- Department of Computer Science, University of Miami, Miami, FL, USA
| | - Carlos Perea-Resa
- Department of Molecular Biology, Harvard Medical School, Boston, MA, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University, Boston, MA, USA
| | - Anne Hinds
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Andrew Tilston-Lunel
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | - Julian H Kwan
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Mark McComb
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Avik Basu
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Valentina Perissi
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Eric J Burks
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Matthew D Layne
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Robert Davey
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Benjamin L Wolozin
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stefan Wuchty
- Department of Computer Science, University of Miami, Miami, FL, USA; Department of Biology, University of Miami, Miami, FL, USA; Miami Institute of Data Science and Computing, Miami, FL, USA
| | - Shawn M Lyons
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Michael Blower
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Molecular Biology, Harvard Medical School, Boston, MA, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA; The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
| | - Andrew Emili
- Center for Network Systems Biology, Boston University, Boston, MA, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; Department of Biology, Boston University, Boston, MA, USA.
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15
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Sarmasti Emami S, Zhang D, Yang X. Interaction of the Hippo Pathway and Phosphatases in Tumorigenesis. Cancers (Basel) 2020; 12:E2438. [PMID: 32867200 PMCID: PMC7564220 DOI: 10.3390/cancers12092438] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 01/05/2023] Open
Abstract
The Hippo pathway is an emerging tumor suppressor signaling pathway involved in a wide range of cellular processes. Dysregulation of different components of the Hippo signaling pathway is associated with a number of diseases including cancer. Therefore, identification of the Hippo pathway regulators and the underlying mechanism of its regulation may be useful to uncover new therapeutics for cancer therapy. The Hippo signaling pathway includes a set of kinases that phosphorylate different proteins in order to phosphorylate and inactivate its main downstream effectors, YAP and TAZ. Thus, modulating phosphorylation and dephosphorylation of the Hippo components by kinases and phosphatases play critical roles in the regulation of the signaling pathway. While information regarding kinase regulation of the Hippo pathway is abundant, the role of phosphatases in regulating this pathway is just beginning to be understood. In this review, we summarize the most recent reports on the interaction of phosphatases and the Hippo pathway in tumorigenesis. We have also introduced challenges in clarifying the role of phosphatases in the Hippo pathway and future direction of crosstalk between phosphatases and the Hippo pathway.
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Affiliation(s)
| | | | - Xiaolong Yang
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada; (S.S.E.); (D.Z.)
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16
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Savage SR, Zhang B. Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. Clin Proteomics 2020; 17:27. [PMID: 32676006 PMCID: PMC7353784 DOI: 10.1186/s12014-020-09290-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 07/04/2020] [Indexed: 12/19/2022] Open
Abstract
Mass spectrometry-based phosphoproteomics is becoming an essential methodology for the study of global cellular signaling. Numerous bioinformatics resources are available to facilitate the translation of phosphopeptide identification and quantification results into novel biological and clinical insights, a critical step in phosphoproteomics data analysis. These resources include knowledge bases of kinases and phosphatases, phosphorylation sites, kinase inhibitors, and sequence variants affecting kinase function, and bioinformatics tools that can predict phosphorylation sites in addition to the kinase that phosphorylates them, infer kinase activity, and predict the effect of mutations on kinase signaling. However, these resources exist in silos and it is challenging to select among multiple resources with similar functions. Therefore, we put together a comprehensive collection of resources related to phosphoproteomics data interpretation, compared the use of tools with similar functions, and assessed the usability from the standpoint of typical biologists or clinicians. Overall, tools could be improved by standardization of enzyme names, flexibility of data input and output format, consistent maintenance, and detailed manuals.
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Affiliation(s)
- Sara R. Savage
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
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17
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Ambreen S, Yasmin A, Aziz S. Isolation and characterization of organophosphorus phosphatases from Bacillus thuringiensis MB497 capable of degrading Chlorpyrifos, Triazophos and Dimethoate. Heliyon 2020; 6:e04221. [PMID: 32642578 PMCID: PMC7334429 DOI: 10.1016/j.heliyon.2020.e04221] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/10/2020] [Accepted: 06/11/2020] [Indexed: 01/03/2023] Open
Abstract
In the current investigation, bacterial strain Bacillus thuringiensis MB497 was examined for production of intracellular and extracellular organophosphorus phosphatase (OPP) enzymes. This strain produced significant amount of extracellular acidic and alkaline phosphatases. Production of neutral phosphatase was negligible. Production of OPP was generally highest at pH 11 and at 45-50 °C. However, activity and stability of OPP was highest at 37 °C and reduced at higher temperatures. OPP production was decreased after 48 h of incubation. Largely, OPP activity was inhibited by SDS and EDTA and significantly enhanced by metals (Zn++, Cu++ and Cd++). Both acidic and alkaline OPPs were capable of bio-precipitation of selected metals (Ni, Mn, Cr and Cd) up to 86-100%. When used against 50 mg/l of three OP pesticides (Chlorpyrifos, Triazophos, and Dimethoate), 81-94.6% degradation of pesticides was observed by alkaline OPP, while acidic OPP showed less degradation (61-70.5%) within 30 min of incubation.
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Affiliation(s)
- Samina Ambreen
- Microbiology & Biotechnology Research Lab, Department of Environmental Sciences, Fatima Jinnah Women University, The Mall, Rawalpindi, Pakistan
| | - Azra Yasmin
- Microbiology & Biotechnology Research Lab, Department of Environmental Sciences, Fatima Jinnah Women University, The Mall, Rawalpindi, Pakistan
| | - Satara Aziz
- Microbiology & Biotechnology Research Lab, Department of Environmental Sciences, Fatima Jinnah Women University, The Mall, Rawalpindi, Pakistan
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18
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Lin S, Wang C, Zhou J, Shi Y, Ruan C, Tu Y, Yao L, Peng D, Xue Y. EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. Brief Bioinform 2020; 22:298-307. [PMID: 32008039 DOI: 10.1093/bib/bbz169] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/25/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
As an important post-translational modification (PTM), protein phosphorylation is involved in the regulation of almost all of biological processes in eukaryotes. Due to the rapid progress in mass spectrometry-based phosphoproteomics, a large number of phosphorylation sites (p-sites) have been characterized but remain to be curated. Here, we briefly summarized the current progresses in the development of data resources for the collection, curation, integration and annotation of p-sites in eukaryotic proteins. Also, we designed the eukaryotic phosphorylation site database (EPSD), which contained 1 616 804 experimentally identified p-sites in 209 326 phosphoproteins from 68 eukaryotic species. In EPSD, we not only collected 1 451 629 newly identified p-sites from high-throughput (HTP) phosphoproteomic studies, but also integrated known p-sites from 13 additional databases. Moreover, we carefully annotated the phosphoproteins and p-sites of eight model organisms by integrating the knowledge from 100 additional resources that covered 15 aspects, including phosphorylation regulator, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein-protein interaction, drug-target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, protein expression/proteomics and subcellular localization. We anticipate that the EPSD can serve as a useful resource for further analysis of eukaryotic phosphorylation. With a data volume of 14.1 GB, EPSD is free for all users at http://epsd.biocuckoo.cn/.
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Affiliation(s)
| | | | - Jiaqi Zhou
- Huazhong University of Science and Technology
| | - Ying Shi
- Huazhong University of Science and Technology
| | - Chen Ruan
- Huazhong University of Science and Technology
| | - Yiran Tu
- Huazhong University of Science and Technology
| | - Lan Yao
- Huazhong University of Science and Technology
| | - Di Peng
- Huazhong University of Science and Technology
| | - Yu Xue
- Huazhong University of Science and Technology
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19
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Kosok M, Alli-Shaik A, Bay BH, Gunaratne J. Comprehensive Proteomic Characterization Reveals Subclass-Specific Molecular Aberrations within Triple-negative Breast Cancer. iScience 2020; 23:100868. [PMID: 32058975 PMCID: PMC7015993 DOI: 10.1016/j.isci.2020.100868] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 12/30/2019] [Accepted: 01/20/2020] [Indexed: 02/07/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer lacking targeted therapies. This is attributed to its high heterogeneity that complicates elucidation of its molecular aberrations. Here, we report identification of specific proteome expression profiles pertaining to two TNBC subclasses, basal A and basal B, through in-depth proteomics analysis of breast cancer cells. We observed that kinases and proteases displayed unique expression patterns within the subclasses. Systematic analyses of protein-protein interaction and co-regulation networks of these kinases and proteases unraveled dysregulated pathways and plausible targets for each TNBC subclass. Among these, we identified kinases AXL, PEAK1, and TGFBR2 and proteases FAP, UCHL1, and MMP2/14 as specific targets for basal B subclass, which represents the more aggressive TNBC cell lines. Our study highlights intricate mechanisms and distinct targets within TNBC and emphasizes that these have to be exploited in a subclass-specific manner rather than a one-for-all TNBC therapy. Proteome profiling reveals functionally distinct subclasses within TNBC Kinases and proteases underlie unique functional signatures among the subclasses Kinase-protease-centric networks highlight subclass-specific molecular rewiring Protein association dysregulations reveal TNBC subclass-specific protein targets
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Affiliation(s)
- Max Kosok
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Asfa Alli-Shaik
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Boon Huat Bay
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore.
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20
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Proteogenomics of Colorectal Cancer Liver Metastases: Complementing Precision Oncology with Phenotypic Data. Cancers (Basel) 2019; 11:cancers11121907. [PMID: 31805664 PMCID: PMC6966481 DOI: 10.3390/cancers11121907] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 12/17/2022] Open
Abstract
Hotspot testing for activating KRAS mutations is used in precision oncology to select colorectal cancer (CRC) patients who are eligible for anti-EGFR treatment. However, even for KRASwildtype tumors anti-EGFR response rates are <30%, while mutated-KRAS does not entirely rule out response, indicating the need for improved patient stratification. We performed proteogenomic phenotyping of KRASwildtype and KRASG12V CRC liver metastases (mCRC). Among >9000 proteins we detected considerable expression changes including numerous proteins involved in progression and resistance in CRC. We identified peptides representing a number of predicted somatic mutations, including KRASG12V. For eight of these, we developed a multiplexed parallel reaction monitoring (PRM) mass spectrometry assay to precisely quantify the mutated and canonical protein variants. This allowed phenotyping of eight mCRC tumors and six paired healthy tissues, by determining mutation rates on the protein level. Total KRAS expression varied between tumors (0.47–1.01 fmol/µg total protein) and healthy tissues (0.13–0.64 fmol/µg). In KRASG12V-mCRC, G12V-mutation levels were 42–100%, while one patient had only 10% KRASG12V but 90% KRASwildtype. This might represent a missed therapeutic opportunity: based on hotspot sequencing, the patient was excluded from anti-EGFR treatment and instead received chemotherapy, while PRM-based tumor-phenotyping indicates the patient might have benefitted from anti-EGFR therapy.
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21
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Wang J, Zhou J, He H, Wu D, Du X, Xu B. Cell-Compatible Nanoprobes for Imaging Intracellular Phosphatase Activities. Chembiochem 2019; 20:526-531. [PMID: 30388302 PMCID: PMC6377289 DOI: 10.1002/cbic.201800495] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Indexed: 11/12/2022]
Abstract
Phosphatases play an important role in cell biology, but only a few probes are suitable for selectively imaging phosphatase activity in live cells, because the current probes require cell fixation or exhibit considerable cytotoxicity. Herein, we show that conjugating a d-peptide to a quinazolinone derivative generates cell-compatible, biostable probes for imaging the phosphatase activity inside live cells. Moreover, our results show that inhibiting ectophosphatases is a critical factor for imaging intracellular phosphatases. As the first example of using selective inhibitors to ensure intracellular function of molecular probes, this work illustrates a facile approach to design molecular probes for profiling the activities of enzymes in a spatial, selective manner in a complicated environment.
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Affiliation(s)
- Jiaqing Wang
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA 02454 (USA),
| | - Jie Zhou
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA 02454 (USA),
| | - Hongjian He
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA 02454 (USA),
| | - Difei Wu
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA 02454 (USA),
| | - Xuewen Du
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA 02454 (USA),
| | - Bing Xu
- Department of Chemistry, Brandeis University, 415 South St. Waltham, MA 02454 (USA),
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22
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Raman D, Pervaiz S. Redox inhibition of protein phosphatase PP2A: Potential implications in oncogenesis and its progression. Redox Biol 2019; 27:101105. [PMID: 30686777 PMCID: PMC6859563 DOI: 10.1016/j.redox.2019.101105] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/04/2019] [Accepted: 01/09/2019] [Indexed: 01/17/2023] Open
Abstract
Cellular processes are dictated by the active signaling of proteins relaying messages to regulate cell proliferation, apoptosis, signal transduction and cell communications. An intricate web of protein kinases and phosphatases are critical to the proper transmission of signals across such cascades. By governing 30–50% of all protein dephosphorylation in the cell, with prominent substrate proteins being key regulators of signaling cascades, the phosphatase PP2A has emerged as a celebrated player in various developmental and tumorigenic pathways, thereby posing as an attractive target for therapeutic intervention in various pathologies wherein its activity is deregulated. This review is mainly focused on refreshing our understanding of the structural and functional complexity that cocoons the PP2A phosphatase, and its expression in cancers. Additionally, we focus on its physiological regulation as well as into recent advents and strategies that have shown promise in countering the deregulation of the phosphatase through its targeted reactivation. Finally, we dwell upon one of the key regulators of PP2A in cancer cells-cellular redox status-its multifarious nature, and its integration into the reactome of PP2A, highlighting some of the significant impacts that ROS can inflict on the structural modifications and functional aspect of PP2A.
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Affiliation(s)
- Deepika Raman
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shazib Pervaiz
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Medical Science Cluster Cancer Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; National University Cancer Institute, National University Health System, Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.
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23
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Damle NP, Köhn M. The human DEPhOsphorylation Database DEPOD: 2019 update. Database (Oxford) 2019; 2019:baz133. [PMID: 31836896 PMCID: PMC6911163 DOI: 10.1093/database/baz133] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/06/2019] [Accepted: 10/29/2019] [Indexed: 01/04/2023]
Abstract
The human Dephosphorylation Database (DEPOD) is a manually curated resource that harbors human phosphatases, their protein and non-protein substrates, dephosphorylation sites and the associated signaling pathways. We report here an update to DEPOD by integrating and/or linking to annotations from 69 other open access databases including disease associations, phosphorylating kinases, protein interactions, and also genome browsers. We also provide tools to visualize protein interactions, protein structures, phosphorylation networks, evolutionary conservation of proteins, dephosphorylation sites, and short linear motifs within various proteins. The updated version of DEPOD contains 254 human phosphatases, 336 protein and 83 non-protein substrates, and 1215 manually curated phosphatase-substrate relationships. In addition, we have improved the data access as all the data in DEPOD can now be easily downloaded in a user-friendly format. With multiple significant improvements, DEPOD continues serving as a key resource for research on phosphatase-kinase networks. Database URL: www.depod.org.
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Affiliation(s)
- Nikhil P Damle
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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24
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Fisgativa H, Tremier A, Saoudi M, Le Roux S, Dabert P. Biochemical and microbial changes reveal how aerobic pre-treatment impacts anaerobic biodegradability of food waste. WASTE MANAGEMENT (NEW YORK, N.Y.) 2018; 80:119-129. [PMID: 30454991 DOI: 10.1016/j.wasman.2018.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 06/09/2023]
Abstract
Aerobic pre-treatment of food waste (FW) was performed at different oxygen concentrations (0%, 5%, 10% and 21%O2) and different durations (1, 2, 3 and 4 days) to investigate its impact on biochemical and microbial community characteristics of the waste and its ability to improve anaerobic biodegradability. Whatever the duration, the highest effect of pre-treatment was observed at full aerobic pre-treatment (21%O2) while 5%O2 and 10%O2 showed lower transformation performances. Biochemical variations at 21%O2 were mainly a decrease of simple carbohydrates, volatile fatty acids (VFA) and low molecular weight water soluble compounds and an increase of high weight water soluble compounds. Microbial community analysis showed a clear modification of populations after 21%O2 aerobic pre-treatment, changing from an initial dominance of lactic acid bacteria to a final dominance of VFA consumers (like Acetobacter) and a higher presence of Fungi. Enzymatic tests showed an increase of exoenzymes content and a higher presence of protein and carbohydrates degrading enzymes. Finally, the aerobic pre-treatment did not negatively impact methane potential of FW (496 NLCH4·kgVS-1) which remained unchanged after two days of pre-treatment at 21%O2. These latter optimal pre-treatment conditions are proposed to be tested in future investigation of anaerobic digestion (AD) process with low inoculum to substrate ratio in order to assess their ability to avoid acidification risk during AD of FW.
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Affiliation(s)
- Henry Fisgativa
- Irstea, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes Cedex, France
| | - Anne Tremier
- Irstea, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes Cedex, France.
| | - Mohamed Saoudi
- Irstea, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes Cedex, France
| | - Sophie Le Roux
- Irstea, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes Cedex, France
| | - Patrick Dabert
- Irstea, UR OPAALE, 17 avenue de Cucillé, CS 64427, F-35044 Rennes Cedex, France
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25
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Joachimiak Ł, Błażewska KM. Phosphorus-Based Probes as Molecular Tools for Proteome Studies: Recent Advances in Probe Development and Applications. J Med Chem 2018; 61:8536-8562. [DOI: 10.1021/acs.jmedchem.8b00249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Łukasz Joachimiak
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego Street 116, 90-924 Łódź, Poland
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26
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Csabai L, Ölbei M, Budd A, Korcsmáros T, Fazekas D. SignaLink: Multilayered Regulatory Networks. Methods Mol Biol 2018; 1819:53-73. [PMID: 30421399 DOI: 10.1007/978-1-4939-8618-7_3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Biological networks are graphs used to represent the inner workings of a biological system. Networks describe the relationships of the elements of biological systems using edges and nodes. However, the resulting representation of the system can sometimes be too simplistic to usefully model reality. By combining several different interaction types within one larger multilayered biological network, tools such as SignaLink provide a more nuanced view than those relying on single-layer networks (where edges only describe one kind of interaction). Multilayered networks display connections between multiple networks (i.e., protein-protein interactions and their transcriptional and posttranscriptional regulators), each one of them describing a specific set of connections. Multilayered networks also allow us to depict cross talk between cellular systems, which is a more realistic way of describing molecular interactions. They can be used to collate networks from different sources into one multilayered structure, which makes them useful as an analytic tool as well.
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Affiliation(s)
| | - Márton Ölbei
- Earlham Institute, Norwich Research Park, Norwich, UK.,Quadram Institute, Norwich Research Park, Norwich, UK
| | - Aidan Budd
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Tamás Korcsmáros
- Eötvös Loránd University, Budapest, Hungary. .,Earlham Institute, Norwich Research Park, Norwich, UK. .,Quadram Institute, Norwich Research Park, Norwich, UK.
| | - Dávid Fazekas
- Eötvös Loránd University, Budapest, Hungary.,Earlham Institute, Norwich Research Park, Norwich, UK
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27
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Kumar P, Munnangi P, Chowdary KR, Shah VJ, Shinde SR, Kolli NR, Halehalli RR, Nagarajaram HA, Maddika S. A Human Tyrosine Phosphatase Interactome Mapped by Proteomic Profiling. J Proteome Res 2017; 16:2789-2801. [PMID: 28675297 PMCID: PMC5548413 DOI: 10.1021/acs.jproteome.7b00065] [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] [Indexed: 11/29/2022]
Abstract
Tyrosine phosphatases play a critical role in many cellular processes and pathogenesis, yet comprehensive analysis of their functional interacting proteins in the cell is limited. By utilizing a proteomic approach, here we present an interaction network of 81 human tyrosine phosphatases built on 1884 high-confidence interactions of which 85% are unreported. Our analysis has linked several phosphatases with new cellular processes and unveiled protein interactions genetically linked to various human diseases including cancer. We validated the functional importance of an identified interaction network by characterizing a distinct novel interaction between PTPN5 and Mob1a. PTPN5 dephosphorylates Mob1a at Y26 residue. Further, we identify that PTPN5 is required for proper midbody abscission during cytokinesis through regulation of Mob1a dephosphorylation. In conclusion, our study provides a valuable resource of tyrosine phosphatase interactions, which can be further utilized to dissect novel cellular functions of these enzymes.
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Affiliation(s)
- Parveen Kumar
- Graduate Studies, Manipal University , Manipal, 576104, India
| | | | | | - Varun J Shah
- Graduate Studies, Manipal University , Manipal, 576104, India
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28
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Ardito F, Giuliani M, Perrone D, Troiano G, Lo Muzio L. The crucial role of protein phosphorylation in cell signaling and its use as targeted therapy (Review). Int J Mol Med 2017; 40:271-280. [PMID: 28656226 PMCID: PMC5500920 DOI: 10.3892/ijmm.2017.3036] [Citation(s) in RCA: 713] [Impact Index Per Article: 101.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022] Open
Abstract
Protein phosphorylation is an important cellular regulatory mechanism as many enzymes and receptors are activated/deactivated by phosphorylation and dephosphorylation events, by means of kinases and phosphatases. In particular, the protein kinases are responsible for cellular transduction signaling and their hyperactivity, malfunction or overexpression can be found in several diseases, mostly tumors. Therefore, it is evident that the use of kinase inhibitors can be valuable for the treatment of cancer. In this review, we discuss the mechanism of action of phosphorylation, with particular attention to the importance of phosphorylation under physiological and pathological conditions. We also discuss the possibility of using kinase inhibitors in the treatment of tumors.
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Affiliation(s)
- Fatima Ardito
- Department of Clinical and Experimental Medicine, Foggia University, I-71122 Foggia, Italy
| | - Michele Giuliani
- Department of Clinical and Experimental Medicine, Foggia University, I-71122 Foggia, Italy
| | - Donatella Perrone
- Department of Clinical and Experimental Medicine, Foggia University, I-71122 Foggia, Italy
| | - Giuseppe Troiano
- Department of Clinical and Experimental Medicine, Foggia University, I-71122 Foggia, Italy
| | - Lorenzo Lo Muzio
- Department of Clinical and Experimental Medicine, Foggia University, I-71122 Foggia, Italy
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29
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Chen MJ, Dixon JE, Manning G. Genomics and evolution of protein phosphatases. Sci Signal 2017; 10:10/474/eaag1796. [DOI: 10.1126/scisignal.aag1796] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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30
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Palma A, Tinti M, Paoluzi S, Santonico E, Brandt BW, Hooft van Huijsduijnen R, Masch A, Heringa J, Schutkowski M, Castagnoli L, Cesareni G. Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases. J Biol Chem 2017; 292:4942-4952. [PMID: 28159843 DOI: 10.1074/jbc.m116.757518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/31/2017] [Indexed: 01/19/2023] Open
Abstract
Reversible tyrosine phosphorylation is a widespread post-translational modification mechanism underlying cell physiology. Thus, understanding the mechanisms responsible for substrate selection by kinases and phosphatases is central to our ability to model signal transduction at a system level. Classical protein-tyrosine phosphatases can exhibit substrate specificity in vivo by combining intrinsic enzymatic specificity with the network of protein-protein interactions, which positions the enzymes in close proximity to their substrates. Here we use a high throughput approach, based on high density phosphopeptide chips, to determine the in vitro substrate preference of 16 members of the protein-tyrosine phosphatase family. This approach helped identify one residue in the substrate binding pocket of the phosphatase domain that confers specificity for phosphopeptides in a specific sequence context. We also present a Bayesian model that combines intrinsic enzymatic specificity and interaction information in the context of the human protein interaction network to infer new phosphatase substrates at the proteome level.
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Affiliation(s)
- Anita Palma
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Michele Tinti
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Serena Paoluzi
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Elena Santonico
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Bernd Willem Brandt
- the Centre for Integrative Bioinformatics, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands, and
| | | | - Antonia Masch
- the Institut für Biochemie & Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06108 Halle, Germany
| | - Jaap Heringa
- the Centre for Integrative Bioinformatics, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands, and
| | - Mike Schutkowski
- the Institut für Biochemie & Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, 06108 Halle, Germany
| | - Luisa Castagnoli
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Gianni Cesareni
- From the Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy,
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31
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Pandey R, Kumar P, Gupta D. KiPho: malaria parasite kinome and phosphatome portal. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:4430889. [PMID: 29220464 PMCID: PMC5737071 DOI: 10.1093/database/bax063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 07/31/2017] [Indexed: 11/23/2022]
Abstract
The Plasmodium kinases and phosphatases play an essential role in the regulation of substrate reversible-phosphorylation and overall cellular homeostasis. Reversible phosphorylation is one of the key post-translational modifications (PTMs) essential for parasite survival. Thus, a complete and comprehensive information of malarial kinases and phosphatases as a single web resource will not only aid in systematic and better understanding of the PTMs, but also facilitate efforts to look for novel drug targets for malaria. In the current work, we have developed KiPho, a comprehensive and one step web-based information resource for Plasmodium kinases and phosphatases. To develop KiPho, we have made use of search methods to retrieve, consolidate and integrate predicted as well as annotated information from several publically available web repositories. Additionally, we have incorporated relevant and manually curated data, which will be updated from time to time with the availability of new information. The KiPho (Malaria Parasite Kinome—Phosphatome) resource is freely available at http://bioinfo.icgeb.res.in/kipho.
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Affiliation(s)
- Rajan Pandey
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pawan Kumar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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32
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Deep Insight into the Phosphatomes of Parasitic Protozoa and a Web Resource ProtozPhosDB. PLoS One 2016; 11:e0167594. [PMID: 27930683 PMCID: PMC5145157 DOI: 10.1371/journal.pone.0167594] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/16/2016] [Indexed: 11/19/2022] Open
Abstract
Phosphorylation dynamically regulates the function of proteins by maintaining a balance between protein kinase and phosphatase activity. A comprehensive understanding of the role phosphatases in cellular signaling is lacking in case of protozoans of medical and veterinary importance worldwide. The drugs used to treat protozoal diseases have many undesired effects and the development of resistance, highlights the need for new effective and safer antiprotozoal agents. In the present study we have analyzed phosphatomes of 15 protozoans of medical significance. We identified ~2000 phosphatases, out of which 21% are uncharacterized proteins. A significant positive correlation between phosphatome and proteome size was observed except for E. histolytica, having highest density of phosphatases irrespective of its proteome size. A difference in the number of phosphatases among different genera shows the variation in the signaling pathways they are involved in. The phosphatome of parasites is dominated by ser/thr phosphatases contrary to the vertebrate host dominated by tyrosine phosphatases. Phosphatases were widely distributed throughout the cell suggesting physiological adaptation of the parasite to regulate its host. 20% to 45% phosphatome of different protozoa consists of ectophosphatases, i.e. crucial for the survival of parasites. A database and a webserver "ProtozPhosDB" can be used to explore the phosphatomes of protozoans of medical significance.
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Abstract
Phosphatases play key roles in normal physiology and diseases. Studying phosphatases has been both essential and challenging, and the application of conventional genetic and biochemical methods has led to crucial but still limited understanding of their mechanisms, substrates, and exclusive functions within highly intricate networks. With the advances in technologies such as cellular imaging and molecular and chemical biology in terms of sensitive tools and methods, the phosphatase field has thrived in the past years and has set new insights for cell signaling studies and for therapeutic development. In this review, we give an overview of the existing interdisciplinary tools for phosphatases, give examples on how they have been applied to increase our understanding of these enzymes, and suggest how they-and other tools yet barely used in the phosphatase field-might be adapted to address future questions and challenges.
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Affiliation(s)
- Sara Fahs
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
| | - Pablo Lujan
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
| | - Maja Köhn
- European Molecular Biology Laboratory, Genome Biology
Unit, Meyerhofstrasse
1, 69117 Heidelberg, Germany
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34
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Perfetto L, Briganti L, Calderone A, Cerquone Perpetuini A, Iannuccelli M, Langone F, Licata L, Marinkovic M, Mattioni A, Pavlidou T, Peluso D, Petrilli LL, Pirrò S, Posca D, Santonico E, Silvestri A, Spada F, Castagnoli L, Cesareni G. SIGNOR: a database of causal relationships between biological entities. Nucleic Acids Res 2015; 44:D548-54. [PMID: 26467481 PMCID: PMC4702784 DOI: 10.1093/nar/gkv1048] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/02/2015] [Indexed: 12/25/2022] Open
Abstract
Assembly of large biochemical networks can be achieved by confronting new cell-specific experimental data with an interaction subspace constrained by prior literature evidence. The SIGnaling Network Open Resource, SIGNOR (available on line at http://signor.uniroma2.it), was developed to support such a strategy by providing a scaffold of prior experimental evidence of causal relationships between biological entities. The core of SIGNOR is a collection of approximately 12,000 manually-annotated causal relationships between over 2800 human proteins participating in signal transduction. Other entities annotated in SIGNOR are complexes, chemicals, phenotypes and stimuli. The information captured in SIGNOR can be represented as a signed directed graph illustrating the activation/inactivation relationships between signalling entities. Each entry is associated to the post-translational modifications that cause the activation/inactivation of the target proteins. More than 4900 modified residues causing a change in protein concentration or activity have been curated and linked to the modifying enzymes (about 351 human kinases and 94 phosphatases). Additional modifications such as ubiquitinations, sumoylations, acetylations and their effect on the modified target proteins are also annotated. This wealth of structured information can support experimental approaches based on multi-parametric analysis of cell systems after physiological or pathological perturbations and to assemble large logic models.
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Affiliation(s)
- Livia Perfetto
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | | | | | | | | | - Luana Licata
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Anna Mattioni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Daniele Peluso
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Stefano Pirrò
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Daniela Posca
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Elena Santonico
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | - Filomena Spada
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Luisa Castagnoli
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
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35
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Corallino S, Iwai LK, Payne LS, Huang PH, Sacco F, Cesareni G, Castagnoli L. Alterations in the phosphoproteomic profile of cells expressing a non-functional form of the SHP2 phosphatase. N Biotechnol 2015; 33:524-36. [PMID: 26316256 DOI: 10.1016/j.nbt.2015.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 08/09/2015] [Accepted: 08/14/2015] [Indexed: 12/13/2022]
Abstract
The phosphatase SHP-2 plays an essential role in growth factor signaling and mutations in its locus is the cause of congenital and acquired pathologies. Mutations of SHP-2 are known to affect the activation of the RAS pathway. Gain-of-function mutations cause the Noonan syndrome, the most common non-chromosomal congenital disorder. In order to obtain a holistic picture of the intricate regulatory mechanisms underlying SHP-2 physiology and pathology, we set out to characterize perturbations of the cell phosphorylation profile caused by an altered localization of SHP-2. To describe the proteins whose activity may be directly or indirectly modulated by SHP-2 activity, we identified tyrosine peptides that are differentially phosphorylated in wild type SHP-2 cells and isogenic cells expressing a non-functional SHP-2 variant that cannot dephosphorylate the physiological substrates due to a defect in cellular localization upon growth factor stimulation. By an iTRAQ based strategy coupled to mass spectrometry, we have identified 63 phosphorylated tyrosine residues in 53 different proteins whose phosphorylation is affected by SHP-2 activity. Some of these confirm already established regulatory mechanisms while many others suggest new possible signaling routes that may contribute to the modulation of the ERK and p38 pathways by SHP-2. Interestingly many new proteins that we found to be regulated by SHP-2 activity are implicated in the formation and regulation of focal adhesions.
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Affiliation(s)
- Salvatore Corallino
- Department of Biology, University of Rome Tor Vergata, Via della ricerca scientifica, 00133 Rome, Italy.
| | - Leo K Iwai
- Protein Networks Team, Division of Cancer Biology, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Leo S Payne
- Protein Networks Team, Division of Cancer Biology, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Paul H Huang
- Protein Networks Team, Division of Cancer Biology, Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Francesca Sacco
- Department of Biology, University of Rome Tor Vergata, Via della ricerca scientifica, 00133 Rome, Italy
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Via della ricerca scientifica, 00133 Rome, Italy; IRCCS Fondazione Santa Lucia, 00143 Rome, Italy.
| | - Luisa Castagnoli
- Department of Biology, University of Rome Tor Vergata, Via della ricerca scientifica, 00133 Rome, Italy.
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36
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Pandey R, Mohmmed A, Pierrot C, Khalife J, Malhotra P, Gupta D. Genome wide in silico analysis of Plasmodium falciparum phosphatome. BMC Genomics 2014; 15:1024. [PMID: 25425018 PMCID: PMC4256932 DOI: 10.1186/1471-2164-15-1024] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/12/2014] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Eukaryotic cellular machineries are intricately regulated by several molecular mechanisms involving transcriptional control, post-translational control and post-translational modifications of proteins (PTMs). Reversible protein phosphorylation/dephosphorylation process, which involves kinases as well as phosphatases, represents an important regulatory mechanism for diverse pathways and systems in all organisms including human malaria parasite, Plasmodium falciparum. Earlier analysis on P. falciparum protein-phosphatome revealed presence of 34 phosphatases in Plasmodium genome. Recently, we re-analysed P. falciparum phosphatome aimed at identifying parasite specific phosphatases. RESULTS Plasmodium database (PlasmoDB 9.2) search, combined with PFAM and CDD searches, revealed 67 candidate phosphatases in P. falciparum. While this number is far less than the number of phosphatases present in Homo sapiens, it is almost the same as in other Plasmodium species. These Plasmodium phosphatase proteins were classified into 13 super families based on NCBI CDD search. Analysis of proteins expression profiles of the 67 phosphatases revealed that 44 phosphatases are expressed in both schizont as well as gametocytes stages. Fourteen phosphatases are common in schizont, ring and trophozoite stages, four phosphatases are restricted to gametocytes, whereas another three restricted to schizont stage. The phylogenetic trees for each of the known phosphatase super families reveal a considerable phylogenetic closeness amongst apicomplexan organisms and a considerable phylogenetic distance with other eukaryotic model organisms included in the study. The GO assignments and predicted interaction partners of the parasite phosphatases indicate its important role in diverse cellular processes. CONCLUSION In the study presented here, we reviewed the P. falciparum phosphatome to show presence of 67 candidate phosphatases in P. falciparum genomes/proteomes. Intriguingly, amongst these phosphatases, we could identify six Plasmodium specific phosphatases and 33 putative phosphatases that do not have human orthologs, thereby suggesting that these phosphatases have the potential to be explored as novel antimalarial drug targets.
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Affiliation(s)
| | | | | | - Jamal Khalife
- Structural and Computational Biology group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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Abstract
Phosphatases are crucial enzymes in health and disease, but the knowledge of their biological roles is still limited. Identifying substrates continues to be a great challenge. To support the research on phosphatase-kinase-substrate networks we present here an update on the human DEPhOsphorylation Database: DEPOD (http://www.depod.org or http://www.koehn.embl.de/depod). DEPOD is a manually curated open access database providing human phosphatases, their protein and non-protein substrates, dephosphorylation sites, pathway involvements and external links to kinases and small molecule modulators. All internal data are fully searchable including a BLAST application. Since the first release, more human phosphatases and substrates, their associated signaling pathways (also from new sources), and interacting proteins for all phosphatases and protein substrates have been added into DEPOD. The user interface has been further optimized; for example, the interactive human phosphatase-substrate network contains now a 'highlight node' function for phosphatases, which includes the visualization of neighbors in the network.
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Affiliation(s)
- Guangyou Duan
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Xun Li
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Maja Köhn
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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Hindle MM, Martin SF, Noordally ZB, van Ooijen G, Barrios-Llerena ME, Simpson TI, Le Bihan T, Millar AJ. The reduced kinome of Ostreococcus tauri: core eukaryotic signalling components in a tractable model species. BMC Genomics 2014; 15:640. [PMID: 25085202 PMCID: PMC4143559 DOI: 10.1186/1471-2164-15-640] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 07/08/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The current knowledge of eukaryote signalling originates from phenotypically diverse organisms. There is a pressing need to identify conserved signalling components among eukaryotes, which will lead to the transfer of knowledge across kingdoms. Two useful properties of a eukaryote model for signalling are (1) reduced signalling complexity, and (2) conservation of signalling components. The alga Ostreococcus tauri is described as the smallest free-living eukaryote. With less than 8,000 genes, it represents a highly constrained genomic palette. RESULTS Our survey revealed 133 protein kinases and 34 protein phosphatases (1.7% and 0.4% of the proteome). We conducted phosphoproteomic experiments and constructed domain structures and phylogenies for the catalytic protein-kinases. For each of the major kinases families we review the completeness and divergence of O. tauri representatives in comparison to the well-studied kinomes of the laboratory models Arabidopsis thaliana and Saccharomyces cerevisiae, and of Homo sapiens. Many kinase clades in O. tauri were reduced to a single member, in preference to the loss of family diversity, whereas TKL and ABC1 clades were expanded. We also identified kinases that have been lost in A. thaliana but retained in O. tauri. For three, contrasting eukaryotic pathways - TOR, MAPK, and the circadian clock - we established the subset of conserved components and demonstrate conserved sites of substrate phosphorylation and kinase motifs. CONCLUSIONS We conclude that O. tauri satisfies our two central requirements. Several of its kinases are more closely related to H. sapiens orthologs than S. cerevisiae is to H. sapiens. The greatly reduced kinome of O. tauri is therefore a suitable model for signalling in free-living eukaryotes.
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Affiliation(s)
| | | | | | | | | | | | | | - Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JD, UK.
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Abstract
Phosphorylation of serine, threonine and tyrosine plays significant roles in cellular signal transduction and in modifying multiple protein functions. Phosphoproteins are coordinated and regulated by a network of kinases, phosphatases and phospho-binding proteins, which modify the phosphorylation states, recognize unique phosphopeptides, or target proteins for degradation. Detailed and complete information on the structure and dynamics of these networks is required to better understand fundamental mechanisms of cellular processes and diseases. High-throughput technologies have been developed to investigate phosphoproteomes in model organisms and human diseases. Among them, mass spectrometry (MS)-based technologies are the major platforms and have been widely applied, which has led to explosive growth of phosphoproteomic data in recent years. New bioinformatics tools are needed to analyze and make sense of these data. Moreover, most research has focused on individual phosphoproteins and kinases. To gain a more complete knowledge of cellular processes, systems biology approaches, including pathways and networks modeling, have to be applied to integrate all components of the phosphorylation machinery, including kinases, phosphatases, their substrates, and phospho-binding proteins. This review presents the latest developments of bioinformatics methods and attempts to apply systems biology to analyze phosphoproteomics data generated by MS-based technologies. Challenges and future directions in this field will be also discussed.
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Sacco F, Boldt K, Calderone A, Panni S, Paoluzi S, Castagnoli L, Ueffing M, Cesareni G. Combining affinity proteomics and network context to identify new phosphatase substrates and adapters in growth pathways. Front Genet 2014; 5:115. [PMID: 24847354 PMCID: PMC4019850 DOI: 10.3389/fgene.2014.00115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/16/2014] [Indexed: 12/22/2022] Open
Abstract
Protein phosphorylation homoeostasis is tightly controlled and pathological conditions are caused by subtle alterations of the cell phosphorylation profile. Altered levels of kinase activities have already been associated to specific diseases. Less is known about the impact of phosphatases, the enzymes that down-regulate phosphorylation by removing the phosphate groups. This is partly due to our poor understanding of the phosphatase-substrate network. Much of phosphatase substrate specificity is not based on intrinsic enzyme specificity with the catalytic pocket recognizing the sequence/structure context of the phosphorylated residue. In addition many phosphatase catalytic subunits do not form a stable complex with their substrates. This makes the inference and validation of phosphatase substrates a non-trivial task. Here, we present a novel approach that builds on the observation that much of phosphatase substrate selection is based on the network of physical interactions linking the phosphatase to the substrate. We first used affinity proteomics coupled to quantitative mass spectrometry to saturate the interactome of eight phosphatases whose down regulations was shown to affect the activation of the RAS-PI3K pathway. By integrating information from functional siRNA with protein interaction information, we develop a strategy that aims at inferring phosphatase physiological substrates. Graph analysis is used to identify protein scaffolds that may link the catalytic subunits to their substrates. By this approach we rediscover several previously described phosphatase substrate interactions and characterize two new protein scaffolds that promote the dephosphorylation of PTPN11 and ERK by DUSP18 and DUSP26, respectively.
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Affiliation(s)
- Francesca Sacco
- Department of Biology, University of Rome Tor Vergata Rome, Italy
| | - Karsten Boldt
- Division of Experimental Ophthalmology, Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen Tuebingen, Germany
| | | | - Simona Panni
- Department DiBEST, University of Calabria Rende, Italy
| | - Serena Paoluzi
- Department of Biology, University of Rome Tor Vergata Rome, Italy
| | - Luisa Castagnoli
- Department of Biology, University of Rome Tor Vergata Rome, Italy
| | - Marius Ueffing
- Division of Experimental Ophthalmology, Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tuebingen Tuebingen, Germany ; Research Unit for Protein Science, Helmholtz Zentrum München Neuherberg, Germany
| | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata Rome, Italy ; Istituto Ricovero e Cura a Carattere Scientifico, Fondazione Santa Lucia Rome, Italy
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Panni S, Rombo SE. Searching for repetitions in biological networks: methods, resources and tools. Brief Bioinform 2013; 16:118-36. [PMID: 24300112 DOI: 10.1093/bib/bbt084] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We present here a compact overview of the data, models and methods proposed for the analysis of biological networks based on the search for significant repetitions. In particular, we concentrate on three problems widely studied in the literature: 'network alignment', 'network querying' and 'network motif extraction'. We provide (i) details of the experimental techniques used to obtain the main types of interaction data, (ii) descriptions of the models and approaches introduced to solve such problems and (iii) pointers to both the available databases and software tools. The intent is to lay out a useful roadmap for identifying suitable strategies to analyse cellular data, possibly based on the joint use of different interaction data types or analysis techniques.
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Anwar T, Gourinath S. Analysis of the Protein phosphotome of Entamoeba histolytica reveals an intricate phosphorylation network. PLoS One 2013; 8:e78714. [PMID: 24236039 PMCID: PMC3827238 DOI: 10.1371/journal.pone.0078714] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 09/22/2013] [Indexed: 01/06/2023] Open
Abstract
Phosphorylation is the most common mechanism for the propagation of intracellular signals. Protein phosphatases and protein kinases play a dynamic antagonistic role in protein phosphorylation. Protein phosphatases make up a significant fraction of eukaryotic proteome. In this article, we report the identification and analysis of protein phosphatases in the intracellular parasite Entamoeba histolytica. Based on an in silico analysis, we classified 250 non-redundant protein phosphatases in E. histolytica. The phosphotome of E. histolytica is 3.1% of its proteome and 1.3 times of the human phosphotome. In this extensive study, we identified 42 new putative phosphatases (39 hypothetical proteins and 3 pseudophosphatases). The presence of pseudophosphatases may have an important role in virulence of E. histolytica. A comprehensive phosphotome analysis of E. histolytica shows spectacular low similarity to human phosphatases, making them potent candidates for drug target.
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Affiliation(s)
- Tamanna Anwar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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PTP-central: a comprehensive resource of protein tyrosine phosphatases in eukaryotic genomes. Methods 2013; 65:156-64. [PMID: 23911837 DOI: 10.1016/j.ymeth.2013.07.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/18/2013] [Accepted: 07/21/2013] [Indexed: 12/28/2022] Open
Abstract
Reversible tyrosine phosphorylation is a fundamental signaling mechanism controlling a diversity of cellular processes. Whereas protein tyrosine kinases have long been implicated in many diseases, aberrant protein tyrosine phosphatase (PTP) activity is also increasingly being associated with a wide spectrum of conditions. PTPs are now regarded as key regulators of biochemical processes instead of simple "off" switches operating in tyrosine kinase signaling pathways. Despite the central importance that PTPs play in the cell's biochemistry, the tyrosine phosphatomes of most species remain uncharted. Here we present a highly sensitive and specific sequence-based method for the automatic classification of PTPs. As proof of principle we re-annotated the human tyrosine phosphatome, and discovered four new PTP genes that had not been reported before. Our method and the predicted tyrosine phosphatomes of 65 eukaryotic genomes are accessible online through the user-friendly PTP-central resource (http://www.PTP-central.org/), where users can also submit their own sequences for prediction. PTP-central is a comprehensive and continually developing resource that currently integrates the predicted tyrosine phosphatomes with structural data and genetic association disease studies, as well as homology relationships. PTP-central thus fills an important void for the systematic study of PTPs, both in model organisms and from an evolutionary perspective.
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Sacco F, Gherardini PF, Paoluzi S, Saez-Rodriguez J, Helmer-Citterich M, Ragnini-Wilson A, Castagnoli L, Cesareni G. Mapping the human phosphatome on growth pathways. Mol Syst Biol 2012; 8:603. [PMID: 22893001 PMCID: PMC3435503 DOI: 10.1038/msb.2012.36] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 07/10/2012] [Indexed: 01/13/2023] Open
Abstract
Large-scale siRNA screenings allow linking the function of poorly characterized genes to phenotypic readouts. According to this strategy, genes are associated with a function of interest if the alteration of their expression perturbs the phenotypic readouts. However, given the intricacy of the cell regulatory network, the mapping procedure is low resolution and the resulting models provide little mechanistic insights. We have developed a new strategy that combines multiparametric analysis of cell perturbation with logic modeling to achieve a more detailed functional mapping of human genes onto complex pathways. A literature-derived optimized model is used to infer the cell activation state following upregulation or downregulation of the model entities. By matching this signature with the experimental profile obtained in the high-throughput siRNA screening it is possible to infer the target of each protein, thus defining its 'entry point' in the network. By this novel approach, 41 phosphatases that affect key growth pathways were identified and mapped onto a human epithelial cell-specific growth model, thus providing insights into the mechanisms underlying their function.
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Affiliation(s)
- Francesca Sacco
- Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
| | | | - Serena Paoluzi
- Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
| | | | | | - Antonella Ragnini-Wilson
- Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
- High-throughput Microscopy Facility, Department of Translational and Cellular Pharmacology, Consorzio Mario Negri Sud, SM Imbaro, Italy
| | - Luisa Castagnoli
- Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
| | - Gianni Cesareni
- Department of Biology, University of Rome ‘Tor Vergata’, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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