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Xiong T, Zhang Z, Fan T, Ye F, Ye Z. Origin, evolution, and diversification of inositol 1,4,5-trisphosphate 3-kinases in plants and animals. BMC Genomics 2024; 25:350. [PMID: 38589807 PMCID: PMC11000326 DOI: 10.1186/s12864-024-10257-7] [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: 01/25/2024] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND In Eukaryotes, inositol polyphosphates (InsPs) represent a large family of secondary messengers and play crucial roes in various cellular processes. InsPs are synthesized through a series of pohophorylation reactions catalyzed by various InsP kinases in a sequential manner. Inositol 1,4,5-trisphosphate 3-kinase (IP3 3-kinase/IP3K), one member of InsP kinase, plays important regulation roles in InsPs metabolism by specifically phosphorylating inositol 1,4,5-trisphosphate (IP3) to inositol 1,3,4,5-tetrakisphosphate (IP4) in animal cells. IP3Ks were widespread in fungi, plants and animals. However, its evolutionary history and patterns have not been examined systematically. RESULTS A total of 104 and 31 IP3K orthologues were identified across 57 plant genomes and 13 animal genomes, respectively. Phylogenetic analyses indicate that IP3K originated in the common ancestor before the divergence of fungi, plants and animals. In most plants and animals, IP3K maintained low-copy numbers suggesting functional conservation during plant and animal evolution. In Brassicaceae and vertebrate, IP3K underwent one and two duplication events, respectively, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for IP3K duplications, and the IP3K duplicates have experienced functional divergence. Finally, a hypothetical evolutionary model for the IP3K proteins is proposed based on phylogenetic theory. CONCLUSION Our study reveals the evolutionary history of IP3K proteins and guides the future functions of animal, plant, and fungal IP3K proteins.
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Affiliation(s)
- Tao Xiong
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Zaibao Zhang
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China.
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
| | - Tianyu Fan
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
| | - Fan Ye
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, Zhejiang, China
| | - Ziyi Ye
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
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2
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Márquez-Moñino MÁ, Ortega-García R, Whitfield H, Riley AM, Infantes L, Garrett SW, Shipton ML, Brearley CA, Potter BVL, González B. Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity. Nat Commun 2024; 15:1502. [PMID: 38374076 PMCID: PMC10876669 DOI: 10.1038/s41467-024-45917-5] [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: 08/19/2023] [Accepted: 02/05/2024] [Indexed: 02/21/2024] Open
Abstract
D-myo-inositol 1,4,5-trisphosphate (InsP3) is a fundamental second messenger in cellular Ca2+ mobilization. InsP3 3-kinase, a highly specific enzyme binding InsP3 in just one mode, phosphorylates InsP3 specifically at its secondary 3-hydroxyl group to generate a tetrakisphosphate. Using a chemical biology approach with both synthetised and established ligands, combining synthesis, crystallography, computational docking, HPLC and fluorescence polarization binding assays using fluorescently-tagged InsP3, we have surveyed the limits of InsP3 3-kinase ligand specificity and uncovered surprisingly unforeseen biosynthetic capacity. Structurally-modified ligands exploit active site plasticity generating a helix-tilt. These facilitated uncovering of unexpected substrates phosphorylated at a surrogate extended primary hydroxyl at the inositol pseudo 3-position, applicable even to carbohydrate-based substrates. Crystallization experiments designed to allow reactions to proceed in situ facilitated unequivocal characterization of the atypical tetrakisphosphate products. In summary, we define features of InsP3 3-kinase plasticity and substrate tolerance that may be more widely exploitable.
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Affiliation(s)
- María Ángeles Márquez-Moñino
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Raquel Ortega-García
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Hayley Whitfield
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Andrew M Riley
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Lourdes Infantes
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain
| | - Shane W Garrett
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Megan L Shipton
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK
| | - Charles A Brearley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Barry V L Potter
- Drug Discovery and Medicinal Chemistry, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.
- Wolfson Laboratory of Medicinal Chemistry, Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Beatriz González
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry Blas Cabrera, CSIC, Serrano 119, 28006, Madrid, Spain.
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3
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Vashishth A, Tehri N, Tehri P, Sharma A, Sharma AK, Kumar V. Unraveling the potential of bacterial phytases for sustainable management of phosphorous. Biotechnol Appl Biochem 2023; 70:1690-1706. [PMID: 37042496 DOI: 10.1002/bab.2466] [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: 09/19/2022] [Accepted: 03/31/2023] [Indexed: 04/13/2023]
Abstract
Phosphorous actively participates in numerous metabolic and regulatory activities of almost all living organisms including animals and humans. Therefore, it is considered as an essential macronutrient required supporting their proper growth. On contrary, phytic acid (PA), an antinutritional substance, is widely known for its strong affinity to chelate essential mineral ions including PO4 3- , Ca2+ , Fe2+ , Mg2+ , and Zn2+ . Being one the major reservoir of PO4 3- ions, PA has great potential to bind PO4 3- ions in diverse range of foods. Once combined with P, PA transforms into an undigested and insoluble complex namely phytate. Produced phytate leads to a notable reduction in the bioavailability of P due to negligible activity of phytases in monogastric animals and humans. This highlights the importance and consequent need of enhancement of phytase level in these life forms. Interestingly, phytases, catalyzing the breakdown of phytate complex and recycling the phosphate into ecosystem to its available form, have naturally been reported in a variety of plants and microorganisms over past few decades. In pursuit of a reliable solution, the focus of this review is to explore the keynote potential of bacterial phytases for sustainable management of phosphorous via efficient utilization of soil phytate. The core of the review covers detailed discussion on bacterial phytases along with their widely reported applications viz. biofertilizers, phosphorus acquisition, and plant growth promotion. Moreover, meticulous description on fermentation-based strategies and future trends on bacterial phytases have also been included.
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Affiliation(s)
- Amit Vashishth
- Department of Science and Humanities, SRM Institute of Science & Technology, Ghaziabad, Uttar Pradesh, India
| | - Nimisha Tehri
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Piyush Tehri
- Department of Applied Sciences, MIET, Meerut, Uttar Pradesh, India
| | - Avinash Sharma
- Faculty of Agricultural Sciences, Arunachal University of Studies, Namsai, Arunachal Pradesh, India
| | - Anil Kumar Sharma
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Vineet Kumar
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Kishangarh, Ajmer, Rajasthan, India
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4
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Myo-D-inositol Trisphosphate Signalling in Oomycetes. Microorganisms 2022; 10:microorganisms10112157. [DOI: 10.3390/microorganisms10112157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Oomycetes are pathogens of plants and animals, which cause billions of dollars of global losses to the agriculture, aquaculture and forestry sectors each year. These organisms superficially resemble fungi, with an archetype being Phytophthora infestans, the cause of late blight of tomatoes and potatoes. Comparison of the physiology of oomycetes with that of other organisms, such as plants and animals, may provide new routes to selectively combat these pathogens. In most eukaryotes, myo-inositol 1,4,5 trisphosphate is a key second messenger that links extracellular stimuli to increases in cytoplasmic Ca2+, to regulate cellular activities. In the work presented in this study, investigation of the molecular components of myo-inositol 1,4,5 trisphosphate signaling in oomycetes has unveiled similarities and differences with that in other eukaryotes. Most striking is that several oomycete species lack detectable phosphoinositide-selective phospholipase C homologues, the enzyme family that generates this second messenger, but still possess relatives of myo-inositol 1,4,5 trisphosphate-gated Ca2+-channels.
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5
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Zubair M, Hamzah R, Griffin R, Ali N. Identification and functional characterization of multiple inositol polyphosphate phosphatase1 (Minpp1) isoform-2 in exosomes with potential to modulate tumor microenvironment. PLoS One 2022; 17:e0264451. [PMID: 35235602 PMCID: PMC8890658 DOI: 10.1371/journal.pone.0264451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/10/2022] [Indexed: 01/06/2023] Open
Abstract
Inositol polyphosphates (InsPs) play key signaling roles in diverse cellular functions, including calcium homeostasis, cell survival and death. Multiple inositol polyphosphate phosphatase 1 (Minpp1) affects the cellular levels of InsPs and cell functions. The Minpp1 is an endoplasmic reticulum (ER) resident but localizes away from its cytosolic InsPs substrates. The current study examines the heterogeneity of Minpp1 and the potential physiologic impact of Minpp1 isoforms, distinct motifs, subcellular distribution, and enzymatic potential. The NCBI database was used to analyze the proteome diversity of Minpp1 using bioinformatics tools. The analysis revealed that translation of three different Minpp1 variants resulted in three isoforms of Minpp1 of varying molecular weights. A link between the minpp1 variant-2 gene and ER-stress, using real-time PCR, suggests a functional similarity between minpp1 variant-1 and variant-2. A detailed study on motifs revealed Minpp1 isoform-2 is the only other isoform, besides isoform-1, that carries a phosphatase motif for InsPs hydrolysis but no ER-retention signal. The confocal microscopy revealed that the Minpp1 isoform-1 predominantly localized near the nucleus with a GRP-78 ER marker, while Minpp1 isoform-2 was scattered more towards the cell periphery where it co-localizes with the plasma membrane-destined multivesicular bodies biomarker CD63. MCF-7 cells were used to establish that Minpp1 isoform-2 is secreted into exosomes. Brefeldin A treatment resulted in overexpression of the exosome-associated Minpp1 isoform-2, suggesting its secretion via an unconventional route involving endocytic-generated vesicles and a link to ER stress. Results further demonstrated that the exosome-associated Minpp1 isoform-2 was enzymatically active. Overall, the data support the possibility that an extracellular form of enzymatically active Minpp1 isoform-2 mitigates any anti-proliferative actions of extracellular InsPs, thereby also impacting the makeup of the tumor microenvironment.
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Affiliation(s)
- Mohd Zubair
- Department of Biology, University of Arkansas at Little Rock, Little Rock, AR, United States of America
| | - Rabab Hamzah
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
- Center for Integrative Nanotechnology Sciences, University of Arkansas at Little Rock, Little Rock, AR, United States of America
| | - Robert Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Nawab Ali
- Department of Biology, University of Arkansas at Little Rock, Little Rock, AR, United States of America
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6
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Liu H, Li X, Zhang Q, Yuan P, Liu L, King GJ, Ding G, Wang S, Cai H, Wang C, Xu F, Shi L. Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate. DNA Res 2021; 28:6369200. [PMID: 34514497 PMCID: PMC8435555 DOI: 10.1093/dnares/dsab011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/28/2021] [Indexed: 01/20/2023] Open
Abstract
Phytate is the storage form of phosphorus in angiosperm seeds and plays vitally important roles during seed development. However, in crop plants phytate decreases bioavailability of seed-sourced mineral elements for humans, livestock and poultry, and contributes to phosphate-related water pollution. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, a panel of 505 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 3.28 × 106 single-nucleotide polymorphisms (SNPs). This identified 119 SNPs significantly associated with phytate concentration (PA_Conc) and phytate content (PA_Cont) and six candidate genes were identified. Of these, BnaA9.MRP5 represented the candidate gene for the significant SNP chrA09_5198034 (27 kb) for both PA_Cont and PA_Conc. Transcription of BnaA9.MRP5 in a low-phytate variety (LPA20) was significantly elevated compared with a high-phytate variety (HPA972). Association and haplotype analysis indicated that inbred lines carrying specific SNP haplotypes within BnaA9.MRP5 were associated with high- and low-phytate phenotypes. No significant differences in seed germination and seed yield were detected between low and high phytate cultivars examined. Candidate genes, favourable haplotypes and the low phytate varieties identified in this study will be useful for low-phytate breeding of B. napus.
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Affiliation(s)
- Haijiang Liu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaojuan Li
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qianwen Zhang
- School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai, 200240, China
| | - Pan Yuan
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, 2480, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, 2480, Australia
| | - Guangda Ding
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sheliang Wang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hongmei Cai
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuang Wang
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangsen Xu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Shi
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
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7
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Malek M, Wawrzyniak AM, Koch P, Lüchtenborg C, Hessenberger M, Sachsenheimer T, Jang W, Brügger B, Haucke V. Inositol triphosphate-triggered calcium release blocks lipid exchange at endoplasmic reticulum-Golgi contact sites. Nat Commun 2021; 12:2673. [PMID: 33976123 PMCID: PMC8113574 DOI: 10.1038/s41467-021-22882-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 04/02/2021] [Indexed: 02/03/2023] Open
Abstract
Vesicular traffic and membrane contact sites between organelles enable the exchange of proteins, lipids, and metabolites. Recruitment of tethers to contact sites between the endoplasmic reticulum (ER) and the plasma membrane is often triggered by calcium. Here we reveal a function for calcium in the repression of cholesterol export at membrane contact sites between the ER and the Golgi complex. We show that calcium efflux from ER stores induced by inositol-triphosphate [IP3] accumulation upon loss of the inositol 5-phosphatase INPP5A or receptor signaling triggers depletion of cholesterol and associated Gb3 from the cell surface, resulting in a blockade of clathrin-independent endocytosis (CIE) of Shiga toxin. This phenotype is caused by the calcium-induced dissociation of oxysterol binding protein (OSBP) from the Golgi complex and from VAP-containing membrane contact sites. Our findings reveal a crucial function for INPP5A-mediated IP3 hydrolysis in the control of lipid exchange at membrane contact sites.
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Affiliation(s)
- Mouhannad Malek
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Anna M. Wawrzyniak
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Peter Koch
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Christian Lüchtenborg
- grid.7700.00000 0001 2190 4373Heidelberg University Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Manuel Hessenberger
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Timo Sachsenheimer
- grid.7700.00000 0001 2190 4373Heidelberg University Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Wonyul Jang
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Britta Brügger
- grid.7700.00000 0001 2190 4373Heidelberg University Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Volker Haucke
- grid.418832.40000 0001 0610 524XLeibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany ,grid.14095.390000 0000 9116 4836Faculty of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
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8
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Role of protons in calcium signaling. Biochem J 2021; 478:895-910. [PMID: 33635336 DOI: 10.1042/bcj20200971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 02/03/2023]
Abstract
Thirty-six years after the publication of the important article by Busa and Nuccitelli on the variability of intracellular pH (pHi) and the interdependence of pHi and intracellular Ca2+ concentration ([Ca2+]i), little research has been carried out on pHi and calcium signaling. Moreover, the results appear to be contradictory. Some authors claim that the increase in [Ca2+]i is due to a reduction in pHi, others that it is caused by an increase in pHi. The reasons for these conflicting results have not yet been discussed and clarified in an exhaustive manner. The idea that variations in pHi are insignificant, because cellular buffers quickly stabilize the pHi, may be a limiting and fundamentally wrong concept. In fact, it has been shown that protons can move and react in the cell before they are neutralized. Variations in pHi have a remarkable impact on [Ca2+]i and hence on some of the basic biochemical mechanisms of calcium signaling. This paper focuses on the possible triggering role of protons during their short cellular cycle and it suggests a new hypothesis for an IP3 proton dependent mechanism of action.
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9
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Zhang J, Zhang S, Li X, Pi H. Relationship of ITPKA expression with the prognosis of breast cancer. Mol Genet Genomic Med 2021; 9:e1598. [PMID: 33624455 PMCID: PMC8123748 DOI: 10.1002/mgg3.1598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/06/2020] [Accepted: 12/15/2020] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Breast cancer (BC) represents a most common cancer among women worldwide. The outcomes of this disease remain dismal due to frequent recurrence and metastasis. Inositol-1,4,5-trisphosphate-3-kinase-A (ITPKA) plays an important role in regulating calcium signaling and actin dynamics. The dysregulation of ITPKA has been observed in several human cancers. The present study aimed to assess ITPKA expression and its prognostic value in BC. METHODS ITPKA expression was examined via quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC) methods. In addition, Kaplan-Meier survival analysis and Cox regression analysis were performed to evaluate prognostic value of ITPKA in BC. RESULTS Upregulated ITPKA expression was found in BC samples, according to both qRT-PCR and IHC analyses (all p < .05). ITPKA expression was positively correlated with lymph node metastasis (p = .021) and TNM stage (p = .009). Moreover, BC patients with high expression of ITPKA had poor overall survival compared with those with low expression (log-rank p < .05). Cox analysis verified that ITPKA expression was an independent prognostic factor for BC patients (HR = 4.239, 95%CI = 2.221-8.093 and p = .000). CONCLUSION BC cases show increased expression of ITPKA. ITPKA may act as an independent prognostic biomarker in BC.
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Affiliation(s)
- Jie Zhang
- Nursing Department, Sixth Medical Center of Chinese PLA Hospital, Medical School of Chinese PLA, Beijing, China
| | - Sujie Zhang
- Department of Oncology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Xiaoyan Li
- Department of Oncology, Chinese PLA General Hospital, Medical School of Chinese PLA, Beijing, China
| | - Hongying Pi
- Nursing Department, Sixth Medical Center of Chinese PLA Hospital, Medical School of Chinese PLA, Beijing, China
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10
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Li LX, Qiao Z, Cai JY, Gu XY, Liang Y, Chen N, Li MH, Guo XY, Miao JH, Wei KH. Mineral element contents and gene expression in Sophora tonkinensis during florescence. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1988707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Lin-xuan Li
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
| | - Zhu Qiao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
| | - Jin-yuan Cai
- Key Laboratory of Medicinal and Edible Homologous Plants, School of Food and Chemical Engineering, Liuzhou Institute of Technology, Liuzhou, PR China
| | - Xiao-yu Gu
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
| | - Ying Liang
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
| | - Namuhan Chen
- Pharmaceutical Laboratory, Inner Mongolia Institute of Traditional Chinese Medicine, Hohhot, Inner Mongolia, PR China
- Pharmaceutical Laboratory, Inner Mongolia Hospital of Traditional Chinese Medicine, Hohhot, Inner Mongolia, PR China
| | - Min-hui Li
- Pharmaceutical Laboratory, Inner Mongolia Institute of Traditional Chinese Medicine, Hohhot, Inner Mongolia, PR China
- Pharmaceutical Laboratory, Inner Mongolia Hospital of Traditional Chinese Medicine, Hohhot, Inner Mongolia, PR China
| | - Xiao-yun Guo
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
| | - Jian-hua Miao
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
| | - Kun-hua Wei
- Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
- Guangxi Engineering Research Center of TCM Resource Intelligent Creation, Guangxi Botanical Garden of Medicinal Plants, Nanning, PR China
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11
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Laha D, Portela-Torres P, Desfougères Y, Saiardi A. Inositol phosphate kinases in the eukaryote landscape. Adv Biol Regul 2020; 79:100782. [PMID: 33422459 PMCID: PMC8024741 DOI: 10.1016/j.jbior.2020.100782] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 01/01/2023]
Abstract
Inositol phosphate encompasses a large multifaceted family of signalling molecules that originate from the combinatorial attachment of phosphate groups to the inositol ring. To date, four distinct inositol kinases have been identified, namely, IPK, ITPK, IPPK (IP5-2K), and PPIP5K. Although, ITPKs have recently been identified in archaea, eukaryotes have taken advantage of these enzymes to create a sophisticated signalling network based on inositol phosphates. However, it remains largely elusive what fundamental biochemical principles control the signalling cascade. Here, we present an evolutionary approach to understand the development of the 'inositol phosphate code' in eukaryotes. Distribution analyses of these four inositol kinase groups throughout the eukaryotic landscape reveal the loss of either ITPK, or of PPIP5K proteins in several species. Surprisingly, the loss of IPPK, an enzyme thought to catalyse the rate limiting step of IP6 (phytic acid) synthesis, was also recorded. Furthermore, this study highlights a noteworthy difference between animal (metazoan) and plant (archaeplastida) lineages. While metazoan appears to have a substantial amplification of IPK enzymes, archaeplastida genomes show a considerable increase in ITPK members. Differential evolution of IPK and ITPK between plant and animal lineage is likely reflective of converging functional adaptation of these two types of inositol kinases. Since, the IPK family comprises three sub-types IPMK, IP6K, and IP3-3K each with dedicated enzymatic specificity in metazoan, we propose that the amplified ITPK group in plant could be classified in sub-types with distinct enzymology.
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Affiliation(s)
- Debabrata Laha
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK
| | - Paloma Portela-Torres
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK
| | - Yann Desfougères
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, WC1E6BT, London, UK.
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12
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Pramitha JL, Rana S, Aggarwal PR, Ravikesavan R, Joel AJ, Muthamilarasan M. Diverse role of phytic acid in plants and approaches to develop low-phytate grains to enhance bioavailability of micronutrients. ADVANCES IN GENETICS 2020; 107:89-120. [PMID: 33641749 DOI: 10.1016/bs.adgen.2020.11.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Natural or synthetic compounds that interfere with the bioavailability of nutrients are called antinutrients. Phytic acid (PA) is one of the major antinutrients present in the grains and acts as a chelator of micronutrients. The presence of six reactive phosphate groups in PA hinders the absorption of micronutrients in the gut of non-ruminants. Consumption of PA-rich diet leads to deficiency of minerals such as iron and zinc among human population. On the contrary, PA is a natural antioxidant, and PA-derived molecules function in various signal transduction pathways. Therefore, optimal concentration of PA needs to be maintained in plants to avoid adverse pleiotropic effects, as well as to ensure micronutrient bioavailability in the diets. Given this, the chapter enumerates the structure, biosynthesis, and accumulation of PA in food grains followed by their roles in growth, development, and stress responses. Further, the chapter elaborates on the antinutritional properties of PA and explains the conventional breeding and transgene-based approaches deployed to develop low-PA varieties. Studies have shown that conventional breeding methods could develop low-PA lines; however, the pleiotropic effects of these methods viz. reduced yield, embryo abnormalities, and poor seed quality hinder the use of breeding strategies. Overexpression of phytase in the endosperm and RNAi-mediated silencing of genes involved in myo-inositol biosynthesis overcome these constraints. Next-generation genome editing approaches, including CRISPR-Cas9 enable the manipulation of more than one gene involved in PA biosynthesis pathway through multiplex editing, and scope exists to deploy such tools in developing varieties with optimal PA levels.
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Affiliation(s)
- J Lydia Pramitha
- Department of Millets, Center for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Sumi Rana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Rajasekaran Ravikesavan
- Department of Millets, Center for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
| | - A John Joel
- Tamil Nadu Rice Research Institute, Tamil Nadu Agricultural University, Aduthurai, Tamil Nadu, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.
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13
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Yang S, Fang G, Zhang A, Ruan B, Jiang H, Ding S, Liu C, Zhang Y, Jaha N, Hu P, Xu Z, Gao Z, Wang J, Qian Q. Rice EARLY SENESCENCE 2, encoding an inositol polyphosphate kinase, is involved in leaf senescence. BMC PLANT BIOLOGY 2020; 20:393. [PMID: 32847519 PMCID: PMC7449006 DOI: 10.1186/s12870-020-02610-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/17/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Early leaf senescence influences yield and yield quality by affecting plant growth and development. A series of leaf senescence-associated molecular mechanisms have been reported in rice. However, the complex genetic regulatory networks that control leaf senescence need to be elucidated. RESULTS In this study, an early senescence 2 (es2) mutant was obtained from ethyl methanesulfonate mutagenesis (EMS)-induced mutational library for the Japonica rice cultivar Wuyugeng 7 (WYG7). Leaves of es2 showed early senescence at the seedling stage and became severe at the tillering stage. The contents of reactive oxygen species (ROS) significantly increased, while chlorophyll content, photosynthetic rate, catalase (CAT) activity significantly decreased in the es2 mutant. Moreover, genes which related to senescence, ROS and chlorophyll degradation were up-regulated, while those associated with photosynthesis and chlorophyll synthesis were down-regulated in es2 mutant compared to WYG7. The ES2 gene, which encodes an inositol polyphosphate kinase (OsIPK2), was fine mapped to a 116.73-kb region on chromosome 2. DNA sequencing of ES2 in the mutant revealed a missense mutation, ES2 was localized to nucleus and plasma membrane of cells, and expressed in various tissues of rice. Complementation test and overexpression experiment confirmed that ES2 completely restored the normal phenotype, with chlorophyll contents and photosynthetic rate increased comparable with the wild type. These results reveal the new role of OsIPK2 in regulating leaf senescence in rice and therefore will provide additional genetic evidence on the molecular mechanisms controlling early leaf senescence. CONCLUSIONS The ES2 gene, encoding an inositol polyphosphate kinase localized in the nucleus and plasma membrane of cells, is essential for leaf senescence in rice. Further study of ES2 will facilitate the dissection of the genetic mechanisms underlying early leaf senescence and plant growth.
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Affiliation(s)
- Shenglong Yang
- Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture/Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Guonan Fang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Anpeng Zhang
- Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture/Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Banpu Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Hongzhen Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Shilin Ding
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Yu Zhang
- Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture/Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Noushin Jaha
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Peng Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China
| | - Zhengjin Xu
- Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture/Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
| | - Jiayu Wang
- Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture/Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, People's Republic of China.
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, 310006, People's Republic of China.
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14
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Zhu H, Zhu N, Peng L, Zhang B, Yu Q, Li M. The inositol polyphosphate kinase Ipk1 transcriptionally regulates mitochondrial functions in Candida albicans. FEMS Yeast Res 2020; 20:5896454. [DOI: 10.1093/femsyr/foaa050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
ABSTRACT
Inositol polyphosphates (IPs) is an important family of signaling molecules that regulate multiple cellular processes, such as chromatin remodeling, transcription and mRNA export. Inositol polyphosphate kinases, as the critical enzymes for production and transformation of IPs, directly determine the intracellular levels of IPs and therefore are involved in many cellular processes. However, its roles in Candida albicans, the leading fungal pathogen in human beings, remain to be investigated. In this study, we identified the inositol polyphosphate kinase Ipk1 in C. albicans and found that it localizes in the nucleus. Moreover, in the ipk1Δ/Δ mutant, the activity of mitochondrial respiratory chain complexes and the mitochondrial function was severely impaired, which were associated with down-regulation of mitochondrial function-related genes revealed by transcription profiling analysis. The ipk1Δ/Δ mutant also displayed hypersensitivity to a series of environmental stresses, such as antifungal drugs, oxidants, cell wall perturbing agents and macrophage attacks, followed by attenuation of virulence in a mouse systematic infection model. These findings firstly reported the importance of inositol polyphosphate kinase Ipk1 in C. albicans, especially its role in mitochondrial function maintenance and pathogenicity.
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Affiliation(s)
- Hangqi Zhu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, No. 94, Weijin Road, Tianjin 300071, P. R. China
| | - Nali Zhu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, No. 94, Weijin Road, Tianjin 300071, P. R. China
| | - Liping Peng
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, No. 94, Weijin Road, Tianjin 300071, P. R. China
| | - Bing Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, No. 94, Weijin Road, Tianjin 300071, P. R. China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, No. 94, Weijin Road, Tianjin 300071, P. R. China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Department of Microbiology, College of Life Science, Nankai University, No. 94, Weijin Road, Tianjin 300071, P. R. China
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15
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Abstract
The multitudinous inositol phosphate family elicits a wide range of molecular effects that regulate countless biological responses. In this review, I provide a methodological viewpoint of the manner in which key advances in the field of inositol phosphate research were made. I also note some of the considerable challenges that still lie ahead.
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Affiliation(s)
- Stephen B Shears
- Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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16
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Pan C, Jin L, Wang X, Li Y, Chun J, Boese AC, Li D, Kang HB, Zhang G, Zhou L, Chen GZ, Saba NF, Shin DM, Magliocca KR, Owonikoko TK, Mao H, Lonial S, Kang S. Inositol-triphosphate 3-kinase B confers cisplatin resistance by regulating NOX4-dependent redox balance. J Clin Invest 2019; 129:2431-2445. [PMID: 31081803 DOI: 10.1172/jci124550] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/26/2019] [Indexed: 12/18/2022] Open
Abstract
How altered metabolism contributes to chemotherapy resistance in cancer cells remains unclear. Through a metabolism-related kinome RNAi screen, we identified inositol-trisphosphate 3-kinase B (ITPKB) as a critical enzyme that contributes to cisplatin-resistant tumor growth. We demonstrated that inositol 1,3,4,5-tetrakisphosphate (IP4), the product of ITPKB, plays a critical role in redox homeostasis upon cisplatin exposure by reducing cisplatin-induced ROS through inhibition of a ROS-generating enzyme, NADPH oxidase 4 (NOX4), which promotes cisplatin-resistant tumor growth. Mechanistically, we identified that IP4 competes with the NOX4 cofactor NADPH for binding and consequently inhibits NOX4. Targeting ITPKB with shRNA or its small-molecule inhibitor resulted in attenuation of NOX4 activity, imbalanced redox status, and sensitized cancer cells to cisplatin treatment in patient-derived xenografts. Our findings provide insight into the crosstalk between kinase-mediated metabolic regulation and platinum-based chemotherapy resistance in human cancers. Our study also suggests a distinctive signaling function of IP4 that regulates NOX4. Furthermore, pharmaceutical inhibition of ITPKB displayed synergistic attenuation of tumor growth with cisplatin, suggesting ITPKB as a promising synthetic lethal target for cancer therapeutic intervention to overcome cisplatin resistance.
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Affiliation(s)
- Chaoyun Pan
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Lingtao Jin
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Xu Wang
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Yuancheng Li
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jaemoo Chun
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Austin C Boese
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Dan Li
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Hee-Bum Kang
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Guojing Zhang
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Lu Zhou
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA
| | - Georgia Z Chen
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Nabil F Saba
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Dong M Shin
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Kelly R Magliocca
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Taofeek K Owonikoko
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Hui Mao
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sagar Lonial
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
| | - Sumin Kang
- Winship Cancer Institute, Department of Hematology and Medical Oncology, and
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17
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Shayanfar S, Broumand A, Pillai SD. Acid stress induces differential accumulation of metabolites in Escherichia coli O26:H11. J Appl Microbiol 2018; 125:1911-1919. [PMID: 30144243 DOI: 10.1111/jam.14081] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/25/2018] [Accepted: 08/14/2018] [Indexed: 11/27/2022]
Abstract
AIMS Acid exposure induces accumulation of certain metabolites in bacteria. The experimental objective was to identify the primary metabolites accumulating in Escherichia coli O26:H11 as a function of acid (pH 3·6) exposure. METHODS AND RESULTS Different buffers of pH 7·5 and 3·6 were used to study the metabolites accumulating in E. coli O26:H11 cells during such pH exposure. After 24 h of acid exposure, there was a 7-log decline in E. coli populations on trypticase soy agar plates. Untargeted metabolomic analysis identified 293 primary metabolites of which 145 metabolites were differentially (P < 0·01) accumulating between pH 7·5 and 3·6 in E. coli O26:H11. CONCLUSIONS After 24 h of acid exposure, 21 different metabolic pathways appeared to be functional, suggesting that the cells were still metabolically active. Among the identifiable pathways, the key differentially expressed pathways were associated with peptidoglycan biosynthesis, purine metabolism, d-Glutamine/d-glutamate metabolism, nitrogen metabolism, unsaturated fatty acid biosynthesis and inositol phosphate metabolism. SIGNIFICANCE AND IMPACT OF THE STUDY Shiga toxin producing non-O157 E. coli strains such as E. coli O26 are responsible for a growing number of food-related illnesses in the United States and around the world. From food production to consumption, micro-organisms in foods experience dramatic pH fluctuations by organic acids introduced either during food processing or by inorganic acids in the stomach. Acid exposure induces specific metabolite accumulation in bacterial cells. Understanding the survival mechanisms of pathogenic micro-organisms by studying the metabolome would be helpful in introducing effective hurdles and thus ensuring food safety.
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Affiliation(s)
- S Shayanfar
- Department of Nutrition and Food Science, National Center for Electron Beam Research, IAEA Collaborating Centre for Electron Beam Technology, Texas A&M University, College Station, TX, USA
| | - A Broumand
- Genomic Signal Processing Lab, Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
| | - S D Pillai
- Department of Nutrition and Food Science, National Center for Electron Beam Research, IAEA Collaborating Centre for Electron Beam Technology, Texas A&M University, College Station, TX, USA
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18
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Punjabi M, Bharadvaja N, Sachdev A, Krishnan V. Molecular characterization, modeling, and docking analysis of late phytic acid biosynthesis pathway gene, inositol polyphosphate 6-/ 3-/ 5-kinase, a potential candidate for developing low phytate crops. 3 Biotech 2018; 8:344. [PMID: 30073129 PMCID: PMC6064606 DOI: 10.1007/s13205-018-1343-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/06/2018] [Indexed: 01/08/2023] Open
Abstract
The coding sequence of inositol polyphosphate 6-/3-/5-kinase (GmIPK2) gene was identified and cloned from popular Indian soybean cultivar Pusa-16. The clone was predicted to encode 279 amino acids long, 30.97 kDa protein. Multiple sequence alignment revealed an inositol phosphate-binding motif, PxxxDxKxG throughout the IPK2 sequences along with other motifs unique to inositol phosphate kinase superfamily. Eight α-helices and eight β-strands in antiparallel β-sheets arrangement were predicted in the secondary structure of GmIPK2. The temporal analysis of GmIPK2 revealed maximum expression in the seed tissues during later stages of development while spatially the transcript levels were lowest in leaf and stem tissues. Endosperm-specific cis-regulatory motifs (GCN4 and Skn_1) which support high levels of expression, as observed in the developing seeds, were detected in its promoter region. The protein structure of GmIPK2 was modeled based on the crystal structure of inositol polyphosphate multikinase from Arabidopsis thaliana (PDB:4FRF) and subsequently docked with inositol phosphate ligands (PDB: 5GUG-I3P and PDB: 4A69-I0P). Molecular dynamics (MD) simulation established the structural stability of both, modeled enzyme and ligand-bound complexes. Docking in combination with trajectory analysis for 50 ns MD run confirmed the participation of Lys105, Lys126 and Arg153 residues in the formation of a network of hydrogen bonds to stabilize the ligand-receptor interaction. Results of the present study thus provide valuable information on structural and functional aspects of GmIPK2 which shall assist in strategizing our long-term goal of achieving phytic acid reduction in soybean by genetic modification of its biosynthetic pathway to develop a nutritionally enhanced crop in the future.
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Affiliation(s)
- Mansi Punjabi
- Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), New Delhi, 110042 India
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Navneeta Bharadvaja
- Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), New Delhi, 110042 India
| | - Archana Sachdev
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Veda Krishnan
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012 India
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19
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Effect of the actin- and calcium-regulating activities of ITPKB on the metastatic potential of lung cancer cells. Biochem J 2018; 475:2057-2071. [DOI: 10.1042/bcj20180238] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 01/10/2023]
Abstract
Inositol-1,4,5-trisphosphate 3-kinase-A (ITPKA) exhibits oncogenic activity in lung cancer cells by regulating Ins(1,4,5)P3-mediated calcium release and cytoskeletal dynamics. Since, in normal cells, ITPKA is mainly expressed in the brain, it is an excellent target for selected therapy of lung cancer. However, ITPKB is strongly expressed in normal lung tissues, but is down-regulated in lung cancer cells by miR-375, assuming that ITPKB might have tumor suppressor activity. In addition, ITPKB binds to F-actin making it likely that, similar to ITPKA, it controls actin dynamics. Thus, the treatment of ITPKA-expressing lung cancer with ITPKA inhibitors simultaneously inhibiting ITPKB may counteract the therapy. Based on these considerations, we analyzed if ITPKB controls actin dynamics and if the protein reduces aggressive progression of lung cancer cells. We found that ITPKB bundled F-actin in cell-free systems. However, the stable expression of ITPKB in H1299 lung cancer cells, exhibiting very low endogenous ITPKB expression, had no significant effect on the actin structure. In addition, our data show that ITPKB negatively controls transmigration of H1299 cells in vitro by blocking Ins(1,4,5)P3-mediated calcium release. On the other hand, colony formation was stimulated by ITPKB, independent of Ins(1,4,5)P3-mediated calcium signals. However, dissemination of H1299 cells from the skin to the lung in NOD scid gamma mice was not significantly affected by ITPKB expression. In summary, ITPKB does not affect the cellular actin structure and does not suppress dissemination of human lung cancer cells in mice. Thus, our initial hypotheses that ITPKB exhibits tumor suppressor activity could not be supported.
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20
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Chakraborty A. The inositol pyrophosphate pathway in health and diseases. Biol Rev Camb Philos Soc 2018; 93:1203-1227. [PMID: 29282838 PMCID: PMC6383672 DOI: 10.1111/brv.12392] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 11/28/2017] [Accepted: 12/05/2017] [Indexed: 12/11/2022]
Abstract
Inositol pyrophosphates (IPPs) are present in organisms ranging from plants, slime moulds and fungi to mammals. Distinct classes of kinases generate different forms of energetic diphosphate-containing IPPs from inositol phosphates (IPs). Conversely, polyphosphate phosphohydrolase enzymes dephosphorylate IPPs to regenerate the respective IPs. IPPs and/or their metabolizing enzymes regulate various cell biological processes by modulating many proteins via diverse mechanisms. In the last decade, extensive research has been conducted in mammalian systems, particularly in knockout mouse models of relevant enzymes. Results obtained from these studies suggest impacts of the IPP pathway on organ development, especially of brain and testis. Conversely, deletion of specific enzymes in the pathway protects mice from various diseases such as diet-induced obesity (DIO), type-2 diabetes (T2D), fatty liver, bacterial infection, thromboembolism, cancer metastasis and aging. Furthermore, pharmacological inhibition of the same class of enzymes in mice validates the therapeutic importance of this pathway in cardio-metabolic diseases. This review critically analyses these findings and summarizes the significance of the IPP pathway in mammalian health and diseases. It also evaluates benefits and risks of targeting this pathway in disease therapies. Finally, future directions of mammalian IPP research are discussed.
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Affiliation(s)
- Anutosh Chakraborty
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, MO 63104, U.S.A
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21
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Dwivedi V, Parida SK, Chattopadhyay D. A repeat length variation in myo-inositol monophosphatase gene contributes to seed size trait in chickpea. Sci Rep 2017; 7:4764. [PMID: 28684754 PMCID: PMC5500587 DOI: 10.1038/s41598-017-05332-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 05/26/2017] [Indexed: 11/11/2022] Open
Abstract
Chickpea (Cicer arietinum L.) is the third most important food legume crop. Seed size is the most economically important trait for chickpea. To understand the genetic regulation of seed size in chickpea, the present study established a three-way association of CT repeat length variation of a simple sequence repeat (SSR) in myo-inositol monophosphatase gene (CaIMP) with seed weight and phytic acid content by large scale validation and genotyping in a set of genetically diverse germplasm accessions and two reciprocal intra-specific mapping populations. Germplasms and mapping individuals with CT repeat-length expansion in the 5' untranslated region of CaIMP exhibited a pronounced increase in CaIMP protein level, enzymatic activity, seed-phytate content and seed weight. A chickpea transient expression system demonstrated this repeat-length variation influenced the translation of CaIMP mRNA, apparently by facilitating translation initiation. Our analyses proposed that the SSR marker derived from 5' UTR of a CaIMP gene is a promising candidate for selection of seed size/weight for agronomic trait improvement of chickpea.
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Affiliation(s)
- Vikas Dwivedi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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22
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Has Inositol Played Any Role in the Origin of Life? Life (Basel) 2017; 7:life7020024. [PMID: 28587245 PMCID: PMC5492146 DOI: 10.3390/life7020024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 12/11/2022] Open
Abstract
Phosphorus, as phosphate, plays a paramount role in biology. Since phosphate transfer reactions are an integral part of contemporary life, phosphate may have been incorporated into the initial molecules at the very beginning. To facilitate the studies into early phosphate utilization, we should look retrospectively to phosphate-rich molecules present in today’s cells. Overlooked by origin of life studies until now, inositol and the inositol phosphates, of which some species possess more phosphate groups that carbon atoms, represent ideal molecules to consider in this context. The current sophisticated association of inositol with phosphate, and the roles that some inositol phosphates play in regulating cellular phosphate homeostasis, intriguingly suggest that inositol might have played some role in the prebiotic process of phosphate exploitation. Inositol can be synthesized abiotically and, unlike glucose or ribose, is chemically stable. This stability makes inositol the ideal candidate for the earliest organophosphate molecules, as primitive inositol phosphates. I also present arguments suggesting roles for some inositol phosphates in early chemical evolution events. Finally, the possible prebiotic synthesis of inositol pyrophosphates could have generated high-energy molecules to be utilized in primitive trans-phosphorylating processes.
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Franco-Echevarría E, Sanz-Aparicio J, Brearley CA, González-Rubio JM, González B. The crystal structure of mammalian inositol 1,3,4,5,6-pentakisphosphate 2-kinase reveals a new zinc-binding site and key features for protein function. J Biol Chem 2017; 292:10534-10548. [PMID: 28450399 PMCID: PMC5481561 DOI: 10.1074/jbc.m117.780395] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/25/2017] [Indexed: 12/28/2022] Open
Abstract
Inositol 1,3,4,5,6-pentakisphosphate 2-kinases (IP5 2-Ks) are part of a family of enzymes in charge of synthesizing inositol hexakisphosphate (IP6) in eukaryotic cells. This protein and its product IP6 present many roles in cells, participating in mRNA export, embryonic development, and apoptosis. We reported previously that the full-length IP5 2-K from Arabidopsis thaliana is a zinc metallo-enzyme, including two separated lobes (the N- and C-lobes). We have also shown conformational changes in IP5 2-K and have identified the residues involved in substrate recognition and catalysis. However, the specific features of mammalian IP5 2-Ks remain unknown. To this end, we report here the first structure for a murine IP5 2-K in complex with ATP/IP5 or IP6. Our structural findings indicated that the general folding in N- and C-lobes is conserved with A. thaliana IP5 2-K. A helical scaffold in the C-lobe constitutes the inositol phosphate-binding site, which, along with the participation of the N-lobe, endows high specificity to this protein. However, we also noted large structural differences between the orthologues from these two eukaryotic kingdoms. These differences include a novel zinc-binding site and regions unique to the mammalian IP5 2-K, as an unexpected basic patch on the protein surface. In conclusion, our findings have uncovered distinct features of a mammalian IP5 2-K and set the stage for investigations into protein-protein or protein-RNA interactions important for IP5 2-K function and activity.
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Affiliation(s)
- Elsa Franco-Echevarría
- From the Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain and
| | - Julia Sanz-Aparicio
- From the Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain and
| | - Charles A Brearley
- the School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Juana M González-Rubio
- From the Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain and
| | - Beatriz González
- From the Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain and
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Inositol-1,4,5-trisphosphate 3-kinase-A (ITPKA) is frequently over-expressed and functions as an oncogene in several tumor types. Biochem Pharmacol 2017; 137:1-9. [PMID: 28377279 DOI: 10.1016/j.bcp.2017.03.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/29/2017] [Indexed: 01/22/2023]
Abstract
At present targeted tumor therapy is based on inhibition of proteins or protein mutants that are up-regulated in tumor but not in corresponding normal cells. The actin bundling Inositol-trisphosphate 3-kinase A (ITPKA) belongs to such molecular targets. ITPKA is expressed in a broad range of tumor types but shows limited expression in normal cells. In lung and breast cancer expression of ITPKA is stimulated by gene body methylation which increases with increasing malignancy of these tumors but is not detectable in the corresponding normal tissues. Since ITPKA gene body methylation occurs early in tumor development, it could serve as biomarker for early detection of lung cancer. Detailed mechanistic studies revealed that down-regulation of ITPKA in lung adenocarcinoma cancers reduced both, tumor growth and metastasis. It is assumed that tumor growth is stimulated by the InsP3Kinase activity of ITPKA and metastasis by its actin bundling activity. A selective inhibitor against the InsP3Kinase activity of ITPKA has been identified but compounds inhibiting the actin bundling activity are not available yet. Since no curative therapy option for metastatic lung or breast tumors exist, therapies that block activities of ITPKA may offer new options for patients with these tumors. Thus, efforts should be made to develop clinical drugs that selectively target InsP3Kinase activity as well as actin bundling activity of ITPKA.
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Balaban NP, Suleimanova AD, Valeeva LR, Chastukhina IB, Rudakova NL, Sharipova MR, V. Shakirov E. Microbial Phytases and Phytate: Exploring Opportunities for Sustainable Phosphorus Management in Agriculture. ACTA ACUST UNITED AC 2017. [DOI: 10.4236/ajmb.2017.71002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
The diverse family of inositol lipids is now known to be central to many aspects of cell biology. The route from the first discovery of inositol to our present day knowledge of inositol lipids spans more than 150 years and is long and complex. This is a brief account of some of the most important stages along that route.
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Affiliation(s)
- Robin F Irvine
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, United Kingdom
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Inositol polyphosphate multikinase (IPMK) in transcriptional regulation and nuclear inositide metabolism. Biochem Soc Trans 2016; 44:279-85. [PMID: 26862216 DOI: 10.1042/bst20150225] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Inositol polyphosphate multikinase (IPMK, ipk2, Arg(82), ArgRIII) is an inositide kinase with unusually flexible substrate specificity and the capacity to partake in many functional protein-protein interactions (PPIs). By merging these two activities, IPMK is able to execute gene regulatory functions that are very unique and only now beginning to be recognized. In this short review, we present a brief history of IPMK, describe the structural biology of the enzyme and highlight a few recent discoveries that have shed more light on the role IPMK plays in inositide metabolism, nuclear signalling and transcriptional regulation.
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Baughman BM, Wang H, An Y, Kireev D, Stashko MA, Jessen HJ, Pearce KH, Frye SV, Shears SB. A High-Throughput Screening-Compatible Strategy for the Identification of Inositol Pyrophosphate Kinase Inhibitors. PLoS One 2016; 11:e0164378. [PMID: 27736936 PMCID: PMC5063353 DOI: 10.1371/journal.pone.0164378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/24/2016] [Indexed: 11/22/2022] Open
Abstract
Pharmacological tools-'chemical probes'-that intervene in cell signaling cascades are important for complementing genetically-based experimental approaches. Probe development frequently begins with a high-throughput screen (HTS) of a chemical library. Herein, we describe the design, validation, and implementation of the first HTS-compatible strategy against any inositol phosphate kinase. Our target enzyme, PPIP5K, synthesizes 'high-energy' inositol pyrophosphates (PP-InsPs), which regulate cell function at the interface between cellular energy metabolism and signal transduction. We optimized a time-resolved, fluorescence resonance energy transfer ADP-assay to record PPIP5K-catalyzed, ATP-driven phosphorylation of 5-InsP7 to 1,5-InsP8 in 384-well format (Z' = 0.82 ± 0.06). We screened a library of 4745 compounds, all anticipated to be membrane-permeant, which are known-or conjectured based on their structures-to target the nucleotide binding site of protein kinases. At a screening concentration of 13 μM, fifteen compounds inhibited PPIP5K >50%. The potency of nine of these hits was confirmed by dose-response analyses. Three of these molecules were selected from different structural clusters for analysis of binding to PPIP5K, using isothermal calorimetry. Acceptable thermograms were obtained for two compounds, UNC10112646 (Kd = 7.30 ± 0.03 μM) and UNC10225498 (Kd = 1.37 ± 0.03 μM). These Kd values lie within the 1-10 μM range generally recognized as suitable for further probe development. In silico docking data rationalizes the difference in affinities. HPLC analysis confirmed that UNC10225498 and UNC10112646 directly inhibit PPIP5K-catalyzed phosphorylation of 5-InsP7 to 1,5-InsP8; kinetic experiments showed inhibition to be competitive with ATP. No other biological activity has previously been ascribed to either UNC10225498 or UNC10112646; moreover, at 10 μM, neither compound inhibits IP6K2, a structurally-unrelated PP-InsP kinase. Our screening strategy may be generally applicable to inhibitor discovery campaigns for other inositol phosphate kinases.
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Affiliation(s)
- Brandi M. Baughman
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Huanchen Wang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
| | - Yi An
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Michael A. Stashko
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Henning J. Jessen
- Institute of Organic Chemistry, Albert-Ludwigs-University of Freiburg, Freiburg 79104, Germany
| | - Kenneth H. Pearce
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Stephen B. Shears
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
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ITPKA Gene Body Methylation Regulates Gene Expression and Serves as an Early Diagnostic Marker in Lung and Other Cancers. J Thorac Oncol 2016; 11:1469-81. [PMID: 27234602 DOI: 10.1016/j.jtho.2016.05.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/03/2016] [Accepted: 05/16/2016] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Despite recent advances in cancer therapy, the overall 5-year survival rate of patients with lung cancer remains low. The aim of our study was to search for novel markers for early diagnosis in patients with lung cancer. METHODS Complementary DNA microarray analysis was performed in primary lung adenocarcinomas and cell lines to search for differentially expressed genes, followed by in vivo and in vitro tumorigenic assays to characterize the oncogenic potential of the candidate genes. Gene body methylation was analyzed by 450K methylation array, bisulfite sequencing, and quantitative methylation-specific polymerase chain reaction assays. In silico analysis of The Cancer Genome Atlas data set was also performed. RESULTS Inositol-trisphosphate 3-kinase A gene (ITPKA), a kinase with limited tissue distribution, was identified as a potential oncogene. We showed that ITPKA expression is up-regulated in many forms of cancers, including lung and breast cancers, and that overexpressed ITPKA contributes to tumorigenesis. We also demonstrated that ITPKA expression is regulated by epigenetic DNA methylation of ITPKA gene body through modulation of the binding of SP1 transcription factor to the ITPKA promoter. ITPKA gene body displayed low or absent levels of methylation in most normal tissue but was significantly methylated in malignant tumors. In lung cancer, ITPKA gene body methylation first appeared at the in situ carcinoma stage and progressively increased after invasion. CONCLUSIONS ITPKA is a potential oncogene that it is overexpressed in most tumors, and its overexpression promotes tumorigenesis. ITPKA gene body methylation regulates its expression and thus serves as a novel and potential biomarker for early cancer detection.
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Indyk HE, Saldo SC, White PM, Dole MN, Gill BD, Woollard DC. The free and total myo-inositol contents of early lactation and seasonal bovine milk. Int Dairy J 2016. [DOI: 10.1016/j.idairyj.2016.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Between spring 1982 and autumn 1984 the physiological role of Ins(1,4,5)P3 as a calcium-mobilizing second messenger was first suggested and then experimentally established. At the same time the unexpected complexity of inositide metabolism began to be exposed by the discovery of Ins(1,3,4)P3. This article recalls my entanglement with these two inositol phosphates.
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Veiga N, Macho I, Gómez K, González G, Kremer C, Torres J. Potentiometric and spectroscopic study of the interaction of 3d transition metal ions with inositol hexakisphosphate. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.05.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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ITPKA expression is a novel prognostic factor in hepatocellular carcinoma. Diagn Pathol 2015; 10:136. [PMID: 26249031 PMCID: PMC4528344 DOI: 10.1186/s13000-015-0374-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/29/2015] [Indexed: 12/15/2022] Open
Abstract
Background Inositol-1,4,5-trisphosphate-3-kinase-A (ITPKA) has recently been found to be implicated in the tumor progression of various cancers. However, the expression and the prognostic value of ITPKA in hepatocellular carcinoma (HCC) remains unexplored. The aim of this study is to investigate the clinical significance of ITPKA expression in HCC. Methods We determined the expression level of ITPKA in 135 cases of HCC tissues and the matched adjacent nontumorous tissues by quantitative real-time RT-PCR. The correlation between ITPKA expression and prognosis of HCC patients was further evaluated by univariate and multivariate analysis. Multivariate analysis of the prognostic factors was performed with Cox proportional hazards model. Results Up-regulation of ITPKA occurred in 48.9 % of primary HCCs compared with their nontumor counterparts (P < 0.001). In addition, high expression of ITPKA was significantly associated with vascular invasion (P = 0.001) and TNM stage (P = 0.005). Kaplan–Meier analysis showed that the 5-year overall survival (OS) and relapse-free survival (RFS) rate in the group with high expression of ITPKA is poorer than that in low expression group (32.2 and 26.8 % versus 59.2 and 57.7 %). Univariate and multivariate analyses revealed that ITPKA was an independent prognostic factor for OS and RFS. Moreover, Stratified analysis revealed that its prognostic significance still existed within the subgroup of patients with early clinical stage (TNM stage I) or normal serum AFP level (≤25 μg/L). Conclusion Our data indicated that ITPKA expression was significantly up-regulated in HCC and could serve as a potential novel prognostic biomarker for HCC patients after surgery.
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Zhan H, Zhong Y, Yang Z, Xia H. Enzyme activities of Arabidopsis inositol polyphosphate kinases AtIPK2α and AtIPK2β are involved in pollen development, pollen tube guidance and embryogenesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:758-71. [PMID: 25846941 DOI: 10.1111/tpj.12846] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 03/16/2015] [Accepted: 03/31/2015] [Indexed: 05/27/2023]
Abstract
Inositol polyphosphate kinase (IPK2) is a key component of inositol polyphosphate signaling. There are two highly homologous inositol polyphosphate kinases (AtIPK2α and AtIPK2β) in Arabidopsis. Previous studies that overexpressed or reduced the expression of AtIPK2α and AtIPK2β revealed their roles in auxiliary shoot branching, abiotic stress responses and root growth. Here, we report that AtIPK2α and AtIPK2β act redundantly during pollen development, pollen tube guidance and embryogenesis. Single knock-out mutants of atipk2α and atipk2β were indistinguishable from the wild type, whereas the atipk2α atipk2β double mutant could not be obtained. Detailed genetic and cytological investigations showed that the mutation of AtIPK2α and AtIPK2β resulted in severely reduced transmission of male gametophyte as a result of abnormal pollen development and defective pollen tube guidance. In addition, the early embryo development of the atipk2α atipk2β double mutant was also aborted. Expressing either catalytically inactive or substrate specificity-altered variants of AtIPK2β could not rescue the male gametophyte and embryogenesis defects of the atipk2α atipk2β double mutant, implying that the kinase activity of AtIPK2 is required for pollen development, pollen tube guidance and embryogenesis. Taken together, our results provide genetic evidence for the requirement of inositol polyphosphate signaling in plant sexual reproduction.
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Affiliation(s)
- Huadong Zhan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Yujiao Zhong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Zhongnan Yang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Huijun Xia
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
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Davis WJ, Lehmann PZ, Li W. Nuclear PI3K signaling in cell growth and tumorigenesis. Front Cell Dev Biol 2015; 3:24. [PMID: 25918701 PMCID: PMC4394695 DOI: 10.3389/fcell.2015.00024] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 03/27/2015] [Indexed: 12/12/2022] Open
Abstract
The PI3K/Akt signaling pathway is a major driving force in a variety of cellular functions. Dysregulation of this pathway has been implicated in many human diseases including cancer. While the activity of the cytoplasmic PI3K/Akt pathway has been extensively studied, the functions of these molecules and their effector proteins within the nucleus are poorly understood. Harboring key cellular processes such as DNA replication and repair as well as nascent messenger RNA transcription, the nucleus provides a unique compartmental environment for protein–protein and protein–DNA/RNA interactions required for cell survival, growth, and proliferation. Here we summarize recent advances made toward elucidating the nuclear PI3K/Akt signaling cascade and its key components within the nucleus as they pertain to cell growth and tumorigenesis. This review covers the spatial and temporal localization of the major nuclear kinases having PI3K activities and the counteracting phosphatases as well as the role of nuclear PI3K/Akt signaling in mRNA processing and exportation, DNA replication and repair, ribosome biogenesis, cell survival, and tumorigenesis.
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Affiliation(s)
- William J Davis
- College of Medical Sciences, Washington State University Spokane, WA, USA
| | - Peter Z Lehmann
- College of Medical Sciences, Washington State University Spokane, WA, USA
| | - Weimin Li
- College of Medical Sciences, Washington State University Spokane, WA, USA
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Abstract
Neutrophils play critical roles in innate immunity and host defense. However, excessive neutrophil accumulation or hyper-responsiveness of neutrophils can be detrimental to the host system. Thus, the response of neutrophils to inflammatory stimuli needs to be tightly controlled. Many cellular processes in neutrophils are mediated by localized formation of an inositol phospholipid, phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), at the plasma membrane. The PtdIns(3,4,5)P3 signaling pathway is negatively regulated by lipid phosphatases and inositol phosphates, which consequently play a critical role in controlling neutrophil function and would be expected to act as ideal therapeutic targets for enhancing or suppressing innate immune responses. Here, we comprehensively review current understanding about the action of lipid phosphatases and inositol phosphates in the control of neutrophil function in infection and inflammation.
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Affiliation(s)
- Hongbo R Luo
- Department of Pathology, Harvard Medical School, Boston, MA, USA Department of Lab Medicine, Children's Hospital Boston, Dana-Farber/Harvard Cancer Center, Boston, MA, USA
| | - Subhanjan Mondal
- Department of Pathology, Harvard Medical School, Boston, MA, USA Department of Lab Medicine, Children's Hospital Boston, Dana-Farber/Harvard Cancer Center, Boston, MA, USA Promega Corporation, Madison, WI, USA
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Leondaritis G, Galanopoulou D. Emerging roles of phosphoinositide-specific phospholipases C in the ciliatesTetrahymenaandParamecium. Commun Integr Biol 2014. [DOI: 10.4161/cib.16295] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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The signaling phospholipid PIP3 creates a new interaction surface on the nuclear receptor SF-1. Proc Natl Acad Sci U S A 2014; 111:15054-9. [PMID: 25288771 DOI: 10.1073/pnas.1416740111] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The signaling phosphatidylinositol lipids PI(4,5)P2 (PIP2) and PI(3,4,5)P3 (PIP3) bind nuclear receptor 5A family (NR5As), but their regulatory mechanisms remain unknown. Here, the crystal structures of human NR5A1 (steroidogenic factor-1, SF-1) ligand binding domain (LBD) bound to PIP2 and PIP3 show the lipid hydrophobic tails sequestered in the hormone pocket, as predicted. However, unlike classic nuclear receptor hormones, the phosphoinositide head groups are fully solvent-exposed and complete the LBD fold by organizing the receptor architecture at the hormone pocket entrance. The highest affinity phosphoinositide ligand PIP3 stabilizes the coactivator binding groove and increases coactivator peptide recruitment. This receptor-ligand topology defines a previously unidentified regulatory protein-lipid surface on SF-1 with the phosphoinositide head group at its nexus and poised to interact with other proteins. This surface on SF-1 coincides with the predicted binding site of the corepressor DAX-1 (dosage-sensitive sex reversal, adrenal hypoplasia critical region on chromosome X), and importantly harbors missense mutations associated with human endocrine disorders. Our data provide the structural basis for this poorly understood cluster of human SF-1 mutations and demonstrates how signaling phosphoinositides function as regulatory ligands for NR5As.
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Woollard DC, Macfadzean C, Indyk HE, McMahon A, Christiansen S. Determination of myo-inositol in infant formulae and milk powders using capillary gas chromatography with flame ionisation detection. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2014.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Martynov VV, Dorokhov DB. Polymorphism of the IPK1 gene among members of the genus Glycine. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414070138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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IP6K structure and the molecular determinants of catalytic specificity in an inositol phosphate kinase family. Nat Commun 2014; 5:4178. [PMID: 24956979 DOI: 10.1038/ncomms5178] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 05/21/2014] [Indexed: 01/27/2023] Open
Abstract
Inositol trisphosphate kinases (IP3Ks) and inositol hexakisphosphate kinases (IP6Ks) each regulate specialized signalling activities by phosphorylating either InsP3 or InsP6 respectively. The molecular basis for these different kinase activities can be illuminated by a structural description of IP6K. Here we describe the crystal structure of an Entamoeba histolytica hybrid IP6K/IP3K, an enzymatic parallel to a 'living fossil'. Through molecular modelling and mutagenesis, we extrapolated our findings to human IP6K2, which retains vestigial IP3K activity. Two structural elements, an α-helical pair and a rare, two-turn 310 helix, together forge a substrate-binding pocket with an open clamshell geometry. InsP6 forms substantial contacts with both structural elements. Relative to InsP6, enzyme-bound InsP3 rotates 55° closer to the α-helices, which provide most of the protein's interactions with InsP3. These data reveal the molecular determinants of IP6K activity, and suggest an unusual evolutionary trajectory for a primordial kinase that could have favored efficient bifunctionality, before propagation of separate IP3Ks and IP6Ks.
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Bang S, Chen Y, Ahima RS, Kim SF. Convergence of IPMK and LKB1-AMPK signaling pathways on metformin action. Mol Endocrinol 2014; 28:1186-93. [PMID: 24877601 DOI: 10.1210/me.2014-1134] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Metformin is a biguanide drug that is widely prescribed for type 2 diabetes. Metformin suppresses hepatic gluconeogenesis and increases fatty acid oxidation. Although studies have suggested that metformin acts, at least in part, via activation of the liver kinase B1 (LKB1)/AMP-activated protein kinase (AMPK) pathway, the specific molecular mechanisms underlying metformin's regulation of glucose and lipid metabolism have not been well delineated. Recently, we have shown that inositol polyphosphate multikinase (IPMK) plays an important role in cellular energy metabolism and glucose-mediated AMPK regulation. Here we investigated the role of IPMK in metformin-induced AMPK activation. We observed that metformin-mediated activation of AMPK was impaired in the absence of IPMK. Overexpression of wild-type IPMK was sufficient to restore LKB1-AMPK activation by either metformin or AICAR in IPMK(-/-) murine embryonic fibroblast cells, suggesting that IPMK may act as an upstream regulator of LKB1-AMPK signaling in response to metformin. Moreover, this regulation was mediated by protein-protein interaction between IPMK and LKB1 as a dominant-negative peptide, which abrogates this interaction, attenuated metformin's ability to activate AMPK. Our data demonstrate that IPMK plays an important role in LKB1/AMPK signaling and may be targeted for treatment of metabolic diseases.
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Affiliation(s)
- Sookhee Bang
- Department of Psychiatry and Pharmacology, Center for Neurobiology and Behavior (S.B., Y.C., S.F.K.); and Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism and the Institute for Diabetes, Obesity, and Metabolism (R.S.A.), Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Yu J, Saiardi A, Greenwood JS, Bewley JD. Molecular and biochemical identification of inositol 1,3,4,5,6-pentakisphosphate 2-kinase encoding mRNA variants in castor bean (Ricinus communis L.) seeds. PLANTA 2014; 239:965-77. [PMID: 24463774 DOI: 10.1007/s00425-014-2028-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
During seed development, phytic acid (PA) associated with mineral cations is stored as phytin and mobilized following germination in support of seedling growth. Two parallel biosynthetic pathways for PA have been proposed; yet the pathway is still poorly understood in terms of its regulation and the enzymes involved. Here, the castor bean (Ricinus communis L.) gene for inositol 1,3,4,5,6-pentakisphosphate 2-kinase (RcIPK1) has been identified. This encodes the enzyme implicated in catalyzing the final reaction in PA biosynthesis, and its expression is enhanced in isolated germinated embryos by application of phosphate and myo-inositol (Ins). Even though only one copy of the RcIPK1 gene is present in the genome, numerous RNA variants are present, most likely due to alternative splicing. These are translated into six closely related protein isoforms according to in silico analysis. Functional analyses using yeast ipk1Δ revealed that only three of the mRNA variants can rescue a temperature-sensitive growth phenotype of this strain. High-performance liquid chromatography (HPLC) analysis of the synthesized inositol phosphates demonstrated that the ability to complement the missing yeast IPK1 enzyme is associated with the production of enzyme activity. The three active isoforms possess unique conserved motifs important for IPK1 catalytic activity.
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MESH Headings
- Base Sequence
- Blotting, Southern
- Ricinus communis/enzymology
- Ricinus communis/genetics
- Ricinus communis/growth & development
- Chromatography, High Pressure Liquid
- Cloning, Molecular
- Computer Simulation
- Gene Expression Regulation, Enzymologic
- Gene Expression Regulation, Plant
- Genes, Plant
- Genetic Complementation Test
- Molecular Sequence Data
- Mutation/genetics
- Phenotype
- Phosphotransferases (Alcohol Group Acceptor)/chemistry
- Phosphotransferases (Alcohol Group Acceptor)/genetics
- Phosphotransferases (Alcohol Group Acceptor)/metabolism
- Phytic Acid/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Saccharomyces cerevisiae/metabolism
- Seeds/enzymology
- Seeds/genetics
- Seeds/growth & development
- Sequence Alignment
- Sequence Analysis, DNA
- Structural Homology, Protein
- Substrate Specificity
- Temperature
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Affiliation(s)
- Jaeju Yu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Veiga N, Torres J, Bazzicalupi C, Bianchi A, Kremer C. The copper(ii)–phytate–terpyridine ternary system: the first crystal structures showing the interaction of phytate with bivalent metal and ammonium cations. Chem Commun (Camb) 2014; 50:14971-4. [DOI: 10.1039/c4cc07226j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work reports the solution and crystallographic study of the Cu(ii)–phytate–terpyridine systems, showing for the first time the phytate binding mode toward a bivalent cation and protonated polyamine groups.
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Affiliation(s)
- Nicolás Veiga
- Departamento Estrella Campos
- Universidad de la República
- Montevideo, Uruguay
| | - Julia Torres
- Departamento Estrella Campos
- Universidad de la República
- Montevideo, Uruguay
| | - Carla Bazzicalupi
- Dipartimento di Chimica “Ugo Schiff”
- Universitá degli Studi di Firenze
- Firenze, Italy
| | - Antonio Bianchi
- Dipartimento di Chimica “Ugo Schiff”
- Universitá degli Studi di Firenze
- Firenze, Italy
| | - Carlos Kremer
- Departamento Estrella Campos
- Universidad de la República
- Montevideo, Uruguay
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45
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Metabolic study of grapevine leaves infected by downy mildew using negative ion electrospray – Fourier transform ion cyclotron resonance mass spectrometry. Anal Chim Acta 2013; 795:44-51. [DOI: 10.1016/j.aca.2013.07.068] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 07/30/2013] [Accepted: 07/31/2013] [Indexed: 12/30/2022]
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46
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Ariza A, Moroz OV, Blagova EV, Turkenburg JP, Waterman J, Roberts SM, Vind J, Sjøholm C, Lassen SF, De Maria L, Glitsoe V, Skov LK, Wilson KS. Degradation of phytate by the 6-phytase from Hafnia alvei: a combined structural and solution study. PLoS One 2013; 8:e65062. [PMID: 23741456 PMCID: PMC3669009 DOI: 10.1371/journal.pone.0065062] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 04/20/2013] [Indexed: 11/19/2022] Open
Abstract
Phytases hydrolyse phytate (myo-inositol hexakisphosphate), the principal form of phosphate stored in plant seeds to produce phosphate and lower phosphorylated myo-inositols. They are used extensively in the feed industry, and have been characterised biochemically and structurally with a number of structures in the PDB. They are divided into four distinct families: histidine acid phosphatases (HAP), β-propeller phytases, cysteine phosphatases and purple acid phosphatases and also split into three enzyme classes, the 3-, 5- and 6-phytases, depending on the position of the first phosphate in the inositol ring to be removed. We report identification, cloning, purification and 3D structures of 6-phytases from two bacteria, Hafnia alvei and Yersinia kristensenii, together with their pH optima, thermal stability, and degradation profiles for phytate. An important result is the structure of the H. alvei enzyme in complex with the substrate analogue myo-inositol hexakissulphate. In contrast to the only previous structure of a ligand-bound 6-phytase, where the 3-phosphate was unexpectedly in the catalytic site, in the H. alvei complex the expected scissile 6-phosphate (sulphate in the inhibitor) is placed in the catalytic site.
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Affiliation(s)
- Antonio Ariza
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Olga V. Moroz
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Elena V. Blagova
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Johan P. Turkenburg
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Jitka Waterman
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Shirley M. Roberts
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | | | | | | | | | | | | | - Keith S. Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
- * E-mail:
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47
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Cigarette smoke (CS) and nicotine delay neutrophil spontaneous death via suppressing production of diphosphoinositol pentakisphosphate. Proc Natl Acad Sci U S A 2013; 110:7726-31. [PMID: 23610437 DOI: 10.1073/pnas.1302906110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Diphosphoinositol pentakisphosphate (InsP7), a higher inositol phosphate containing energetic pyrophosphate bonds, is beginning to emerge as a key cellular signaling molecule. However, the various physiological and pathological processes that involve InsP7 are not completely understood. Here we report that cigarette smoke (CS) extract and nicotine reduce InsP7 levels in aging neutrophils. This subsequently leads to suppression of Akt deactivation, a causal mediator of neutrophil spontaneous death, and delayed neutrophil death. The effect of CS extract and nicotine on neutrophil death can be suppressed by either directly inhibiting the PtdIns(3,4,5)P3/Akt pathway, or increasing InsP7 levels via overexpression of InsP6K1, an inositol hexakisphosphate (InsP6) kinase responsible for InsP7 production in neutrophils. Delayed neutrophil death contributes to the pathogenesis of CS-induced chronic obstructive pulmonary disease. Therefore, disruption of InsP6K1 augments CS-induced neutrophil accumulation and lung damage. Taken together, these results suggest that CS and nicotine delay neutrophil spontaneous death by suppressing InsP7 production and consequently blocking Akt deactivation in aging neutrophils. Modifying neutrophil death via this pathway provides a strategy and therapeutic target for the treatment of tobacco-induced chronic obstructive pulmonary disease.
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The kinetic properties of a human PPIP5K reveal that its kinase activities are protected against the consequences of a deteriorating cellular bioenergetic environment. Biosci Rep 2013; 33:e00022. [PMID: 23240582 PMCID: PMC3564036 DOI: 10.1042/bsr20120115] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We obtained detailed kinetic characteristics--stoichiometry, reaction rates, substrate affinities and equilibrium conditions--of human PPIP5K2 (diphosphoinositol pentakisphosphate kinase 2). This enzyme synthesizes 'high-energy' PP-InsPs (diphosphoinositol polyphosphates) by metabolizing InsP₆ (inositol hexakisphosphate) and 5-InsP₇ (5-diphosphoinositol 1,2,3,4,6-pentakisphosphate) to 1-InsP₇ (1-diphosphoinositol 2,3,4,5,6-pentakisphosphate) and InsP₈ (1,5-bis-diphosphoinositol 2,3,4,6-tetrakisphosphate), respectively. These data increase our insight into the PPIP5K2 reaction mechanism and clarify the interface between PPIP5K catalytic activities and cellular bioenergetic status. For example, stochiometric analysis uncovered non-productive, substrate-stimulated ATPase activity (thus, approximately 2 and 1.2 ATP molecules are utilized to synthesize each molecule of 1-InsP₇ and InsP₈, respectively). Impaired ATPase activity of a PPIP5K2-K248A mutant increased atomic-level insight into the enzyme's reaction mechanism. We found PPIP5K2 to be fully reversible as an ATP-synthase in vitro, but our new data contradict previous perceptions that significant 'reversibility' occurs in vivo. PPIP5K2 was insensitive to physiological changes in either [AMP] or [ATP]/[ADP] ratios. Those data, together with adenine nucleotide kinetics (ATP Km=20-40 μM), reveal how insulated PPIP5K2 is from cellular bioenergetic challenges. Finally, the specificity constants for PPIP5K2 revise upwards by one-to-two orders of magnitude the inherent catalytic activities of this enzyme, and we show its equilibrium point favours 80-90% depletion of InsP₆/₅-InsP₇.
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Shears SB, Weaver JD, Wang H. Structural insight into inositol pyrophosphate turnover. Adv Biol Regul 2013; 53:19-27. [PMID: 23107997 PMCID: PMC3570603 DOI: 10.1016/j.jbior.2012.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 10/04/2012] [Indexed: 11/28/2022]
Abstract
The diphosphoinositol polyphosphates ("inositol pyrophosphates"; PP-InsPs) regulate many cellular processes in eukaryotes, including stress responses, apoptosis, vesicle trafficking, cytoskeletal dynamics, exocytosis, telomere maintenance, insulin signaling and neutrophil activation. Thus, the enzymes that control the metabolism of the PP-InsPs serve important cell signaling roles. In order to fully characterize how these enzymes are regulated, we need to determine the atomic-level architecture of their active sites. Only then can we fully appreciate reaction mechanisms and their modes of regulation. In this review, we summarize published information obtained from the structural analysis of a human diphosphoinositol polyphosphate phosphohydrolase (DIPP), and a human diphosphoinositol polyphosphate kinase (PPIP5K). This work includes the analysis of crystal complexes with substrates, products, transition state analogs, and a novel phosphonoacetate substrate analog.
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Affiliation(s)
- Stephen B Shears
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, PO Box 12233, NC 27709, USA.
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50
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Ganapathi SB, Wei SG, Zaremba A, Lamb FS, Shears SB. Functional regulation of ClC-3 in the migration of vascular smooth muscle cells. Hypertension 2013; 61:174-9. [PMID: 23150504 PMCID: PMC3521842 DOI: 10.1161/hypertensionaha.112.194209] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 10/22/2012] [Indexed: 12/17/2022]
Abstract
Migration of vascular smooth muscle cells (VSMCs) into neointima contributes to atherosclerosis and restenosis. This migration requires coordinated plasmalemmal fluxes of water and ions. Here, we show that aortic VSMC migration depends on the regulation of transmembrane Cl(-) flux by ClC-3, a Cl(-) channel/transporter. The contribution of ClC-3 to plasmalemmal Cl(-) current was studied in VSMCs by electrophysiological recordings. Cl(-) current was negligible in cells perfused with 0 [Ca(2+)]. Raising intracellular [Ca(2+)] to 0.5 μM activated a Cl(-) current (I(Cl.Ca)), approximately half of which was eliminated on inhibition by KN-93 of calmodulin-dependent protein kinase II. I(Cl.Ca) was also halved by inositol-3,4,5,6-tetrakisphosphate, a cellular signal with the biological function of specifically preventing calmodulin-dependent protein kinase II from activating I(Cl.Ca). Gene disruption of ClC-3 reduced I(Cl.Ca) by 50%. Moreover, I(Cl.Ca) in the ClC-3 null VSMCs was not affected by either KN-93 or inositol-3,4,5,6-tetrakisphosphate. We conclude that I(Cl.Ca) is composed of 2 components, one is ClC-3 independent whereas the other is ClC-3 dependent, activated by calmodulin-dependent protein kinase II and inhibited by inositol-3,4,5,6-tetrakisphosphate. We also assayed VSMC migration in transwell assays. Migration was halved in ClC-3 null cells versus wild-type cells. In addition, inhibition of ClC-3 by niflumic acid, KN-93, or inositol-3,4,5,6-tetrakisphosphate each reduced cell migration in wild-type cells but not in ClC-3 null cells. These cell-signaling roles of ClC-3 in VSMC migration suggest new therapeutic approaches to vascular remodeling diseases.
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MESH Headings
- Animals
- Aorta/cytology
- Aorta/drug effects
- Aorta/metabolism
- Benzylamines/pharmacology
- Calcium-Calmodulin-Dependent Protein Kinase Type 2/antagonists & inhibitors
- Cell Movement/drug effects
- Cell Movement/physiology
- Cells, Cultured
- Chloride Channels/genetics
- Chloride Channels/metabolism
- Inositol Phosphates/pharmacology
- Mice
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Myocytes, Smooth Muscle/cytology
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/metabolism
- Niflumic Acid/pharmacology
- Protein Kinase Inhibitors/pharmacology
- Signal Transduction/drug effects
- Signal Transduction/physiology
- Sulfonamides/pharmacology
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Affiliation(s)
- Sindura B. Ganapathi
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, PO Box 12233, NC 27709, USA
| | - Shun-Guang Wei
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, PO Box 12233, NC 27709, USA
| | - Angelika Zaremba
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, PO Box 12233, NC 27709, USA
| | - Fred S. Lamb
- Department of Pediatrics, University of Iowa Children’s Hospital, Iowa City, Iowa 52242, USA
| | - Stephen B. Shears
- Inositol Signaling Group, Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, PO Box 12233, NC 27709, USA
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