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Qiao K, Lv J, Hao J, Zhao C, Fan S, Ma Q. Identification of cotton PIP5K genes and role of GhPIP5K9a in primary root development. Gene 2024; 921:148532. [PMID: 38705423 DOI: 10.1016/j.gene.2024.148532] [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: 12/15/2023] [Revised: 04/24/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Phosphatidylinositol 4 phosphate 5-kinase (PIP5K) is crucial for the phosphatidylinositol (PI) signaling pathway. It plays a significant role in plant growth and development, as well as stress response. However, its effects on cotton are unknown. This study identified PIP5K genes from four cotton species and conducted bioinformatic analyses, with a particular emphasis on the functions of GhPIP5K9a in primary roots. The results showed that cotton PIP5Ks were classified into four subgroups. Analysis of gene structure and motif composition showed obvious conservation within each subgroup. Synteny analysis suggested that the PIP5K gene family experienced significant expansion due to both whole-genome duplication (WGD) and segmental duplication. Transcriptomic data analysis revealed that the majority of GhPIP5K genes had the either low or undetectable levels of expression. Moreover, GhPIP5K9a is highly expressed in the root and was located in plasmalemma. Suppression of GhPIP5K9a transcripts resulted in longer primary roots, longer primary root cells and increased auxin polar transport-related genes expression, and decreased abscisic acid (ABA) content, indicating that GhPIP5K9a negatively regulates cotton primary root growth. This study lays the foundation for further exploration of the role of the PIP5K genes in cotton.
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Affiliation(s)
- Kaikai Qiao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Jiaoyan Lv
- Anyang Academy of Agricultural Sciences, Anyang 455000, China
| | - Juxin Hao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China
| | - Chenglong Zhao
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China
| | - Shuli Fan
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.
| | - Qifeng Ma
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.
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Ratchatasunthorn A, Sakagami H, Kondo H, Hipkaeo W, Chomphoo S. Temporal involvement of phosphatidylinositol 4-phosphate 5-kinase γ in differentiation of Z-bands and myofilament bundles as well as intercalated discs in mouse heart at mid-gestation. J Anat 2024; 244:1030-1039. [PMID: 38275211 PMCID: PMC11095301 DOI: 10.1111/joa.14008] [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: 08/12/2023] [Revised: 12/25/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
Considering the occurrence of serious heart failure in a gene knockout mouse of PIP5Kγ and in congenital abnormal cases in humans in which the gene was defective as reported by others, the present study attempted to localize PIP5Kγ in the heart during prenatal stages. It was done on the basis of the supposition that phenotypes caused by gene mutation of a given molecule are owed to the functional deterioration of selective cellular sites normally expressing it at significantly higher levels in wild mice. PIP5Kγ-immunoreactivity was the highest in the heart at E10 in contrast to almost non-significant levels of the immunoreactivity in surrounding organs and tissues such as liver. The immunoreactivity gradually weakened in the heart with the prenatal age, and it was at non-significant levels at newborn and postnatal stages. Six patterns in localization of distinct immunoreactivity for PIP5Kγ were recognized in cardiomyocytes: (1) its localization on the plasma membranes and subjacent cytoplasm without association with short myofibrils and (2) its localization on them as well as short myofibrils in association with them in cardiomyocytes of early differentiation at E10; (3) its spot-like localization along long myofibrils in cardiomyocytes of advanced differentiation at E10; (4) rare occurrences of such spot-like localization along long myofibrils in cardiomyocytes of advanced differentiation at E14; (5) its localization at Z-bands of long myofibrils; and (6) its localization at intercellular junctions including the intercalated discs in cardiomyocytes of advanced differentiation at E10 and E14, especially dominant at the latter stage. No distinct localization of PIP5Kγ-immunoreactivity of any patterns was seen in the heart at E18 and P1D. The present finding suggests that sites of PIP5Kγ-appearance and probably of its high activity in cardiomyocytes are shifted from the plasma membranes through short myofibrils subjacent to the plasma membranes and long myofibrils, to Z-bands as well as to the intercalated discs during the mid-term gestation. It is further suggested that PIP5Kγ is involved in the differentiation of myofibrils as well as intercellular junctions including the intercalated discs at later stages of the mid-term gestation. Failures in its involvement in the differentiation of these structural components are thus likely to cause the mid-term gestation lethality of the mutant mice for PIP5Kγ.
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Affiliation(s)
- A Ratchatasunthorn
- Electron Microscopy Unit, Department of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - H Sakagami
- Department of Anatomy, School of Medicine, Kitasato University, Sagamihara, Japan
| | - H Kondo
- Electron Microscopy Unit, Department of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Department of Anatomy, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - W Hipkaeo
- Electron Microscopy Unit, Department of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - S Chomphoo
- Electron Microscopy Unit, Department of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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Jensen TD, Ni B, Reuter CM, Gorzynski JE, Fazal S, Bonner D, Ungar RA, Goddard PC, Raja A, Ashley EA, Bernstein JA, Zuchner S, Greicius MD, Montgomery SB, Schatz MC, Wheeler MT, Battle A. Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.22.24304565. [PMID: 38585781 PMCID: PMC10996727 DOI: 10.1101/2024.03.22.24304565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that don't incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression towards improving the prioritization of functional SVs and TREs in rare disease patients.
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Zhang F, Guo H, Zhou X, Deng Z, Xu Q, Wang Q, Yuan H, Luo J. Novel PIP5K1C variant identified in a Chinese pedigree with lethal congenital contractural syndrome 3. BMC Pediatr 2024; 24:182. [PMID: 38491417 PMCID: PMC10941444 DOI: 10.1186/s12887-024-04674-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Biallelic pathogenic variants in PIP5K1C (MIM #606,102) lead to lethal congenital contractural syndrome 3 (LCCS3, MIM #611,369), a rare autosomal recessive genetic disorder characterized by small gestational age, severe multiple joint contractures and muscle atrophy, early death due to respiratory failure. Currently, 5 individuals with LCCS3 were reported and 5 pathogenic variants in PIP5K1C were identified. Here, we reported the two fetuses in a Chinese pedigree who displayed multiple joint contractures and other congenital anomalies. METHODS Trio-based whole-exome sequencing (WES) was performed for the parents and the recent fetus to detect the genetic cause for fetus phenotype. RESULTS A novel variant, NM_012398.3: c.949_952dup, p.S318Ifs*28 and a previously reported variant, c.688_689del, p.G230Qfs*114 (ClinVar database) in PIP5K1C, were detected in the individuals, and these variants were inherited from the mother and father, respectively. We described the features of multiple joint contractures in our fetuses, including bilateral talipes equinovarus, stiffness in the limbs, extended knees, persistently closed hands and overlapping fingers, which have not been delineated detailedly in previously reported LCCS3 individuals. Furthermore, novel phenotype, bilateral dilated lateral ventricles, was revealed in one fetus. CONCLUSIONS These findings expanded the genetic variant spectrum of PIP5K1C and enriched the clinical features of LCCS3, which will help with the prenatal diagnosis and genetic counseling for this family.
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Affiliation(s)
- Fang Zhang
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Hongmei Guo
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Xinlong Zhou
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
- Key Laboratory for Precision Diagnosis and Treatment of Severe Infectious Diseases in Children, Dongguan, 523120, China
| | - Zhengxi Deng
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Qiuhong Xu
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Qingming Wang
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
- Department of Medical Genetics, Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Haiming Yuan
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.
- Department of Medical Genetics, Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.
| | - Jianhua Luo
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.
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Lin S, Tao C, Yan Q, Gao H, Qin L, Zhong Y, Yao Q, Zhang P, Yang J, Zou X, Xiao G. Pip5k1c expression in osteocytes regulates bone remodeling in mice. J Orthop Translat 2024; 45:36-47. [PMID: 38495744 PMCID: PMC10943313 DOI: 10.1016/j.jot.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 03/19/2024] Open
Abstract
Research background The role of osteocytes in maintaining bone mass has been progressively emphasized. Pip5k1c is the most critical isoform among PIP5KIs, which can regulate cytoskeleton, biomembrane, and Ca2+ release of cells and participate in many processes, such as cell adhesion, differentiation, and apoptosis. However, its expression and function in osteocytes are still unclear. Materials and methods To determine the function of Pip5k1c in osteocytes, the expression of Pip5k1c in osteocytes was deleted by breeding the 10-kb mouse Dmp1-Cre transgenic mice with the Pip5k1cfl/fl mice. Bone histomorphometry, micro-computerized tomography analysis, immunofluorescence staining and western blotting were used to determine the effects of Pip5k1c loss on bone mass. In vitro, we explored the mechanism by siRNA knockdown of Pip5k1c in MLO-Y4 cells. Results Pip5k1c expression was decreased in osteocytes in senescent and osteoporotic tissues both in humans and mice. Loss of Pip5k1c in osteocytes led to a low bone mass in long bones and spines and impaired biomechanical properties in femur, without changes in calvariae. The loss of Pip5k1c resulted in the reduction of the protein level of type 1 collagen in tibiae and MLO-Y4 cells. Osteocyte Pip5k1c loss reduced the osteoblast and bone formation rate with high expression of sclerostin, impacting the osteoclast activities at the same time. Moreover, Pip5k1c loss in osteocytes reduced expression of focal adhesion proteins and promoted apoptosis. Conclusion Our studies demonstrate the critical role and mechanism of Pip5k1c in osteocytes in regulating bone remodeling. The translational potential of this article Osteocyte has been considered to a key role in regulating bone homeostasis. The present study has demonstrated that the significance of Pip5k1c in bone homeostasis by regulating the expression of collagen, sclerostin and focal adhesion expression, which provided a possible therapeutic target against human metabolic bone disease.
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Affiliation(s)
- Sixiong Lin
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Department of Spinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, 518055, China
| | - Chu Tao
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, 518055, China
| | - Qinnan Yan
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, 518055, China
| | - Huanqing Gao
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Qin
- Department of Orthopedics, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, 518000, China
| | - Yiming Zhong
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, 518055, China
| | - Qing Yao
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, 518055, China
| | - Peijun Zhang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, 518055, China
| | - Jiaming Yang
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, 518055, China
- Department of Orthopaedics & Traumatology, Stem Cells and Regenerative Medicine Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, China
| | - Xuenong Zou
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Department of Spinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510080, China
| | - Guozhi Xiao
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, 518055, China
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Hernández-Cáceres MP, Pinto-Nuñez D, Rivera P, Burgos P, Díaz-Castro F, Criollo A, Yañez MJ, Morselli E. Role of lipids in the control of autophagy and primary cilium signaling in neurons. Neural Regen Res 2024; 19:264-271. [PMID: 37488876 PMCID: PMC10503597 DOI: 10.4103/1673-5374.377414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/09/2023] [Accepted: 04/27/2023] [Indexed: 07/26/2023] Open
Abstract
The brain is, after the adipose tissue, the organ with the greatest amount of lipids and diversity in their composition in the human body. In neurons, lipids are involved in signaling pathways controlling autophagy, a lysosome-dependent catabolic process essential for the maintenance of neuronal homeostasis and the function of the primary cilium, a cellular antenna that acts as a communication hub that transfers extracellular signals into intracellular responses required for neurogenesis and brain development. A crosstalk between primary cilia and autophagy has been established; however, its role in the control of neuronal activity and homeostasis is barely known. In this review, we briefly discuss the current knowledge regarding the role of autophagy and the primary cilium in neurons. Then we review the recent literature about specific lipid subclasses in the regulation of autophagy, in the control of primary cilium structure and its dependent cellular signaling in physiological and pathological conditions, specifically focusing on neurons, an area of research that could have major implications in neurodevelopment, energy homeostasis, and neurodegeneration.
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Affiliation(s)
- María Paz Hernández-Cáceres
- Instituto de Investigación en Ciencias Odontológicas (ICOD), Facultad de Odontología, Universidad de Chile, Santiago, Chile
- Department of Basic Sciences, Faculty of Medicine and Science, Universidad San Sebastián, Santiago, Chile
| | - Daniela Pinto-Nuñez
- Department of Basic Sciences, Faculty of Medicine and Science, Universidad San Sebastián, Santiago, Chile
| | - Patricia Rivera
- Department of Basic Sciences, Faculty of Medicine and Science, Universidad San Sebastián, Santiago, Chile
- Physiology Department, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paulina Burgos
- Department of Basic Sciences, Faculty of Medicine and Science, Universidad San Sebastián, Santiago, Chile
| | - Francisco Díaz-Castro
- Department of Basic Sciences, Faculty of Medicine and Science, Universidad San Sebastián, Santiago, Chile
- Physiology Department, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alfredo Criollo
- Instituto de Investigación en Ciencias Odontológicas (ICOD), Facultad de Odontología, Universidad de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Facultad de Ciencias Químicas y Farmacéuticas & Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Autophagy Research Center, Santiago, Chile
| | - Maria Jose Yañez
- Department of Basic Sciences, Faculty of Medicine and Science, Universidad San Sebastián, Santiago, Chile
| | - Eugenia Morselli
- Department of Basic Sciences, Faculty of Medicine and Science, Universidad San Sebastián, Santiago, Chile
- Autophagy Research Center, Santiago, Chile
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Ling P, Ju J, Zhang X, Wei W, Luo J, Li Y, Hai H, Shang B, Cheng H, Wang C, Zhang X, Su J. The Silencing of GhPIP5K2 and GhPIP5K22 Weakens Abiotic Stress Tolerance in Upland Cotton ( Gossypium hirsutum). Int J Mol Sci 2024; 25:1511. [PMID: 38338791 PMCID: PMC10855785 DOI: 10.3390/ijms25031511] [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: 11/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 02/12/2024] Open
Abstract
Phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks), essential enzymes in the phosphatidylinositol signaling pathway, are crucial for the abiotic stress responses and the overall growth and development of plants. However, the GhPIP5Ks had not been systematically studied, and their function in upland cotton was unknown. This study identified a total of 28 GhPIP5Ks, and determined their chromosomal locations, gene structures, protein motifs and cis-acting elements via bioinformatics analysis. A quantitative real-time PCR (qRT‒PCR) analysis showed that most GhPIP5Ks were upregulated under different stresses. A virus-induced gene silencing (VIGS) assay indicated that the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities were significantly decreased, while malondialdehyde (MDA) content were significantly increased in GhPIP5K2- and GhPIP5K22-silenced upland cotton plants under abiotic stress. Furthermore, the expression of the stress marker genes GhHSFB2A, GhHSFB2B, GhDREB2A, GhDREB2C, GhRD20-1, GhRD29A, GhBIN2, GhCBL3, GhNHX1, GhPP2C, GhCBF1, GhSnRK2.6 and GhCIPK6 was significantly decreased in the silenced plants after exposure to stress. These results revealed that the silencing of GhPIP5K2 and GhPIP5K22 weakened the tolerance to abiotic stresses. These discoveries provide a foundation for further inquiry into the actions of the GhPIP5K gene family in regulating the response and resistance mechanisms of cotton to abiotic stresses.
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Affiliation(s)
- Pingjie Ling
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Jisheng Ju
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Xueli Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Wei Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Jin Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Ying Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Han Hai
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Bowen Shang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Hongbo Cheng
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Caixiang Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Xianliang Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
| | - Junji Su
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
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Wang Z, Wang Z, Li X, Chen Z, Liu Y, Zhang F, Dai Q, Yu Q, Li N. Identification and Analysis of the Expression of the PIP5K Gene Family in Tomatoes. Int J Mol Sci 2023; 25:159. [PMID: 38203328 PMCID: PMC10778592 DOI: 10.3390/ijms25010159] [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: 11/10/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
To explore the function of phosphatidylinositol 4-phosphate 5-kinase (PIP5K) in tomatoes, members of the tomato PIP5K family were identified and characterized using bioinformatic methods, and their expression patterns were also analyzed under salt stress and in different tissues. Twenty-one PIP5K members-namely, SlPIP5K1-SlPIP5K21-were identified from ten chromosomes, and these were divided into three groups according to a phylogenetic analysis. Further bioinformatic analysis showed four pairs of collinear relationships and fragment replication events among the SlPIP5K family members. To understand the possible roles of the SlPIP5Ks, a cis-acting element analysis was conducted, which indicated that tomato PIP5Ks could be associated with plant growth, hormones, and stress responses. We further validated the results of the in silico analysis by integrating RNA-seq and qRT-PCR techniques for salt- and hormone-treated tomato plants. Our results showed that SlPIP5K genes exhibited tissue- and treatment-specific patterns, and some of the SlPIP5Ks exhibited significantly altered expressions after our treatments, suggesting that they might be involved in these stresses. We selected one of the SlPIP5Ks that responded to our treatments, SlPIP5K2, to further understand its subcellular localization. Our results showed that SlPIP5K2 was located on the membrane. This study lays a foundation for the analysis of the biological functions of the tomato SlPIP5K genes and can also provide a theoretical basis for the selection and breeding of new tomato varieties and germplasm innovation, especially under salt stress.
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Affiliation(s)
- Zepeng Wang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Zhongyu Wang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Xianguo Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Zhaolong Chen
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yuxiang Liu
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Fulin Zhang
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Qi Dai
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Qinghui Yu
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Ning Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
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9
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Wills RC, Doyle CP, Zewe JP, Pacheco J, Hansen SD, Hammond GRV. A novel homeostatic mechanism tunes PI(4,5)P2-dependent signaling at the plasma membrane. J Cell Sci 2023; 136:jcs261494. [PMID: 37534432 PMCID: PMC10482388 DOI: 10.1242/jcs.261494] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023] Open
Abstract
The lipid molecule phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] controls all aspects of plasma membrane (PM) function in animal cells, from its selective permeability to the attachment of the cytoskeleton. Although disruption of PI(4,5)P2 is associated with a wide range of diseases, it remains unclear how cells sense and maintain PI(4,5)P2 levels to support various cell functions. Here, we show that the PIP4K family of enzymes, which synthesize PI(4,5)P2 via a minor pathway, also function as sensors of tonic PI(4,5)P2 levels. PIP4Ks are recruited to the PM by elevated PI(4,5)P2 levels, where they inhibit the major PI(4,5)P2-synthesizing PIP5Ks. Perturbation of this simple homeostatic mechanism reveals differential sensitivity of PI(4,5)P2-dependent signaling to elevated PI(4,5)P2 levels. These findings reveal that a subset of PI(4,5)P2-driven functions might drive disease associated with disrupted PI(4,5)P2 homeostasis.
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Affiliation(s)
- Rachel C. Wills
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Colleen P. Doyle
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - James P. Zewe
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Jonathan Pacheco
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Scott D. Hansen
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA
| | - Gerald R. V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
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10
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Morleo M, Venditti R, Theodorou E, Briere LC, Rosello M, Tirozzi A, Tammaro R, Al-Badri N, High FA, Shi J, Putti E, Ferrante L, Cetrangolo V, Torella A, Walker MA, Tenconi R, Iascone M, Mei D, Guerrini R, van der Smagt J, Kroes HY, van Gassen KLI, Bilal M, Umair M, Pingault V, Attie-Bitach T, Amiel J, Ejaz R, Rodan L, Zollino M, Agrawal PB, Del Bene F, Nigro V, Sweetser DA, Franco B. De novo missense variants in phosphatidylinositol kinase PIP5KIγ underlie a neurodevelopmental syndrome associated with altered phosphoinositide signaling. Am J Hum Genet 2023; 110:1377-1393. [PMID: 37451268 PMCID: PMC10432144 DOI: 10.1016/j.ajhg.2023.06.012] [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: 01/24/2023] [Revised: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Phosphoinositides (PIs) are membrane phospholipids produced through the local activity of PI kinases and phosphatases that selectively add or remove phosphate groups from the inositol head group. PIs control membrane composition and play key roles in many cellular processes including actin dynamics, endosomal trafficking, autophagy, and nuclear functions. Mutations in phosphatidylinositol 4,5 bisphosphate [PI(4,5)P2] phosphatases cause a broad spectrum of neurodevelopmental disorders such as Lowe and Joubert syndromes and congenital muscular dystrophy with cataracts and intellectual disability, which are thus associated with increased levels of PI(4,5)P2. Here, we describe a neurodevelopmental disorder associated with an increase in the production of PI(4,5)P2 and with PI-signaling dysfunction. We identified three de novo heterozygous missense variants in PIP5K1C, which encodes an isoform of the phosphatidylinositol 4-phosphate 5-kinase (PIP5KIγ), in nine unrelated children exhibiting intellectual disability, developmental delay, acquired microcephaly, seizures, visual abnormalities, and dysmorphic features. We provide evidence that the PIP5K1C variants result in an increase of the endosomal PI(4,5)P2 pool, giving rise to ectopic recruitment of filamentous actin at early endosomes (EEs) that in turn causes dysfunction in EE trafficking. In addition, we generated an in vivo zebrafish model that recapitulates the disorder we describe with developmental defects affecting the forebrain, including the eyes, as well as craniofacial abnormalities, further demonstrating the pathogenic effect of the PIP5K1C variants.
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Affiliation(s)
- Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy.
| | - Rossella Venditti
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II," Medical School, Naples, Italy
| | - Evangelos Theodorou
- Center for Genomic Medicine, Divisions of Pediatric Hematology/Oncology and Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren C Briere
- Center for Genomic Medicine, Divisions of Pediatric Hematology/Oncology and Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Marion Rosello
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France
| | - Alfonsina Tirozzi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy; Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
| | - Roberta Tammaro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Nour Al-Badri
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France
| | - Frances A High
- Division of Medical Genetics & Metabolism, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Jiahai Shi
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Elena Putti
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France
| | - Luigi Ferrante
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Viviana Cetrangolo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - Melissa A Walker
- Department of Neurology, Division of Neurogenetics, Child Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Romano Tenconi
- Clinical Genetics Unit, Department of Women and Children's Health, University of Padova, Padova, Italy
| | - Maria Iascone
- Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Davide Mei
- Meyer Children's Hospital IRCCS, Neuroscience Department, Florence, Italy
| | - Renzo Guerrini
- Meyer Children's Hospital IRCCS, Neuroscience Department, Florence, Italy
| | - Jasper van der Smagt
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hester Y Kroes
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Muhammad Bilal
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center & King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Veronica Pingault
- Service de Médecine Génomique des Maladies Rares, et Institut Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | - Tania Attie-Bitach
- Service de Médecine Génomique des Maladies Rares, et Institut Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | - Jeannine Amiel
- Service de Médecine Génomique des Maladies Rares, et Institut Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | - Resham Ejaz
- Division of Genetics, Department of Pediatrics, McMaster Children's Hospital, Hamilton, ON, Canada
| | - Lance Rodan
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Marcella Zollino
- Institute of Medical Genetics, A. Gemelli School of Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Pankaj B Agrawal
- Divisions of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA; Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Filippo Del Bene
- Sorbonne Université, INSERM U968, CNRS UMR 7210, Institut de la Vision, Paris, France
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Department of Precision Medicine, University of Campania "Luigi Vanvitelli," Naples, Italy
| | - David A Sweetser
- Center for Genomic Medicine, Divisions of Pediatric Hematology/Oncology and Medical Genetics and Metabolism, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy; Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, Naples, Italy; Medical Genetics, Department of Translational Medicine, University of Naples "Federico II," Via Sergio Pansini, 80131 Naples, Italy
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11
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Bura A, Čabrijan S, Đurić I, Bruketa T, Jurak Begonja A. A Plethora of Functions Condensed into Tiny Phospholipids: The Story of PI4P and PI(4,5)P 2. Cells 2023; 12:1411. [PMID: 37408244 DOI: 10.3390/cells12101411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 07/07/2023] Open
Abstract
Phosphoinositides (PIs) are small, phosphorylated lipids that serve many functions in the cell. They regulate endo- and exocytosis, vesicular trafficking, actin reorganization, and cell mobility, and they act as signaling molecules. The most abundant PIs in the cell are phosphatidylinositol-4-monophosphate (PI4P) and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. PI4P is mostly localized at the Golgi apparatus where it regulates the anterograde trafficking from the Golgi apparatus to the plasma membrane (PM), but it also localizes at the PM. On the other hand, the main localization site of PI(4,5)P2 is the PM where it regulates the formation of endocytic vesicles. The levels of PIs are regulated by many kinases and phosphatases. Four main kinases phosphorylate the precursor molecule phosphatidylinositol into PI4P, divided into two classes (PI4KIIα, PI4KIIβ, PI4KIIIα, and PI4KIIIβ), and three main kinases phosphorylate PI4P to form PI(4,5)P2 (PI4P5KIα, PI4P5KIβ, and PI4P5KIγ). In this review, we discuss the localization and function of the kinases that produce PI4P and PI(4,5)P2, as well as the localization and function of their product molecules with an overview of tools for the detection of these PIs.
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Affiliation(s)
- Ana Bura
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Sara Čabrijan
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Iris Đurić
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Tea Bruketa
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
| | - Antonija Jurak Begonja
- Laboratory of Hematopoiesis, Department of Biotechnology, University of Rijeka, R. Matejcic 2, 51000 Rijeka, Croatia
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12
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Hipkaeo W, Kondo H. Localization of phospholipid-related signal molecules in salivary glands of rodents: A review. J Oral Biosci 2023; 65:146-155. [PMID: 37061129 DOI: 10.1016/j.job.2023.04.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/08/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023]
Abstract
BACKGROUND In the 1950s, Hokin conducted initial studies on phosphoinositide turnover/cycle in salivary glandular cells. From these studies, the idea emerged that receptor-mediated changes in intramembranous levels of phosphoinositides represent an early step in the stimulus-response pathway. Based on this idea and the general view that knowledge of the exact localization of a given endogenous molecule in cells in situ is important for understanding its functional significance, we have reviewed available information about the localization of several representative phosphoinositide-signaling molecules in the salivary glands in situ in mice. HIGHLIGHT We focused on phosphatidylinositol 4-kinase, phosphatidylinositol 4 phosphate 5-kinase α, β, γ, phospholipase Cβ, muscarinic cholinoceptors 1 and 3, diacylglycerol kinase ζ, phospholipase D1 and 2, ADP-ribosylation factor 6 and its exchange factors for Arf6, and cannabinoid receptors. These molecules individually exhibit differential localization in a spatiotemporal manner in the exocrine glands, making it possible to deduce their functional significance, such as their involvement in secretion and cell differentiation. CONCLUSION Although phosphoinositide-signaling molecules whose in situ localization in glandular cells has been clarified are still limited, the obtained information on their localization suggests that their functional significance is more valuable in glandular ducts than in acini. It thus suggests the necessity of greater attention to the ducts in their physio-pharmacological analyses. The purpose of this review is to encourage more in situ localization studies of phosphoinositide-signaling molecules with an aim to further understand their possible involvement in the pathogenesis of salivary gland diseases.
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Affiliation(s)
- Wiphawi Hipkaeo
- Electron Microscopy Laboratory, Division of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
| | - Hisatake Kondo
- Electron Microscopy Laboratory, Division of Anatomy, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Department of Anatomy, Graduate School of Medicine, Tohoku University, Sendai, JAPAN
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13
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Llorente A, Arora GK, Grenier SF, Emerling BM. PIP kinases: A versatile family that demands further therapeutic attention. Adv Biol Regul 2023; 87:100939. [PMID: 36517396 PMCID: PMC9992244 DOI: 10.1016/j.jbior.2022.100939] [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: 11/21/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Phosphoinositides are membrane-localized phospholipids that regulate a plethora of essential cellular processes. These lipid signaling molecules are critical for cell homeostasis and therefore their levels are strictly regulated by the coordinated action of several families of lipid kinases and phosphatases. In this review, we provide a focused perspective on the phosphatidylinositol phosphate kinase (PIPK) family and the three subfamilies that compose it: Type I PIPKs or phosphatidylinositol-4-phosphate 5-kinases (PI4P5Ks), Type II PIPKs or phosphatidylinositol-5-phosphate 4-kinases (PI5P4Ks), and Type III PIPKs or phosphatidylinositol-3-phosphate 5-kinases (PIKfyve). Each subfamily is responsible for catalyzing a hydroxyl phosphorylation on specific phosphoinositide species to generate a double phosphorylated lipid, therefore regulating the levels of both substrate and product. Here, we summarize our current knowledge about the functions and regulation of each PIPK subfamily. Further, we highlight the roles of these kinases in various in vivo genetic models and give an overview of their involvement in multiple pathological conditions. The phosphoinositide field has been long focused on targeting PI3K signaling, but growing evidence suggests that it is time to draw attention to the other phosphoinositide kinases. The discovery of the involvement of PIPKs in the pathogenesis of multiple diseases has prompted substantial efforts to turn these enzymes into pharmacological targets. An increasingly refined knowledge of the biology of PIPKs in a variety of in vitro and in vivo models will facilitate the development of effective approaches for therapeutic intervention with the potential to translate into meaningful clinical benefits for patients suffering from cancer, immunological and infectious diseases, and neurodegenerative disorders.
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Affiliation(s)
- Alicia Llorente
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Gurpreet K Arora
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Shea F Grenier
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA
| | - Brooke M Emerling
- Cell and Molecular Biology of Cancer Program, Sanford Burnham Prebys, La Jolla, CA, 92037, USA.
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14
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Chen C, Hu J, Ling K. The Role of Primary Cilia-Associated Phosphoinositide Signaling in Development. J Dev Biol 2022; 10:51. [PMID: 36547473 PMCID: PMC9785882 DOI: 10.3390/jdb10040051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/07/2022] Open
Abstract
Primary cilia are microtube-based organelles that extend from the cell surface and function as biochemical and mechanical extracellular signal sensors. Primary cilia coordinate a series of signaling pathways during development. Cilia dysfunction leads to a pleiotropic group of developmental disorders, termed ciliopathy. Phosphoinositides (PIs), a group of signaling phospholipids, play a crucial role in development and tissue homeostasis by regulating membrane trafficking, cytoskeleton reorganization, and organelle identity. Accumulating evidence implicates the involvement of PI species in ciliary defects and ciliopathies. The abundance and localization of PIs in the cell are tightly regulated by the opposing actions of kinases and phosphatases, some of which are recently discovered in the context of primary cilia. Here, we review several cilium-associated PI kinases and phosphatases, including their localization along cilia, function in regulating the ciliary biology under normal conditions, as well as the connection of their disease-associated mutations with ciliopathies.
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Affiliation(s)
- Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - Jinghua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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15
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Wills RC, Hammond GRV. PI(4,5)P2: signaling the plasma membrane. Biochem J 2022; 479:2311-2325. [PMID: 36367756 PMCID: PMC9704524 DOI: 10.1042/bcj20220445] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022]
Abstract
In the almost 70 years since the first hints of its existence, the phosphoinositide, phosphatidyl-D-myo-inositol 4,5-bisphosphate has been found to be central in the biological regulation of plasma membrane (PM) function. Here, we provide an overview of the signaling, transport and structural roles the lipid plays at the cell surface in animal cells. These include being substrate for second messenger generation, direct modulation of receptors, control of membrane traffic, regulation of ion channels and transporters, and modulation of the cytoskeleton and cell polarity. We conclude by re-evaluating PI(4,5)P2's designation as a signaling molecule, instead proposing a cofactor role, enabling PM-selective function for many proteins.
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Affiliation(s)
- Rachel C. Wills
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Gerald R. V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
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16
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Abstract
Phosphoinositides are signalling lipids derived from phosphatidylinositol, a ubiquitous phospholipid in the cytoplasmic leaflet of eukaryotic membranes. Initially discovered for their roles in cell signalling, phosphoinositides are now widely recognized as key integrators of membrane dynamics that broadly impact on all aspects of cell physiology and on disease. The past decade has witnessed a vast expansion of our knowledge of phosphoinositide biology. On the endocytic and exocytic routes, phosphoinositides direct the inward and outward flow of membrane as vesicular traffic is coupled to the conversion of phosphoinositides. Moreover, recent findings on the roles of phosphoinositides in autophagy and the endolysosomal system challenge our view of lysosome biology. The non-vesicular exchange of lipids, ions and metabolites at membrane contact sites in between organelles has also been found to depend on phosphoinositides. Here we review our current understanding of how phosphoinositides shape and direct membrane dynamics to impact on cell physiology, and provide an overview of emerging concepts in phosphoinositide regulation.
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17
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Chomphoo S, Sakagami H, Kondo H, Hipkaeo W. Localization of PIP5Kγ selectively in proprioceptive peripheral fields and also in sensory ganglionic satellite cells as well as neuronal cell membranes and their central terminals. J Anat 2021; 239:1196-1206. [PMID: 34151437 PMCID: PMC8546504 DOI: 10.1111/joa.13491] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/10/2021] [Accepted: 06/04/2021] [Indexed: 12/14/2022] Open
Abstract
Based on a previous study by others reporting that PIP5Kγ (phosphatidylinositol 4-phosphate 5-kinase γ) and its product, phosphatidylinositol 4,5 bisphosphate (PIP2 ), are involved in the regulation of nociception, the present immunohistochemical study examined the localization of PIP5Kγ-immunoreactivity in dorsal root ganglia (DRG) and their peripheral and central terminal fields. PIP5Kγ-immunoreactivity was localized for the first time in the muscle spindles, in which it was found in I-bands of polar regions of intrafusal muscle fibers and also in sensory nerve terminals abutting on equatorial regions of the muscle fibers. This finding indicates the involvement of PIP5Kγ in the proprioception and suggests somehow complicated mechanisms of its involvement because of its heterogeneous localization in intra-I-band structures. In DRG, on the other hand, PIP5Kγ-immunoreactivity was shown to be localized heterogeneously, but not evenly, over apposed plasma membranes of both neurons and ganglionic satellite cells in immune electron microscopy. In addition, no peripheral nerve terminals of DRG showing its distinct immunoreactivity were found in most peripheral fields of nociception and any other sensory perception except for the proprioception through muscle spindles. In contrast, numerous central terminals of DRG in the spinal posterior horn were immunoreactive for it. This finding leads us to consider the possibility that the regulation by PIP5Kγ of nociception is dominantly exerted in DRG and sensory neural tracts central, rather than peripheral, to DRG.
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Affiliation(s)
- Surang Chomphoo
- Electron Microscopy UnitDepartment of AnatomyFaculty of MedicineKhon Kaen UniversityKhon KaenThailand
| | - Hiroyuki Sakagami
- Department of AnatomySchool of MedicineKitasato UniversitySagamiharaJapan
| | - Hisatake Kondo
- Electron Microscopy UnitDepartment of AnatomyFaculty of MedicineKhon Kaen UniversityKhon KaenThailand
- Department of AnatomyGraduate School of MedicineTohoku UniversitySendaiJapan
| | - Wiphawi Hipkaeo
- Electron Microscopy UnitDepartment of AnatomyFaculty of MedicineKhon Kaen UniversityKhon KaenThailand
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18
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Whittle J, Johnson A, Dobbs MB, Gurnett CA. Models of Distal Arthrogryposis and Lethal Congenital Contracture Syndrome. Genes (Basel) 2021; 12:genes12060943. [PMID: 34203046 PMCID: PMC8234565 DOI: 10.3390/genes12060943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 12/28/2022] Open
Abstract
Distal arthrogryposis and lethal congenital contracture syndromes describe a broad group of disorders that share congenital limb contractures in common. While skeletal muscle sarcomeric genes comprise many of the first genes identified for Distal Arthrogyposis, other mechanisms of disease have been demonstrated, including key effects on peripheral nerve function. While Distal Arthrogryposis and Lethal Congenital Contracture Syndromes display superficial similarities in phenotype, the underlying mechanisms for these conditions are diverse but overlapping. In this review, we discuss the important insights gained into these human genetic diseases resulting from in vitro molecular studies and in vivo models in fruit fly, zebrafish, and mice.
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Affiliation(s)
- Julia Whittle
- Department of Neurology, Washington University in St Louis, St Louis, MO 63130, USA;
| | - Aaron Johnson
- Department of Developmental Biology, Washington University in St Louis, St Louis, MO 63130, USA;
| | - Matthew B. Dobbs
- Paley Orthopaedic and Spine Institute, West Palm Beach, FL 33407, USA;
| | - Christina A. Gurnett
- Department of Neurology, Washington University in St Louis, St Louis, MO 63130, USA;
- Correspondence:
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Chen C, Xu Q, Zhang Y, Davies BA, Huang Y, Katzmann DJ, Harris PC, Hu J, Ling K. Ciliopathy protein HYLS1 coordinates the biogenesis and signaling of primary cilia by activating the ciliary lipid kinase PIPKIγ. SCIENCE ADVANCES 2021; 7:7/26/eabe3401. [PMID: 34162535 PMCID: PMC8221637 DOI: 10.1126/sciadv.abe3401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/10/2021] [Indexed: 05/04/2023]
Abstract
Mutation of ciliopathy protein HYLS1 causes the perinatal lethal hydrolethalus syndrome (HLS), yet the underlying molecular etiology and pathogenesis remain elusive. Here, we reveal unexpected mechanistic insights into the role of mammalian HYLS1 in regulating primary cilia. HYLS1 is recruited to the ciliary base via a direct interaction with the type Iγ phosphatidylinositol 4-phosphate [PI(4)P] 5-kinase (PIPKIγ). HYLS1 activates PIPKIγ by interrupting the autoinhibitory dimerization of PIPKIγ, which thereby expedites depletion of centrosomal PI(4)P to allow axoneme nucleation. HYLS1 deficiency interrupts the assembly of ciliary NPHP module and agonist-induced ciliary exit of β-arrestin, which, in turn, disturbs the removal of ciliary Gpr161 and activation of hedgehog (Hh) signaling. Consistent with this model of pathogenesis, the HLS mutant HYLS1D211G supports ciliogenesis but not activation of Hh signaling. These results implicate mammalian HYLS1 as a multitasking protein that facilitates ciliogenesis and ciliary signaling by coordinating with the ciliary lipid kinase PIPKIγ.
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Affiliation(s)
- Chuan Chen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - Qingwen Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuxia Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - Brian A Davies
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yan Huang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - David J Katzmann
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Peter C Harris
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - Jinghua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
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Genome-wide systematic characterization and expression analysis of the phosphatidylinositol 4-phosphate 5-kinases in plants. Gene 2020; 756:144915. [PMID: 32580009 DOI: 10.1016/j.gene.2020.144915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/07/2020] [Accepted: 06/17/2020] [Indexed: 12/18/2022]
Abstract
Phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) are key enzymes in the process of phosphatidylinositol signaling pathway and have essential functions in growth, development, and biotic and abiotic stresses responses in plants. However, the evolutionary history and patterns of PIP5K genes in plants have not been examined systematically. Here, we use whole-genome sequences from eight plant species of land plants and algae to define the evolutionary relationships between these proteins in plants. 85 PIP5K genes were identified and divided into two subfamilies based on phylogenetic analyses. PIP5K members in subfamily II underwent several duplication events in land plants, resulting in multiple gene copies in angiosperms, while PIP5K members in subfamily I displayed low-copy numbers and lost in eudicots. Furthermore, PIP5K genes within the same subfamily had similar motifs and intron/exon features. Nine duplicated soybean gene pairs, four duplicated Arabidopsis gene pairs and two rice duplicated gene pairs were identified and many of them localized in synteny genomic regions. These duplicate events were formed by Whole-genome duplication (WGD)/segmental duplications. In addition, the ratios of non-synonymous to synonymous substitutions (Ka/Ks) showed that the PIP5K family had undergone purifying selection in higher plants. Expression analysis showed that PIP5K genes had complex and variable expression patterns in different developmental stages. The specificity of these genes is utilized to provide evidence for selective expression in the evolutionary process.
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Volpatti JR, Al-Maawali A, Smith L, Al-Hashim A, Brill JA, Dowling JJ. The expanding spectrum of neurological disorders of phosphoinositide metabolism. Dis Model Mech 2019; 12:12/8/dmm038174. [PMID: 31413155 PMCID: PMC6737944 DOI: 10.1242/dmm.038174] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Phosphoinositides (PIPs) are a ubiquitous group of seven low-abundance phospholipids that play a crucial role in defining localized membrane properties and that regulate myriad cellular processes, including cytoskeletal remodeling, cell signaling cascades, ion channel activity and membrane traffic. PIP homeostasis is tightly regulated by numerous inositol kinases and phosphatases, which phosphorylate and dephosphorylate distinct PIP species. The importance of these phospholipids, and of the enzymes that regulate them, is increasingly being recognized, with the identification of human neurological disorders that are caused by mutations in PIP-modulating enzymes. Genetic disorders of PIP metabolism include forms of epilepsy, neurodegenerative disease, brain malformation syndromes, peripheral neuropathy and congenital myopathy. In this Review, we provide an overview of PIP function and regulation, delineate the disorders associated with mutations in genes that modulate or utilize PIPs, and discuss what is understood about gene function and disease pathogenesis as established through animal models of these diseases. Summary: This Review highlights the intersection between phosphoinositides and the enzymes that regulate their metabolism, which together are crucial regulators of myriad cellular processes and neurological disorders.
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Affiliation(s)
- Jonathan R Volpatti
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Almundher Al-Maawali
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman
| | - Lindsay Smith
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aqeela Al-Hashim
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Department of Neuroscience, King Fahad Medical City, Riyadh 11525, Saudi Arabia
| | - Julie A Brill
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Program in Cell Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - James J Dowling
- Division of Neurology and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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Khadka B, Gupta RS. Novel Molecular Signatures in the PIP4K/PIP5K Family of Proteins Specific for Different Isozymes and Subfamilies Provide Important Insights into the Evolutionary Divergence of this Protein Family. Genes (Basel) 2019; 10:genes10040312. [PMID: 31010098 PMCID: PMC6523245 DOI: 10.3390/genes10040312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 02/07/2023] Open
Abstract
Members of the PIP4K/PIP5K family of proteins, which generate the highly important secondary messenger phosphatidylinositol-4,5-bisphosphate, play central roles in regulating diverse signaling pathways. In eukaryotic organisms, multiple isozymes and subfamilies of PIP4K/PIP5K proteins are found and it is of much interest to understand their evolution and species distribution and what unique molecular and biochemical characteristics distinguish specific isozymes and subfamilies of proteins. We report here the species distribution of different PIP4K/PIP5K family of proteins in eukaryotic organisms and phylogenetic analysis based on their protein sequences. Our results indicate that the distinct homologs of both PIP4K and PIP5K are found in different organisms belonging to the Holozoa clade of eukaryotes, which comprises of various metazoan phyla as well as their close unicellular relatives Choanoflagellates and Filasterea. In contrast, the deeper-branching eukaryotic lineages, as well as plants and fungi, contain only a single homolog of the PIP4K/PIP5K proteins. In parallel, our comparative analyses of PIP4K/PIP5K protein sequences have identified six highly-specific molecular markers consisting of conserved signature indels (CSIs) that are uniquely shared by either the PIP4K or PIP5K proteins, or both, or specific subfamilies of these proteins. Of these molecular markers, 2 CSIs are distinctive characteristics of all PIP4K homologs, 1 CSI distinguishes the PIP4K and PIP5K homologs from the Holozoa clade of species from the ancestral form of PIP4K/PIP5K found in deeper-branching eukaryotic lineages. The remaining three CSIs are specific for the PIP5Kα, PIP5Kβ, and PIP4Kγ subfamilies of proteins from vertebrate species. These molecular markers provide important means for distinguishing different PIP4K/PIP5K isozymes as well as some of their subfamilies. In addition, the distribution patterns of these markers in different isozymes provide important insights into the evolutionary divergence of PIP4K/PIP5K proteins. Our results support the view that the Holozoa clade of eukaryotic organisms shared a common ancestor exclusive of the other eukaryotic lineages and that the initial gene duplication event leading to the divergence of distinct types of PIP4K and PIP5K homologs occurred in a common ancestor of this clade. Based on the results gleaned from different studies presented here, a model for the evolutionary divergence of the PIP4K/PIP5K family of proteins is presented.
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Affiliation(s)
- Bijendra Khadka
- Department of Biochemistry and Biomedical Sciences McMaster University, Hamilton, ON L8N 3Z5, Canada.
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences McMaster University, Hamilton, ON L8N 3Z5, Canada.
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Genes involved in angiogenesis and circulatory system development are differentially expressed in porcine epithelial oviductal cells during long-term primary in vitro culture – a transcriptomic study. ACTA ACUST UNITED AC 2019. [DOI: 10.2478/acb-2018-0026] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Abstract
An oviduct is an essential organ for gamete transport, oocyte maturation, fertilization, spermatozoon capacitation and early embryo development. The epithelium plays an important role in oviduct functioning. The products of secretory cells provide an optimal environment and influence gamete activities and embryonic development. The oviduct physiology changes during the female cycle, thus, the ratio of the secreted molecules in the oviduct fluid differs between phases. In this study, a differential gene expression in porcine oviduct epithelial cells was examined during the long-term primary in vitro culture. The microarray expression analysis revealed 2552 genes, 1537 of which were upregulated and 995 were downregulated after 7 days of culture, with subsequent changes in expression during 30 day-long culture. The obtained genes were classified into 8 GO BP terms, connected with angiogenesis and circulatory system development, extracted by DAVID software. Among all genes, 10 most up-regulated and 10 most down-regulated genes were selected for further investigation. Interactions between genes were indicated by STRING software and REACTOME FIViz application to the Cytoscape 3.6.0 software. Most of the genes belonged to more than one ontology group. Although studied genes are mostly responsible for angiogenesis and circulatory system development, they can also be found to be expressed in processes connected with fertilization and early embryo development. The latter function is focused on more, considering the fact that these genes were expressed in epithelial cells of the fallopian tube which is largely responsible for reproductive processes.
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Mochel F. Lipids and synaptic functions. J Inherit Metab Dis 2018; 41:1117-1122. [PMID: 29869164 DOI: 10.1007/s10545-018-0204-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/16/2018] [Accepted: 05/18/2018] [Indexed: 10/14/2022]
Abstract
Synaptic functions have long been thought to be driven by proteins, especially the SNARE complex, contrasting with a relatively passive role for lipids constituting cell membranes. It is now clear that not only lipids, i.e. glycerophospholipids, sphingolipids and sterols, play a determinant role in the dynamics of synaptic membranes but they also actively contribute to the endocytosis and exocytosis of synaptic vesicles in conjunction with synaptic proteins. On the other hand, a growing number of inborn errors of metabolism affecting the nervous system have been related to defects in the synthesis and remodelling of fatty acids, phospholipids and sphingolipids. Alterations of the metabolism of these lipids would be expected to affect the dynamics of synaptic membranes and synaptic vesicles. Still, only few examples are currently documented. It remains to be determined to which extent the pathophysiology of disorders of complex lipids biosynthesis and remodelling share common pathogenic mechanisms with the more traditional synaptopathies.
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Affiliation(s)
- Fanny Mochel
- Sorbonne Université, UPMC-Paris 6, UMR S 1127 and Inserm U 1127, and CNRS UMR 7225, and ICM, F-75013, Paris, France.
- Sorbonne Université, GRC no. 13, Neurométabolisme, Paris, France.
- Department of Genetics and Reference Centre for Adult Neurometabolic Diseases, AP-HP, La Pitié-Salpêtriere University Hospital, Paris, France.
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Adam S, Coetzee M, Honey EM. Pena-Shokeir syndrome: current management strategies and palliative care. APPLICATION OF CLINICAL GENETICS 2018; 11:111-120. [PMID: 30498368 PMCID: PMC6207248 DOI: 10.2147/tacg.s154643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Pena-Shokeir syndrome (PSS) type 1, also known as fetal akinesia deformation sequence, is a rare genetic syndrome that almost always results in intrauterine or early neonatal death. It is characterized by markedly decreased fetal movements, intrauterine growth restriction, joint contractures, short umbilical cord, and features of pulmonary hypoplasia. Antenatal diagnosis can be difficult. Ultrasound features are varied and may overlap with those of Trisomy 18. The poor prognosis of PSS is due to pulmonary hypoplasia, which is an important feature that distinguishes PSS from arthrogryposis multiplex congenital without pulmonary hypoplasia, which has a better prognosis. If diagnosed in the antenatal period, a late termination of pregnancy can be considered following ethical discussion (if the law allows). In most cases, a diagnosis is only made in the neonatal period. Parents of a baby affected with PSS require detailed counseling that includes information on the imprecise recurrence risks and a plan for subsequent pregnancies.
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Affiliation(s)
- Sumaiya Adam
- Department of Obstetrics and Gynaecology, Steve Biko Academic Hospital, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa,
| | - Melantha Coetzee
- Division of Neonatology, Department of Pediatrics and Child Health, Steve Biko Academic Hospital, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Engela Magdalena Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
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26
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Loo L, Zylka M. Conditional deletion of Pip5k1c in sensory ganglia and effects on nociception and inflammatory sensitization. Mol Pain 2018; 13:1744806917737907. [PMID: 29020859 PMCID: PMC5656109 DOI: 10.1177/1744806917737907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Abstract Phosphatidylinositol 4-phosphate 5-kinase type 1 gamma (Pip5k1c) generates phosphatidylinositol 4,5-bisphosphate, also
known as PI(4,5)P2 or PIP2. Many pronociceptive signaling pathways and receptor tyrosine kinases signal via PIP2 hydrolysis.
Previously, we found that pain signaling and pain sensitization were reduced in Pip5k1cþ/ global heterozygous knockout
mice. Here, we sought to evaluate the extent to which dorsal root ganglia selective deletion of Pip5k1c affected nociception
in mice. Initially, we crossed sensory neuron-selective Advillin-Cre mice with a conditional Pip5k1c knockout (cKO) allele
(Pip5k1cfl/fl). However, these mice displayed an early onset proprioceptive deficit. To bypass this early onset phenotype,
we used two different tamoxifen-inducible Cre lines (Brn3a-Cre-ERT2 and Advillin-Cre-ERT2) to conditionally delete Pip5k1c in
adults. Tamoxifen induced high efficiency deletion of PIP5K1C in dorsal root ganglia and slightly reduced PIP5K1C in spinal
cord and brain in Brn3a-Cre-ERT2 Pip5k1cfl/fl (Brn3a cKO) mice while PIP5K1C was selectively deleted in dorsal root ganglia
with no changes in spinal cord or brain in Advillin-Cre-ERT2 Pip5k1cfl/fl (Advil cKO) mice. Acute thermosensation and
mechanosensation were not altered in either line relative to wild-type mice. However, thermal hypersensitivity and mechanical
allodynia recovered more rapidly in Brn3a cKO mice, but not Advil cKO mice, following hind paw inflammation.
These data collectively suggest that PIP5K1C regulates nociceptive sensitization in more regions of the nervous system
than dorsal root ganglia alone.
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Affiliation(s)
- Lipin Loo
- Department of Cell Biology and Physiology and UNC Neuroscience Center, The University of North Carolina, Chapel Hill, USA
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Structural insights into lethal contractural syndrome type 3 (LCCS3) caused by a missense mutation of PIP5Kγ. Biochem J 2018; 475:2257-2269. [PMID: 29959184 DOI: 10.1042/bcj20180326] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Signaling molecule phosphatidylinositol 4,5-bisphosphate is produced primarily by phosphatidylinositol 4-phosphate 5-kinase (PIP5K). PIP5K is essential for the development of the human neuronal system, which has been exemplified by a recessive genetic disorder, lethal congenital contractural syndrome type 3, caused by a single aspartate-to-asparagine mutation in the kinase domain of PIP5Kγ. So far, the exact role of this aspartate residue has yet to be elucidated. In this work, we conducted structural, functional and computational studies on a zebrafish PIP5Kα variant with a mutation at the same site. Compared with the structure of the wild-type (WT) protein in the ATP-bound state, the ATP-associating glycine-rich loop of the mutant protein was severely disordered and the temperature factor of ATP was significantly higher. Both observations suggest a greater degree of disorder of the bound ATP, whereas neither the structure of the catalytic site nor the Km toward ATP was substantially affected by the mutation. Microsecond molecular dynamics simulation revealed that negative charge elimination caused by the mutation destabilized the involved hydrogen bonds and affected key electrostatic interactions in the close proximity of ATP. Taken together, our data indicated that the disease-related aspartate residue is a key node in the interaction network crucial for effective ATP binding. This work provides a paradigm of how a subtle but critical structural perturbation caused by a single mutation at the ATP-binding site abolishes the kinase activity, emphasizing that stabilizing substrate in a productive conformational state is crucial for catalysis.
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Wegener M, Müller-McNicoll M. Nuclear retention of mRNAs - quality control, gene regulation and human disease. Semin Cell Dev Biol 2017; 79:131-142. [PMID: 29102717 DOI: 10.1016/j.semcdb.2017.11.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/21/2022]
Abstract
Nuclear retention of incompletely spliced or mature mRNAs emerges as a novel, previously underappreciated layer of gene regulation, which enables the cell to rapidly respond to stress, viral infection, differentiation cues or changing environmental conditions. Focusing on mammalian cells, we discuss recent insights into the mechanisms and functions of nuclear retention, describe retention-promoting features in protein-coding transcripts and propose mechanisms for their regulated release into the cytoplasm. Moreover, we discuss examples of how aberrant nuclear retention of mRNAs may lead to human diseases.
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Affiliation(s)
- Marius Wegener
- RNA Regulation Group, Cluster of Excellence 'Macromolecular Complexes', Goethe University Frankfurt, Institute of Cell Biology and Neuroscience, Max-von-Laue-Str. 13, 60438 Frankfurt/Main, Germany
| | - Michaela Müller-McNicoll
- RNA Regulation Group, Cluster of Excellence 'Macromolecular Complexes', Goethe University Frankfurt, Institute of Cell Biology and Neuroscience, Max-von-Laue-Str. 13, 60438 Frankfurt/Main, Germany.
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29
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Yoshida A, Hayashi H, Tanabe K, Fujita A. Segregation of phosphatidylinositol 4-phosphate and phosphatidylinositol 4,5-bisphosphate into distinct microdomains on the endosome membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017. [PMID: 28648675 DOI: 10.1016/j.bbamem.2017.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Phosphatidylinositol 4-phosphate (PtdIns(4)P) is the immediate precursor of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), which is located on the cytoplasmic leaflet of the plasma membrane and has been reported to possess multiple cellular functions. Although PtdIns(4)P and PtdIns(4,5)P2 have been reported to localize to multiple intracellular compartments and to each function as regulatory molecules, their generation, regulation and functions in most intracellular compartments are not well-defined. To analyze PtdIns(4)P and PtdIns(4,5)P2 distributions, at a nanoscale, we employed an electron microscopy technique that specifically labels PtdIns(4)P and PtdIns(4,5)P2 on the freeze-fracture replica of intracellular biological membranes. This method minimizes the possibility of artificial perturbation, because molecules in the membrane are physically immobilized in situ. Using this technique, we found that PtdIns(4)P was localized to the cytoplasmic leaflet of Golgi apparatus and vesicular-shaped structures. The PtdIns(4,5)P2 labeling was observed in the cytoplasmic leaflet of the mitochondrial inner membrane and vesicular-shaped structures. Double labeling of PtdIns(4)P and PtdIns(4,5)P2 with endosome markers illustrated that PtdIns(4)P and PtdIns(4,5)P2 were mainly localized to the late endosome/lysosome and early endosome, respectively. PtdIns(4)P and PtdIns(4,5)P2 were colocalized in some endosomes, with the two phospholipids separated into distinct microdomains on the same endosomes. This is the first report showing, at a nanoscale, segregation of PtdIns(4)P- and PtdIns(4,5)P2-enriched microdomains in the endosome, of likely importance for endosome functionality.
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Affiliation(s)
- Akane Yoshida
- Field of Veterinary Pathobiology, Basic Veterinary Science, Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Hiroki Hayashi
- Field of Veterinary Pathobiology, Basic Veterinary Science, Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan
| | - Kenji Tanabe
- Medical Research Institute, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo 162-8666, Japan
| | - Akikazu Fujita
- Field of Veterinary Pathobiology, Basic Veterinary Science, Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine, Kagoshima University, Korimoto 1-21-24, Kagoshima 890-0065, Japan.
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30
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Wiessner M, Roos A, Munn CJ, Viswanathan R, Whyte T, Cox D, Schoser B, Sewry C, Roper H, Phadke R, Marini Bettolo C, Barresi R, Charlton R, Bönnemann CG, Abath Neto O, Reed UC, Zanoteli E, Araújo Martins Moreno C, Ertl-Wagner B, Stucka R, De Goede C, Borges da Silva T, Hathazi D, Dell’Aica M, Zahedi RP, Thiele S, Müller J, Kingston H, Müller S, Curtis E, Walter MC, Strom TM, Straub V, Bushby K, Muntoni F, Swan LE, Lochmüller H, Senderek J. Mutations in INPP5K, Encoding a Phosphoinositide 5-Phosphatase, Cause Congenital Muscular Dystrophy with Cataracts and Mild Cognitive Impairment. Am J Hum Genet 2017; 100:523-536. [PMID: 28190456 PMCID: PMC5339217 DOI: 10.1016/j.ajhg.2017.01.024] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/12/2017] [Indexed: 12/26/2022] Open
Abstract
Phosphoinositides are small phospholipids that control diverse cellular downstream signaling events. Their spatial and temporal availability is tightly regulated by a set of specific lipid kinases and phosphatases. Congenital muscular dystrophies are hereditary disorders characterized by hypotonia and weakness from birth with variable eye and central nervous system involvement. In individuals exhibiting congenital muscular dystrophy, early-onset cataracts, and mild intellectual disability but normal cranial magnetic resonance imaging, we identified bi-allelic mutations in INPP5K, encoding inositol polyphosphate-5-phosphatase K. Mutations impaired phosphatase activity toward the phosphoinositide phosphatidylinositol (4,5)-bisphosphate or altered the subcellular localization of INPP5K. Downregulation of INPP5K orthologs in zebrafish embryos disrupted muscle fiber morphology and resulted in abnormal eye development. These data link congenital muscular dystrophies to defective phosphoinositide 5-phosphatase activity that is becoming increasingly recognized for its role in mediating pivotal cellular mechanisms contributing to disease.
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Mechanism of substrate specificity of phosphatidylinositol phosphate kinases. Proc Natl Acad Sci U S A 2016; 113:8711-6. [PMID: 27439870 PMCID: PMC4978281 DOI: 10.1073/pnas.1522112113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The phosphatidylinositol phosphate kinase (PIPK) family of enzymes is primarily responsible for converting singly phosphorylated phosphatidylinositol derivatives to phosphatidylinositol bisphosphates. As such, these kinases are central to many signaling and membrane trafficking processes in the eukaryotic cell. The three types of phosphatidylinositol phosphate kinases are homologous in sequence but differ in catalytic activities and biological functions. Type I and type II kinases generate phosphatidylinositol 4,5-bisphosphate from phosphatidylinositol 4-phosphate and phosphatidylinositol 5-phosphate, respectively, whereas the type III kinase produces phosphatidylinositol 3,5-bisphosphate from phosphatidylinositol 3-phosphate. Based on crystallographic analysis of the zebrafish type I kinase PIP5Kα, we identified a structural motif unique to the kinase family that serves to recognize the monophosphate on the substrate. Our data indicate that the complex pattern of substrate recognition and phosphorylation results from the interplay between the monophosphate binding site and the specificity loop: the specificity loop functions to recognize different orientations of the inositol ring, whereas residues flanking the phosphate binding Arg244 determine whether phosphatidylinositol 3-phosphate is exclusively bound and phosphorylated at the 5-position. This work provides a thorough picture of how PIPKs achieve their exquisite substrate specificity.
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Thapa N, Tan X, Choi S, Lambert PF, Rapraeger AC, Anderson RA. The Hidden Conundrum of Phosphoinositide Signaling in Cancer. Trends Cancer 2016; 2:378-390. [PMID: 27819060 DOI: 10.1016/j.trecan.2016.05.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Phosphoinositide 3-kinase (PI3K) generation of PI(3,4,5)P3 from PI(4,5)P2 and the subsequent activation of Akt and its downstream signaling cascades (e.g. mTORC1) dominates the landscape of phosphoinositide signaling axis in cancer research. However, PI(4,5)P2 is breaking its boundary as merely a substrate for PI3K and phospholipase C (PLC), and is now an established lipid messenger pivotal for different cellular events in cancer. Here, we review the phosphoinositide signaling axis in cancer, giving due weight to PI(4,5)P2 and its generating enzymes, the phosphatidylinositol phosphate (PIP) kinases (PIPKs). We highlighted how PI(4,5)P2 and PIP kinases serve as a proximal node in phosphoinositide signaling axis and how its interaction with cytoskeletal proteins regulates migratory and invasive nexus of metastasizing tumor cells.
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Affiliation(s)
- Narendra Thapa
- University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Xiaojun Tan
- Program in Molecular and Cellular Pharmacology, 1300 University Avenue, Madison, WI 53706, USA
| | - Suyong Choi
- University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Paul F Lambert
- Department of Oncology, 1300 University Avenue, Madison, WI 53706, USA; McArdle Laboratory for Cancer Research, 1300 University Avenue, Madison, WI 53706, USA; University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Alan C Rapraeger
- Program in Molecular and Cellular Pharmacology, 1300 University Avenue, Madison, WI 53706, USA; Department of Human Oncology, 1300 University Avenue, Madison, WI 53706, USA; University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
| | - Richard A Anderson
- Program in Molecular and Cellular Pharmacology, 1300 University Avenue, Madison, WI 53706, USA; University of Wisconsin-Madison School of Medicine and Public Health, 1300 University Avenue, Madison, WI 53706, USA
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Membrane Lipids in Presynaptic Function and Disease. Neuron 2016; 90:11-25. [DOI: 10.1016/j.neuron.2016.02.033] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/28/2016] [Accepted: 02/18/2016] [Indexed: 12/20/2022]
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Bong SM, Son KB, Yang SW, Park JW, Cho JW, Kim KT, Kim H, Kim SJ, Kim YJ, Lee BI. Crystal Structure of Human Myotubularin-Related Protein 1 Provides Insight into the Structural Basis of Substrate Specificity. PLoS One 2016; 11:e0152611. [PMID: 27018598 PMCID: PMC4809516 DOI: 10.1371/journal.pone.0152611] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 03/16/2016] [Indexed: 01/07/2023] Open
Abstract
Myotubularin-related protein 1 (MTMR1) is a phosphatase that belongs to the tyrosine/dual-specificity phosphatase superfamily. MTMR1 has been shown to use phosphatidylinositol 3-monophosphate (PI(3)P) and/or phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) as substrates. Here, we determined the crystal structure of human MTMR1. The refined model consists of the Pleckstrin homology (PH)-GRAM and phosphatase (PTP) domains. The overall structure was highly similar to the previously reported MTMR2 structure. Interestingly, two phosphate molecules were coordinated by strictly conserved residues located in the C(X)5R motif of the active site. Additionally, our biochemical studies confirmed the substrate specificity of MTMR1 for PI(3)P and PI(3,5)P2 over other phosphatidylinositol phosphates. Our structural and enzymatic analyses provide insight into the catalytic mechanism and biochemical properties of MTMR1.
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Affiliation(s)
- Seoung Min Bong
- Research institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
| | - Kka-bi Son
- Department of Biomedical Chemistry, Konkuk University, Chungju 27478, Republic of Korea
| | - Seung-Won Yang
- Research institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
| | - Jae-Won Park
- Research institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
| | - Jea-Won Cho
- Research institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
| | - Kyung-Tae Kim
- Research institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
| | - Hackyoung Kim
- Department of Biomedical Chemistry, Konkuk University, Chungju 27478, Republic of Korea
| | - Seung Jun Kim
- Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Young Jun Kim
- Department of Biomedical Chemistry, Konkuk University, Chungju 27478, Republic of Korea
- * E-mail: (YJK); (BIL)
| | - Byung Il Lee
- Research institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
- * E-mail: (YJK); (BIL)
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Knierim E, Hirata H, Wolf NI, Morales-Gonzalez S, Schottmann G, Tanaka Y, Rudnik-Schöneborn S, Orgeur M, Zerres K, Vogt S, van Riesen A, Gill E, Seifert F, Zwirner A, Kirschner J, Goebel HH, Hübner C, Stricker S, Meierhofer D, Stenzel W, Schuelke M. Mutations in Subunits of the Activating Signal Cointegrator 1 Complex Are Associated with Prenatal Spinal Muscular Atrophy and Congenital Bone Fractures. Am J Hum Genet 2016; 98:473-489. [PMID: 26924529 DOI: 10.1016/j.ajhg.2016.01.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/05/2016] [Indexed: 12/31/2022] Open
Abstract
Transcriptional signal cointegrators associate with transcription factors or nuclear receptors and coregulate tissue-specific gene transcription. We report on recessive loss-of-function mutations in two genes (TRIP4 and ASCC1) that encode subunits of the nuclear activating signal cointegrator 1 (ASC-1) complex. We used autozygosity mapping and whole-exome sequencing to search for pathogenic mutations in four families. Affected individuals presented with prenatal-onset spinal muscular atrophy (SMA), multiple congenital contractures (arthrogryposis multiplex congenita), respiratory distress, and congenital bone fractures. We identified homozygous and compound-heterozygous nonsense and frameshift TRIP4 and ASCC1 mutations that led to a truncation or the entire absence of the respective proteins and cosegregated with the disease phenotype. Trip4 and Ascc1 have identical expression patterns in 17.5-day-old mouse embryos with high expression levels in the spinal cord, brain, paraspinal ganglia, thyroid, and submandibular glands. Antisense morpholino-mediated knockdown of either trip4 or ascc1 in zebrafish disrupted the highly patterned and coordinated process of α-motoneuron outgrowth and formation of myotomes and neuromuscular junctions and led to a swimming defect in the larvae. Immunoprecipitation of the ASC-1 complex consistently copurified cysteine and glycine rich protein 1 (CSRP1), a transcriptional cofactor, which is known to be involved in spinal cord regeneration upon injury in adult zebrafish. ASCC1 mutant fibroblasts downregulated genes associated with neurogenesis, neuronal migration, and pathfinding (SERPINF1, DAB1, SEMA3D, SEMA3A), as well as with bone development (TNFRSF11B, RASSF2, STC1). Our findings indicate that the dysfunction of a transcriptional coactivator complex can result in a clinical syndrome affecting the neuromuscular system.
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Affiliation(s)
- Ellen Knierim
- Department of Neuropediatrics, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany; NeuroCure Clinical Research Center, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Hiromi Hirata
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara 252-5258, Japan; Center for Frontier Research, National Institute of Genetics, Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Mishima 411-8540, Japan.
| | - Nicole I Wolf
- Department of Child Neurology, Neuroscience Campus Amsterdam, VU University Medical Center, 1007 MB Amsterdam, the Netherlands
| | - Susanne Morales-Gonzalez
- Department of Neuropediatrics, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany; NeuroCure Clinical Research Center, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Gudrun Schottmann
- Department of Neuropediatrics, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany; NeuroCure Clinical Research Center, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Yu Tanaka
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara 252-5258, Japan
| | - Sabine Rudnik-Schöneborn
- Institute of Human Genetics and University Hospital, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany; Division of Human Genetics, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Mickael Orgeur
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Free University Berlin, Institute for Chemistry and Biochemistry, 14195 Berlin, Germany
| | - Klaus Zerres
- Institute of Human Genetics and University Hospital, Rheinisch-Westfälische Technische Hochschule Aachen University, 52074 Aachen, Germany
| | - Stefanie Vogt
- Medizinisches Versorgungszentrum Dr. Eberhard & Partner, 44137 Dortmund, Germany
| | - Anne van Riesen
- Department of Neuropediatrics, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Esther Gill
- Department of Neuropediatrics, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany; NeuroCure Clinical Research Center, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Franziska Seifert
- Department of Neuropediatrics, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany; NeuroCure Clinical Research Center, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Angelika Zwirner
- Department of Neuropediatrics, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany; NeuroCure Clinical Research Center, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Janbernd Kirschner
- Department of Neuropediatrics and Muscle Disorders, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Hans Hilmar Goebel
- Department of Neuropathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Christoph Hübner
- Department of Neuropediatrics, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Sigmar Stricker
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Free University Berlin, Institute for Chemistry and Biochemistry, 14195 Berlin, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Werner Stenzel
- Department of Neuropathology, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Markus Schuelke
- Department of Neuropediatrics, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany; NeuroCure Clinical Research Center, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
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36
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Phosphatidylinositol phosphate kinase PIPKIγ and phosphatase INPP5E coordinate initiation of ciliogenesis. Nat Commun 2016; 7:10777. [PMID: 26916822 PMCID: PMC4773430 DOI: 10.1038/ncomms10777] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/19/2016] [Indexed: 02/08/2023] Open
Abstract
Defective primary cilia are causative to a wide spectrum of human genetic disorders, termed ciliopathies. Although the regulation of ciliogenesis is intensively studied, how it is initiated remains unclear. Here we show that type Iγ phosphatidylinositol 4-phosphate (PtdIns(4)P) 5-kinase (PIPKIγ) and inositol polyphosphate-5-phosphatase E (INPP5E), a Joubert syndrome protein, localize to the centrosome and coordinate the initiation of ciliogenesis. PIPKIγ counteracts INPP5E in regulating tau-tubulin kinase-2 (TTBK2) recruitment to the basal body, which promotes the removal of microtubule capping protein CP110 and the subsequent axoneme elongation. Interestingly, INPP5E and its product—PtdIns(4)P—accumulate at the centrosome/basal body in non-ciliated, but not ciliated, cells. PtdIns(4)P binding to TTBK2 and the distal appendage protein CEP164 compromises the TTBK2-CEP164 interaction and inhibits the recruitment of TTBK2. Our results reveal that PtdIns(4)P homoeostasis, coordinated by PIPKIγ and INPP5E at the centrosome/ciliary base, is vital for ciliogenesis by regulating the CEP164-dependent recruitment of TTBK2. The primary cilium is essential for embryonic development and tissue pattern formation. Here the authors show that PIPKIγ localizes to the basal body of the primary cilium and cooperates with the Joubert Syndrome associated protein INPP5E to regulate the initiation of ciliogenesis.
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Seytanoglu A, Alsomali NI, Valori CF, McGown A, Kim HR, Ning K, Ramesh T, Sharrack B, Wood JD, Azzouz M. Deficiency in the mRNA export mediator Gle1 impairs Schwann cell development in the zebrafish embryo. Neuroscience 2016; 322:287-97. [PMID: 26921650 DOI: 10.1016/j.neuroscience.2016.02.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 02/17/2016] [Accepted: 02/17/2016] [Indexed: 12/12/2022]
Abstract
GLE1 mutations cause lethal congenital contracture syndrome 1 (LCCS1), a severe autosomal recessive fetal motor neuron disease, and more recently have been associated with amyotrophic lateral sclerosis (ALS). The gene encodes a highly conserved protein with an essential role in mRNA export. The mechanism linking Gle1 function to motor neuron degeneration in humans has not been elucidated, but increasing evidence implicates abnormal RNA processing as a key event in the pathogenesis of several motor neuron diseases. Homozygous gle1(-/-) mutant zebrafish display various aspects of LCCS, showing severe developmental abnormalities including motor neuron arborization defects and embryonic lethality. A previous gene expression study on spinal cord from LCCS fetuses indicated that oligodendrocyte dysfunction may be an important factor in LCCS. We therefore set out to investigate the development of myelinating glia in gle1(-/-) mutant zebrafish embryos. While expression of myelin basic protein (mbp) in hindbrain oligodendrocytes appeared relatively normal, our studies revealed a prominent defect in Schwann cell precursor proliferation and differentiation in the posterior lateral line nerve. Other genes mutated in LCCS have important roles in Schwann cell development, thereby suggesting that Schwann cell deficits may be a common factor in LCCS pathogenesis. These findings illustrate the potential importance of glial cells such as myelinating Schwann cells in motor neuron diseases linked to RNA processing defects.
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Affiliation(s)
- A Seytanoglu
- The Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - N I Alsomali
- The Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - C F Valori
- The Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - A McGown
- The Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - H R Kim
- Bateson Centre, Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - K Ning
- The Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - T Ramesh
- The Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK
| | - B Sharrack
- The Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK; Department of Neurology, Royal Hallamshire Hospital, Sheffield Teaching Hospitals Foundation Trust, Glossop Road, Sheffield S10 2JF, UK
| | - J D Wood
- The Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK; Bateson Centre, Department of Biomedical Science, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - M Azzouz
- The Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, 385A Glossop Road, Sheffield S10 2HQ, UK; Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia.
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Viaud J, Mansour R, Antkowiak A, Mujalli A, Valet C, Chicanne G, Xuereb JM, Terrisse AD, Séverin S, Gratacap MP, Gaits-Iacovoni F, Payrastre B. Phosphoinositides: Important lipids in the coordination of cell dynamics. Biochimie 2015; 125:250-8. [PMID: 26391221 DOI: 10.1016/j.biochi.2015.09.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/02/2015] [Indexed: 01/21/2023]
Abstract
By interacting specifically with proteins, phosphoinositides organize the spatiotemporal formation of protein complexes involved in the control of intracellular signaling, vesicular trafficking and cytoskeleton dynamics. A set of specific kinases and phosphatases ensures the production, degradation and inter-conversion of phosphoinositides to achieve a high level of precision in the regulation of cellular dynamics coordinated by these lipids. The direct involvement of these enzymes in cancer, genetic or infectious diseases, and the recent arrival of inhibitors targeting specific phosphoinositide kinases in clinic, emphasize the importance of these lipids and their metabolism in the biomedical field.
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Affiliation(s)
- Julien Viaud
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France.
| | - Rana Mansour
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Adrien Antkowiak
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Abdulrahman Mujalli
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Colin Valet
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Gaëtan Chicanne
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Jean-Marie Xuereb
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Anne-Dominique Terrisse
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Sonia Séverin
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Marie-Pierre Gratacap
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Frédérique Gaits-Iacovoni
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France
| | - Bernard Payrastre
- INSERM UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Université Toulouse III Paul Sabatier, 1 Avenue Jean Poulhès, BP84225, 31432 Toulouse Cedex 04, France; Centre Hospitalier Universitaire de Toulouse, Laboratoire d'Hématologie, 31059 Toulouse Cedex 03, France.
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39
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Waugh MG. PIPs in neurological diseases. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:1066-82. [PMID: 25680866 DOI: 10.1016/j.bbalip.2015.02.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 12/19/2022]
Abstract
Phosphoinositide (PIP) lipids regulate many aspects of cell function in the nervous system including receptor signalling, secretion, endocytosis, migration and survival. Levels of PIPs such as PI4P, PI(4,5)P2 and PI(3,4,5)P3 are normally tightly regulated by phosphoinositide kinases and phosphatases. Deregulation of these biochemical pathways leads to lipid imbalances, usually on intracellular endosomal membranes, and these changes have been linked to a number of major neurological diseases including Alzheimer's, Parkinson's, epilepsy, stroke, cancer and a range of rarer inherited disorders including brain overgrowth syndromes, Charcot-Marie-Tooth neuropathies and neurodevelopmental conditions such as Lowe's syndrome. This article analyses recent progress in this area and explains how PIP lipids are involved, to varying degrees, in almost every class of neurological disease. This article is part of a Special Issue entitled Brain Lipids.
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Affiliation(s)
- Mark G Waugh
- Lipid and Membrane Biology Group, Institute for Liver and Digestive Health, UCL, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom.
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40
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Mendelian disorders of PI metabolizing enzymes. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1851:867-81. [PMID: 25510381 DOI: 10.1016/j.bbalip.2014.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/18/2014] [Accepted: 12/01/2014] [Indexed: 12/18/2022]
Abstract
More than twenty different genetic diseases have been described that are caused by mutations in phosphoinositide metabolizing enzymes, mostly in phosphoinositide phosphatases. Although generally ubiquitously expressed, mutations in these enzymes, which are mainly loss-of-function, result in tissue-restricted clinical manifestations through mechanisms that are not completely understood. Here we analyze selected disorders of phosphoinositide metabolism grouped according to the principle tissue affected: the nervous system, muscle, kidney, the osteoskeletal system, the eye, and the immune system. We will highlight what has been learnt so far from the study of these disorders about not only the cellular and molecular pathways that are involved or are governed by phosphoinositides, but also the many gaps that remain to be filled to gain a full understanding of the pathophysiological mechanisms underlying the clinical manifestations of this steadily growing class of diseases, most of which still remain orphan in terms of treatment. This article is part of a Special Issue entitled Phosphoinositides.
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41
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Patel N, Smith LL, Faqeih E, Mohamed J, Gupta VA, Alkuraya FS. ZBTB42 mutation defines a novel lethal congenital contracture syndrome (LCCS6). Hum Mol Genet 2014; 23:6584-93. [PMID: 25055871 DOI: 10.1093/hmg/ddu384] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Lethal congenital contracture syndrome (LCCS) is a lethal autosomal recessive form of arthrogryposis multiplex congenita (AMC). LCCS is genetically heterogeneous with mutations in five genes identified to date, all with a role in the innervation or contractile apparatus of skeletal muscles. In a consanguineous Saudi family with multiple stillbirths presenting with LCCS, we excluded linkage to all known LCCS loci and combined autozygome analysis and whole-exome sequencing to identify a novel homozygous variant in ZBTB42, which had been shown to be enriched in skeletal muscles, especially at the neuromuscular junction. Knockdown experiments of zbtb42 in zebrafish consistently resulted in grossly abnormal skeletal muscle development and myofibrillar disorganization at the microscopic level. This severe muscular phenotype is successfully rescued with overexpression of the human wild-type ZBTB42 gene, but not with the mutant form of ZBTB42 that models the human missense change. Our data assign a novel muscular developmental phenotype to ZBTB42 in vertebrates and establish a new LCCS6 type caused by ZBTB42 mutation.
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Affiliation(s)
- Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Laura L Smith
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Eissa Faqeih
- Department of Pediatrics, King Fahad Medical City, Riyadh, Saudi Arabia and
| | - Jawahir Mohamed
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Vandana A Gupta
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA,
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia, Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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42
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Wright BD, Loo L, Street SE, Ma A, Taylor-Blake B, Stashko MA, Jin J, Janzen WP, Frye SV, Zylka MJ. The lipid kinase PIP5K1C regulates pain signaling and sensitization. Neuron 2014; 82:836-47. [PMID: 24853942 DOI: 10.1016/j.neuron.2014.04.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2014] [Indexed: 02/07/2023]
Abstract
Numerous pain-producing (pronociceptive) receptors signal via phosphatidylinositol 4,5-bisphosphate (PIP2) hydrolysis. However, it is currently unknown which lipid kinases generate PIP2 in nociceptive dorsal root ganglia (DRG) neurons and if these kinases regulate pronociceptive receptor signaling. Here, we found that phosphatidylinositol 4-phosphate 5 kinase type 1C (PIP5K1C) is expressed at higher levels than any other PIP5K and, based on experiments with Pip5k1c(+/-) mice, generates at least half of all PIP2 in DRG neurons. Additionally, Pip5k1c haploinsufficiency reduces pronociceptive receptor signaling and TRPV1 sensitization in DRG neurons as well as thermal and mechanical hypersensitivity in mouse models of chronic pain. We identified a small molecule inhibitor of PIP5K1C (UNC3230) in a high-throughput screen. UNC3230 lowered PIP2 levels in DRG neurons and attenuated hypersensitivity when administered intrathecally or into the hindpaw. Our studies reveal that PIP5K1C regulates PIP2-dependent nociceptive signaling and suggest that PIP5K1C is a therapeutic target for chronic pain.
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Affiliation(s)
- Brittany D Wright
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lipin Loo
- Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sarah E Street
- Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anqi Ma
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bonnie Taylor-Blake
- Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael A Stashko
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jian Jin
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William P Janzen
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephen V Frye
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Center for Integrative Chemical Biology and Drug Discovery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mark J Zylka
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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43
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Identification of cellular proteins that interact with human cytomegalovirus immediate-early protein 1 by protein array assay. Viruses 2013; 6:89-105. [PMID: 24385082 PMCID: PMC3917433 DOI: 10.3390/v6010089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 12/10/2013] [Accepted: 12/20/2013] [Indexed: 12/13/2022] Open
Abstract
Human cytomegalovirus (HCMV) gene expression during infection is characterized as a sequential process including immediate-early (IE), early (E), and late (L)-stage gene expression. The most abundantly expressed gene at the IE stage of infection is the major IE (MIE) gene that produces IE1 and IE2. IE1 has been the focus of study because it is an important protein, not only for viral gene expression but also for viral replication. It is believed that IE1 plays important roles in viral gene regulation by interacting with cellular proteins. In the current study, we performed protein array assays and identified 83 cellular proteins that interact with IE1. Among them, seven are RNA-binding proteins that are important in RNA processing; more than half are nuclear proteins that are involved in gene regulations. Tumorigenesis-related proteins are also found to interact with IE1, implying that the role of IE1 in tumorigenesis might need to be reevaluated. Unexpectedly, cytoplasmic proteins, such as Golgi autoantigen and GGA1 (both related to the Golgi trafficking protein), are also found to be associated with IE1. We also employed a coimmunoprecipitation assay to test the interactions of IE1 and some of the proteins identified in the protein array assays and confirmed that the results from the protein array assays are reliable. Many of the proteins identified by the protein array assay have not been previously reported. Therefore, the functions of the IE1-protein interactions need to be further explored in the future.
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Bayot A, Reichman S, Lebon S, Csaba Z, Aubry L, Sterkers G, Husson I, Rak M, Rustin P. Cis-silencing of PIP5K1B evidenced in Friedreich's ataxia patient cells results in cytoskeleton anomalies. Hum Mol Genet 2013; 22:2894-904. [PMID: 23552101 DOI: 10.1093/hmg/ddt144] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Friedreich's ataxia (FRDA) is a progressive neurodegenerative disease characterized by ataxia, variously associating heart disease, diabetes mellitus and/or glucose intolerance. It results from intronic expansion of GAA triplet repeats at the FXN locus. Homozygous expansions cause silencing of the FXN gene and subsequent decreased expression of the encoded mitochondrial frataxin. Detailed analyses in fibroblasts and neuronal tissues from FRDA patients have revealed profound cytoskeleton anomalies. So far, however, the molecular mechanism underlying these cytoskeleton defects remains unknown. We show here that gene silencing spreads in cis over the PIP5K1B gene in cells from FRDA patients (circulating lymphocytes and primary fibroblasts), correlating with expanded GAA repeat size. PIP5K1B encodes phosphatidylinositol 4-phosphate 5-kinase β type I (pip5k1β), an enzyme functionally linked to actin cytoskeleton dynamics that phosphorylates phosphatidylinositol 4-phosphate [PI(4)P] to generate phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. Accordingly, loss of pip5k1β function in FRDA cells was accompanied by decreased PI(4,5)P2 levels and was shown instrumental for destabilization of the actin network and delayed cell spreading. Knockdown of PIP5K1B in control fibroblasts using shRNA reproduced abnormal actin cytoskeleton remodeling, whereas over-expression of PIP5K1B, but not FXN, suppressed this phenotype in FRDA cells. In addition to provide new insights into the consequences of the FXN gene expansion, these findings raise the question whether PIP5K1B silencing may contribute to the variable manifestation of this complex disease.
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Affiliation(s)
- Aurélien Bayot
- Hôpital Robert Debré, INSERM UMR 676 Faculté de Médecine Denis Diderot, Université Paris 7, 75019 Paris, France.
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45
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Abstract
Phosphoinositides (PIs) make up only a small fraction of cellular phospholipids, yet they control almost all aspects of a cell's life and death. These lipids gained tremendous research interest as plasma membrane signaling molecules when discovered in the 1970s and 1980s. Research in the last 15 years has added a wide range of biological processes regulated by PIs, turning these lipids into one of the most universal signaling entities in eukaryotic cells. PIs control organelle biology by regulating vesicular trafficking, but they also modulate lipid distribution and metabolism via their close relationship with lipid transfer proteins. PIs regulate ion channels, pumps, and transporters and control both endocytic and exocytic processes. The nuclear phosphoinositides have grown from being an epiphenomenon to a research area of its own. As expected from such pleiotropic regulators, derangements of phosphoinositide metabolism are responsible for a number of human diseases ranging from rare genetic disorders to the most common ones such as cancer, obesity, and diabetes. Moreover, it is increasingly evident that a number of infectious agents hijack the PI regulatory systems of host cells for their intracellular movements, replication, and assembly. As a result, PI converting enzymes began to be noticed by pharmaceutical companies as potential therapeutic targets. This review is an attempt to give an overview of this enormous research field focusing on major developments in diverse areas of basic science linked to cellular physiology and disease.
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Affiliation(s)
- Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
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46
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Sun Y, Thapa N, Hedman AC, Anderson RA. Phosphatidylinositol 4,5-bisphosphate: targeted production and signaling. Bioessays 2013; 35:513-22. [PMID: 23575577 DOI: 10.1002/bies.201200171] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI4,5P(2)) is a key lipid signaling molecule that regulates a vast array of biological activities. PI4,5P(2) can act directly as a messenger or can be utilized as a precursor to generate other messengers: inositol trisphosphate, diacylglycerol, or phosphatidylinositol 3,4,5-trisphosphate. PI4,5P(2) interacts with hundreds of different effector proteins. The enormous diversity of PI4,5P(2) effector proteins and the spatio-temporal control of PI4,5P(2) generation allow PI4,5P(2) signaling to control a broad spectrum of cellular functions. PI4,5P(2) is synthesized by phosphatidylinositol phosphate kinases (PIPKs). The array of PIPKs in cells enables their targeting to specific subcellular compartments through interactions with targeting factors that are often PI4,5P(2) effectors. These interactions are a mechanism to define spatial and temporal PI4,5P(2) synthesis and the specificity of PI4,5P(2) signaling. In turn, the regulation of PI4,5P(2) effectors at specific cellular compartments has implications for understanding how PI4,5P(2) controls cellular processes and its role in diseases.
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Affiliation(s)
- Yue Sun
- University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
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47
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Nowaczyk MJM, Thompson BA, Zeesman S, Moog U, Sanchez-Lara PA, Magoulas PL, Falk RE, Hoover-Fong JE, Batista DAS, Amudhavalli SM, White SM, Graham GE, Rauen KA. Deletion of MAP2K2/MEK2: a novel mechanism for a RASopathy? Clin Genet 2013; 85:138-46. [PMID: 23379592 DOI: 10.1111/cge.12116] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 01/28/2013] [Accepted: 01/28/2013] [Indexed: 11/29/2022]
Abstract
RASopathies are a class of genetic syndromes caused by germline mutations in genes encoding Ras/mitogen-activated protein kinase (Ras/MAPK) pathway components. Cardio-facio-cutaneous (CFC) syndrome is a RASopathy characterized by distinctive craniofacial features, skin and hair abnormalities, and congenital heart defects caused by activating mutations of BRAF, MEK1, MEK2, and KRAS. We define the phenotype of seven patients with de novo deletions of chromosome 19p13.3 including MEK2; they present with a distinct phenotype but have overlapping features with CFC syndrome. Phenotypic features of all seven patients include tall forehead, thick nasal tip, underdeveloped cheekbones, long midface, sinuous upper vermilion border, tall chin, angular jaw, and facial asymmetry. Patients also have developmental delay, hypotonia, heart abnormalities, failure to thrive, obstructive sleep apnea, gastroesophageal reflux and integument abnormalities. Analysis of epidermal growth factor-stimulated fibroblasts revealed that P-MEK1/2 was ∼50% less abundant in cells carrying the MEK2 deletion compared to the control. Significant differences in total MEK2 and Sprouty1 abundance were also observed. Our cohort of seven individuals with MEK2 deletions has overlapping features associated with RASopathies. This is the first report suggesting that, in addition to activating mutations, MEK2 haploinsufficiency can lead to dysregulation of the MAPK pathway.
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Affiliation(s)
- M J M Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada; Department of Pediatrics, McMaster University, Hamilton, Canada
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48
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Filges I, Hall JG. Failure to identify antenatal multiple congenital contractures and fetal akinesia - proposal of guidelines to improve diagnosis. Prenat Diagn 2013; 33:61-74. [DOI: 10.1002/pd.4011] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Isabel Filges
- Department of Medical Genetics, BC Children's and Women's Hospital, Child and Family Research Institute; University of British Columbia; Vancouver Canada
- Division of Medical Genetics, University Children's Hospital and Department of Biomedicine; University of Basel; Basel Switzerland
| | - Judith G. Hall
- Department of Medical Genetics, BC Children's and Women's Hospital, Child and Family Research Institute; University of British Columbia; Vancouver Canada
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Phosphatidylinositol 4-Kinases and PI4P Metabolism in the Nervous System: Roles in Psychiatric and Neurological Diseases. Mol Neurobiol 2012; 47:361-72. [DOI: 10.1007/s12035-012-8358-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 09/27/2012] [Indexed: 01/18/2023]
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50
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Markus B, Narkis G, Landau D, Birk RZ, Cohen I, Birk OS. Autosomal recessive lethal congenital contractural syndrome type 4 (LCCS4) caused by a mutation in MYBPC1. Hum Mutat 2012; 33:1435-8. [PMID: 22610851 DOI: 10.1002/humu.22122] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 05/07/2012] [Indexed: 11/08/2022]
Abstract
Autosomal recessive lethal congenital contractural syndrome (LCCS) is a severe form of neuromuscular arthrogryposis. We previously showed that this phenotype is caused in two unrelated inbred Bedouin tribes by different defects in the phosphatidylinositol pathway. However, the molecular basis of the same phenotype in other tribes remained elusive. Whole exome sequencing identified a novel LCCS founder mutation within a minimal shared homozygosity locus of approximately 1 Mb in two affected individuals of different tribes: a homozygous premature stop producing mutation in MYBPC1, encoding myosin-binding protein C, slow type. A dominant missense mutation in MYBPC1 was previously shown to cause mild distal arthrogryposis. We now show that a recessive mutation abrogating all functional domains in the same gene leads to LCCS.
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Affiliation(s)
- Barak Markus
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev, Ben Gurion University, Beer-Sheva, Israel
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