1
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Goldberg A, O'Connor P, Gonzalez C, Ouren M, Rivera L, Radde N, Nguyen M, Ponce-Herrera F, Lloyd A, Gonzalez A. Genetic interaction between TTG2 and AtPLC1 reveals a role for phosphoinositide signaling in a co-regulated suite of Arabidopsis epidermal pathways. Sci Rep 2024; 14:9752. [PMID: 38679676 PMCID: PMC11056374 DOI: 10.1038/s41598-024-60530-8] [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: 01/27/2024] [Accepted: 04/24/2024] [Indexed: 05/01/2024] Open
Abstract
The TTG2 transcription factor of Arabidopsis regulates a set of epidermal traits, including the differentiation of leaf trichomes, flavonoid pigment production in cells of the inner testa (or seed coat) layer and mucilage production in specialized cells of the outer testa layer. Despite the fact that TTG2 has been known for over twenty years as an important regulator of multiple developmental pathways, little has been discovered about the downstream mechanisms by which TTG2 co-regulates these epidermal features. In this study, we present evidence of phosphoinositide lipid signaling as a mechanism for the regulation of TTG2-dependent epidermal pathways. Overexpression of the AtPLC1 gene rescues the trichome and seed coat phenotypes of the ttg2-1 mutant plant. Moreover, in the case of seed coat color rescue, AtPLC1 overexpression restored expression of the TTG2 flavonoid pathway target genes, TT12 and TT13/AHA10. Consistent with these observations, a dominant AtPLC1 T-DNA insertion allele (plc1-1D) promotes trichome development in both wild-type and ttg2-3 plants. Also, AtPLC1 promoter:GUS analysis shows expression in trichomes and this expression appears dependent on TTG2. Taken together, the discovery of a genetic interaction between TTG2 and AtPLC1 suggests a role for phosphoinositide signaling in the regulation of trichome development, flavonoid pigment biosynthesis and the differentiation of mucilage-producing cells of the seed coat. This finding provides new avenues for future research at the intersection of the TTG2-dependent developmental pathways and the numerous molecular and cellular phenomena influenced by phospholipid signaling.
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Grants
- 52006985, 52008124 Howard Hughes Medical Institute
- 52006985, 52008124 Howard Hughes Medical Institute
- 52006985, 52008124 Howard Hughes Medical Institute
- 52006985, 52008124 Howard Hughes Medical Institute
- 52006985, 52008124 Howard Hughes Medical Institute
- 52006985, 52008124 Howard Hughes Medical Institute
- 52006985, 52008124 Howard Hughes Medical Institute
- 52006985, 52008124 Howard Hughes Medical Institute
- 52006985, 52008124 Howard Hughes Medical Institute
- 52006985, 52008124 Howard Hughes Medical Institute
- US National Science Foundation
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Affiliation(s)
- Aleah Goldberg
- The Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Patrick O'Connor
- The Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Cassandra Gonzalez
- The Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Mason Ouren
- The Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Luis Rivera
- The Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Noor Radde
- The Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Michael Nguyen
- The Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Felipe Ponce-Herrera
- The Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Alan Lloyd
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway, Austin, TX, 78712, USA
| | - Antonio Gonzalez
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway, Austin, TX, 78712, USA.
- The Freshman Research Initiative, The University of Texas at Austin, Austin, TX, 78712, USA.
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2
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Vidalle MC, Sheth B, Fazio A, Marvi MV, Leto S, Koufi FD, Neri I, Casalin I, Ramazzotti G, Follo MY, Ratti S, Manzoli L, Gehlot S, Divecha N, Fiume R. Nuclear Phosphoinositides as Key Determinants of Nuclear Functions. Biomolecules 2023; 13:1049. [PMID: 37509085 PMCID: PMC10377365 DOI: 10.3390/biom13071049] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Polyphosphoinositides (PPIns) are signalling messengers representing less than five per cent of the total phospholipid concentration within the cell. Despite their low concentration, these lipids are critical regulators of various cellular processes, including cell cycle, differentiation, gene transcription, apoptosis and motility. PPIns are generated by the phosphorylation of the inositol head group of phosphatidylinositol (PtdIns). Different pools of PPIns are found at distinct subcellular compartments, which are regulated by an array of kinases, phosphatases and phospholipases. Six of the seven PPIns species have been found in the nucleus, including the nuclear envelope, the nucleoplasm and the nucleolus. The identification and characterisation of PPIns interactor and effector proteins in the nucleus have led to increasing interest in the role of PPIns in nuclear signalling. However, the regulation and functions of PPIns in the nucleus are complex and are still being elucidated. This review summarises our current understanding of the localisation, biogenesis and physiological functions of the different PPIns species in the nucleus.
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Affiliation(s)
- Magdalena C Vidalle
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Bhavwanti Sheth
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Antonietta Fazio
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Maria Vittoria Marvi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Leto
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Foteini-Dionysia Koufi
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Neri
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Irene Casalin
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Giulia Ramazzotti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Matilde Y Follo
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Stefano Ratti
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Lucia Manzoli
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Sonakshi Gehlot
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Nullin Divecha
- Inositide Laboratory, School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Life Sciences Building 85, Highfield, Southampton SO17 1BJ, UK
| | - Roberta Fiume
- Department of Biomedical Sciences (DIBINEM), University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
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3
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Zarreen F, Kumar K, Chakraborty S. Phosphoinositides in plant-pathogen interaction: trends and perspectives. STRESS BIOLOGY 2023; 3:4. [PMID: 37676371 PMCID: PMC10442044 DOI: 10.1007/s44154-023-00082-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 02/15/2023] [Indexed: 09/08/2023]
Abstract
Phosphoinositides are important regulatory membrane lipids, with a role in plant development and cellular function. Emerging evidence indicates that phosphoinositides play crucial roles in plant defence and are also utilized by pathogens for infection. In this review, we highlight the role of phosphoinositides in plant-pathogen interaction and the implication of this remarkable convergence in the battle against plant diseases.
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Affiliation(s)
- Fauzia Zarreen
- Molecular Virology Laboratory, School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Kamal Kumar
- Molecular Virology Laboratory, School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India.
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4
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Wang YH, Sheetz MP. When PIP 2 Meets p53: Nuclear Phosphoinositide Signaling in the DNA Damage Response. Front Cell Dev Biol 2022; 10:903994. [PMID: 35646908 PMCID: PMC9136457 DOI: 10.3389/fcell.2022.903994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The mechanisms that maintain genome stability are critical for preventing tumor progression. In the past decades, many strategies were developed for cancer treatment to disrupt the DNA repair machinery or alter repair pathway selection. Evidence indicates that alterations in nuclear phosphoinositide lipids occur rapidly in response to genotoxic stresses. This implies that nuclear phosphoinositides are an upstream element involved in DNA damage signaling. Phosphoinositides constitute a new signaling interface for DNA repair pathway selection and hence a new opportunity for developing cancer treatment strategies. However, our understanding of the underlying mechanisms by which nuclear phosphoinositides regulate DNA damage repair, and particularly the dynamics of those processes, is rather limited. This is partly because there are a limited number of techniques that can monitor changes in the location and/or abundance of nuclear phosphoinositide lipids in real time and in live cells. This review summarizes our current knowledge regarding the roles of nuclear phosphoinositides in DNA damage response with an emphasis on the dynamics of these processes. Based upon recent findings, there is a novel model for p53's role with nuclear phosphoinositides in DNA damage response that provides new targets for synthetic lethality of tumors.
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Affiliation(s)
| | - Michael P. Sheetz
- Biochemistry and Molecular Biology Dept., University of Texas Medical Branch, Galveston, TX, United States
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5
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Lin F, Zheng J, Xie Y, Jing W, Zhang Q, Zhang W. Emerging roles of phosphoinositide-associated membrane trafficking in plant stress responses. J Genet Genomics 2022; 49:726-734. [DOI: 10.1016/j.jgg.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 10/18/2022]
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6
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Unconventional metabolites in chromatin regulation. Biosci Rep 2022; 42:230604. [PMID: 34988581 PMCID: PMC8777195 DOI: 10.1042/bsr20211558] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Chromatin, the complex of DNA and histone proteins, serves as a main integrator of cellular signals. Increasing evidence links cellular functional to chromatin state. Indeed, different metabolites are emerging as modulators of chromatin function and structure. Alterations in chromatin state are decisive for regulating all aspects of genome function and ultimately have the potential to produce phenotypic changes. Several metabolites such as acetyl-CoA, S-adenosylmethionine (SAM) or adenosine triphosphate (ATP) have now been well characterized as main substrates or cofactors of chromatin-modifying enzymes. However, there are other metabolites that can directly interact with chromatin influencing its state or that modulate the properties of chromatin regulatory factors. Also, there is a growing list of atypical enzymatic and nonenzymatic chromatin modifications that originate from different cellular pathways that have not been in the limelight of chromatin research. Here, we summarize different properties and functions of uncommon regulatory molecules originating from intermediate metabolism of lipids, carbohydrates and amino acids. Based on the various modes of action on chromatin and the plethora of putative, so far not described chromatin-regulating metabolites, we propose that there are more links between cellular functional state and chromatin regulation to be discovered. We hypothesize that these connections could provide interesting starting points for interfering with cellular epigenetic states at a molecular level.
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7
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Morales JA, Gonzalez-Kantun WA, Rodriguez-Zapata LC, Ramón-Ugalde J, Castano E. The effect of plant stress on phosphoinositides. Cell Biochem Funct 2019; 37:553-559. [PMID: 31478243 DOI: 10.1002/cbf.3432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/20/2019] [Accepted: 08/05/2019] [Indexed: 01/22/2023]
Abstract
Phosphoinositides are very versatile molecules with a plethora of functions such as cytokinesis, chemotaxis, cell survival, and cell death. Their functions depend on the proteins with which they interact. Thus, when interacting with phospholipases, phosphatases, or kinases, they can be precursors of second messengers in different signalling pathways. They could be second messengers themselves and interact directly with other proteins to modulate their functions trough changing its localization and activity or enhancing its synthesis rate. Because they are more abundant in animal cells and their importance in diseases such as cancer has taken priority, the study of the phosphoinositides in plants has not evolved to the same extent. Nevertheless, several studies have shown the significance of these lipids in plant cells viability and environmental response. This review focuses on phosphoinositides response to abiotic and biotic stress, showing their implication in plant survival during different stages of development. SIGNIFICANCE OF THE STUDY: This review is focused on plant PIPs functions in stress, highlighting in the main differences between plant and mammal PIPs and the novel interactions that could be extrapolated to animal models to contribute in a better understanding of these pivotal molecules.
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Affiliation(s)
- Javier Adrian Morales
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Wilma A Gonzalez-Kantun
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | | | - Julio Ramón-Ugalde
- Centro de Selección y Reproducción Ovina (CeSyRO), Instituto Tecnológico de Conkal (ITC), Mérida, Mexico
| | - Enrique Castano
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
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8
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Xing L, Li Y, Qi S, Zhang C, Ma W, Zuo X, Liang J, Gao C, Jia P, Shah K, Zhang D, An N, Zhao C, Han M, Zhao J. Comparative RNA-Sequencing and DNA Methylation Analyses of Apple (Malus domestica Borkh.) Buds with Diverse Flowering Capabilities Reveal Novel Insights into the Regulatory Mechanisms of Flower Bud Formation. PLANT & CELL PHYSIOLOGY 2019; 60:1702-1721. [PMID: 31077318 DOI: 10.1093/pcp/pcz080] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
In plants, DNA methylation (i.e. chromatin modification) is important for various biological processes, including growth, development and flowering. Because 'Fuji' apple trees are alternate bearing and have a long ripening period and poor-quality flower buds, we used bud types with diverse flowering capabilities to investigate the epigenetic regulatory mechanisms influencing flower bud formation. We examined the DNA methylation changes and the transcriptional responses in the selected apple bud types. We observed that in the apple genome, approximately 79.5%, 67.4% and 23.7% of the CG, CHG and CHH sequences are methylated, respectively. For each sequence context, differentially methylated regions exhibited distinct methylation patterns among the analyzed apple bud types. Global methylation and transcriptional analyses revealed that nonexpressed genes or genes expressed at low levels were highly methylated in the gene-body regions, suggesting that gene-body methylation is negatively correlated with gene expression. Moreover, genes with methylated promoters were more highly expressed than genes with unmethylated promoters, implying promoter methylation and gene expression are positively correlated. Additionally, flowering-related genes (e.g. SOC1, AP1 and SPLs) and some transcription factor genes (e.g. GATA, bHLH, bZIP and WOX) were highly expressed in spur buds (highest flowering rate), but were associated with low methylation levels in the gene-body regions. Our findings indicate a potential correlation between DNA methylation and gene expression in apple buds with diverse flowering capabilities, suggesting an epigenetic regulatory mechanism influences apple flower bud formation.
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Affiliation(s)
- Libo Xing
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
- Ministry of Agriculture Rural Affairs, Key Laboratory of Agricultural Internet of Things, Yangling, Shaanxi, P. R. China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, Yangling, Shaanxi, P. R. China
| | - Youmei Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Siyan Qi
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Chenguang Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Wenchun Ma
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Xiya Zuo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Jiayan Liang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Cai Gao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Pen Jia
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Kamran Shah
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Dong Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Na An
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Caiping Zhao
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Mingyu Han
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi, P. R. China
| | - Juan Zhao
- Ministry of Agriculture Rural Affairs, Key Laboratory of Agricultural Internet of Things, Yangling, Shaanxi, P. R. China
- Shaanxi Key Laboratory of Agriculture Information Perception and Intelligent Service, Yangling, Shaanxi, P. R. China
- College of Mechanical and Electronic Engineering, Northwest A & F University, Yangling, Shaanxi, P. R. China
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9
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Nuclear Phosphoinositides-Versatile Regulators of Genome Functions. Cells 2019; 8:cells8070649. [PMID: 31261688 PMCID: PMC6678639 DOI: 10.3390/cells8070649] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/21/2019] [Accepted: 06/25/2019] [Indexed: 12/17/2022] Open
Abstract
The many functions of phosphoinositides in cytosolic signaling were extensively studied; however, their activities in the cell nucleus are much less clear. In this review, we summarize data about their nuclear localization and metabolism, and review the available literature on their involvements in chromatin remodeling, gene transcription, and RNA processing. We discuss the molecular mechanisms via which nuclear phosphoinositides, in particular phosphatidylinositol (4,5)-bisphosphate (PI(4,5)P2), modulate nuclear processes. We focus on PI(4,5)P2’s role in the modulation of RNA polymerase I activity, and functions of the nuclear lipid islets—recently described nucleoplasmic PI(4,5)P2-rich compartment involved in RNA polymerase II transcription. In conclusion, the high impact of the phosphoinositide–protein complexes on nuclear organization and genome functions is only now emerging and deserves further thorough studies.
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10
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Polyphosphoinositides in the nucleus: Roadmap of their effectors and mechanisms of interaction. Adv Biol Regul 2019; 72:7-21. [PMID: 31003946 DOI: 10.1016/j.jbior.2019.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 01/01/2023]
Abstract
Biomolecular interactions between proteins and polyphosphoinositides (PPIn) are essential in the regulation of the vast majority of cellular processes. Consequently, alteration of these interactions is implicated in the development of many diseases. PPIn are phosphorylated derivatives of phosphatidylinositol and consist of seven species with different phosphate combinations. PPIn signal by recruiting proteins via canonical domains or short polybasic motifs. Although their actions are predominantly documented on cytoplasmic membranes, six of the seven PPIn are present within the nucleus together with the PPIn kinases, phosphatases and phospholipases that regulate their turnover. Importantly, the contribution of nuclear PPIn in the regulation of nuclear processes has led to an increased recognition of their importance compared to their more accepted cytoplasmic roles. This review summarises our knowledge on the identification and functional characterisation of nuclear PPIn-effector proteins as well as their mode of interactions, which tend to favour polybasic motifs.
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11
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Avramova Z. Defence-related priming and responses to recurring drought: Two manifestations of plant transcriptional memory mediated by the ABA and JA signalling pathways. PLANT, CELL & ENVIRONMENT 2019; 42:983-997. [PMID: 30299553 DOI: 10.1111/pce.13458] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 09/26/2018] [Accepted: 10/02/2018] [Indexed: 05/20/2023]
Abstract
Collective evidence from agricultural practices and from scientific research has demonstrated that plants can alter their phenotypic responses to repeated biotic and abiotic stresses or their elicitors. A coordinated reaction at the organismal, cellular, and genome levels has suggested that plants can "remember" an earlier stress and modify their future responses, accordingly. Stress memory may increase a plant's survival chances by improving its tolerance/avoidance abilities and may provide a mechanism for acclimation and adaptation. Understanding the mechanisms that regulate plant stress memory is not only an intellectually challenging topic but has important implications for agricultural practices as well. Here, I focus exclusively on specific aspects of the transcription memory in response to recurring dehydration stresses and the memory-type responses to insect damage in a process known as "priming." The questions discussed are (a) whether/how the two memory phenomena are connected at the level of transcriptional regulation; (b) how differential transcription is achieved mechanistically under a repeated stress; and (c) whether similar molecular and/or epigenetic mechanisms are involved. Possible biological relevance of transcriptional stress memory and its preservation in plant evolution are also discussed.
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Affiliation(s)
- Zoya Avramova
- School of Biological Sciences, UNL, Lincoln, Nebraska
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12
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Phospholipids and inositol phosphates linked to the epigenome. Histochem Cell Biol 2018; 150:245-253. [DOI: 10.1007/s00418-018-1690-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2018] [Indexed: 12/17/2022]
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13
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Nagpal A, Hassan A, Ndamukong I, Avramova Z, Baluška F. Myotubularins, PtdIns5P, and ROS in ABA-mediated stomatal movements in dehydrated Arabidopsis seedlings. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:259-266. [PMID: 32291040 DOI: 10.1071/fp17116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 05/23/2017] [Indexed: 06/11/2023]
Abstract
Myotubularins (MTMs) are lipid phosphoinositide 3-phosphate phosphatases and the product of their enzyme activity - phosphoinositide 5-phosphate (PtdIns5P) - functions as a signalling molecule in pathways involved in membrane dynamics and cell signalling. Two Arabidopsis genes, AtMTM1 and AtMTM2, encode enzymatically active phosphatases but although AtMTM1 deficiency results in increased tolerance to dehydration stress and a decrease in cellular PtdIns5P, the role of AtMTM2 is less clear, as it does not contribute to the PtdIns5P pool upon dehydration stress. Here we analysed the involvement of AtMTM1, AtMTM2 and PtdIns5P in the response of Arabidopsis seedlings to dehydration stress/ABA, and found that both AtMTM1 and AtMTM2 were involved but affected oppositely stomata movement and the accumulation of reactive oxygen species (ROS, e.g. H2O2). Acting as a secondary messenger in the ABA-induced ROS production in guard cells, PtdIns5P emerges as an evolutionarily conserved signalling molecule that calibrates cellular ROS under stress. We propose the biological relevance of the counteracting AtMTM1 and AtMTM2 activities is to balance the ABA-induced ROS accumulation and cellular homeostasis under dehydration stress.
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Affiliation(s)
- Akanksha Nagpal
- IZMB, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - Ammar Hassan
- IZMB, University of Bonn, Kirschallee 1, D-53115 Bonn, Germany
| | - Ivan Ndamukong
- School of Biological Sciences, UNL, Lincoln, NE 68588-6008, USA
| | - Zoya Avramova
- School of Biological Sciences, UNL, Lincoln, NE 68588-6008, USA
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14
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Chen HC, Hsieh-Feng V, Liao PC, Cheng WH, Liu LY, Yang YW, Lai MH, Chang MC. The function of OsbHLH068 is partially redundant with its homolog, AtbHLH112, in the regulation of the salt stress response but has opposite functions to control flowering in Arabidopsis. PLANT MOLECULAR BIOLOGY 2017; 94:531-548. [PMID: 28631168 PMCID: PMC5504132 DOI: 10.1007/s11103-017-0624-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 06/12/2017] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE The homologous genes OsbHLH068 and AtbHLH112 have partially redundant functions in the regulation of the salt stress response but opposite functions to control flowering in Arabidopsis. The transcription factor (TF) basic/Helix-Loop-Helix (bHLH) is important for plant growth, development, and stress responses. OsbHLH068, which is a homologous gene of AtbHLH112 that is up-regulated under drought and salt stresses, as indicated by previous microarray data analysis. However, the intrinsic function of OsbHLH068 remains unknown. In the present study, we characterized the function and compared the role of OsbHLH068 with that of its homolog, AtbHLH112. Histochemical GUS staining indicated that OsbHLH068 and AtbHLH112 share a similar expression pattern in transgenic Arabidopsis during the juvenile-to-adult phase transition. Heterologous overexpression of OsbHLH068 in Arabidopsis delays seed germination, decreases salt-induced H2O2 accumulation, and promotes root elongation, whereas AtbHLH112 knock-out mutant displays an opposite phenotype. Both OsbHLH068-overexpressing transgenic Arabidopsis seedlings and the Atbhlh112 mutant display a late-flowering phenotype. Moreover, the expression of OsbHLH068-GFP driven by an AtbHLH112 promoter can compensate for the germination deficiency in the Atbhlh112 mutant, but the delayed-flowering phenotype tends to be more severe. Further analysis by microarray and qPCR indicated that the expression of FT is down-regulated in both OsbHLH068-overexpressing Arabidopsis plants and Atbhlh112 mutant plants, whereas SOC1 but not FT is highly expressed in AtbHLH112-overexpressing Arabidopsis plants. A comparative transcriptomic analysis also showed that several stress-responsive genes, such as AtERF15 and AtPUB23, were affected in both OsbHLH068- and AtbHLH112-overexpressing transgenic Arabidopsis plants. Thus, we propose that OsbHLH068 and AtbHLH112 share partially redundant functions in the regulation of abiotic stress responses but have opposite functions to control flowering in Arabidopsis, presumably due to the evolutionary functional divergence of homolog-encoded proteins.
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Affiliation(s)
- Hung-Chi Chen
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Vicki Hsieh-Feng
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Pei-Chun Liao
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Wan-Hsing Cheng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Li-Yu Liu
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Yun-Wei Yang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, Taichung, Taiwan, ROC
| | - Men-Chi Chang
- Department of Agronomy, National Taiwan University, Taipei, Taiwan, ROC.
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15
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Lu C, Tian Y, Wang S, Su Y, Mao T, Huang T, Chen Q, Xu Z, Ding Y. Phosphorylation of SPT5 by CDKD;2 Is Required for VIP5 Recruitment and Normal Flowering in Arabidopsis thaliana. THE PLANT CELL 2017; 29:277-291. [PMID: 28188267 PMCID: PMC5354186 DOI: 10.1105/tpc.16.00568] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 01/10/2017] [Accepted: 02/09/2017] [Indexed: 05/10/2023]
Abstract
The elongation factor suppressor of Ty 5 homolog (Spt5) is a regulator of transcription and histone methylation. In humans, phosphorylation of SPT5 by P-TEFb, a protein kinase composed of Cyclin-dependent kinase 9 (CDK9) and cyclin T, interacts with the RNA polymerase II-associated factor1 (PAF1) complex. However, the mechanism of SPT5 phosphorylation is not well understood in plants. Here, we examine the function of SPT5 in Arabidopsis thaliana and find that spt5 mutant flowers early under long-day and short-day conditions. SPT5 interacts with the CDK-activating kinase 4 (CAK4; CDKD;2) and is specifically phosphorylated by CDKD;2 at threonines. The phosphorylated SPT5 binds VERNALIZATION INDEPENDENCE5 (VIP5), a subunit of the PAF1 complex. Genetic analysis showed that VIP5 acts downstream of SPT5 and CDKD;2 Loss of SPT5 or CDKD;2 function results in early flowering because of decreased amounts of FLOWERING LOCUS C (FLC) transcript. Importantly, CDKD;2 and SPT5 are required for the deposition of VIP5 and the enhancement of trimethylation of histone 3 lysine 4 in the chromatin of the FLC locus. Together, our results provide insight into the mechanism by which the Arabidopsis elongation factor SPT5 recruits the PAF1 complex via the posttranslational modification of proteins and suggest that the phosphorylation of SPT5 by CDKD;2 enables it to recruit VIP5 to regulate chromatin and transcription in Arabidopsis.
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Affiliation(s)
- Chengyuan Lu
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Yongke Tian
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Shiliang Wang
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Yanhua Su
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Ting Mao
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Tongtong Huang
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Qingqing Chen
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Zuntao Xu
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
| | - Yong Ding
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Anhui, China 230027
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16
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Nagpal A, Ndamukong I, Hassan A, Avramova Z, Baluška F. Subcellular localizations of Arabidopsis myotubularins MTM1 and MTM2 suggest possible functions in vesicular trafficking between ER and cis-Golgi. JOURNAL OF PLANT PHYSIOLOGY 2016; 200:45-52. [PMID: 27340857 DOI: 10.1016/j.jplph.2016.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/03/2016] [Accepted: 06/03/2016] [Indexed: 06/06/2023]
Abstract
The two Arabidopsis genes AtMTM1 and AtMTM2 encode highly similar phosphoinositide 3-phosphatases from the myotubularin family. Despite the high-level conservation of structure and biochemical activities, their physiological roles have significantly diverged. The nature of a membrane and the concentrations of their membrane-anchored substrates (PtdIns3P or PtdIns3,5P2) and/or products (PtdIns5P and PtdIns) are considered critical for determining the functional specificity of myotubularins. We have performed comprehensive analyses of the subcellular localization of AtMTM1 and AtMTM2 using a variety of specific constructs transiently expressed in Nicotiana benthamiana leaf epidermal cells under the control of 35S promoter. AtMTM1 co-localized preferentially with cis-Golgi membranes, while AtMTM2 associated predominantly with ER membranes. In a stark contrast with animal/human MTMs, neither AtMTM1 nor AtMTM2 co-localizes with early or late endosomes or with TGN/EE compartments, making them unlikely participants in the endosomal trafficking system. Localization of the AtMTM2 is sensitive to cold and osmotic stress challenges. In contrast to animal myotubularins, Arabidopsis myotubularins do not associate with endosomes. Our results suggest that Arabidopsis myotubularins play a role in the vesicular trafficking between ER exit sites and cis-Golgi elements. The significance of these results is discussed also in the context of stress biology and plant autophagy.
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Affiliation(s)
| | - Ivan Ndamukong
- School of Biological Sciences, UNL, Lincoln NE, 68588, United States
| | - Ammar Hassan
- IZMB, University of Bonn, Kirschalle 1, 53115 Bonn, Germany
| | - Zoya Avramova
- School of Biological Sciences, UNL, Lincoln NE, 68588, United States.
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17
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Hou Q, Ufer G, Bartels D. Lipid signalling in plant responses to abiotic stress. PLANT, CELL & ENVIRONMENT 2016; 39:1029-48. [PMID: 26510494 DOI: 10.1111/pce.12666] [Citation(s) in RCA: 320] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 05/18/2023]
Abstract
Lipids are one of the major components of biological membranes including the plasma membrane, which is the interface between the cell and the environment. It has become clear that membrane lipids also serve as substrates for the generation of numerous signalling lipids such as phosphatidic acid, phosphoinositides, sphingolipids, lysophospholipids, oxylipins, N-acylethanolamines, free fatty acids and others. The enzymatic production and metabolism of these signalling molecules are tightly regulated and can rapidly be activated upon abiotic stress signals. Abiotic stress like water deficit and temperature stress triggers lipid-dependent signalling cascades, which control the expression of gene clusters and activate plant adaptation processes. Signalling lipids are able to recruit protein targets transiently to the membrane and thus affect conformation and activity of intracellular proteins and metabolites. In plants, knowledge is still scarce of lipid signalling targets and their physiological consequences. This review focuses on the generation of signalling lipids and their involvement in response to abiotic stress. We describe lipid-binding proteins in the context of changing environmental conditions and compare different approaches to determine lipid-protein interactions, crucial for deciphering the signalling cascades.
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Affiliation(s)
- Quancan Hou
- University of Bonn IMBIO Bonn Germany, Kirschallee 1, Bonn, D-53115, Germany
| | - Guido Ufer
- University of Bonn IMBIO Bonn Germany, Kirschallee 1, Bonn, D-53115, Germany
| | - Dorothea Bartels
- University of Bonn IMBIO Bonn Germany, Kirschallee 1, Bonn, D-53115, Germany
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18
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Gu T, Han Y, Huang R, McAvoy RJ, Li Y. Identification and characterization of histone lysine methylation modifiers in Fragaria vesca. Sci Rep 2016; 6:23581. [PMID: 27049067 PMCID: PMC4822149 DOI: 10.1038/srep23581] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/09/2016] [Indexed: 12/31/2022] Open
Abstract
The diploid woodland strawberry (Fragaria vesca) is an important model for fruit crops because of several unique characteristics including the small genome size, an ethylene-independent fruit ripening process, and fruit flesh derived from receptacle tissues rather than the ovary wall which is more typical of fruiting plants. Histone methylation is an important factor in gene regulation in higher plants but little is known about its roles in fruit development. We have identified 45 SET methyltransferase, 22 JmjC demethylase and 4 LSD demethylase genes in F. vesca. The analysis of these histone modifiers in eight plant species supports the clustering of those genes into major classes consistent with their functions. We also provide evidence that whole genome duplication and dispersed duplications via retrotransposons may have played pivotal roles in the expansion of histone modifier genes in F. vesca. Furthermore, transcriptome data demonstrated that expression of some SET genes increase as the fruit develops and peaks at the turning stage. Meanwhile, we have observed that expression of those SET genes responds to cold and heat stresses. Our results indicate that regulation of histone methylation may play a critical role in fruit development as well as responses to abiotic stresses in strawberry.
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Affiliation(s)
- Tingting Gu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Yuhui Han
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Ruirui Huang
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China
| | - Richard J McAvoy
- Department of Plant Science and Landscape Architecture, University of Connecticut, CT 06269, USA
| | - Yi Li
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, P. R. China.,Department of Plant Science and Landscape Architecture, University of Connecticut, CT 06269, USA
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19
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Cocco L, Manzoli L, Faenza I, Ramazzotti G, Yang YR, McCubrey JA, Suh PG, Follo MY. Modulation of nuclear PI-PLCbeta1 during cell differentiation. Adv Biol Regul 2016; 60:1-5. [PMID: 26525203 DOI: 10.1016/j.jbior.2015.10.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 10/21/2015] [Indexed: 06/05/2023]
Abstract
PI-PLCbeta1 plays an important role in cell differentiation, and particularly in myogenesis, osteogenesis and hematopoiesis. Indeed, the increase of PI-PLCbeta1, along with Cyclin D3, has been detected in C2C12 mouse myoblasts induced to differentiate, as well as in human cells obtained from myotonic dystrophy. Also in the case of osteogenic differentiation there is a specific induction of PI-PLCbeta1, but in this case the role of PI-PLCbeta1 seems to be independent from Cyclin D3, so that a different mechanism could be involved. As for the hematopoietic system, PI-PLCbeta1 has a peculiar behavior: it increases during myeloid differentiation and decreases during erythroid differentiation, thus confirming the role of PI-PLCbeta1 as a modulator of hematopoiesis.
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Affiliation(s)
- Lucio Cocco
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Bologna, Italy
| | - Lucia Manzoli
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Bologna, Italy
| | - Irene Faenza
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Bologna, Italy
| | - Giulia Ramazzotti
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Bologna, Italy
| | - Yong Ryoul Yang
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Pann-Ghill Suh
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Matilde Y Follo
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Bologna, Italy.
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20
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Nakamura Y. Function of polar glycerolipids in flower development in Arabidopsis thaliana. Prog Lipid Res 2015; 60:17-29. [DOI: 10.1016/j.plipres.2015.09.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 09/22/2015] [Indexed: 11/28/2022]
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21
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Avramova Z. Transcriptional 'memory' of a stress: transient chromatin and memory (epigenetic) marks at stress-response genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:149-59. [PMID: 25788029 DOI: 10.1111/tpj.12832] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/10/2015] [Accepted: 03/13/2015] [Indexed: 05/17/2023]
Abstract
Drought, salinity, extreme temperature variations, pathogen and herbivory attacks are recurring environmental stresses experienced by plants throughout their life. To survive repeated stresses, plants provide responses that may be different from their response during the first encounter with the stress. A different response to a similar stress represents the concept of 'stress memory'. A coordinated reaction at the organismal, cellular and gene/genome levels is thought to increase survival chances by improving the plant's tolerance/avoidance abilities. Ultimately, stress memory may provide a mechanism for acclimation and adaptation. At the molecular level, the concept of stress memory indicates that the mechanisms responsible for memory-type transcription during repeated stresses are not based on repetitive activation of the same response pathways activated by the first stress. Some recent advances in the search for transcription 'memory factors' are discussed with an emphasis on super-induced dehydration stress memory response genes in Arabidopsis.
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Affiliation(s)
- Zoya Avramova
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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22
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Stijf-Bultsma Y, Sommer L, Tauber M, Baalbaki M, Giardoglou P, Jones DR, Gelato KA, van Pelt J, Shah Z, Rahnamoun H, Toma C, Anderson KE, Hawkins P, Lauberth SM, Haramis APG, Hart D, Fischle W, Divecha N. The basal transcription complex component TAF3 transduces changes in nuclear phosphoinositides into transcriptional output. Mol Cell 2015; 58:453-67. [PMID: 25866244 PMCID: PMC4429956 DOI: 10.1016/j.molcel.2015.03.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 01/20/2015] [Accepted: 03/06/2015] [Indexed: 12/17/2022]
Abstract
Phosphoinositides (PI) are important signaling molecules in the nucleus that influence gene expression. However, if and how nuclear PI directly affects the transcriptional machinery is not known. We report that the lipid kinase PIP4K2B regulates nuclear PI5P and the expression of myogenic genes during myoblast differentiation. A targeted screen for PI interactors identified the PHD finger of TAF3, a TATA box binding protein-associated factor with important roles in transcription regulation, pluripotency, and differentiation. We show that the PI interaction site is distinct from the known H3K4me3 binding region of TAF3 and that PI binding modulates association of TAF3 with H3K4me3 in vitro and with chromatin in vivo. Analysis of TAF3 mutants indicates that TAF3 transduces PIP4K2B-mediated alterations in PI into changes in specific gene transcription. Our study reveals TAF3 as a direct target of nuclear PI and further illustrates the importance of basal transcription components as signal transducers.
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Affiliation(s)
- Yvette Stijf-Bultsma
- The Inositide Laboratory, Centre for Biological Sciences, Highfield Campus, University of Southampton, Southampton SO171BJ, UK; The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK
| | - Lilly Sommer
- The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK
| | - Maria Tauber
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Mai Baalbaki
- University of California, San Francisco, Mail Code 3120, Smith Cardiovascular Research Building, 555 Mission Bay Boulevard, South San Francisco, CA 94158-9001, USA
| | - Panagiota Giardoglou
- Institute of Biology (IBL), Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - David R Jones
- The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK
| | - Kathy A Gelato
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jason van Pelt
- Institute of Biology (IBL), Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Zahid Shah
- The Inositide Laboratory, Centre for Biological Sciences, Highfield Campus, University of Southampton, Southampton SO171BJ, UK
| | - Homa Rahnamoun
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Clara Toma
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Karen E Anderson
- Signaling Laboratory, The Babraham Institute, Cambridge, Cambridgeshire CB22 3AT, UK
| | - Philip Hawkins
- Signaling Laboratory, The Babraham Institute, Cambridge, Cambridgeshire CB22 3AT, UK
| | - Shannon M Lauberth
- Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Anna-Pavlina G Haramis
- Institute of Biology (IBL), Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, the Netherlands
| | - Daniel Hart
- University of California, San Francisco, Mail Code 3120, Smith Cardiovascular Research Building, 555 Mission Bay Boulevard, South San Francisco, CA 94158-9001, USA
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Nullin Divecha
- The Inositide Laboratory, Centre for Biological Sciences, Highfield Campus, University of Southampton, Southampton SO171BJ, UK; The Inositide Laboratory, the CRUK Manchester Institute, the University of Manchester, Wilmslow Road, Manchester M204BX, UK.
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23
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Jude JG, Spencer GJ, Huang X, Somerville TDD, Jones DR, Divecha N, Somervaille TCP. A targeted knockdown screen of genes coding for phosphoinositide modulators identifies PIP4K2A as required for acute myeloid leukemia cell proliferation and survival. Oncogene 2015; 34:1253-1262. [PMID: 24681948 PMCID: PMC4130659 DOI: 10.1038/onc.2014.77] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 01/28/2014] [Accepted: 02/20/2014] [Indexed: 02/06/2023]
Abstract
Given the importance of deregulated phosphoinositide (PI) signaling in leukemic hematopoiesis, genes coding for proteins that regulate PI metabolism may have significant and as yet unappreciated roles in leukemia. We performed a targeted knockdown (KD) screen of PI modulator genes in human acute myeloid leukemia (AML) cells and identified candidates required to sustain proliferation or prevent apoptosis. One of these, the lipid kinase phosphatidylinositol-5-phosphate 4-kinase, type II, alpha (PIP4K2A) regulates cellular levels of phosphatidylinositol-5-phosphate (PtsIns5P) and phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P₂). We found PIP4K2A to be essential for the clonogenic and leukemia-initiating potential of human AML cells, and for the clonogenic potential of murine MLL-AF9 AML cells. Importantly, PIP4K2A is also required for the clonogenic potential of primary human AML cells. Its KD results in accumulation of the cyclin-dependent kinase inhibitors CDKN1A and CDKN1B, G₁ cell cycle arrest and apoptosis. Both CDKN1A accumulation and apoptosis were partially dependent on activation of the mTOR pathway. Critically, however, PIP4K2A KD in normal hematopoietic stem and progenitor cells, both murine and human, did not adversely impact either clonogenic or multilineage differentiation potential, indicating a selective dependency that we suggest may be the consequence of the regulation of different transcriptional programs in normal versus malignant cells. Thus, PIP4K2A is a novel candidate therapeutic target in myeloid malignancy.
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Affiliation(s)
- Julian G Jude
- Inositide Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Gary J Spencer
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Xu Huang
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Tim D D Somerville
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - David R Jones
- Inositide Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Nullin Divecha
- Inositide Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
| | - Tim C P Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4BX, United Kingdom
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24
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Bulley SJ, Clarke JH, Droubi A, Giudici ML, Irvine RF. Exploring phosphatidylinositol 5-phosphate 4-kinase function. Adv Biol Regul 2014; 57:193-202. [PMID: 25311266 PMCID: PMC4359101 DOI: 10.1016/j.jbior.2014.09.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 11/30/2022]
Abstract
The family of phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) is emerging from a comparative backwater in inositide signalling into the mainstream, as is their substrate, phosphatidylinositol 5-phosphate (PI5P). Here we review some of the key questions about the PI5P4Ks, their localisation, interaction, and regulation and also we summarise our current understanding of how PI5P is synthesised and what its cellular functions might be. Finally, some of the evidence for the involvement of PI5P4Ks in pathology is discussed.
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Affiliation(s)
- Simon J Bulley
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Jonathan H Clarke
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
| | - Alaa Droubi
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK
| | | | - Robin F Irvine
- Department of Pharmacology, Tennis Court Road, Cambridge, CB2 1PD, UK.
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25
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Fromm M, Avramova Z. ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis genes? CURRENT OPINION IN PLANT BIOLOGY 2014; 21:75-82. [PMID: 25047977 DOI: 10.1016/j.pbi.2014.07.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 06/26/2014] [Accepted: 07/02/2014] [Indexed: 06/03/2023]
Abstract
Despite the proven correlation between gene transcriptional activity and the levels of tri-methyl marks on histone 3 lysine4 (H3K4me3) of their nucleosomes, whether H3K4me3 contributes to, or 'registers', activated transcription is still controversial. Other questions of broad relevance are whether histone-modifying proteins are involved in the recruitment of Pol II and the general transcription machinery and whether they have roles other than their enzyme activities. We address these questions as well as the roles of the ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), of the COMPASS-related (AtCOMPASS) protein complex, and of their product, H3K4me3, at ATX1-dependent genes. We suggest that the ambiguity about the role of H3K4me3 as an activating mark is due to the unknown duality of the ATX1/AtCOMPASS to facilitate PIC assembly and to generate H3K4me3, which is essential for activating transcriptional elongation.
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Affiliation(s)
- Michael Fromm
- Department of Agronomy and Plant Science Innovation, UNL, Lincoln, NE 68588-6008, USA
| | - Zoya Avramova
- School of Biological Science, UNL, Lincoln, NE 68588-6008, USA.
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Han SK, Wagner D. Role of chromatin in water stress responses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2785-99. [PMID: 24302754 PMCID: PMC4110454 DOI: 10.1093/jxb/ert403] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
As sessile organisms, plants are exposed to environmental stresses throughout their life. They have developed survival strategies such as developmental and morphological adaptations, as well as physiological responses, to protect themselves from adverse environments. In addition, stress sensing triggers large-scale transcriptional reprogramming directed at minimizing the deleterious effect of water stress on plant cells. Here, we review recent findings that reveal a role of chromatin in water stress responses. In addition, we discuss data in support of the idea that chromatin remodelling and modifying enzymes may be direct targets of stress signalling pathways. Modulation of chromatin regulator activity by these signaling pathways may be critical in minimizing potential trade-offs between growth and stress responses. Alterations in the chromatin organization and/or in the activity of chromatin remodelling and modifying enzymes may furthermore contribute to stress memory. Mechanistic insight into these phenomena derived from studies in model plant systems should allow future engineering of broadly drought-tolerant crop plants that do not incur unnecessary losses in yield or growth.
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Affiliation(s)
- Soon-Ki Han
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Kissoudis C, van de Wiel C, Visser RGF, van der Linden G. Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk. FRONTIERS IN PLANT SCIENCE 2014; 5:207. [PMID: 24904607 PMCID: PMC4032886 DOI: 10.3389/fpls.2014.00207] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/28/2014] [Indexed: 05/18/2023]
Abstract
Plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. Research has so far been limited to responses to individual stresses, and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. Omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. Taking into account that most data originate from imposition of individual stress factors, this review summarizes these findings in a physiological context, following the pathogenesis timeline and highlighting potential differential interactions occurring between abiotic and biotic stress signaling across the different cellular compartments and at the whole plant level. Potential effects of abiotic stress on resistance components such as extracellular receptor proteins, R-genes and systemic acquired resistance will be elaborated, as well as crosstalk at the levels of hormone, reactive oxygen species, and redox signaling. Breeding targets and strategies are proposed focusing on either manipulation and deployment of individual common regulators such as transcription factors or pyramiding of non- (negatively) interacting components such as R-genes with abiotic stress resistance genes. We propose that dissection of broad spectrum stress tolerance conferred by priming chemicals may provide an insight on stress cross regulation and additional candidate genes for improving crop performance under combined stress. Validation of the proposed strategies in lab and field experiments is a first step toward the goal of achieving tolerance to combinatorial stress in crops.
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Gelato KA, Tauber M, Ong MS, Winter S, Hiragami-Hamada K, Sindlinger J, Lemak A, Bultsma Y, Houliston S, Schwarzer D, Divecha N, Arrowsmith CH, Fischle W. Accessibility of different histone H3-binding domains of UHRF1 is allosterically regulated by phosphatidylinositol 5-phosphate. Mol Cell 2014; 54:905-919. [PMID: 24813945 DOI: 10.1016/j.molcel.2014.04.004] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/11/2014] [Accepted: 04/02/2014] [Indexed: 11/30/2022]
Abstract
UHRF1 is a multidomain protein crucially linking histone H3 modification states and DNA methylation. While the interaction properties of its specific domains are well characterized, little is known about the regulation of these functionalities. We show that UHRF1 exists in distinct active states, binding either unmodified H3 or the H3 lysine 9 trimethylation (H3K9me3) modification. A polybasic region (PBR) in the C terminus blocks interaction of a tandem tudor domain (TTD) with H3K9me3 by occupying an essential peptide-binding groove. In this state the plant homeodomain (PHD) mediates interaction with the extreme N terminus of the unmodified H3 tail. Binding of the phosphatidylinositol phosphate PI5P to the PBR of UHRF1 results in a conformational rearrangement of the domains, allowing the TTD to bind H3K9me3. Our results define an allosteric mechanism controlling heterochromatin association of an essential regulatory protein of epigenetic states and identify a functional role for enigmatic nuclear phosphatidylinositol phosphates.
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Affiliation(s)
- Kathy A Gelato
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Maria Tauber
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michelle S Ong
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Stefan Winter
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kyoko Hiragami-Hamada
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Julia Sindlinger
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
| | - Alexander Lemak
- Princess Margaret Cancer Center, TMDT, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Yvette Bultsma
- Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Scott Houliston
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Center, TMDT, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
| | - Nullin Divecha
- Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Center, TMDT, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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Peremarti A, Marè C, Aprile A, Roncaglia E, Cattivelli L, Villegas D, Royo C. Transcriptomic and proteomic analyses of a pale-green durum wheat mutant shows variations in photosystem components and metabolic deficiencies under drought stress. BMC Genomics 2014; 15:125. [PMID: 24521234 PMCID: PMC3937041 DOI: 10.1186/1471-2164-15-125] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 02/04/2014] [Indexed: 01/08/2023] Open
Abstract
Background Leaf pigment content is an important trait involved in environmental interactions. In order to determine its impact on drought tolerance in wheat, we characterized a pale-green durum wheat mutant (Triticum turgidum L. var. durum) under contrasting water availability conditions. Results The pale-green mutant was investigated by comparing pigment content and gene/protein expression profiles to wild-type plants at anthesis. Under well-watered (control) conditions the mutant had lower levels of chlorophylls and carotenoids, but higher levels of xanthophyll de-epoxidation compared to wild-type. Transcriptomic analysis under control conditions showed that defense genes (encoding e.g. pathogenesis-related proteins, peroxidases and chitinases) were upregulated in the mutant, suggesting the presence of mild oxidative stress that was compensated without altering the net rate of photosynthesis. Transcriptomic analysis under terminal water stress conditions, revealed the modulation of antioxidant enzymes, photosystem components, and enzymes representing carbohydrate metabolism and the tricarboxylic acid cycle, indicating that the mutant was exposed to greater oxidative stress than the wild-type plants, but had a limited capacity to respond. We also compared the two genotypes under irrigated and rain-fed field conditions over three years, finding that the greater oxidative stress and corresponding molecular changes in the pale-green mutant were associated to a yield reduction. Conclusions This study provides insight on the effect of pigment content in the molecular response to drought. Identified genes differentially expressed under terminal water stress may be valuable for further studies addressing drought resistance in wheat.
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Affiliation(s)
- Ariadna Peremarti
- Agrotecnio Center, Av, Alcalde Rovira Roure 191, Lleida E-25198, Spain.
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Viaud J, Boal F, Tronchère H, Gaits-Iacovoni F, Payrastre B. Phosphatidylinositol 5-phosphate: A nuclear stress lipid and a tuner of membranes and cytoskeleton dynamics. Bioessays 2013; 36:260-72. [DOI: 10.1002/bies.201300132] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Julien Viaud
- Inserm U1048; I2MC and Université Paul Sabatier; Toulouse France
| | - Frédéric Boal
- Inserm U1048; I2MC and Université Paul Sabatier; Toulouse France
| | - Hélène Tronchère
- Inserm U1048; I2MC and Université Paul Sabatier; Toulouse France
| | | | - Bernard Payrastre
- Inserm U1048; I2MC and Université Paul Sabatier; Toulouse France
- CHU de Toulouse; Laboratoire d'Hématologie; Toulouse France
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31
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Shah ZH, Jones DR, Sommer L, Foulger R, Bultsma Y, D'Santos C, Divecha N. Nuclear phosphoinositides and their impact on nuclear functions. FEBS J 2013; 280:6295-310. [PMID: 24112514 DOI: 10.1111/febs.12543] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/11/2013] [Accepted: 09/16/2013] [Indexed: 12/23/2022]
Abstract
Polyphosphoinositides (PPIn) are important lipid molecules whose levels are de-regulated in human diseases such as cancer, neurodegenerative disorders and metabolic syndromes. PPIn are synthesized and degraded by an array of kinases, phosphatases and lipases which are localized to various subcellular compartments and are subject to regulation in response to both extra- and intracellular cues. Changes in the activities of enzymes that metabolize PPIn lead to changes in the profiles of PPIn in various subcellular compartments. Understanding how subcellular PPIn are regulated and how they affect downstream signaling is critical to understanding their roles in human diseases. PPIn are present in the nucleus, and their levels are changed in response to various stimuli, suggesting that they may serve to regulate specific nuclear functions. However, the lack of nuclear downstream targets has hindered the definition of which pathways nuclear PPIn affect. Over recent years, targeted and global proteomic studies have identified a plethora of potential PPIn-interacting proteins involved in many aspects of transcription, chromatin remodelling and mRNA maturation, suggesting that PPIn signalling within the nucleus represents a largely unexplored novel layer of complexity in the regulation of nuclear functions.
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Affiliation(s)
- Zahid H Shah
- Cancer Research UK Inositide Laboratory, Paterson Institute for Cancer Research, Manchester, UK
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32
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Keune WJ, Sims AH, Jones DR, Bultsma Y, Lynch JT, Jirström K, Landberg G, Divecha N. Low PIP4K2B expression in human breast tumors correlates with reduced patient survival: A role for PIP4K2B in the regulation of E-cadherin expression. Cancer Res 2013; 73:6913-25. [PMID: 24127122 DOI: 10.1158/0008-5472.can-13-0424] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Phosphatidylinositol-5-phosphate (PtdIns5P) 4-kinase β (PIP4K2B) directly regulates the levels of two important phosphoinositide second messengers, PtdIns5P and phosphatidylinositol-(4,5)-bisphosphate [PtdIns(4,5)P2]. PIP4K2B has been linked to the regulation of gene transcription, to TP53 and AKT activation, and to the regulation of cellular reactive oxygen accumulation. However, its role in human tumor development and on patient survival is not known. Here, we have interrogated the expression of PIP4K2B in a cohort (489) of patients with breast tumor using immunohistochemical staining and by a meta-analysis of gene expression profiles from 2,999 breast tumors, both with associated clinical outcome data. Low PIP4K2B expression was associated with increased tumor size, high Nottingham histological grade, Ki67 expression, and distant metastasis, whereas high PIP4K2B expression strongly associated with ERBB2 expression. Kaplan-Meier curves showed that both high and low PIP4K2B expression correlated with poorer patient survival compared with intermediate expression. In normal (MCF10A) and tumor (MCF7) breast epithelial cell lines, mimicking low PIP4K2B expression, using short hairpin RNA interference-mediated knockdown, led to a decrease in the transcription and expression of the tumor suppressor protein E-cadherin (CDH1). In MCF10A cells, knockdown of PIP4K2B enhanced TGF-β-induced epithelial to mesenchymal transition (EMT), a process required during the development of metastasis. Analysis of gene expression datasets confirmed the association between low PIP4K2B and low CDH1expression. Decreased CDH1 expression and enhancement of TGF-β-induced EMT by reduced PIP4K2B expression might, in part, explain the association between low PIP4K2B expression and poor patient survival.
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Affiliation(s)
- Willem-Jan Keune
- Authors' Affiliations: The CRUK Inositide Laboratory; Breakthrough Breast Cancer Research Unit; Leukaemia Biology, Inositide Group Cancer Research UK Manchester Institute, The University of Manchester, Manchester; Applied Bioinformatics of Cancer, University of Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom; and Center for Molecular Pathology, Department of Laboratory Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
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Coordinating metabolite changes with our perception of plant abiotic stress responses: emerging views revealed by integrative-omic analyses. Metabolites 2013; 3:761-86. [PMID: 24958149 PMCID: PMC3901284 DOI: 10.3390/metabo3030761] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 08/21/2013] [Accepted: 08/28/2013] [Indexed: 11/17/2022] Open
Abstract
Metabolic configuration and adaptation under a range of abiotic stresses, including drought, heat, salinity, cold, and nutrient deprivation, are subjected to an intricate span of molecular pathways that work in parallel in order to enhance plant fitness and increase stress tolerance. In recent years, unprecedented advances have been made in identifying and linking different abiotic stresses, and the current challenge in plant molecular biology is deciphering how the signaling responses are integrated and transduced throughout metabolism. Metabolomics have often played a fundamental role in elucidating the distinct and overlapping biochemical changes that occur in plants. However, a far greater understanding and appreciation of the complexity in plant metabolism under specific stress conditions have become apparent when combining metabolomics with other—omic platforms. This review focuses on recent advances made in understanding the global changes occurring in plant metabolism under abiotic stress conditions using metabolite profiling as an integrated discovery platform.
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34
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Shisheva A. PtdIns5P: news and views of its appearance, disappearance and deeds. Arch Biochem Biophys 2013; 538:171-80. [PMID: 23916588 DOI: 10.1016/j.abb.2013.07.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 07/22/2013] [Indexed: 12/24/2022]
Abstract
Accumulated evidence indicates that PtdIns5P, one of the seven phosphoinositides, found now to be constitutively present in yeast, plants and metazoa, serves as a signaling molecule to modulate pleiotropic cellular functions in both the nucleus and the cytoplasm. The enzymatic routes in biogenesis of basal PtdIns5P have remained incompletely understood. The role for candidate kinase PIKfyve that is principally involved in PtdIns(3,5)P2 production, has been questioned. In this review article we scrutinize the past obstacles that prevented the definitive implication of PIKfyve in PtdIns5P biosynthesis from PtdIns and focus on the recent pharmacological and genetic advancements that now make this conclusion well supported. We further summarize our current knowledge of the diverse stimuli modulating PtdIns5P levels, binding partners and regulated cellular process, with particular reference to the available mechanistic insights for the relevant signaling pathways.
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Affiliation(s)
- Assia Shisheva
- Department of Physiology, Wayne State University School of Medicine, 540 E. Canfield, Detroit, MI 48201, United States.
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35
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Lam SM, Shui G. Lipidomics as a Principal Tool for Advancing Biomedical Research. J Genet Genomics 2013; 40:375-90. [DOI: 10.1016/j.jgg.2013.06.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/04/2013] [Accepted: 06/19/2013] [Indexed: 01/22/2023]
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36
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Jones DR, Ramirez IBR, Lowe M, Divecha N. Measurement of phosphoinositides in the zebrafish Danio rerio. Nat Protoc 2013; 8:1058-72. [DOI: 10.1038/nprot.2013.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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37
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Elouarrat D, van der Velden YU, Jones DR, Moolenaar WH, Divecha N, Haramis APG. Role of phosphatidylinositol 5-phosphate 4-kinase α in zebrafish development. Int J Biochem Cell Biol 2013; 45:1293-301. [PMID: 23542014 DOI: 10.1016/j.biocel.2013.03.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 10/27/2022]
Abstract
Phosphatidylinositol 5-phosphate 4-kinases (PIP4Ks) phosphorylate phosphatidylinositol 5-phosphate (PI5P) to generate phosphatidylinositol 4,5-bisphosphate; their most likely function is the regulation of the levels of PI5P, a putative signalling intermediate. There are three mammalian PIP4Ks isoforms (α, β and γ), but their physiological roles remain poorly understood. In the present study, we identified the zebrafish orthologue (zPIP4Kα) of the high-activity human PIP4K α isoform and analyzed its role in embryonic development. RT-PCR analysis and whole-mount in situ hybridization experiments showed that zPIP4Kα is maternally expressed. At later embryonic stages, high PIP4Kα expression was detected in the head and the pectoral fins. Knockdown of zPIP4Kα by antisense morpholino oligonucleotides led to severe morphological abnormalities, including midbody winding defects at 48hpf. The abnormal phenotype could be rescued, at least in large part, by injection of human PIP4Kα mRNA. Our results reveal a key role for PIP4Kα and its activity in vertebrate tissue homeostasis and organ development.
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Affiliation(s)
- Dalila Elouarrat
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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38
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Zong W, Zhong X, You J, Xiong L. Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress. PLANT MOLECULAR BIOLOGY 2013. [PMID: 23192746 DOI: 10.1007/s11103-012-9990-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Histone modifications affect gene expression level. Several studies have shown that they may play key roles in regulating gene expression in plants under abiotic stress, but genome-wide surveys of such stress-related modifications are very limited, especially for crops. By using ChIP-Seq and RNA-Seq, we investigated the genome-wide distribution pattern of histone H3 lysine4 tri-methylation (H3K4me3) and the pattern's association with whole genome expression profiles of rice (Oryza sativa L.) under drought stress, one of the major and representative abiotic stresses. We detected 51.1 and 48 % of annotated genes with H3K4me3 modification in rice seedlings under normal growth (control) and drought stress conditions, respectively. By RNA-Seq, 76.7 and 79 % of annotated genes were detected with expression in rice seedlings under the control and drought stress conditions, respectively. Furthermore, 4,837 genes were differentially H3K4me3-modified (H3M), (3,927 genes with increased H3M; 910 genes with decreased H3M) and 5,866 genes were differentially expressed (2,145 up-regulated; 3,721 down-regulated) in drought stress. Differential H3K4me3 methylation only affects a small proportion of stress-responsive genes, and the H3K4me3 modification level was significantly and positively correlated with transcript level only for a subset of genes showing changes both in modification and expression with drought stress. Moreover, for the H3K4me3-regulated stress-related genes, the H3K4me3 modification level was mainly increased in genes with low expression and decreased in genes with high expression under drought stress. The comprehensive data of H3K4me3 and gene expression profiles in rice under drought stress provide a useful resource for future epigenomic regulation studies in plants under abiotic stresses.
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Affiliation(s)
- Wei Zong
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
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39
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Jones DR, Foulger R, Keune WJ, Bultsma Y, Divecha N. PtdIns5P is an oxidative stress-induced second messenger that regulates PKB activation. FASEB J 2012; 27:1644-56. [PMID: 23241309 DOI: 10.1096/fj.12-218842] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Oxidative stress initiates signaling pathways, which protect from stress-induced cellular damage, initiate apoptosis, or drive cells into senescence or into tumorigenesis. Oxidative stress regulates the activity of the cell survival factor PKB, through the regulation of PtdIns(3,4,5)P₃ synthesis. Whether oxidative stress regulates other phosphoinositides to control PKB activation is not clear. Here we show that PtdIns5P is a redox-regulated second messenger. In response to hydrogen peroxide (H₂O₂), we measured an increase in PtdIns5P in cells derived from human osteosarcoma, U2OS (5-fold); breast tumors, MDA-MB-468 (2-fold); and fibrosarcoma, HT1080 (3-fold); and in p53-null murine embryonic fibroblasts (8-fold). In U2OS cells, the increase in H₂O₂-dependent PtdIns5P did not require mTOR, PDK1, PKB, ERK, and p38 signaling or PIKfyve, a lipid kinase that increases PtdIns5P in response to osmotic and oncogenic signaling. A reduction in H₂O₂-induced PtdIns5P levels by the overexpression of PIP4K revealed its role in PKB activation. Suppression of H₂O₂-induced PtdIns5P generation reduced PKB activation and, surprisingly, reduced cell sensitivity to growth inhibition by H₂O₂. These data suggest that inhibition of PIP4K signaling might be useful as a novel strategy to increase the susceptibility of tumor cells to therapeutics that function through increased oxidative stress.
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Affiliation(s)
- David R Jones
- Cancer Research UK Inositide Laboratory, The Paterson Institute for Cancer Research, University of Manchester, Manchester, UK
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40
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Keune WJ, Jones DR, Bultsma Y, Sommer L, Zhou XZ, Lu KP, Divecha N. Regulation of phosphatidylinositol-5-phosphate signaling by Pin1 determines sensitivity to oxidative stress. Sci Signal 2012. [PMID: 23193159 DOI: 10.1126/scisignal.2003223] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Oxidative signaling and oxidative stress contribute to aging, cancer, and diseases resulting from neurodegeneration. Pin1 is a proline isomerase that recognizes phosphorylated substrates and regulates the localization and conformation of its targets. Pin1(-/-) mice show phenotypes associated with premature aging, yet mouse embryonic fibroblasts (MEFs) from these mice are resistant to hydrogen peroxide (H(2)O(2))-induced cell death. We found that the abundance of phosphatidylinositol-5-phosphate (PtdIns5P) was increased in response to H(2)O(2), an effect that was enhanced in Pin1(-/-) MEFs. Reduction of H(2)O(2)-induced PtdIns5P compromised cell viability in response to oxidative stress, suggesting that PtdIns5P contributed to the enhanced cell viability of Pin1(-/-) MEFs exposed to oxidative stress. The increased PtdIns5P in the Pin1(-/-) MEFs stimulated the expression of genes involved in defense against oxidative stress and reduced the accumulation of reactive oxygen species. Pin1 and PtdIns5P 4-kinases (PIP4Ks), enzymes that phosphorylate and thereby reduce the amount of PtdIns5P, interacted in a manner dependent on the phosphorylation of PIP4K. Although reintroduction of Pin1 into the Pin1(-/-) MEFs reduced the amount of PtdIns5P produced in response to H(2)O(2), in vitro assays indicated that the isomerase activity of Pin1 inhibited PIP4K activity. Whether this isomerise-mediated inhibition of PIP4K occurs in cells remains an open question, but the data suggest that the regulation of PIP4K by Pin1 may be complex.
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Affiliation(s)
- Willem-Jan Keune
- CRUK Inositide Laboratory, Paterson Institute for Cancer Research, The University of Manchester, Manchester M20 4BX, UK
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41
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Dieck CB, Wood A, Brglez I, Rojas-Pierce M, Boss WF. Increasing phosphatidylinositol (4,5) bisphosphate biosynthesis affects plant nuclear lipids and nuclear functions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 57:32-44. [PMID: 22677448 PMCID: PMC3601448 DOI: 10.1016/j.plaphy.2012.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 05/09/2012] [Indexed: 05/21/2023]
Abstract
In order to characterize the effects of increasing phosphatidylinositol(4,5)bisphosphate (PtdIns(4,5)P(2)) on nuclear function, we expressed the human phosphatidylinositol (4)-phosphate 5-kinase (HsPIP5K) 1α in Nicotiana tabacum (NT) cells. The HsPIP5K-expressing (HK) cells had altered nuclear lipids and nuclear functions. HK cell nuclei had 2-fold increased PIP5K activity and increased steady state PtdIns(4,5)P(2). HK nuclear lipid classes showed significant changes compared to NT (wild type) nuclear lipid classes including increased phosphatidylserine (PtdSer) and phosphatidylcholine (PtdCho) and decreased lysolipids. Lipids isolated from protoplast plasma membranes (PM) were also analyzed and compared with nuclear lipids. The lipid profiles revealed similarities and differences in the plasma membrane and nuclei from the NT and transgenic HK cell lines. A notable characteristic of nuclear lipids from both cell types is that PtdIns accounts for a higher mol% of total lipids compared to that of the protoplast PM lipids. The lipid molecular species composition of each lipid class was also analyzed for nuclei and protoplast PM samples. To determine whether expression of HsPIP5K1α affected plant nuclear functions, we compared DNA replication, histone 3 lysine 9 acetylation (H3K9ac) and phosphorylation of the retinoblastoma protein (pRb) in NT and HK cells. The HK cells had a measurable decrease in DNA replication, histone H3K9 acetylation and pRB phosphorylation.
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Affiliation(s)
| | - Austin Wood
- Department of Biochemistry, North Carolina State University, Raleigh, NC
| | - Irena Brglez
- Department of Plant Biology, North Carolina State University, Raleigh, NC
| | | | - Wendy F. Boss
- Department of Plant Biology, North Carolina State University, Raleigh, NC
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42
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Ding Y, Ndamukong I, Zhao Y, Xia Y, Riethoven JJ, Jones DR, Divecha N, Avramova Z. Divergent functions of the myotubularin (MTM) homologs AtMTM1 and AtMTM2 in Arabidopsis thaliana: evolution of the plant MTM family. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:866-878. [PMID: 22324391 DOI: 10.1111/j.1365-313x.2012.04936.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Myotubularin and myotubularin-related proteins are evolutionarily conserved in eukaryotes. Defects in their function result in muscular dystrophy, neuronal diseases and leukemia in humans. In contrast to the animal lineage, where genes encoding both active and inactive myotubularins (phosphoinositide 3-phosphatases) have appeared and proliferated in the basal metazoan group, myotubularin genes are not found in the unicellular relatives of green plants. However, they are present in land plants encoding proteins highly similar to the active metazoan enzymes. Despite their remarkable structural conservation, plant and animal myotubularins have significantly diverged in their functions. While loss of myotubularin function causes severe disease phenotypes in humans it is not essential for the cellular homeostasis under normal conditions in Arabidopsis thaliana. Instead, myotubularin deficiency is associated with altered tolerance to dehydration stress. The two Arabidopsis genes AtMTM1 and AtMTM2 have originated from a segmental chromosomal duplication and encode catalytically active enzymes. However, only AtMTM1 is involved in elevating the cellular level of phosphatidylinositol 5-phosphate in response to dehydration stress, and the two myotubularins differentially affect the Arabidopsis dehydration stress-responding transcriptome. AtMTM1 and AtMTM2 display different localization patterns in the cell, consistent with the idea that they associate with different membranes to perform specific functions. A single amino acid mutation in AtMTM2 (L250W) results in a dramatic loss of subcellular localization. Mutations in this region are linked to disease conditions in humans.
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MESH Headings
- Amino Acid Substitution
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- Chromosome Duplication
- Chromosomes, Plant/genetics
- Chromosomes, Plant/metabolism
- Dehydration/metabolism
- Enzyme Activation
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Genes, Plant
- Mitochondrial Proteins/genetics
- Mitochondrial Proteins/metabolism
- Oligonucleotide Array Sequence Analysis/methods
- Phosphatidylinositol Phosphates/metabolism
- Phosphoric Monoester Hydrolases/genetics
- Phosphoric Monoester Hydrolases/metabolism
- Plant Cells/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Protein Structure, Tertiary
- Protein Tyrosine Phosphatases, Non-Receptor/genetics
- Protein Tyrosine Phosphatases, Non-Receptor/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Soil
- Stress, Physiological
- Transcriptome
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Affiliation(s)
- Yong Ding
- School of Biological Sciences, University of Nebraska at Lincoln, Lincoln, NE 68588, USA
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43
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The emerging role of PtdIns5P: another signalling phosphoinositide takes its place. Biochem Soc Trans 2012; 40:257-61. [PMID: 22260701 DOI: 10.1042/bst20110617] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Of the seven phosphoinositides, PtdIns5P remains the most enigmatic. However, recent research has begun to elucidate its physiological functions. It is now clear that PtdIns5P is found in several distinct subcellular locations, and the identification of a number of PtdIns5P-binding proteins points to its involvement in a variety of key processes, including signal transduction, membrane trafficking and regulation of gene expression. Although the mechanisms that control its turnover are not yet fully understood, the existence of multiple pathways for PtdIns5P regulation is consistent with this emerging versatility.
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Viiri K, Maki M, Lohi O. Phosphoinositides as Regulators of Protein-Chromatin Interactions. Sci Signal 2012; 5:pe19. [DOI: 10.1126/scisignal.2002917] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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45
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Dieck CB, Boss WF, Perera IY. A role for phosphoinositides in regulating plant nuclear functions. FRONTIERS IN PLANT SCIENCE 2012; 3:50. [PMID: 22645589 PMCID: PMC3355785 DOI: 10.3389/fpls.2012.00050] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 02/27/2012] [Indexed: 05/21/2023]
Abstract
Nuclear localized inositol phospholipids and inositol phosphates are important for regulating many essential processes in animal and yeast cells such as DNA replication, recombination, RNA processing, mRNA export and cell cycle progression. An overview of the current literature indicates the presence of a plant nuclear phosphoinositide (PI) pathway. Inositol phospholipids, inositol phosphates, and enzymes of the PI pathway have been identified in plant nuclei and are implicated in DNA replication, chromatin remodeling, stress responses and hormone signaling. In this review, the potential functions of the nuclear PI pathway in plants are discussed within the context of the animal and yeast literature. It is anticipated that future research will help shed light on the functional significance of the nuclear PI pathway in plants.
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Affiliation(s)
| | - Wendy F. Boss
- Department of Plant Biology, North Carolina State UniversityRaleigh, NC, USA
| | - Imara Y. Perera
- Department of Plant Biology, North Carolina State UniversityRaleigh, NC, USA
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46
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Gao XQ, Zhang XS. Metabolism and roles of phosphatidylinositol 3-phosphate in pollen development and pollen tube growth in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2012; 7:165-9. [PMID: 22307045 PMCID: PMC3405687 DOI: 10.4161/psb.18743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Phosphoinositides play important roles in eukaryotic cells, although they constitute a minor fraction of total cellular lipids. Specific kinases and phosphatases function on the regulation of phosphoinositide levels. Phosphatidylinositol 3-phosphate (PtdIns3P), a molecule of phosphoinositides regulates multiple aspects of plant growth and development. In this mini-review, we introduce and discuss the kinases and phosphatases involved in PtdIns3P metabolism and their roles in pollen development and pollen tube growth in Arabidopsis.
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47
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Fiume R, Keune WJ, Faenza I, Bultsma Y, Ramazzotti G, Jones DR, Martelli AM, Somner L, Follo MY, Divecha N, Cocco L. Nuclear phosphoinositides: location, regulation and function. Subcell Biochem 2012; 59:335-361. [PMID: 22374096 DOI: 10.1007/978-94-007-3015-1_11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Lipid signalling in human disease is an important field of investigation and stems from the fact that phosphoinositide signalling has been implicated in the control of nearly all the important cellular pathways including metabolism, cell cycle control, membrane trafficking, apoptosis and neuronal conduction. A distinct nuclear inositide signalling metabolism has been identified, thus defining a new role for inositides in the nucleus, which are now considered essential co-factors for several nuclear processes, including DNA repair, transcription regulation, and RNA dynamics. Deregulation of phoshoinositide metabolism within the nuclear compartment may contribute to disease progression in several disorders, such as chronic inflammation, cancer, metabolic, and degenerative syndromes. In order to utilize these very druggable pathways for human benefit there is a need to identify how nuclear inositides are regulated specifically within this compartment and what downstream nuclear effectors process and integrate inositide signalling cascades in order to specifically control nuclear function. Here we describe some of the facets of nuclear inositide metabolism with a focus on their relationship to cell cycle control and differentiation.
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Affiliation(s)
- Roberta Fiume
- Cellular Signalling Laboratory, Department of Human Anatomical Sciences, University of Bologna, Bologna, Italy,
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48
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Valluru R, Van den Ende W. Myo-inositol and beyond--emerging networks under stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:387-400. [PMID: 21889044 DOI: 10.1016/j.plantsci.2011.07.009] [Citation(s) in RCA: 200] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 05/18/2023]
Abstract
Myo-inositol is a versatile compound that generates diversified derivatives upon phosphorylation by lipid-dependent and -independent pathways. Phosphatidylinositols form one such group of myo-inositol derivatives that act both as membrane structural lipid molecules and as signals. The significance of these compounds lies in their dual functions as signals as well as key metabolites under stress. Several stress- and non-stress related pathways regulated by phosphatidylinositol isoforms and associated enzymes, kinases and phosphatases, appear to function in parallel to coordinatively adapt growth and stress responses in plants. Recent evidence also postulates their crucial roles in nuclear functions as they interact with the key players of chromatin structure, yet other nuclear functions remain largely unknown. Phosphatidylinositol monophosphate 5-kinase interacts with and represses a cytosolic neutral invertase, a key enzyme of sugar metabolism suggesting a crosstalk between lipid and sugar signaling. Besides phosphatidylinositol, myo-inositol derived galactinol and associated raffinose-family oligosaccharides are emerging as antioxidants and putative signaling compounds too. Importantly, myo-inositol polyphosphate 5-phosphatase (5PTase) acts, depending on sugar status, as a positive or negative regulator of a global energy sensor, SnRK1. This implies that both myo-inositol- and sugar-derived (e.g. trehalose 6-phosphate) molecules form part of a broad regulatory network with SnRK1 as the central regulator. Recently, it was shown that the transcription factor bZIP11 also takes part in this network. Moreover, a functional coordination between neutral invertase and hexokinase is emerging as a sweet network that contributes to oxidative stress homeostasis in plants. In this review, we focus on myo-inositol, its direct and more downstream derivatives (galactinol, raffinose), and the contribution of their associated networks to plant stress tolerance.
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Affiliation(s)
- Ravi Valluru
- Ecophysiology of Plants Under Environmental Stress, INRA-SUPAGRO, Institute of Integrative Plant Biology, 2 Place Viala, Montpellier, France
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49
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Munnik T, Nielsen E. Green light for polyphosphoinositide signals in plants. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:489-97. [PMID: 21775194 DOI: 10.1016/j.pbi.2011.06.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 06/21/2011] [Accepted: 06/23/2011] [Indexed: 05/04/2023]
Abstract
Plant genomes lack homologues of the inositol 1,4,5-trisphosphate receptor and protein kinase C, which are important components of the canonical phospholipase C signalling system in animals. Instead, plants seem to utilize alternative downstream signalling molecules, that is, InsP(6) and phosphatidic acid. Inositol lipids may also function as second messengers themselves. By reversible phosphorylation of the inositol headgroup, five biologically active plant polyphosphoinositides can be detected. Protein targets interact with specific polyphosphoinositide isomers via selective lipid-binding domains, thereby altering their intracellular localization and/or enzymatic activity. Such lipid-binding domains have also been used to create GFP based-lipid biosensors to visualize PPIs dynamics in vivo. Here, we highlight some recent advances and ideas on PPIs' role in plant signalling.
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Affiliation(s)
- Teun Munnik
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098XH Amsterdam, The Netherlands.
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50
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Yaish MW, Colasanti J, Rothstein SJ. The role of epigenetic processes in controlling flowering time in plants exposed to stress. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3727-35. [PMID: 21633082 DOI: 10.1093/jxb/err177] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants interact with their environment by modifying gene expression patterns. One mechanism for this interaction involves epigenetic modifications that affect a number of aspects of plant growth and development. Thus, the epigenome is highly dynamic in response to environmental cues and developmental changes. Flowering is controlled by a set of genes that are affected by environmental conditions through an alteration in their expression pattern. This ensures the production of flowers even when plants are growing under adverse conditions, and thereby enhances transgenerational seed production. In this review recent findings on the epigenetic changes associated with flowering in Arabidopsis thaliana grown under abiotic stress conditions such as cold, drought, and high salinity are discussed. These epigenetic modifications include DNA methylation, histone modifications, and the production of micro RNAs (miRNAs) that mediate epigenetic modifications. The roles played by the phytohormones abscisic acid (ABA) and auxin in chromatin remodelling are also discussed. It is shown that there is a crucial relationship between the epigenetic modifications associated with floral initiation and development and modifications associated with stress tolerance. This relationship is demonstrated by the common epigenetic pathways through which plants control both flowering and stress tolerance, and can be used to identify new epigenomic players.
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Affiliation(s)
- Mahmoud W Yaish
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman.
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