Arabidopsis inositol polyphosphate kinases IPK1 and ITPK1 modulate crosstalks between SA-dependent immunity and phosphate-starvation responses

AbstractThe propensity for polyphosphorylation makes myo-inositol derivatives, the inositol polyphosphates (InsPs), especially phytic acid or inositol hexakisphosphate (InsP6) the major form of phosphate storage in plants. Acts of pyrophosphorylation on InsP6 generates InsP7 or InsP8 containing high-energy phosphoanhydride bonds that are harnessed during energy requirements of a cell. Also implicated as co-factors for several phytohormone signaling networks, InsP7/InsP8 modulate key developmental processes. With recent identification as the common moeity for transducing both jasmonic acid (JA) and phosphate-starvation responses (PSR), InsP8 is the classic example of a metabolite that may moonlight crosstalks to different cellular pathways during diverse stress adaptations. We show here that Arabidopsis thaliana INOSITOL PENTAKISPHOSPHATE 2-KINASE (IPK1), INOSITOL 1,3,4-TRISPHOSPHATE 5/6-KINASE 1 (ITPK1), and DIPHOSPHOINOSITOL PENTAKISPHOSPHATE KINASE 2 (VIH2), but not other InsP-kinases, suppress basal salicylic acid (SA)-dependent immunity. In ipk1, itpk1 or vih2 mutants, elevated endogenous SA levels and constitutive activation of defense signaling lead to enhanced resistance against the virulent Pseudomonas syringae pv tomato DC3000 (PstDC3000) strain. Our data reveal that activated SA-signaling sectors in these mutants modulate expression amplitudes of phosphate-starvation inducible (PSI)-genes, reported earlier. In turn, via mutualism the heightened basal defenses in these mutants require upregulated PSI-gene expressions likely highlighting the increased demand of phosphates required to support immunity. We demonstrate that SA is induced in phosphate-deprived plants, however its defense-promoting functions are likely diverted to PSR-supportive roles. Overall, our investigations reveal selective InsPs as crosstalk mediators among diverse signaling networks programming stress-appropriate adaptations.

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An ATP-responsive metabolic cassette comprised of inositol tris/tetrakisphosphate kinase 1 (ITPK1) and inositol pentakisphosphate 2-kinase (IPK1) buffers diphosphosphoinositol phosphate levels

Biochemical Journal ◽

10.1042/bcj20200423 ◽

2020 ◽

Vol 477 (14) ◽

pp. 2621-2638 ◽

Cited By ~ 5

Author(s):

Hayley Whitfield ◽

Gaye White ◽

Colleen Sprigg ◽

Andrew M. Riley ◽

Barry V.L. Potter ◽

...

Keyword(s):

Mammalian Cells ◽

Inositol Phosphate ◽

High Energy ◽

Dependent Manner ◽

Inositol Polyphosphate ◽

Inositol Polyphosphates ◽

Inositol Pyrophosphate ◽

Relative Contribution ◽

Chromatographic Resolution ◽

Molecular Signals

Inositol polyphosphates are ubiquitous molecular signals in metazoans, as are their pyrophosphorylated derivatives that bear a so-called ‘high-energy’ phosphoanhydride bond. A structural rationale is provided for the ability of Arabidopsis inositol tris/tetrakisphosphate kinase 1 to discriminate between symmetric and enantiomeric substrates in the production of diverse symmetric and asymmetric myo-inositol phosphate and diphospho-myo-inositol phosphate (inositol pyrophosphate) products. Simple tools are applied to chromatographic resolution and detection of known and novel diphosphoinositol phosphates without resort to radiolabeling approaches. It is shown that inositol tris/tetrakisphosphate kinase 1 and inositol pentakisphosphate 2-kinase comprise a reversible metabolic cassette converting Ins(3,4,5,6)P4 into 5-InsP7 and back in a nucleotide-dependent manner. Thus, inositol tris/tetrakisphosphate kinase 1 is a nexus of bioenergetics status and inositol polyphosphate/diphosphoinositol phosphate metabolism. As such, it commands a role in plants that evolution has assigned to a different class of enzyme in mammalian cells. The findings and the methods described will enable a full appraisal of the role of diphosphoinositol phosphates in plants and particularly the relative contribution of reversible inositol phosphate hydroxykinase and inositol phosphate phosphokinase activities to plant physiology.

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On Exact and Approximate Approaches for Stochastic Receptor-Ligand Competition Dynamics—An Ecological Perspective

Mathematics ◽

10.3390/math8061014 ◽

2020 ◽

Vol 8 (6) ◽

pp. 1014

Author(s):

Polly-Anne Jeffrey ◽

Martín López-García ◽

Mario Castro ◽

Grant Lythe ◽

Carmen Molina-París

Keyword(s):

Summary Statistics ◽

Steady State Distribution ◽

State Distribution ◽

Cellular Receptors ◽

Stochastic Description ◽

The Matrix ◽

Common Resource ◽

A Cell ◽

The Common ◽

Cellular Medium

Cellular receptors on the cell membrane can bind ligand molecules in the extra-cellular medium to form ligand-bound monomers. These interactions ultimately determine the fate of a cell through the resulting intra-cellular signalling cascades. Often, several receptor types can bind a shared ligand leading to the formation of different monomeric complexes, and in turn to competition for the common ligand. Here, we describe competition between two receptors which bind a common ligand in terms of a bi-variate stochastic process. The stochastic description is important to account for fluctuations in the number of molecules. Our interest is in computing two summary statistics—the steady-state distribution of the number of bound monomers and the time to reach a threshold number of monomers of a given kind. The matrix-analytic approach developed in this manuscript is exact, but becomes impractical as the number of molecules in the system increases. Thus, we present novel approximations which can work under low-to-moderate competition scenarios. Our results apply to systems with a larger number of population species (i.e., receptors) competing for a common resource (i.e., ligands), and to competition systems outside the area of molecular dynamics, such as Mathematical Ecology.

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Emulation with Organic Memristive Devices of Impairment of LTP Mechanism in Neurodegenerative Disease Pathology

Neural Plasticity ◽

10.1155/2017/6090312 ◽

2017 ◽

Vol 2017 ◽

pp. 1-8 ◽

Cited By ~ 4

Author(s):

Silvia Battistoni ◽

Victor Erokhin ◽

Salvatore Iannotta

Keyword(s):

Neural Network ◽

Information Transmission ◽

Common Sense ◽

Artificial Neuron ◽

Cell Network ◽

Neuron Networks ◽

A Cell ◽

The Common ◽

Major Progress ◽

Single Synapse

We explore and demonstrate the extension of the synapse-mimicking properties of memristive devices to a dysfunctional synapse as it occurs in the Alzheimer’s disease (AD) pathology. The ability of memristive devices to reproduce synapse properties such as LTP, LTD, and STDP has been already widely demonstrated, and moreover, they were used for developing artificial neuron networks (perceptrons) able to simulate the information transmission in a cell network. However, a major progress would be to extend the common sense of neuromorphic device even to the case of dysfunction of natural synapses. Can memristors efficiently simulate them? We provide here evidences of the ability of emulating the dysfunctional synaptic behavior typical of the AD pathology with organic memristive devices considering the effect of the disease not only on a single synapse but also in the case of a neural network, composed by numerous synapses.

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Mating type control in Saccharomyces cerevisiae: a frameshift mutation at the common DNA sequence, X, of the HML alpha locus

Molecular and Cellular Biology ◽

10.1128/mcb.4.1.203-211.1984 ◽

1984 ◽

Vol 4 (1) ◽

pp. 203-211

Author(s):

K Tanaka ◽

T Oshima ◽

H Araki ◽

S Harashima ◽

Y Oshima

Keyword(s):

Mating Type ◽

Base Pair ◽

Reading Frame ◽

Base Pair Deletion ◽

A Cell ◽

Alpha Gene ◽

The Common ◽

Type Switch ◽

Diploid Cells ◽

Mat Locus

A mutation defective in the homothallic switching of mating type alleles, designated hml alpha-2, has previously been characterized. The mutation occurred in a cell having the HO MATa HML alpha HMRa genotype, and the mutant culture consisted of ca. 10% a mating type cells, 90% nonmater cells of haploid cell size, and 0.1% sporogenous diploid cells. Genetic analyses revealed that nonmater haploid cells have a defect in the alpha 2 cistron at the MAT locus. This defect was probably caused by transposition of a cassette originating from the hml alpha-2 allele by the process of the homothallic mating type switch. That the MAT locus of the nonmater cells is occupied by a DNA fragment indistinguishable from the Y alpha sequence in electrophoretic mobility was demonstrated by Southern hybridization of the EcoRI-HindIII fragment encoding the MAT locus with a cloned HML alpha gene as the probe. The hml alpha-2 mutation was revealed to be a one-base-pair deletion at the ninth base pair in the X region from the X and Y boundary of the HML locus. This mutation gave rise to a shift in the open reading frame of the alpha 2 cistron. A molecular mechanism for the mating type switch associated with the occurrence of sporogenous diploid cells in the mutant culture is discussed.

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Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62

eLife ◽

10.7554/elife.17290 ◽

2016 ◽

Vol 5 ◽

Cited By ~ 78

Author(s):

Rowena DeJesus ◽

Francesca Moretti ◽

Gregory McAllister ◽

Zuncai Wang ◽

Phil Bergman ◽

...

Keyword(s):

Adaptor Protein ◽

Er Stress Response ◽

Genome Wide ◽

A Genome ◽

Crispr Screen ◽

Selection Step ◽

A Cell ◽

Cell Type Specific ◽

Cellular Pathways ◽

Mtor Signalling

SQSTM1 is an adaptor protein that integrates multiple cellular signaling pathways and whose expression is tightly regulated at the transcriptional and post-translational level. Here, we describe a forward genetic screening paradigm exploiting CRISPR-mediated genome editing coupled to a cell selection step by FACS to identify regulators of SQSTM1. Through systematic comparison of pooled libraries, we show that CRISPR is superior to RNAi in identifying known SQSTM1 modulators. A genome-wide CRISPR screen exposed MTOR signalling and the entire macroautophagy machinery as key regulators of SQSTM1 and identified several novel modulators including HNRNPM, SLC39A14, SRRD, PGK1 and the ufmylation cascade. We show that ufmylation regulates SQSTM1 by eliciting a cell type-specific ER stress response which induces SQSTM1 expression and results in its accumulation in the cytosol. This study validates pooled CRISPR screening as a powerful method to map the repertoire of cellular pathways that regulate the fate of an individual target protein.

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Subcellular optogenetic activation of Cdc42 controls local and distal signaling to drive immune cell migration

Molecular Biology of the Cell ◽

10.1091/mbc.e15-12-0832 ◽

2016 ◽

Vol 27 (9) ◽

pp. 1442-1450 ◽

Cited By ~ 33

Author(s):

Patrick R. O’Neill ◽

Vani Kalyanaraman ◽

N. Gautam

Keyword(s):

Cell Migration ◽

Intracellular Signaling ◽

Immune Cell ◽

Leading Edge ◽

Signaling Networks ◽

Membrane Protrusions ◽

A Cell ◽

Immune Cell Migration ◽

Directional Cell Migration ◽

Rhoa Signaling

Migratory immune cells use intracellular signaling networks to generate and orient spatially polarized responses to extracellular cues. The monomeric G protein Cdc42 is believed to play an important role in controlling the polarized responses, but it has been difficult to determine directly the consequences of localized Cdc42 activation within an immune cell. Here we used subcellular optogenetics to determine how Cdc42 activation at one side of a cell affects both cell behavior and dynamic molecular responses throughout the cell. We found that localized Cdc42 activation is sufficient to generate polarized signaling and directional cell migration. The optically activated region becomes the leading edge of the cell, with Cdc42 activating Rac and generating membrane protrusions driven by the actin cytoskeleton. Cdc42 also exerts long-range effects that cause myosin accumulation at the opposite side of the cell and actomyosin-mediated retraction of the cell rear. This process requires the RhoA-activated kinase ROCK, suggesting that Cdc42 activation at one side of a cell triggers increased RhoA signaling at the opposite side. Our results demonstrate how dynamic, subcellular perturbation of an individual signaling protein can help to determine its role in controlling polarized cellular responses.

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Cardiac physiologic-metabolic changes after chronic low-level heavy metal feeding

AJP Heart and Circulatory Physiology ◽

10.1152/ajpheart.1980.239.1.h22 ◽

1980 ◽

Vol 239 (1) ◽

pp. H22-H30 ◽

Cited By ~ 1

Author(s):

S. J. Kopp ◽

M. Perry ◽

T. Glonek ◽

M. Erlanger ◽

E. F. Perry ◽

...

Keyword(s):

Heavy Metal ◽

Atrioventricular Node ◽

High Energy ◽

Spectroscopic Techniques ◽

Sodium Pentobarbital ◽

His Bundle ◽

Metabolite Profiles ◽

The Common ◽

Blood Pressure Responses ◽

And Control

Female Long-Evans hooded rats received 0 or 5 parts per million Cd, Pb, or Cd + Pb in the drinking water from weaning to 20 mo. Growth, measured as body weight, and organ weights were comparable among heavy metal and control animals. Indirect blood pressure responses measured trimonthly are discussed. Analysis of His bundle electrograms (HBE) and electrocardiograms recorded in sodium pentobarbital-anesthetized animals at 20 mo demonstrated that Cd selectively depressed conduction system excitability proximal to the common His bundle (atrioventricular node region), whereas Pb and Pb + Cd impaired conductivity distal to the common His bundle (His-Purkinje system). Perchloric acid extracts of liquid N2-freeze-clamped isolated perfused hearts, derived from a subpopulation of control and Cd-fed rats in which HBE analyses were not performed, were analyzed by phosphorus-31 nuclear magnetic resonance (31P-NMR) spectroscopic techniques to quantitate [31P]phosphate metabolite profiles. Cardiac active tension and atrioventricular node excitability were depressed in the Cd group. High-energy phosphate and glycerol 3-phosphorylcholine concentrations were depressed. Results demonstrate potentially significant pathophysiological changes within cardiovascular tissues that develop in the absence of overt heavy metal toxicity manifestations.

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Eukaryotic Ribosome Assembly

Annual Review of Biochemistry ◽

10.1146/annurev-biochem-013118-110817 ◽

2019 ◽

Vol 88 (1) ◽

pp. 281-306 ◽

Cited By ~ 60

Author(s):

Jochen Baßler ◽

Ed Hurt

Keyword(s):

Ribosomal Rna ◽

Nuclear Export ◽

Ribosomal Proteins ◽

Ribosome Biogenesis ◽

Cryo Electron Microscopy ◽

A Cell ◽

Cellular Pathways ◽

Nucleolar Rnas ◽

Shed Light

Ribosomes, which synthesize the proteins of a cell, comprise ribosomal RNA and ribosomal proteins, which coassemble hierarchically during a process termed ribosome biogenesis. Historically, biochemical and molecular biology approaches have revealed how preribosomal particles form and mature in consecutive steps, starting in the nucleolus and terminating after nuclear export into the cytoplasm. However, only recently, due to the revolution in cryo–electron microscopy, could pseudoatomic structures of different preribosomal particles be obtained. Together with in vitro maturation assays, these findings shed light on how nascent ribosomes progress stepwise along a dynamic biogenesis pathway. Preribosomes assemble gradually, chaperoned by a myriad of assembly factors and small nucleolar RNAs, before they reach maturity and enter translation. This information will lead to a better understanding of how ribosome synthesis is linked to other cellular pathways in humans and how it can cause diseases, including cancer, if disturbed.

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Inositol Polyphosphate-Based Compounds as Inhibitors of Phosphoinositide 3-Kinase-Dependent Signaling

International Journal of Molecular Sciences ◽

10.3390/ijms21197198 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7198

Author(s):

Tania Maffucci ◽

Marco Falasca

Keyword(s):

Therapeutic Strategy ◽

Therapeutic Potential ◽

Deep Understanding ◽

Inositol Polyphosphate ◽

Inositol Polyphosphates ◽

Downstream Effectors ◽

Protein Membrane ◽

Phosphoinositide 3 Kinase ◽

Cancer Settings ◽

Established Role

Signaling pathways regulated by the phosphoinositide 3-kinase (PI3K) enzymes have a well-established role in cancer development and progression. Over the past 30 years, the therapeutic potential of targeting this pathway has been well recognized, and this has led to the development of a multitude of drugs, some of which have progressed into clinical trials, with few of them currently approved for use in specific cancer settings. While many inhibitors compete with ATP, hence preventing the catalytic activity of the kinases directly, a deep understanding of the mechanisms of PI3K-dependent activation of its downstream effectors led to the development of additional strategies to prevent the initiation of this signaling pathway. This review summarizes previously published studies that led to the identification of inositol polyphosphates as promising parent molecules to design novel inhibitors of PI3K-dependent signals. We focus our attention on the inhibition of protein–membrane interactions mediated by binding of pleckstrin homology domains and phosphoinositides that we proposed 20 years ago as a novel therapeutic strategy.

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Targeted removal of PML-RARα protein is required prior to inhibition of histone deacetylase for overcoming all-trans retinoic acid differentiation resistance in acute promyelocytic leukemia

Blood ◽

10.1182/blood.v100.3.1008 ◽

2002 ◽

Vol 100 (3) ◽

pp. 1008-1013 ◽

Cited By ~ 27

Author(s):

Yongkui Jing ◽

Lijuan Xia ◽

Samuel Waxman

Keyword(s):

Retinoic Acid ◽

Histone Deacetylase ◽

Acute Promyelocytic Leukemia ◽

Promyelocytic Leukemia ◽

Dominant Negative ◽

Gene Expressions ◽

Trans Retinoic Acid ◽

All Trans Retinoic Acid ◽

Nitroblue Tetrazolium Reduction ◽

A Cell

Abstract All-trans retinoic acid (tRA)–induced differentiation in NB4 cells, a cell line derived from an acute promyelocytic leukemia patient with t(15;17) translocation, is markedly facilitated by sodium butyrate (NaB), a histone deacetylase inhibitor (HDACI), or by hexamethylene bisacetamide (HMBA), a non–HDACI tRA-differentiation inducer, as determined by nitroblue tetrazolium reduction. The tRA-induced expression of RIG-G, Bfl-1/A1, and p21waf1 and, to a lesser extent, of CCAAT/enhancer binding protein–ε (C/EBPε) are also enhanced by such combined treatments. Both responses are associated with a facilitated diminution of the leukemogenic PML-RARα protein and retained ΔPML-RARα, a cleavage product. Treatment with tRA in tRA differentiation–resistant NB4 subclones R4 and MR-2 does not result in PML-RARα diminution and the tested gene expressions. Moreover, the addition of HMBA or NaB with tRA results in only minimal increase of differentiation in the tRA differentiation–resistant subclones. The increases in acetylated histone H3 (AcH3) and AcH4 in NaB-treated NB4, R4, and MR-2 cells are similar and do not correlate with the extent of differentiation induction when NaB and HMBA are given in combination with tRA. Arsenic trioxide (As2O3) treatment results in the total degradation of PML-RARα without increasing AcH3 or AcH4 or inducing differentiation in R4 cells. As2O3 in combination with tRA induces gene (Bfl-1/A1 and C/EBPε) expression and partial differentiation. Both NaB and HMBA addition to As2O3-plus-tRA–treated R4 cells further enhances differentiation. These results suggest that elimination of the dominant negative PML-RARα protein is required prior to inhibition of histone deacetylase to fully overcome tRA-differentiation resistance in APL cells.

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