International Journal of Molecular Sciences

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8 pages, 270 KiB

Open AccessEditorial

New Horizons in Plant Cell Signaling

by Aloysius Wong and Christoph Gehring

Int. J. Mol. Sci. 2022, 23(10), 5826; https://doi.org/10.3390/ijms23105826 - 23 May 2022

Cited by 1 | Viewed by 2184

Abstract

Responding to environmental stimuli with appropriate molecular mechanisms is essential to all life forms and particularly so in sessile organisms such as plants [...] Full article

(This article belongs to the Special Issue New Horizons in Plant Cell Signaling)

Research

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14 pages, 3128 KiB

Open AccessArticle

In Search of Monocot Phosphodiesterases: Identification of a Calmodulin Stimulated Phosphodiesterase from Brachypodium distachyon

by Mateusz Kwiatkowski, Aloysius Wong, Anna Kozakiewicz-Piekarz, Christoph Gehring and Krzysztof Jaworski

Int. J. Mol. Sci. 2021, 22(17), 9654; https://doi.org/10.3390/ijms22179654 - 6 Sep 2021

Cited by 9 | Viewed by 2584

Abstract

In plants, rapid and reversible biological responses to environmental cues may require complex cellular reprograming. This is enabled by signaling molecules such as the cyclic nucleotide monophosphates (cNMPs) cAMP and cGMP, as well as Ca²⁺. While the roles and synthesis of [...] Read more.

In plants, rapid and reversible biological responses to environmental cues may require complex cellular reprograming. This is enabled by signaling molecules such as the cyclic nucleotide monophosphates (cNMPs) cAMP and cGMP, as well as Ca²⁺. While the roles and synthesis of cAMP and cGMP in plants are increasingly well-characterized, the “off signal” afforded by cNMP-degrading enzymes, the phosphodiesterases (PDEs), is, however, poorly understood, particularly so in monocots. Here, we identified a candidate PDE from the monocot Brachypodium distachyon (BDPDE1) and showed that it can hydrolyze cNMPs to 5′NMPs but with a preference for cAMP over cGMP in vitro. Notably, the PDE activity was significantly enhanced by Ca²⁺ only in the presence of calmodulin (CaM), which interacts with BDPDE1, most likely at a predicted CaM-binding site. Finally, based on our biochemical, mutagenesis and structural analyses, we constructed a comprehensive amino acid consensus sequence extracted from the catalytic centers of annotated and/or experimentally validated PDEs across species to enable a broad application of this search motif for the identification of similar active sites in eukaryotes and prokaryotes. Full article

(This article belongs to the Special Issue New Horizons in Plant Cell Signaling)

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21 pages, 4221 KiB

Open AccessArticle

Deciphering the Binding of Salicylic Acid to Arabidopsis thaliana Chloroplastic GAPDH-A1

by Igor Pokotylo, Denis Hellal, Tahar Bouceba, Miguel Hernandez-Martinez, Volodymyr Kravets, Luis Leitao, Christophe Espinasse, Isabelle Kleiner and Eric Ruelland

Int. J. Mol. Sci. 2020, 21(13), 4678; https://doi.org/10.3390/ijms21134678 - 30 Jun 2020

Cited by 8 | Viewed by 3633 | Correction

Abstract

Salicylic acid (SA) has an essential role in the responses of plants to pathogens. SA initiates defence signalling via binding to proteins. NPR1 is a transcriptional co-activator and a key target of SA binding. Many other proteins have recently been shown to [...] Read more.

Salicylic acid (SA) has an essential role in the responses of plants to pathogens. SA initiates defence signalling via binding to proteins. NPR1 is a transcriptional co-activator and a key target of SA binding. Many other proteins have recently been shown to bind SA. Amongst these proteins are important enzymes of primary metabolism. This fact could stand behind SA’s ability to control energy fluxes in stressed plants. Nevertheless, only sparse information exists on the role and mechanisms of such binding. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was previously demonstrated to bind SA both in human and plants. Here, we detail that the A1 isomer of chloroplastic glyceraldehyde 3-phosphate dehydrogenase (GAPA1) from Arabidopsis thaliana binds SA with a K_D of 16.7 nM, as shown in surface plasmon resonance experiments. Besides, we show that SA inhibits its GAPDH activity in vitro. To gain some insight into the underlying molecular interactions and binding mechanism, we combined in silico molecular docking experiments and molecular dynamics simulations on the free protein and protein–ligand complex. The molecular docking analysis yielded to the identification of two putative binding pockets for SA. A simulation in water of the complex between SA and the protein allowed us to determine that only one pocket—a surface cavity around Asn35—would efficiently bind SA in the presence of solvent. In silico mutagenesis and simulations of the ligand/protein complexes pointed to the importance of Asn35 and Arg81 in the binding of SA to GAPA1. The importance of this is further supported through experimental biochemical assays. Indeed, mutating GAPA1 Asn35 into Gly or Arg81 into Leu strongly diminished the ability of the enzyme to bind SA. The very same cavity is responsible for the NADP⁺ binding to GAPA1. More precisely, modelling suggests that SA binds to the very site where the pyrimidine group of the cofactor fits. NADH inhibited in a dose-response manner the binding of SA to GAPA1, validating our data. Full article

(This article belongs to the Special Issue New Horizons in Plant Cell Signaling)

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19 pages, 6197 KiB

Open AccessArticle

Mg²⁺ is a Missing Link in Plant Cell Ca²⁺ Signalling and Homeostasis—A Study on Vicia faba Guard Cells

by Fouad Lemtiri-Chlieh, Stefan T. Arold and Chris Gehring

Int. J. Mol. Sci. 2020, 21(11), 3771; https://doi.org/10.3390/ijms21113771 - 27 May 2020

Cited by 10 | Viewed by 3057

Abstract

Hyperpolarization-activated calcium channels (HACCs) are found in the plasma membrane and tonoplast of many plant cell types, where they have an important role in Ca²⁺-dependent signalling. The unusual gating properties of HACCs in plants, i.e., activation by membrane hyperpolarization rather than [...] Read more.

Hyperpolarization-activated calcium channels (HACCs) are found in the plasma membrane and tonoplast of many plant cell types, where they have an important role in Ca²⁺-dependent signalling. The unusual gating properties of HACCs in plants, i.e., activation by membrane hyperpolarization rather than depolarization, dictates that HACCs are normally open in the physiological hyperpolarized resting membrane potential state (the so-called pump or P-state); thus, if not regulated, they would continuously leak Ca²⁺ into cells. HACCs are permeable to Ca²⁺, Ba²⁺, and Mg²⁺; activated by H₂O₂ and the plant hormone abscisic acid (ABA); and their activity in guard cells is greatly reduced by increasing amounts of free cytosolic Ca²⁺ ([Ca²⁺]_Cyt), and hence closes during [Ca²⁺]_Cyt surges. Here, we demonstrate that the presence of the commonly used Mg-ATP inside the guard cell greatly reduces HACC activity, especially at voltages ≤ −200 mV, and that Mg²⁺ causes this block. Therefore, we firstly conclude that physiological cytosolic Mg²⁺ levels affect HACC gating and that channel opening requires either high negative voltages (≥−200 mV) or displacement of Mg²⁺ away from the immediate vicinity of the channel. Secondly, based on structural comparisons with a Mg²⁺-sensitive animal inward-rectifying K⁺ channel, we propose that the likely candidate HACCs described here are cyclic nucleotide gated channels (CNGCs), many of which also contain a conserved diacidic Mg²⁺ binding motif within their pores. This conclusion is consistent with the electrophysiological data. Finally, we propose that Mg²⁺, much like in animal cells, is an important component in Ca²⁺ signalling and homeostasis in plants. Full article

(This article belongs to the Special Issue New Horizons in Plant Cell Signaling)

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12 pages, 1892 KiB

Open AccessArticle

Molecular Dissection of TaLTP1 Promoter Reveals Functional Cis-Elements Regulating Epidermis-Specific Expression

by Guiping Wang, Guanghui Yu, Yongchao Hao, Xinxin Cheng, Jinxiao Zhao, Silong Sun and Hongwei Wang

Int. J. Mol. Sci. 2020, 21(7), 2261; https://doi.org/10.3390/ijms21072261 - 25 Mar 2020

Cited by 2 | Viewed by 2823

Abstract

Plant epidermis serves important functions in shoot growth, plant defense and lipid metabolism, though mechanisms of related transcriptional regulation are largely unknown. Here, we identified cis-elements specific to shoot epidermis expression by dissecting the promoter of Triticum aestivum lipid transfer protein 1 [...] Read more.

Plant epidermis serves important functions in shoot growth, plant defense and lipid metabolism, though mechanisms of related transcriptional regulation are largely unknown. Here, we identified cis-elements specific to shoot epidermis expression by dissecting the promoter of Triticum aestivum lipid transfer protein 1 (TaLTP1). A preliminary promoter deletion analysis revealed that a truncated fragment within 400 bp upstream from the translation start site was sufficient to confer conserved epidermis-specific expression in transgenic Brachypodium distachyon and Arabidopsis thaliana. Further, deletion or mutation of a GC(N4)GGCC motif at position −380 bp caused a loss of expression in pavement cells. With an electrophoretic mobility shift assay (EMSA) and transgenic reporter assay, we found that a light-responsive CcATC motif at position −268 bp was also involved in regulating pavement cell-specific expression that is evolutionary conserved. Moreover, expression specific to leaf trichome cells was found to be independently regulated by a CCaacAt motif at position −303 bp. Full article

(This article belongs to the Special Issue New Horizons in Plant Cell Signaling)

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Review

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12 pages, 865 KiB

Open AccessReview

Function and Regulation of microRNA171 in Plant Stem Cell Homeostasis and Developmental Programing

by Han Han and Yun Zhou

Int. J. Mol. Sci. 2022, 23(5), 2544; https://doi.org/10.3390/ijms23052544 - 25 Feb 2022

Cited by 15 | Viewed by 3399

Abstract

MicroRNA171 (miR171), a group of 21-nucleotide single-strand small RNAs, is one ancient and conserved microRNA family in land plants. This review focuses on the recent progress in understanding the role of miR171 in plant stem cell homeostasis and developmental patterning, and the regulation [...] Read more.

MicroRNA171 (miR171), a group of 21-nucleotide single-strand small RNAs, is one ancient and conserved microRNA family in land plants. This review focuses on the recent progress in understanding the role of miR171 in plant stem cell homeostasis and developmental patterning, and the regulation of miR171 by developmental cues and environmental signals. Specifically, miR171 regulates shoot meristem activity and phase transition through repressing the HAIRYMERISTEM (HAM) family genes. In the model species Arabidopsis, miR171 serves as a short-range mobile signal, which initiates in the epidermal layer of shoot meristems and moves downwards within a limited distance, to pattern the apical-basal polarity of gene expression and drive stem cell dynamics. miR171 levels are regulated by light and various abiotic stresses, suggesting miR171 may serve as a linkage between environmental factors and cell fate decisions. Furthermore, miR171 family members also demonstrate both conserved and lineage-specific functions in land plants, which are summarized and discussed here. Full article

(This article belongs to the Special Issue New Horizons in Plant Cell Signaling)

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15 pages, 1125 KiB

Open AccessReview

Recent Advances Clarifying the Structure and Function of Plant Apyrases (Nucleoside Triphosphate Diphosphohydrolases)

by Greg Clark, Katherine A. Brown, Manas K. Tripathy and Stanley J. Roux

Int. J. Mol. Sci. 2021, 22(6), 3283; https://doi.org/10.3390/ijms22063283 - 23 Mar 2021

Cited by 16 | Viewed by 3163

Abstract

Studies implicating an important role for apyrase (NTPDase) enzymes in plant growth and development began appearing in the literature more than three decades ago. After early studies primarily in potato, Arabidopsis and legumes, especially important discoveries that advanced an understanding of the biochemistry, [...] Read more.

Studies implicating an important role for apyrase (NTPDase) enzymes in plant growth and development began appearing in the literature more than three decades ago. After early studies primarily in potato, Arabidopsis and legumes, especially important discoveries that advanced an understanding of the biochemistry, structure and function of these enzymes have been published in the last half-dozen years, revealing that they carry out key functions in diverse other plants. These recent discoveries about plant apyrases include, among others, novel findings on its crystal structures, its biochemistry, its roles in plant stress responses and its induction of major changes in gene expression when its expression is suppressed or enhanced. This review will describe and discuss these recent advances and the major questions about plant apyrases that remain unanswered. Full article

(This article belongs to the Special Issue New Horizons in Plant Cell Signaling)

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21 pages, 1715 KiB

Open AccessReview

Moonlighting Proteins Shine New Light on Molecular Signaling Niches

by Ilona Turek and Helen Irving

Int. J. Mol. Sci. 2021, 22(3), 1367; https://doi.org/10.3390/ijms22031367 - 29 Jan 2021

Cited by 30 | Viewed by 4285

Abstract

Plants as sessile organisms face daily environmental challenges and have developed highly nuanced signaling systems to enable suitable growth, development, defense, or stalling responses. Moonlighting proteins have multiple tasks and contribute to cellular signaling cascades where they produce additional variables adding to the [...] Read more.

Plants as sessile organisms face daily environmental challenges and have developed highly nuanced signaling systems to enable suitable growth, development, defense, or stalling responses. Moonlighting proteins have multiple tasks and contribute to cellular signaling cascades where they produce additional variables adding to the complexity or fuzziness of biological systems. Here we examine roles of moonlighting kinases that also generate 3′,5′-cyclic guanosine monophosphate (cGMP) in plants. These proteins include receptor like kinases and lipid kinases. Their guanylate cyclase activity potentiates the development of localized cGMP-enriched nanodomains or niches surrounding the kinase and its interactome. These nanodomains contribute to allosteric regulation of kinase and other molecules in the immediate complex directly or indirectly modulating signal cascades. Effects include downregulation of kinase activity, modulation of other members of the protein complexes such as cyclic nucleotide gated channels and potential triggering of cGMP-dependent degradation cascades terminating signaling. The additional layers of information provided by the moonlighting kinases are discussed in terms of how they may be used to provide a layer of fuzziness to effectively modulate cellular signaling cascades. Full article

(This article belongs to the Special Issue New Horizons in Plant Cell Signaling)

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Other

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2 pages, 448 KiB

Open AccessCorrection

Correction: Pokotylo, I., et al. Deciphering the Binding of Salicylic Acid to Arabidopsis thaliana Chloroplastic GAPDH-A1. Int. J. Mol. Sci. 2020, 21, 4678

by Igor Pokotylo, Denis Hellal, Tahar Bouceba, Miguel Hernandez-Martinez, Volodymyr Kravets, Luis Leitao, Christophe Espinasse, Isabelle Kleiner and Eric Ruelland

Int. J. Mol. Sci. 2020, 21(20), 7435; https://doi.org/10.3390/ijms21207435 - 9 Oct 2020

Cited by 2 | Viewed by 1515

Abstract

The authors wish to make the following correction to their published paper [...] Full article

(This article belongs to the Special Issue New Horizons in Plant Cell Signaling)

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