1
|
Abdullah SNA, Ariffin N, Hatta MAM, Kemat N. Opportunity for genome engineering to enhance phosphate homeostasis in crops. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:1055-1070. [PMID: 39100872 PMCID: PMC11291846 DOI: 10.1007/s12298-024-01479-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 06/15/2024] [Accepted: 06/24/2024] [Indexed: 08/06/2024]
Abstract
Plants maintain cellular homeostasis of phosphate (Pi) through an integrated response pathway regulated by different families of transcription factors including MYB, WRKY, BHLH, and ZFP. The systemic response to Pi limitation showed the critical role played by inositol pyrophosphate (PP-InsPs) as signaling molecule and SPX (SYG1/PHO81/XPR1) domain proteins as sensor of cellular Pi status. Binding of SPX to PP-InsPs regulates the transcriptional activity of the MYB-CC proteins, phosphate starvation response factors (PHR/PHL) as the central regulator of Pi-deficiency response in plants. Vacuolar phosphate transporter, VPT may sense the cellular Pi status by its SPX domain, and vacuolar sequestration is activated under Pi replete condition and the stored Pi is an important resource to be mobilized under Pi deficiency. Proteomic approaches led to new discoveries of proteins associated with Pi-deficient response pathways and post-translational events that may influence plants in achieving Pi homeostasis. This review provides current understanding on the molecular mechanisms at the transcriptional and translational levels for achieving Pi homeostasis in plants. The potential strategies for employing the CRISPR technology to modify the gene sequences of key regulatory and response proteins for attaining plant Pi homeostasis are discussed.
Collapse
Affiliation(s)
- Siti Nor Akmar Abdullah
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
- Institute of Plantation Studies (IKP), Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Norazrin Ariffin
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Muhammad Asyraf Md Hatta
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| | - Nurashikin Kemat
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Darul Ehsan Malaysia
| |
Collapse
|
2
|
Xiong T, Zhang Z, Fan T, Ye F, Ye Z. Origin, evolution, and diversification of inositol 1,4,5-trisphosphate 3-kinases in plants and animals. BMC Genomics 2024; 25:350. [PMID: 38589807 PMCID: PMC11000326 DOI: 10.1186/s12864-024-10257-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND In Eukaryotes, inositol polyphosphates (InsPs) represent a large family of secondary messengers and play crucial roes in various cellular processes. InsPs are synthesized through a series of pohophorylation reactions catalyzed by various InsP kinases in a sequential manner. Inositol 1,4,5-trisphosphate 3-kinase (IP3 3-kinase/IP3K), one member of InsP kinase, plays important regulation roles in InsPs metabolism by specifically phosphorylating inositol 1,4,5-trisphosphate (IP3) to inositol 1,3,4,5-tetrakisphosphate (IP4) in animal cells. IP3Ks were widespread in fungi, plants and animals. However, its evolutionary history and patterns have not been examined systematically. RESULTS A total of 104 and 31 IP3K orthologues were identified across 57 plant genomes and 13 animal genomes, respectively. Phylogenetic analyses indicate that IP3K originated in the common ancestor before the divergence of fungi, plants and animals. In most plants and animals, IP3K maintained low-copy numbers suggesting functional conservation during plant and animal evolution. In Brassicaceae and vertebrate, IP3K underwent one and two duplication events, respectively, resulting in multiple gene copies. Whole-genome duplication (WGD) was the main mechanism for IP3K duplications, and the IP3K duplicates have experienced functional divergence. Finally, a hypothetical evolutionary model for the IP3K proteins is proposed based on phylogenetic theory. CONCLUSION Our study reveals the evolutionary history of IP3K proteins and guides the future functions of animal, plant, and fungal IP3K proteins.
Collapse
Affiliation(s)
- Tao Xiong
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Zaibao Zhang
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China.
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China.
| | - Tianyu Fan
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
| | - Fan Ye
- College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, Zhejiang, China
| | - Ziyi Ye
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
| |
Collapse
|
3
|
Mihiret YE, Schaaf G, Kamleitner M. Protein pyrophosphorylation by inositol phosphates: a novel post-translational modification in plants? FRONTIERS IN PLANT SCIENCE 2024; 15:1347922. [PMID: 38455731 PMCID: PMC10917965 DOI: 10.3389/fpls.2024.1347922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
Inositol pyrophosphates (PP-InsPs) are energy-rich molecules harboring one or more diphosphate moieties. PP-InsPs are found in all eukaryotes evaluated and their functional versatility is reflected in the various cellular events in which they take part. These include, among others, insulin signaling and intracellular trafficking in mammals, as well as innate immunity and hormone and phosphate signaling in plants. The molecular mechanisms by which PP-InsPs exert such functions are proposed to rely on the allosteric regulation via direct binding to proteins, by competing with other ligands, or by protein pyrophosphorylation. The latter is the focus of this review, where we outline a historical perspective surrounding the first findings, almost 20 years ago, that certain proteins can be phosphorylated by PP-InsPs in vitro. Strikingly, in vitro phosphorylation occurs by an apparent enzyme-independent but Mg2+-dependent transfer of the β-phosphoryl group of an inositol pyrophosphate to an already phosphorylated serine residue at Glu/Asp-rich protein regions. Ribosome biogenesis, vesicle trafficking and transcription are among the cellular events suggested to be modulated by protein pyrophosphorylation in yeast and mammals. Here we discuss the latest efforts in identifying targets of protein pyrophosphorylation, pointing out the methodological challenges that have hindered the full understanding of this unique post-translational modification, and focusing on the latest advances in mass spectrometry that finally provided convincing evidence that PP-InsP-mediated pyrophosphorylation also occurs in vivo. We also speculate about the relevance of this post-translational modification in plants in a discussion centered around the protein kinase CK2, whose activity is critical for pyrophosphorylation of animal and yeast proteins. This enzyme is widely present in plant species and several of its functions overlap with those of PP-InsPs. Until now, there is virtually no data on pyrophosphorylation of plant proteins, which is an exciting field that remains to be explored.
Collapse
Affiliation(s)
| | | | - Marília Kamleitner
- Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| |
Collapse
|
4
|
Whitfield H, Rodriguez RF, Shipton ML, Li AW, Riley AM, Potter BV, Hemmings AM, Brearley CA. Crystal Structure and Enzymology of Solanum tuberosum Inositol Tris/Tetrakisphosphate Kinase 1 ( StITPK1). Biochemistry 2024; 63:42-52. [PMID: 38146842 PMCID: PMC10765375 DOI: 10.1021/acs.biochem.3c00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 12/27/2023]
Abstract
Inositol phosphates and their pyrophosphorylated derivatives are responsive to the phosphate supply and are agents of phosphate homeostasis and other aspects of physiology. It seems likely that the enzymes that interconvert these signals work against the prevailing milieu of mixed populations of competing substrates and products. The synthesis of inositol pyrophosphates is mediated in plants by two classes of ATP-grasp fold kinase: PPIP5 kinases, known as VIH, and members of the inositol tris/tetrakisphosphate kinase (ITPK) family, specifically ITPK1/2. A molecular explanation of the contribution of ITPK1/2 to inositol pyrophosphate synthesis and turnover in plants is incomplete: the absence of nucleotide in published crystal structures limits the explanation of phosphotransfer reactions, and little is known of the affinity of potential substrates and competitors for ITPK1. Herein, we describe a complex of ADP and StITPK1 at 2.26 Å resolution and use a simple fluorescence polarization approach to compare the affinity of binding of diverse inositol phosphates, inositol pyrophosphates, and analogues. By simple HPLC, we reveal the novel catalytic capability of ITPK1 for different inositol pyrophosphates and show Ins(3,4,5,6)P4 to be a potent inhibitor of the inositol pyrophosphate-synthesizing activity of ITPK1. We further describe the exquisite specificity of ITPK1 for the myo-isomer among naturally occurring inositol hexakisphosphates.
Collapse
Affiliation(s)
- Hayley
L. Whitfield
- School
of Biological Sciences, University of East
Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Raquel Faba Rodriguez
- School
of Biological Sciences, University of East
Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Megan L. Shipton
- Medicinal
Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
| | - Arthur W.H. Li
- School
of Biological Sciences, University of East
Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Andrew M. Riley
- Medicinal
Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
| | - Barry V.L. Potter
- Medicinal
Chemistry & Drug Discovery, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, U.K.
| | - Andrew M. Hemmings
- School
of Biological Sciences, University of East
Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
- School
of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
- College
of Food Science and Technology, Shanghai
Ocean University, Shanghai 201306, China
| | - Charles A. Brearley
- School
of Biological Sciences, University of East
Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| |
Collapse
|
5
|
Cadena-Zamudio JD, Monribot-Villanueva JL, Pérez-Torres CA, Alatorre-Cobos F, Guerrero-Analco JA, Ibarra-Laclette E. Non-Targeted Metabolomic Analysis of Arabidopsis thaliana (L.) Heynh: Metabolic Adaptive Responses to Stress Caused by N Starvation. Metabolites 2023; 13:1021. [PMID: 37755301 PMCID: PMC10535036 DOI: 10.3390/metabo13091021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
As sessile organisms, plants develop the ability to respond and survive in changing environments. Such adaptive responses maximize phenotypic and metabolic fitness, allowing plants to adjust their growth and development. In this study, we analyzed the metabolic plasticity of Arabidopsis thaliana in response to nitrate deprivation by untargeted metabolomic analysis and using wild-type (WT) genotypes and the loss-of-function nia1/nia2 double mutant. Secondary metabolites were identified using seedlings grown on a hydroponic system supplemented with optimal or limiting concentrations of N (4 or 0.2 mM, respectively) and harvested at 15 and 30 days of age. Then, spectral libraries generated from shoots and roots in both ionization modes (ESI +/-) were compared. Totals of 3407 and 4521 spectral signals (m/z_rt) were obtained in the ESI+ and ESI- modes, respectively. Of these, approximately 50 and 65% were identified as differentially synthetized/accumulated. This led to the presumptive identification of 735 KEGG codes (metabolites) belonging to 79 metabolic pathways. The metabolic responses in the shoots and roots of WT genotypes at 4 mM of N favor the synthesis/accumulation of metabolites strongly related to growth. In contrast, for the nia1/nia2 double mutant (similar as the WT genotype at 0.2 mM N), metabolites identified as differentially synthetized/accumulated help cope with stress, regulating oxidative stress and preventing programmed cell death, meaning that metabolic responses under N starvation compromise growth to prioritize a defensive response.
Collapse
Affiliation(s)
- Jorge David Cadena-Zamudio
- Red de Estudios Moleculares Avanzados (REMAV), Instituto de Ecología, A.C. (INECOL), Xalapa 91073, Veracruz, Mexico; (J.D.C.-Z.); (J.L.M.-V.); (C.-A.P.-T.); (J.A.G.-A.)
| | - Juan Luis Monribot-Villanueva
- Red de Estudios Moleculares Avanzados (REMAV), Instituto de Ecología, A.C. (INECOL), Xalapa 91073, Veracruz, Mexico; (J.D.C.-Z.); (J.L.M.-V.); (C.-A.P.-T.); (J.A.G.-A.)
| | - Claudia-Anahí Pérez-Torres
- Red de Estudios Moleculares Avanzados (REMAV), Instituto de Ecología, A.C. (INECOL), Xalapa 91073, Veracruz, Mexico; (J.D.C.-Z.); (J.L.M.-V.); (C.-A.P.-T.); (J.A.G.-A.)
- Consejo Nacional de Ciencia y Tecnología, Unidad de Bioquímica y Biología Molecular de Plantas, Merida 97205, Yucatan, Mexico;
| | - Fulgencio Alatorre-Cobos
- Consejo Nacional de Ciencia y Tecnología, Unidad de Bioquímica y Biología Molecular de Plantas, Merida 97205, Yucatan, Mexico;
- Centro de Investigación Científica de Yucatán (CICY), Unidad de Biotecnología, Merida 97205, Yucatan, Mexico
| | - José Antonio Guerrero-Analco
- Red de Estudios Moleculares Avanzados (REMAV), Instituto de Ecología, A.C. (INECOL), Xalapa 91073, Veracruz, Mexico; (J.D.C.-Z.); (J.L.M.-V.); (C.-A.P.-T.); (J.A.G.-A.)
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados (REMAV), Instituto de Ecología, A.C. (INECOL), Xalapa 91073, Veracruz, Mexico; (J.D.C.-Z.); (J.L.M.-V.); (C.-A.P.-T.); (J.A.G.-A.)
| |
Collapse
|
6
|
Pullagurla NJ, Shome S, Yadav R, Laha D. ITPK1 Regulates Jasmonate-Controlled Root Development in Arabidopsis thaliana. Biomolecules 2023; 13:1368. [PMID: 37759768 PMCID: PMC10526342 DOI: 10.3390/biom13091368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/26/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Jasmonic acid (JA) is a plant hormone that regulates a plethora of physiological processes including immunity and development and is perceived by the F-Box protein, Coronatine-insensitive protein 1 (COI1). The discovery of inositol phosphates (InsPs) in the COI1 receptor complex highlights their role in JAperception. InsPs are phosphate-rich signaling molecules that control many aspects of plant physiology. Inositol pyrophosphates (PP-InsPs) are diphosphate containing InsP species, of which InsP7 and InsP8 are the best characterized ones. Different InsP and PP-InsP species are linked with JA-related plant immunity. However, role of PP-InsP species in regulating JA-dependent developmental processes are poorly understood. Recent identification of ITPK1 kinase, responsible for the production of 5-InsP7 from InsP6in planta, provides a platform to investigate the possible involvement of ITPK-derived InsP species in JA-related plant development. Here, in this study, we report that ITPK1-defective plants exhibit increased root growth inhibition to bioactive JA treatment. The itpk1 plants also show increased lateral root density when treated with JA. Notably, JA treatment does not increase ITPK1 protein levels. Gene expression analyses revealed that JA-biosynthetic genes are not differentially expressed in ITPK1-deficient plants. We further demonstrate that genes encoding different JAZ repressor proteins are severely down-regulated in ITPK1-defective plants. Taken together, our study highlights the role of ITPK1 in regulating JA-dependent root architecture development through controlling the expression of different JAZ repressor proteins.
Collapse
Affiliation(s)
| | | | | | - Debabrata Laha
- Department of Biochemistry, Division of Biological Sciences, Indian Institute of Science (IISc), Bengaluru 560012, India; (N.J.P.); (S.S.); (R.Y.)
| |
Collapse
|
7
|
Lahuta LB, Szablińska-Piernik J, Stałanowska K, Horbowicz M, Górecki RJ, Railean V, Pomastowski P, Buszewski B. Exogenously Applied Cyclitols and Biosynthesized Silver Nanoparticles Affect the Soluble Carbohydrate Profiles of Wheat ( Triticum aestivum L.) Seedling. PLANTS (BASEL, SWITZERLAND) 2023; 12:1627. [PMID: 37111851 PMCID: PMC10145852 DOI: 10.3390/plants12081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/24/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
Cyclitols, such as myo-inositol and its isomers and methyl derivatives (i.e., d-chiro-inositol and d-pinitol (3-O-methyl-chiro-inositol)), are classified as osmolytes and osmoprotectants and are significantly involved in plant responses to abiotic stresses, such as drought, salinity and cold. Moreover, d-pinitol demonstrates a synergistic effect with glutathione (GSH), increasing its antioxidant properties. However, the role of cyclitols in plant protection against stresses caused by metal nanoparticles is not yet known. Therefore, the present study examined the effects of myo-inositol, d-chiro-inositol and d-pinitol on wheat germination, seedling growth and changes in the profile of soluble carbohydrates in response to biologically synthesized silver nanoparticles ((Bio)Ag NPs). It was found that cyclitols were absorbed by germinating grains and transported within the growing seedlings but this process was disrupted by (Bio)Ag NPs. Cyclitols applied alone induced sucrose and 1-kestose accumulation in seedlings slightly, while (Bio)Ag NP doubled the concentrations of both sugars. This coincided with a decrease in monosaccharides; i.e., fructose and glucose. Cyclitols and (Bio)Ag NPs present in the endosperm resulted in reductions in monosaccharides, maltose and maltotriose, with no effect on sucrose and 1-kestose. Similar changes occurred in seedlings developing from primed grains. Cyclitols that accumulated in grain and seedlings during grain priming with d-pinitol and glutathione did not prevent the phytotoxic effects of (Bio)Ag NPs.
Collapse
Affiliation(s)
- Lesław B. Lahuta
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury, Oczapowskiego Street 1A/103, 10-719 Olsztyn, Poland
| | - Joanna Szablińska-Piernik
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury, Oczapowskiego Street 1A/103, 10-719 Olsztyn, Poland
| | - Karolina Stałanowska
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury, Oczapowskiego Street 1A/103, 10-719 Olsztyn, Poland
| | - Marcin Horbowicz
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury, Oczapowskiego Street 1A/103, 10-719 Olsztyn, Poland
| | - Ryszard J. Górecki
- Department of Plant Physiology, Genetics and Biotechnology, University of Warmia and Mazury, Oczapowskiego Street 1A/103, 10-719 Olsztyn, Poland
| | - Viorica Railean
- Department of Infectious, Invasive Diseases and Veterinary Administration, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100 Toruń, Poland
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University in Torun, 87-100 Toruń, Poland
| | - Paweł Pomastowski
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University in Torun, 87-100 Toruń, Poland
| | - Bogusław Buszewski
- Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University in Torun, 87-100 Toruń, Poland
| |
Collapse
|