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Xiang RH, Wang JQ, Li ZG. Crosstalk of methylglyoxal and calcium signaling in maize (Zea mays L.) thermotolerance through methylglyoxal-scavenging system. JOURNAL OF PLANT PHYSIOLOGY 2024; 303:154362. [PMID: 39395220 DOI: 10.1016/j.jplph.2024.154362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 09/24/2024] [Accepted: 09/24/2024] [Indexed: 10/14/2024]
Abstract
Methylglyoxal (MG) and calcium ion (Ca2+) can increase multiple-stress tolerance including plant thermotolerance. However, whether crosstalk of MG and Ca2+ exists in the formation of maize thermotolerance and underlying mechanism still remain elusive. In this paper, maize seedlings were irrigated with MG and calcium chloride alone or in combination, and then exposed to heat stress (HS). The results manifested that, compared with the survival percentage (SP, 45.3%) of the control seedlings, the SP of MG and Ca2+ alone or in combination was increased to 72.4%, 74.2%, and 83.4% under HS conditions, indicating that Ca2+ and MG alone or in combination could upraise seedling thermotolerance. Also, the MG-upraised SP was separately weakened to 42.2%, 40.3%, 52.1%, and 39.4% by Ca2+ chelator (ethylene glycol tetraacetic acid, EGTA), plasma membrane Ca2+ channel blocker (lanthanum chloride, LaCl3), intracellular Ca2+ channel blocker (neomycin, NEC), and calmodulin (CaM) antagonist (trifluoperazine, TFP). However, significant effect of MG scavengers N-acetylcysteine (NAC) and aminoguanidine (AG) on Ca2+-induced thermotolerance was not observed. Similarly, an endogenous Ca2+ level in seedlings was increased by exogenous MG under non-HS and HS conditions, while exogenous Ca2+ had no significant effect on endogenous MG. These data implied that Ca2+ signaling, at least partly, mediated MG-upraised thermotolerance in maize seedlings. Moreover, the activity and gene expression of glyoxalase system (glyoxalase I, glyoxalase II, and glyoxalase III) and non-glyoxalase system (MG reductase, aldehyde reductase, aldo-keto reductase, and lactate dehydrogenase) were up-regulated to a certain extent by Ca2+ and MG alone in seedlings under non-HS and HS conditions. The up-regulated MG-scavenging system by MG was enhanced by Ca2+, while impaired by EGTA, LaCl3, NEC, or TFP. These data suggest that the crosstalk of MG and Ca2+ signaling in maize thermotolerance through MG-scavenging system. These findings provided a theoretical basis for breeding climate-resilient maize crop and developing smart agriculture.
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Affiliation(s)
- Ru-Hua Xiang
- School of Life Sciences, Yunnan Normal University, Kunming, 650092, PR China; Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650092, PR China; Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Province, Yunnan Normal University, Kunming, 650092, PR China
| | - Jia-Qi Wang
- School of Life Sciences, Yunnan Normal University, Kunming, 650092, PR China; Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650092, PR China; Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Province, Yunnan Normal University, Kunming, 650092, PR China
| | - Zhong-Guang Li
- School of Life Sciences, Yunnan Normal University, Kunming, 650092, PR China; Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, 650092, PR China; Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Province, Yunnan Normal University, Kunming, 650092, PR China.
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Wang Z, Zhang Y, Wu Y, Lai D, Deng Y, Ju C, Sun L, Huang P, Wang C. CPK10 protein kinase regulates Arabidopsis tolerance to boron deficiency through phosphorylation and activation of BOR1 transporter. THE NEW PHYTOLOGIST 2024; 243:1795-1809. [PMID: 38622812 DOI: 10.1111/nph.19712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/12/2024] [Indexed: 04/17/2024]
Abstract
Boron (B) is crucial for plant growth and development. B deficiency can impair numerous physiological and metabolic processes, particularly in root development and pollen germination, seriously impeding crop growth and yield. However, the molecular mechanism underlying boron signal perception and signal transduction is rather limited. In this study, we discovered that CPK10, a calcium-dependent protein kinase in the CPK family, has the strongest interaction with the boron transporter BOR1. Mutations in CPK10 led to growth and root development defects under B-deficiency conditions, while constitutively active CPK10 enhanced plant tolerance to B deficiency. Furthermore, we found that CPK10 interacted with and phosphorylated BOR1 at the Ser689 residue. Through various biochemical analyses and complementation of B transport in yeast and plants, we revealed that Ser689 of BOR1 is important for its transport activity. In summary, these findings highlight the significance of the CPK10-BOR1 signaling pathway in maintaining B homeostasis in plants and provide targets for the genetic improvement of crop tolerance to B-deficiency stress.
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Affiliation(s)
- Zhangqing Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yanting Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yaru Wu
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Duoduo Lai
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yuan Deng
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chuanfeng Ju
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lv Sun
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Panpan Huang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cun Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Sarkar S, Rhein HS, Pittman JK, Hirschi KD. A dominant-negative Arabidopsis cation exchanger 1 (CAX1): N-terminal autoinhibition and membrane topology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39175446 DOI: 10.1111/tpj.16966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/20/2024] [Accepted: 07/25/2024] [Indexed: 08/24/2024]
Abstract
Calcium (Ca2+) is essential for plant growth and cellular homeostasis, with cation exchangers (CAXs) regulating Ca2+ transport into plant vacuoles. In Arabidopsis, multiple CAXs feature a common structural arrangement, comprising an N-terminal autoinhibitory domain followed by two pseudosymmetrical modules. Mutations in CAX1 enhance stress tolerance, notably tolerance to anoxia (a condition marked by oxygen depletion), crucial for flood resilience. Here we engineered a dominant-negative CAX1 variant, named ½N-CAX1, incorporating the autoinhibitory domain and the N-terminal pseudosymmetrical module, which, when expressed in wild-type Arabidopsis plants, phenocopied the anoxia tolerance of cax1. Physiological evaluations, yeast assays, and calcium imaging demonstrated that wild-type plants expressing ½N-CAX1 have phenotypes consistent with inhibition of CAX1, which is likely through direct interaction of ½N-CAX1 with CAX1. Eliminating segments within the N-terminal pseudosymmetrical module, as well as incorporating modules from other plant CAXs and expressing these variants into wild-type plants, failed to produce anoxia tolerance. This underscores the requirement for both the CAX1 autoinhibitory domain and the intact pseudosymmetrical module to produce the dominant-negative phenotype. Our study elucidates the interaction of this ½N-CAX1 variant with CAX1 and its impact on anoxia tolerance, offering insights into further approaches for engineering plant stress tolerance.
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Affiliation(s)
- Shayan Sarkar
- Pediatrics Nutrition, Children's Nutrition Research, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Hormat Shadgou Rhein
- Pediatrics Nutrition, Children's Nutrition Research, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jon K Pittman
- Faculty of Science and Engineering, School of Natural Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Kendal D Hirschi
- Pediatrics Nutrition, Children's Nutrition Research, Baylor College of Medicine, Houston, Texas, 77030, USA
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Mathieu D, Bryson AE, Hamberger B, Singan V, Keymanesh K, Wang M, Barry K, Mondo S, Pangilinan J, Koriabine M, Grigoriev IV, Bonito G, Hamberger B. Multilevel analysis between Physcomitrium patens and Mortierellaceae endophytes explores potential long-standing interaction among land plants and fungi. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:304-323. [PMID: 38265362 DOI: 10.1111/tpj.16605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/16/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024]
Abstract
The model moss species Physcomitrium patens has long been used for studying divergence of land plants spanning from bryophytes to angiosperms. In addition to its phylogenetic relationships, the limited number of differential tissues, and comparable morphology to the earliest embryophytes provide a system to represent basic plant architecture. Based on plant-fungal interactions today, it is hypothesized these kingdoms have a long-standing relationship, predating plant terrestrialization. Mortierellaceae have origins diverging from other land fungi paralleling bryophyte divergence, are related to arbuscular mycorrhizal fungi but are free-living, observed to interact with plants, and can be found in moss microbiomes globally. Due to their parallel origins, we assess here how two Mortierellaceae species, Linnemannia elongata and Benniella erionia, interact with P. patens in coculture. We also assess how Mollicute-related or Burkholderia-related endobacterial symbionts (MRE or BRE) of these fungi impact plant response. Coculture interactions are investigated through high-throughput phenomics, microscopy, RNA-sequencing, differential expression profiling, gene ontology enrichment, and comparisons among 99 other P. patens transcriptomic studies. Here we present new high-throughput approaches for measuring P. patens growth, identify novel expression of over 800 genes that are not expressed on traditional agar media, identify subtle interactions between P. patens and Mortierellaceae, and observe changes to plant-fungal interactions dependent on whether MRE or BRE are present. Our study provides insights into how plants and fungal partners may have interacted based on their communications observed today as well as identifying L. elongata and B. erionia as modern fungal endophytes with P. patens.
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Affiliation(s)
- Davis Mathieu
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Abigail E Bryson
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Britta Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Vasanth Singan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Keykhosrow Keymanesh
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Mei Wang
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Stephen Mondo
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Maxim Koriabine
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, 94720, USA
| | - Gregory Bonito
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Björn Hamberger
- Genetics and Genome Science Graduate Program, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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5
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Bouard W, Ouellet F, Houde M. Modulation of the wheat transcriptome by TaZFP13D under well-watered and drought conditions. PLANT MOLECULAR BIOLOGY 2024; 114:16. [PMID: 38332456 PMCID: PMC10853348 DOI: 10.1007/s11103-023-01403-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/16/2023] [Indexed: 02/10/2024]
Abstract
Maintaining global food security in the context of climate changes will be an important challenge in the next century. Improving abiotic stress tolerance of major crops such as wheat can contribute to this goal. This can be achieved by the identification of the genes involved and their use to develop tools for breeding programs aiming to generate better adapted cultivars. Recently, we identified the wheat TaZFP13D gene encoding Zinc Finger Protein 13D as a new gene improving water-stress tolerance. The current work analyzes the TaZFP13D-dependent transcriptome modifications that occur in well-watered and dehydration conditions to better understand its function during normal growth and during drought. Plants that overexpress TaZFP13D have a higher biomass under well-watered conditions, indicating a positive effect of the protein on growth. Survival rate and stress recovery after a severe drought stress are improved compared to wild-type plants. The latter is likely due the higher activity of key antioxidant enzymes and concomitant reduction of drought-induced oxidative damage. Conversely, down-regulation of TaZFP13D decreases drought tolerance and protection against drought-induced oxidative damage. RNA-Seq transcriptome analysis identified many genes regulated by TaZFP13D that are known to improve drought tolerance. The analysis also revealed several genes involved in the photosynthetic electron transfer chain known to improve photosynthetic efficiency and chloroplast protection against drought-induced ROS damage. This study highlights the important role of TaZFP13D in wheat drought tolerance, contributes to unravel the complex regulation governed by TaZFPs, and suggests that it could be a promising marker to select wheat cultivars with higher drought tolerance.
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Affiliation(s)
- William Bouard
- Département des Sciences biologiques, Université du Québec à Montréal, Montréal, QC, H3C 3P8, Canada
| | - François Ouellet
- Département des Sciences biologiques, Université du Québec à Montréal, Montréal, QC, H3C 3P8, Canada
| | - Mario Houde
- Département des Sciences biologiques, Université du Québec à Montréal, Montréal, QC, H3C 3P8, Canada.
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Ye K, Shen W, Zhao Y. External application of brassinolide enhances cold resistance of tea plants (Camellia sinensis L.) by integrating calcium signals. PLANTA 2023; 258:114. [PMID: 37943407 DOI: 10.1007/s00425-023-04276-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 10/28/2023] [Indexed: 11/10/2023]
Abstract
MAIN CONCLUSION Exogenous brassinolide can activate the expression of key genes in the calcium signalling pathway to enhance cold resistance of tea plants. Brassinolide is an endogenous sterol phytohormone containing multiple hydroxyl groups that has the important function of improving plant cold resistance and alleviating freeze damage. To explore the molecular mechanism of how brassinolide improves the cold resistance of tea plants, "Qiancha 1" was used as the material, and the method of spraying brassinolide on the leaves was adopted to explore its effects on the tea plants under 4 °C low-temperature treatment. The results showed that brassinolide can significantly increase the protective enzyme activity of tea plants under cold stress and reduce cold damage. At the transcriptome level, brassinolide significantly enhanced the expression of key genes involved in calcium signal transduction, Calmodulin (CaM), Calcium-dependent protein kinase (CDPK), calcineurin B-like protein (CBL) and calmodulin-binding transcriptional activators (CAMTA), which then activated the downstream key genes transcriptional regulator CBF1 (CBF1) and transcription factor ICE1 (ICE1) during cold induction. Quantitative real-time PCR (qRT‒PCR) results showed that the expression of these genes was significantly induced after treatment with brassinolide, especially CaM and CBF1. When calcium signalling was inhibited, the upregulated expression of CBF1 and ICE1 disappeared, and when CAMTA was knocked down, the expression of other genes under cold stress was also significantly reduced. The above results indicate that brassinolide combined with the calcium signalling pathway can improve the cold resistance of tea plants. This study provides a new theoretical basis for the study of the cold resistance mechanism of brassinolide.
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Affiliation(s)
- Kun Ye
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Tea Sciences, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Weijian Shen
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Tea Sciences, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Yichen Zhao
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Tea Sciences, College of Life Sciences, Guizhou University, Guiyang, 550025, China.
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Khan MI, Pandith SA, Shah MA, Reshi ZA. Calcium Oxalate Crystals, the Plant 'Gemstones': Insights into Their Synthesis and Physiological Implications in Plants. PLANT & CELL PHYSIOLOGY 2023; 64:1124-1138. [PMID: 37498947 DOI: 10.1093/pcp/pcad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
From simple algal forms to the most advanced angiosperms, calcium oxalate (CaOx) crystals (CRs) occur in the majority of taxonomic groups of photosynthetic organisms. Various studies have demonstrated that this biomineralization is not a simple or random event but a genetically regulated coordination between calcium uptake, oxalate (OX) synthesis and, sometimes, environmental stresses. Certainly, the occurrence of CaOx CRs is old; however, questions related to their genesis, biosynthesis, significance and genetics exhibit robust evolution. Moreover, their speculated roles in bulk calcium regulation, heavy metal/OX detoxification, light reflectance and photosynthesis, and protection against grazing and herbivory, besides other characteristics, are gaining much interest. Thus, it is imperative to understand their synthesis and regulation in relation to the ascribed key functions to reconstruct future perspectives in harnessing their potential to achieve nutritious and pest-resistant crops amid anticipated global climatic perturbations. This review critically addresses the basic and evolving concepts of the origin (and recycling), synthesis, significance, regulation and fate vis-à-vis various functional aspects of CaOx CRs in plants (and soil). Overall, insights and conceptual future directions present them as potential biominerals to address future climate-driven issues.
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Affiliation(s)
- Mohd Ishfaq Khan
- Department of Botany, University of Kashmir, Hazratbal Srinagar, Jammu and Kashmir 190006, India
| | - Shahzad A Pandith
- Department of Botany, University of Kashmir, Hazratbal Srinagar, Jammu and Kashmir 190006, India
| | - Manzoor A Shah
- Department of Botany, University of Kashmir, Hazratbal Srinagar, Jammu and Kashmir 190006, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Hazratbal Srinagar, Jammu and Kashmir 190006, India
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Li L, Guo N, Cao Y, Zhai X, Fan G. Genome-Wide Characterization of Calmodulin and Calmodulin-like Protein Gene Families in Paulownia fortunei and Identification of Their Potential Involvement in Paulownia Witches' Broom. Genes (Basel) 2023; 14:1540. [PMID: 37628592 PMCID: PMC10454933 DOI: 10.3390/genes14081540] [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: 05/08/2023] [Revised: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 08/27/2023] Open
Abstract
As significant Ca2+ sensors, calmodulin (CaM) and calmodulin-like proteins (CML), have been associated with a variety of environmental conditions in plants. However, whether CaMs/CMLs are related to the stress of phytoplasma infection has not been reported in Paulownia fortunei. In the current study, 5 PfCaMs and 58 PfCMLs were detected through a genome-wide investigation. The number of EF-hand motifs in all PfCaMs/CMLs varied. Bioinformatics analyses, including protein characteristics, conserved domain, gene structure, cis-elements, evolutionary relationship, collinearity, chromosomal location, post-translation modification site, subcellular localization and expression pattern analyses, represented the conservation and divergence of PfCaMs/CMLs. Furthermore, some PfCaMs/CMLs might be involved in plants' reaction to phytoplasma infection and exogenous calcium therapy, indicating these genes may play a role in abiotic as well as biotic stress responses. In addition, subcellular localization analysis showed that PfCML10 was located in the cell membrane and nucleus. In summary, these findings establish a stronger platform for their subsequent functional investigation in trees and further characterize their roles in Paulownia witches' broom (PaWB) occurrence.
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Affiliation(s)
- Lijiao Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (L.L.); (N.G.); (Y.C.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Na Guo
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (L.L.); (N.G.); (Y.C.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | - Yabing Cao
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (L.L.); (N.G.); (Y.C.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
| | | | - Guoqiang Fan
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China; (L.L.); (N.G.); (Y.C.)
- Institute of Paulownia, Henan Agricultural University, Zhengzhou 450002, China
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Balasubramaniam S, Somathilaka S, Sun S, Ratwatte A, Pierobon M. Realizing Molecular Machine Learning through Communications for Biological AI: Future Directions and Challenges. IEEE NANOTECHNOLOGY MAGAZINE 2023; 17:10-20. [PMID: 38855043 PMCID: PMC11160936 DOI: 10.1109/mnano.2023.3262099] [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] [Indexed: 06/11/2024]
Abstract
Artificial Intelligence (AI) and Machine Learning (ML) are weaving their way into the fabric of society, where they are playing a crucial role in numerous facets of our lives. As we witness the increased deployment of AI and ML in various types of devices, we benefit from their use into energy-efficient algorithms for low powered devices. In this paper, we investigate a scale and medium that is far smaller than conventional devices as we move towards molecular systems that can be utilized to perform machine learning functions, i.e., Molecular Machine Learning (MML). Fundamental to the operation of MML is the transport, processing, and interpretation of information propagated by molecules through chemical reactions. We begin by reviewing the current approaches that have been developed for MML, before we move towards potential new directions that rely on gene regulatory networks inside biological organisms as well as their population interactions to create neural networks. We then investigate mechanisms for training machine learning structures in biological cells based on calcium signaling and demonstrate their application to build an Analog to Digital Converter (ADC). Lastly, we look at potential future directions as well as challenges that this area could solve.
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Affiliation(s)
| | - Samitha Somathilaka
- School of Computing, University of Nebraska-Lincoln, NE, USA
- Walton Institute, South East Technological University, Ireland
| | - Sehee Sun
- School of Computing, University of Nebraska-Lincoln, NE, USA
| | - Adrian Ratwatte
- School of Computing, University of Nebraska-Lincoln, NE, USA
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Tansley C, Houghton J, Rose AME, Witek B, Payet RD, Wu T, Miller JB. CIPK-B is essential for salt stress signalling in Marchantia polymorpha. THE NEW PHYTOLOGIST 2023; 237:2210-2223. [PMID: 36660914 PMCID: PMC10953335 DOI: 10.1111/nph.18633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/13/2022] [Indexed: 06/17/2023]
Abstract
Calcium signalling is central to many plant processes, with families of calcium decoder proteins having expanded across the green lineage and redundancy existing between decoders. The liverwort Marchantia polymorpha has fast become a new model plant, but the calcium decoders that exist in this species remain unclear. We performed phylogenetic analyses to identify the calcineurin B-like (CBL) and CBL-interacting protein kinase (CIPK) network of M. polymorpha. We analysed CBL-CIPK expression during salt stress, and determined protein-protein interactions using yeast two-hybrid and bimolecular fluorescence complementation. We also created genetic knockouts using CRISPR/Cas9. We confirm that M. polymorpha has two CIPKs and three CBLs. Both CIPKs and one CBL show pronounced salt-responsive transcriptional changes. All M. polymorpha CBL-CIPKs interact with each other in planta. Knocking out CIPK-B causes increased sensitivity to salt, suggesting that this CIPK is involved in salt signalling. We have identified CBL-CIPKs that form part of a salt tolerance pathway in M. polymorpha. Phylogeny and interaction studies imply that these CBL-CIPKs form an evolutionarily conserved salt overly sensitive pathway. Hence, salt responses may be some of the early functions of CBL-CIPK networks and increased abiotic stress tolerance required for land plant emergence.
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Affiliation(s)
- Connor Tansley
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - James Houghton
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Althea M. E. Rose
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Bartosz Witek
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Rocky D. Payet
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - Taoyang Wu
- School of Computing SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
| | - J. Benjamin Miller
- School of Biological SciencesUniversity of East AngliaNorwich Research ParkNorwichNR4 7TJUK
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Folke Olsen L. Complex dynamics in an unexplored simple model of the peroxidase-oxidase reaction. CHAOS (WOODBURY, N.Y.) 2023; 33:023102. [PMID: 36859227 DOI: 10.1063/5.0129095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
A previously overlooked version of the so-called Olsen model of the peroxidase-oxidase reaction has been studied numerically using 2D isospike stability and maximum Lyapunov exponent diagrams and reveals a rich variety of dynamic behaviors not observed before. The model has a complex bifurcation structure involving mixed-mode and bursting oscillations as well as quasiperiodic and chaotic dynamics. In addition, multiple periodic and non-periodic attractors coexist for the same parameters. For some parameter values, the model also reveals formation of mosaic patterns of complex dynamic states. The complex dynamic behaviors exhibited by this model are compared to those of another version of the same model, which has been studied in more detail. The two models show similarities, but also notable differences between them, e.g., the organization of mixed-mode oscillations in parameter space and the relative abundance of quasiperiodic and chaotic oscillations. In both models, domains with chaotic dynamics contain apparently disorganized subdomains of periodic attractors with dinoflagellate-like structures, while the domains with mainly quasiperiodic behavior contain subdomains with periodic attractors organized as regular filamentous structures. These periodic attractors seem to be organized according to Stern-Brocot arithmetics. Finally, it appears that toroidal (quasiperiodic) attractors develop into first wrinkled and then fractal tori before they break down to chaotic attractors.
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Affiliation(s)
- Lars Folke Olsen
- PhyLife, Institute of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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Allan C, Tayagui A, Hornung R, Nock V, Meisrimler CN. A dual-flow RootChip enables quantification of bi-directional calcium signaling in primary roots. FRONTIERS IN PLANT SCIENCE 2023; 13:1040117. [PMID: 36704158 PMCID: PMC9871814 DOI: 10.3389/fpls.2022.1040117] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/13/2022] [Indexed: 06/18/2023]
Abstract
One sentence summary: Bi-directional-dual-flow-RootChip to track calcium signatures in Arabidopsis primary roots responding to osmotic stress. Plant growth and survival is fundamentally linked with the ability to detect and respond to abiotic and biotic factors. Cytosolic free calcium (Ca2+) is a key messenger in signal transduction pathways associated with a variety of stresses, including mechanical, osmotic stress and the plants' innate immune system. These stresses trigger an increase in cytosolic Ca2+ and thus initiate a signal transduction cascade, contributing to plant stress adaptation. Here we combine fluorescent G-CaMP3 Arabidopsis thaliana sensor lines to visualise Ca2+ signals in the primary root of 9-day old plants with an optimised dual-flow RootChip (dfRC). The enhanced polydimethylsiloxane (PDMS) bi-directional-dual-flow-RootChip (bi-dfRC) reported here adds two adjacent inlet channels at the base of the observation chamber, allowing independent or asymmetric chemical stimulation at either the root differentiation zone or tip. Observations confirm distinct early spatio-temporal patterns of salinity (sodium chloride, NaCl) and drought (polyethylene glycol, PEG)-induced Ca2+ signals throughout different cell types dependent on the first contact site. Furthermore, we show that the primary signal always dissociates away from initially stimulated cells. The observed early signaling events induced by NaCl and PEG are surprisingly complex and differ from long-term changes in cytosolic Ca2+ reported in roots. Bi-dfRC microfluidic devices will provide a novel approach to challenge plant roots with different conditions simultaneously, while observing bi-directionality of signals. Future applications include combining the bi-dfRC with H2O2 and redox sensor lines to test root systemic signaling responses to biotic and abiotic factors.
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Affiliation(s)
- Claudia Allan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Ayelen Tayagui
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
| | | | - Volker Nock
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, New Zealand
- MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington, New Zealand
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Calcium decoders and their targets: The holy alliance that regulate cellular responses in stress signaling. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 134:371-439. [PMID: 36858741 DOI: 10.1016/bs.apcsb.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Calcium (Ca2+) signaling is versatile communication network in the cell. Stimuli perceived by cells are transposed through Ca2+-signature, and are decoded by plethora of Ca2+ sensors present in the cell. Calmodulin, calmodulin-like proteins, Ca2+-dependent protein kinases and calcineurin B-like proteins are major classes of proteins that decode the Ca2+ signature and serve in the propagation of signals to different parts of cells by targeting downstream proteins. These decoders and their targets work together to elicit responses against diverse stress stimuli. Over a period of time, significant attempts have been made to characterize as well as summarize elements of this signaling machinery. We begin with a structural overview and amalgamate the newly identified Ca2+ sensor protein in plants. Their ability to bind Ca2+, undergo conformational changes, and how it facilitates binding to a wide variety of targets is further embedded. Subsequently, we summarize the recent progress made on the functional characterization of Ca2+ sensing machinery and in particular their target proteins in stress signaling. We have focused on the physiological role of Ca2+, the Ca2+ sensing machinery, and the mode of regulation on their target proteins during plant stress adaptation. Additionally, we also discuss the role of these decoders and their mode of regulation on the target proteins during abiotic, hormone signaling and biotic stress responses in plants. Finally, here, we have enumerated the limitations and challenges in the Ca2+ signaling. This article will greatly enable in understanding the current picture of plant response and adaptation during diverse stimuli through the lens of Ca2+ signaling.
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Parmagnani AS, Maffei ME. Calcium Signaling in Plant-Insect Interactions. PLANTS (BASEL, SWITZERLAND) 2022; 11:2689. [PMID: 36297718 PMCID: PMC9609891 DOI: 10.3390/plants11202689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
In plant-insect interactions, calcium (Ca2+) variations are among the earliest events associated with the plant perception of biotic stress. Upon herbivory, Ca2+ waves travel long distances to transmit and convert the local signal to a systemic defense program. Reactive oxygen species (ROS), Ca2+ and electrical signaling are interlinked to form a network supporting rapid signal transmission, whereas the Ca2+ message is decoded and relayed by Ca2+-binding proteins (including calmodulin, Ca2+-dependent protein kinases, annexins and calcineurin B-like proteins). Monitoring the generation of Ca2+ signals at the whole plant or cell level and their long-distance propagation during biotic interactions requires innovative imaging techniques based on sensitive sensors and using genetically encoded indicators. This review summarizes the recent advances in Ca2+ signaling upon herbivory and reviews the most recent Ca2+ imaging techniques and methods.
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Damineli DSC, Portes MT, Feijó JA. Electrifying rhythms in plant cells. Curr Opin Cell Biol 2022; 77:102113. [PMID: 35809387 DOI: 10.1016/j.ceb.2022.102113] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 05/10/2022] [Accepted: 06/05/2022] [Indexed: 12/12/2022]
Abstract
Physiological oscillations (or rhythms) pervade all spatiotemporal scales of biological organization, either because they perform critical functions or simply because they can arise spontaneously and may be difficult to prevent. Regardless of the case, they reflect regulatory relationships between control points of a given system and offer insights as read-outs of the concerted regulation of a myriad of biological processes. Here we review recent advances in understanding ultradian oscillations (period < 24h) in plant cells, with a special focus on single-cell oscillations. Ion channels are at the center stage due to their involvement in electrical/excitabile phenomena associated with oscillations and cell-cell communication. We highlight the importance of quantitative approaches to measure oscillations in appropriate physiological conditions, which are essential strategies to deal with the complexity of biological rhythms. Future development of optogenetics techniques in plants will further boost research on the role of membrane potential in oscillations and waves across multiple cell types.
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Affiliation(s)
- Daniel S C Damineli
- Department of Computer Science, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, SP 05508-090, Brazil.
| | - Maria Teresa Portes
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, SP 05508-090, Brazil
| | - José A Feijó
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742-5815, USA
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