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Shannon D, Cerdan K, Kim M, Mecklenburg M, Su J, Chen Y, Helgeson ME, Valentine MT, Hawker CJ. Bioinspired Metal-Ligand Networks with Enhanced Stability and Performance: Facile Preparation of Hydroxypyridinone (HOPO)-Functionalized Materials. Macromolecules 2024; 57:11339-11349. [PMID: 39741960 PMCID: PMC11684171 DOI: 10.1021/acs.macromol.4c02250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 11/19/2024] [Accepted: 11/22/2024] [Indexed: 01/03/2025]
Abstract
Bioinspired hydroxypyridinone (HOPO)functionalized materials are shown to display a remarkable capacity for stability and for chelating a wide array of metal ions. This allows for the synthesis of multifunctional networks with diverse physical properties when compared to traditional catechol systems. In the present study, we report a facile, one-pot synthesis of an amino HOPO ligand and simple, scalable incorporation into PEG-acrylate based networks via active ester chemistry. This modular network approach allows for fabrication of patterned HOPO containing networks which can chelate a range of metal ions, such as transition metals (Fe3+) and lanthanides (Ho3+, Tb3+), leading to modulation of mechanical, magnetic, and fluorescent properties. Moreover, networks with tailored, heterogeneous properties can be prepared through localization of metal ion incorporation in 3-dimensions via masking techniques, creating distinctly soft, hard, magnetic, and fluorescent domains.
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Affiliation(s)
- Declan
P. Shannon
- Materials
Department, University of California Santa
Barbara, Santa
Barbara, California 93106-5050, United States
- Materials
Research Laboratory, University of California
Santa Barbara, Santa Barbara, California 93106-5121, United States
| | - Kenneth Cerdan
- Department
of Mechanical Engineering, University of
California, Santa Barbara, Santa
Barbara, California 93106-5070, United States
- Department
of Chemical Engineering, University of California,
Santa Barbara, Santa Barbara, California 93106-5080, United States
| | - Minseong Kim
- Materials
Department, University of California Santa
Barbara, Santa
Barbara, California 93106-5050, United States
- Materials
Research Laboratory, University of California
Santa Barbara, Santa Barbara, California 93106-5121, United States
| | - Matthew Mecklenburg
- California
NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Judy Su
- California
NanoSystems Institute, University of California, Los Angeles, California 90095, United States
| | - Yueyun Chen
- California
NanoSystems Institute, University of California, Los Angeles, California 90095, United States
- Department
of Physics and Astronomy, University of
California, Los Angeles, California 90095, United States
| | - Matthew E. Helgeson
- Department
of Chemical Engineering, University of California,
Santa Barbara, Santa Barbara, California 93106-5080, United States
| | - Megan T. Valentine
- Department
of Mechanical Engineering, University of
California, Santa Barbara, Santa
Barbara, California 93106-5070, United States
| | - Craig J. Hawker
- Materials
Department, University of California Santa
Barbara, Santa
Barbara, California 93106-5050, United States
- Department
of Chemistry & Biochemistry, University
of California Santa Barbara, Santa
Barbara, California 93106-9510, United States
- Materials
Research Laboratory, University of California
Santa Barbara, Santa Barbara, California 93106-5121, United States
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Chakraborty S, Dwivedi S, Schuster S. Mathematical modeling predicts that endemics by generalist insects are eradicated if nearly all plants produce constitutive defense. Sci Rep 2024; 14:25771. [PMID: 39468088 PMCID: PMC11519633 DOI: 10.1038/s41598-024-74771-0] [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: 06/11/2024] [Accepted: 09/30/2024] [Indexed: 10/30/2024] Open
Abstract
Plants with constitutive defense chemicals exist widely in nature. The phenomenon is backed by abundant data from plant chemical ecology. Sufficient data are also available to conclude that plant defenses act as deterrent and repellent to attacking herbivores, particularly deleterious generalist insects. In the wild, generalist species are usually not endemic, meaning they are not restricted to certain plant species in a region. Therefore, our objective is to inspect theoretically whether evolution of chemical defenses in all plant species eradicate an endemic by any generalist species. The objective is addressed by developing deterministic ordinary differential equations under the following conditions: Plants without constitutive defenses are susceptible to oviposition by generalist insects, while they become defended against generalists by storing chemical defenses. From the models, we explicitly obtain that a generalist-free stable state is only possible if the vast majority of all plant individuals have chemical defenses. The model also allows one to predict the highest possible percentage of undefended plant individuals, which may be considered as free-riders.
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Affiliation(s)
- Suman Chakraborty
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Pl. 2, Jena, 07743, Thuringia, Germany
- International Max Planck Research School 'Chemical Communication in Ecological Systems', Jena, 07745, Thuringia, Germany
| | - Shalu Dwivedi
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Pl. 2, Jena, 07743, Thuringia, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Pl. 2, Jena, 07743, Thuringia, Germany.
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Borthakur D, Busov V, Cao XH, Du Q, Gailing O, Isik F, Ko JH, Li C, Li Q, Niu S, Qu G, Vu THG, Wang XR, Wei Z, Zhang L, Wei H. Current status and trends in forest genomics. FORESTRY RESEARCH 2022; 2:11. [PMID: 39525413 PMCID: PMC11524260 DOI: 10.48130/fr-2022-0011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2024]
Abstract
Forests are not only the most predominant of the Earth's terrestrial ecosystems, but are also the core supply for essential products for human use. However, global climate change and ongoing population explosion severely threatens the health of the forest ecosystem and aggravtes the deforestation and forest degradation. Forest genomics has great potential of increasing forest productivity and adaptation to the changing climate. In the last two decades, the field of forest genomics has advanced quickly owing to the advent of multiple high-throughput sequencing technologies, single cell RNA-seq, clustered regularly interspaced short palindromic repeats (CRISPR)-mediated genome editing, and spatial transcriptomes, as well as bioinformatics analysis technologies, which have led to the generation of multidimensional, multilayered, and spatiotemporal gene expression data. These technologies, together with basic technologies routinely used in plant biotechnology, enable us to tackle many important or unique issues in forest biology, and provide a panoramic view and an integrative elucidation of molecular regulatory mechanisms underlying phenotypic changes and variations. In this review, we recapitulated the advancement and current status of 12 research branches of forest genomics, and then provided future research directions and focuses for each area. Evidently, a shift from simple biotechnology-based research to advanced and integrative genomics research, and a setup for investigation and interpretation of many spatiotemporal development and differentiation issues in forest genomics have just begun to emerge.
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Affiliation(s)
- Dulal Borthakur
- Dulal Borthakur, Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Honolulu, HI 96822, USA
| | - Victor Busov
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Xuan Hieu Cao
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Qingzhang Du
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Oliver Gailing
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Fikret Isik
- Cooperative Tree Improvement Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Jae-Heung Ko
- Department of Plant & Environmental New Resources, Kyung Hee University, 1732 Deogyeong-daero, Yongin 17104, Republic of Korea
| | - Chenghao Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, P.R. China
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100093, P.R. China
| | - Shihui Niu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Guanzheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, P.R. China
| | - Thi Ha Giang Vu
- Forest Genetics and Forest Tree Breeding, Faculty for Forest Sciences and Forest Ecology, University of Göttingen, Büsgenweg 2, 37077 Göttingen, Germany
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå 90187, Sweden
| | - Zhigang Wei
- College of Life Sciences, Heilongjiang University, Harbin 150080, P. R. China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha 410004, Hunan Province, P.R. China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
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Bageel AM, Kam A, Borthakur D. Transcriptional Analyses of Genes Related to Fodder Qualities in Giant Leucaena Under Different Stress Environments. FRONTIERS IN PLANT SCIENCE 2022; 13:885366. [PMID: 35783950 PMCID: PMC9243426 DOI: 10.3389/fpls.2022.885366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Leucaena leucocephala subsp. glabrata (giant leucaena) is a tree legume, whose foliage is used as a fodder for animals because of its high protein content. In spite of being a highly nutritious fodder, giant leucaena foliage has two undesirable secondary metabolites, mimosine and tannin. The amounts of mimosine and tannin in giant leucaena foliage are known to vary under different environmental conditions. Giant leucaena was grown under different salinity, pH and nitrogen availability conditions. It produced the highest amounts of mimosine at pH 6.0-7.0, whereas, variation in soil pH did not affect tannin concentrations. Salinity stress had negative effects on both mimosine and tannin concentrations, while nitrogen abundance promoted both mimosine and tannin production. Seven genes for mimosine and tannin metabolism were isolated from a transcriptome library of giant leucaena. These were mimosine synthase, mimosinase, chalcone synthase, flavanone 3β-hydroxylase, dihydroflavonol reductase, leucoanthocyanidin reductase, and anthocyanidin reductase. The highest level of mimosine synthase activity was observed in the absence of salt in the soils. Mimosine synthase activities had strong positive correlation with mimosine concentrations in the foliage (R2 = 0.78) whereas mimosinase expression did not appear to have a direct relationship with salt concentrations. The expression of mimosine synthase was significantly higher in the leucaena foliage under nitrogen abundant condition than in nitrogen deficiency conditions, while mimosinase expression was significantly higher under nitrogen deficiency condition than in nitrogen abundance conditions. Mimosine concentrations in the foliage were positively correlated with the expression levels of mimosine synthase but not mimosinase. Similarly, the concentrations of tannin were positively correlated with expression levels of dihydroflavonol reductase, leucoanthocyanidin reductase, and anthocyanidin reductase. Understanding of the environmental conditions that promote or inhibit transcription of the genes for mimosine and tannin biosynthesis should help to design environmental conditions that inhibit transcription of these genes, resulting in reduced levels of these compounds in the leucaena foliage.
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Carrillo JT, Borthakur D. Heterologous expression and characterization of a thermoalkaliphilic SAM-synthetase from giant leucaena (Leucaena leucocephala subsp glabrata). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 181:42-49. [PMID: 35429803 DOI: 10.1016/j.plaphy.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
The cDNA encoding S-adenosylmethionine (SAM) synthetase was isolated from giant leucaena (Leucaena leucocephala subsp. glabrata) root tissue mRNA. Transcriptome data and 5'-RLM-RACE were used to obtain the transcript sequence and clone into the T7-expression vector pEt14b. N-terminal Histidine-tagged recombinant protein was expressed highly in Escherichia coli, purified and characterized by activity assays. A straightforward method using isocratic reverse-phase HPLC analysis (mobile phase: 0.02M o-phosphoric acid) of enzyme assays determined optimal enzyme activity at pH 10.0, 55 °C and 200 mM KCl. In addition to thermophilic activity, giant leucaena SAM-synthetase remains highly active in solutions containing up to 4 M KCl and accepts Na+ to some extent as a substitute for K+, a known required cofactor for SAM-synthetases. The enzyme followed Michaelis-Menten kinetics (Km = 1.82 mM, Kcat = 1.17 s-1, Vmax 243.9 μM. min-1) and was not inhibited by spermidine, spermine or nicotianamine. Giant leucaena SAM-synthetase is a highly tolerant enzyme to extreme conditions, suggesting further studies on plant SAM-synthetases.
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Affiliation(s)
- James T Carrillo
- University of Hawaii at Manoa, Department of Molecular Biosciences and Bioengineering, 1955 East-West Road, Agricultural Sciences 218, Honolulu, HI, 96822, USA.
| | - Dulal Borthakur
- University of Hawaii at Manoa, Department of Molecular Biosciences and Bioengineering, 1955 East-West Road, Agricultural Sciences 218, Honolulu, HI, 96822, USA.
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da Silva Rodrigues-Honda KC, Honda MDH, Borthakur D, Fett-Neto AG. Methods of Mimosine Extraction from Leucaena leucocephala (Lam.) de Wit Leaves. Methods Mol Biol 2022; 2469:231-237. [PMID: 35508843 DOI: 10.1007/978-1-0716-2185-1_19] [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] [Indexed: 06/14/2023]
Abstract
Mimosine is a nonprotein amino acid biosynthesized from OAS (O-acetylserine) and 3H4P (3-hydroxy-4-pyridone or its tautoisomer 3,4-dihydroxypyridine). This amino acid constitutively occurs in all parts of Leucaena leucocephala (Lam.) de Wit plants and is found at higher concentrations in seeds and leaves. This metabolite has several useful activities, such as antioxidant, allelochemical, insecticidal, antimicrobial, metal chelating, and antitumor. Mimosine is well studied in biomedical research due its ability to inhibit cells in the late G1 phase and to induce cell apoptosis. Two simple methods of mimosine extraction from leucaena leaves, pulverized and whole maceration, are described herein in detail.
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Affiliation(s)
- Kelly Cristine da Silva Rodrigues-Honda
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
| | - Michael David Hideo Honda
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Dulal Borthakur
- Department of Molecular Biosciences and Bioengineering, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Arthur G Fett-Neto
- Center for Biotechnology and Department of Botany, Plant Physiology Laboratory, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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Carrillo JT, Borthakur D. Methods for metal chelation in plant homeostasis: Review. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 163:95-107. [PMID: 33826996 DOI: 10.1016/j.plaphy.2021.03.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/20/2021] [Indexed: 05/01/2023]
Abstract
Metal uptake, transport and storage in plants depend on specialized ligands with closely related functions. Individual studies differing by species, nutrient availability, tissue type, etc. are not comprehensive enough to understand plant metal homeostasis in its entirety. A thorough review is required that distinguishes the role of ligands directly involved in chelation from the myriad of plant responses to general stress. Distinguishing between the functions of metal chelating compounds is the primary focus of this review; reactive oxygen species mediation and other aspects of metal homeostasis are also discussed. High molecular weight ligands (polysaccharides, phytochelatin, metallothionein), low molecular weight ligands (nicotianamine, histidine, secondary metabolites) and select studies which demonstrate the complex nature of plant metal homeostasis are explored.
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Affiliation(s)
- James T Carrillo
- University of Hawaii at Manoa, Department of Molecular Biology and Bioengineering, 1955 East-West Road, Agricultural Sciences 218, Honolulu, HI, 96822, USA.
| | - Dulal Borthakur
- University of Hawaii at Manoa, Department of Molecular Biology and Bioengineering, 1955 East-West Road, Agricultural Sciences 218, Honolulu, HI, 96822, USA.
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Biochemistry of plants N-heterocyclic non-protein amino acids. Amino Acids 2021; 53:801-812. [PMID: 33950299 DOI: 10.1007/s00726-021-02990-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Plants catalyze the biosynthesis of a large number of non-protein amino acids, which are usually toxic for other organisms. In this review, the chemistry and metabolism of N-heterocyclic non-protein amino acids from plants are described. These N-heterocyclic non-protein amino acids are composed of β-substituted alanines and include mimosine, β-pyrazol-1-yl-L-alanine, willardiine, isowillardiine, and lathyrine. These β-substituted alanines consisted of an N-heterocyclic moiety and an alanyl side chain. This review explains how these individual moieties are derived from their precursors and how they are used as the substrate for biosynthesizing the respective N-heterocyclic non-protein amino acids. In addition, known catabolism and possible role of these non-protein amino acids in the actual host is explained.
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