1
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Wang T, Chen X, Ju C, Wang C. Calcium signaling in plant mineral nutrition: From uptake to transport. PLANT COMMUNICATIONS 2023; 4:100678. [PMID: 37635354 PMCID: PMC10721523 DOI: 10.1016/j.xplc.2023.100678] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/26/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
Plant mineral nutrition is essential for crop yields and human health. However, the uneven distribution of mineral elements over time and space leads to a lack or excess of available mineral elements in plants. Among the essential nutrients, calcium (Ca2+) stands out as a prominent second messenger that plays crucial roles in response to extracellular stimuli in all eukaryotes. Distinct Ca2+ signatures with unique parameters are induced by different stresses and deciphered by various Ca2+ sensors. Recent research on the participation of Ca2+ signaling in regulation of mineral elements has made great progress. In this review, we focus on the impact of Ca2+ signaling on plant mineral uptake and detoxification. Specifically, we emphasize the significance of Ca2+ signaling for regulation of plant mineral nutrition and delve into key points and novel avenues for future investigations, aiming to offer new insights into plant ion homeostasis.
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Affiliation(s)
- Tian Wang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Xuanyi Chen
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China
| | - Chuanfeng Ju
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China.
| | - Cun Wang
- National Key Laboratory of Crop Improvement for Stress Tolerance and Production, College of Life Sciences, Northwest Agriculture & Forestry University, Yangling, Shaanxi 712100, China.
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2
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Lepri A, Longo C, Messore A, Kazmi H, Madia VN, Di Santo R, Costi R, Vittorioso P. Plants and Small Molecules: An Up-and-Coming Synergy. PLANTS (BASEL, SWITZERLAND) 2023; 12:1729. [PMID: 37111951 PMCID: PMC10145415 DOI: 10.3390/plants12081729] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 06/19/2023]
Abstract
The emergence of Arabidopsis thaliana as a model system has led to a rapid and wide improvement in molecular genetics techniques for studying gene function and regulation. However, there are still several drawbacks that cannot be easily solved with molecular genetic approaches, such as the study of unfriendly species, which are of increasing agronomic interest but are not easily transformed, thus are not prone to many molecular techniques. Chemical genetics represents a methodology able to fill this gap. Chemical genetics lies between chemistry and biology and relies on small molecules to phenocopy genetic mutations addressing specific targets. Advances in recent decades have greatly improved both target specificity and activity, expanding the application of this approach to any biological process. As for classical genetics, chemical genetics also proceeds with a forward or reverse approach depending on the nature of the study. In this review, we addressed this topic in the study of plant photomorphogenesis, stress responses and epigenetic processes. We have dealt with some cases of repurposing compounds whose activity has been previously proven in human cells and, conversely, studies where plants have been a tool for the characterization of small molecules. In addition, we delved into the chemical synthesis and improvement of some of the compounds described.
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Affiliation(s)
- A. Lepri
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - C. Longo
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - A. Messore
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - H. Kazmi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - V. N. Madia
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Di Santo
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Costi
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - P. Vittorioso
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
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3
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Umeda-Hara C, Iwakawa H, Ohtani M, Demura T, Matsumoto T, Kikuchi J, Murata K, Umeda M. Tetraploidization promotes radial stem growth in poplars. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:215-220. [PMID: 36349238 PMCID: PMC9592956 DOI: 10.5511/plantbiotechnology.22.0716a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/16/2022] [Indexed: 06/16/2023]
Abstract
Somatic polyploidization often increases cell and organ size, thereby contributing to plant biomass production. However, as most woody plants do not undergo polyploidization, explaining the polyploidization effect on organ growth in trees remains difficult. Here we developed a new method to generate tetraploid lines in poplars through colchicine treatment of lateral buds. We found that tetraploidization induced cell enlargement in the stem, suggesting that polyploidization can increase cell size in woody plants that cannot induce polyploidization in normal development. Greenhouse growth analysis revealed that radial growth was enhanced in the basal stem of tetraploids, whereas longitudinal growth was retarded, producing the same amount of stem biomass as diploids. Woody biomass characteristics were also comparable in terms of wood substance density, saccharification efficiency, and cell wall profiling. Our results reveal tetraploidization as an effective strategy for improving woody biomass production when combined with technologies that promote longitudinal stem growth by enhancing metabolite production and/or transport.
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Affiliation(s)
- Chikage Umeda-Hara
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Hidekazu Iwakawa
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanaagawa 230-0045, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanaagawa 230-0045, Japan
| | - Tomoko Matsumoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanaagawa 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanaagawa 230-0045, Japan
| | - Koji Murata
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
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4
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Nakano Y, Endo H, Gerber L, Hori C, Ihara A, Sekimoto M, Matsumoto T, Kikuchi J, Ohtani M, Demura T. Enhancement of Secondary Cell Wall Formation in Poplar Xylem Using a Self-Reinforced System of Secondary Cell Wall-Related Transcription Factors. FRONTIERS IN PLANT SCIENCE 2022; 13:819360. [PMID: 35371169 PMCID: PMC8967175 DOI: 10.3389/fpls.2022.819360] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/17/2022] [Indexed: 05/06/2023]
Abstract
The secondary cell wall (SCW) in the xylem is one of the largest sink organs of carbon in woody plants, and is considered a promising sustainable bioresource for biofuels and biomaterials. To enhance SCW formation in poplar (Populus sp.) xylem, we developed a self-reinforced system of SCW-related transcription factors from Arabidopsis thaliana, involving VASCULAR-RELATED NAC-DOMAIN7 (VND7), SECONDARY WALL-ASSOCIATED NAC-DOMAIN PROTEIN 1/NAC SECONDARY WALL THICKENING-PROMOTING FACTOR3 (SND1/NST3), and MYB46. In this system, these transcription factors were fused with the transactivation domain VP16 and expressed under the control of the Populus trichocarpa CesA18 (PtCesA18) gene promoter, creating the chimeric genes PtCesA18pro::AtVND7:VP16, PtCesA18pro::AtSND1:VP16, and PtCesA18pro::AtMYB46:VP16. The PtCesA18 promoter is active in tissues generating SCWs, and can be regulated by AtVND7, AtSND1, and AtMYB46; thus, the expression levels of PtCesA18pro::AtVND7:VP16, PtCesA18pro::AtSND1:VP16, and PtCesA18pro::AtMYB46:VP16 are expected to be boosted in SCW-generating tissues. In the transgenic hybrid aspens (Populus tremula × tremuloides T89) expressing PtCesA18pro::AtSND1:VP16 or PtCesA18pro::AtMYB46:VP16 grown in sterile half-strength Murashige and Skoog growth medium, SCW thickening was significantly enhanced in the secondary xylem cells, while the PtCesA18pro::AtVND7:VP16 plants showed stunted xylem formation, possibly because of the enhanced programmed cell death (PCD) in the xylem regions. After acclimation, the transgenic plants were transferred from the sterile growth medium to pots of soil in the greenhouse, where only the PtCesA18pro::AtMYB46:VP16 aspens survived. A nuclear magnetic resonance footprinting cell wall analysis and enzymatic saccharification analysis demonstrated that PtCesA18pro::AtMYB46:VP16 influences cell wall properties such as the ratio of syringyl (S) and guaiacyl (G) units of lignin, the abundance of the lignin β-aryl ether and resinol bonds, and hemicellulose acetylation levels. Together, these data indicate that we have created a self-reinforced system using SCW-related transcription factors to enhance SCW accumulation.
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Affiliation(s)
- Yoshimi Nakano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Hitoshi Endo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Lorenz Gerber
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Chiaki Hori
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ayumi Ihara
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Masayo Sekimoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- *Correspondence: Misato Ohtani,
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Taku Demura,
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5
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Akiyoshi N, Ihara A, Matsumoto T, Takebayashi A, Hiroyama R, Kikuchi J, Demura T, Ohtani M. Functional Analysis of Poplar Sombrero-Type NAC Transcription Factors Yields a Strategy to Modify Woody Cell Wall Properties. PLANT & CELL PHYSIOLOGY 2021; 62:1963-1974. [PMID: 34226939 DOI: 10.1093/pcp/pcab102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 06/08/2021] [Accepted: 07/05/2021] [Indexed: 05/22/2023]
Abstract
Woody cells generate lignocellulosic biomass, which is a promising sustainable bioresource for wide industrial applications. Woody cell differentiation in vascular plants, including the model plant poplar (Populus trichocarpa), is regulated by a set of NAC family transcription factors, the VASCULAR-RELATED NAC-DOMAIN (VND), NAC SECONDARY CELL WALL THICKENING PROMOTING FACTOR (NST)/SND, and SOMBRERO (SMB) (VNS)-related proteins, but the precise contributions of each VNS protein to wood quality are unknown. Here, we performed a detailed functional analysis of the poplar SMB-type VNS proteins PtVNS13-PtVNS16. PtVNS13-PtVNS16 were preferentially expressed in the roots of young poplar plantlets, similar to the Arabidopsis thalianaSMB gene. PtVNS13 and PtVNS14, as well as the NST-type PtVNS11, suppressed the abnormal root cap phenotype of the Arabidopsis sombrero-3 mutant, whereas the VND-type PtVNS07 gene did not, suggesting a functional gap between SMB- or NST-type VNS proteins and VND-type VNS proteins. Overexpressing PtVNS13-PtVNS16 in Arabidopsis seedlings and poplar leaves induced ectopic xylem-vessel-like cells with secondary wall deposition, and a transient expression assay showed that PtVNS13-16 transactivated woody-cell-related genes. Interestingly, although any VNS protein rescued the pendant stem phenotype of the Arabidopsis nst1-1 nst3-1 mutant, the resulting inflorescence stems exhibited distinct cell wall properties: poplar VNS genes generated woody cell walls with higher enzymatic saccharification efficiencies compared with Arabidopsis VNS genes. Together, our data reveal clear functional diversity among VNS proteins in woody cell differentiation and demonstrate a novel VNS-based strategy for modifying woody cell wall properties toward enhanced utilization of woody biomass.
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Affiliation(s)
- Nobuhiro Akiyoshi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Ayumi Ihara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Tomoko Matsumoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Arika Takebayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Ryoko Hiroyama
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Taku Demura
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8915-5 Takayama-cho, Ikoma 630-0192, Japan
| | - Misato Ohtani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8915-5 Takayama-cho, Ikoma 630-0192, Japan
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6
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Butuzova O, Minarsky A, Bessonov N, Soulé C, Morozova N. Determinism and variability of the morphogenesis pathways. Dev Biol 2021; 479:1-10. [PMID: 34314693 DOI: 10.1016/j.ydbio.2021.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/17/2021] [Accepted: 07/16/2021] [Indexed: 11/30/2022]
Abstract
Along with a strict determinism of early embryogenesis in most living organisms, some of them exhibit variability of cell fates and developmental pathways. Here we discuss the phenomena of determinism and variability of developmental pathways, defining its dependence upon cell potency, cell sensitivity to the external signals and cell signaling. We propose a set of conjectures on the phenomenon of variability of developmental pathways, and denote a difference between a normal (local) variability, leading to an invariant final structure (e.g., embryo shape), and fundamental one, which is a switching between different developmental pathways, leading to different possible structures. For illustrating our conjectures, we analyzed early developmental stages of plant embryos with different levels of variability of morphogenesis pathways, and provide a set of computational experiments by Morphogenesis Software.
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Affiliation(s)
| | | | | | | | - Nadya Morozova
- BIN RAS, St-Petersburg, Russia; IHES, France; I2BC, CEA, CNRS, Université Paris-Sud, Université Paris Saclay, France.
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7
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Phan NV, Wright T, Rahman MM, Xu J, Coburn JM. In Vitro Biocompatibility of Decellularized Cultured Plant Cell-Derived Matrices. ACS Biomater Sci Eng 2020; 6:822-832. [PMID: 33464854 DOI: 10.1021/acsbiomaterials.9b00870] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There has been a recent increase in exploring the use of decellularized plant tissue as a novel "green" material for biomedical applications. As part of this effort, we have developed a technique to decellularize cultured plant cells (tobacco BY-2 cells and rice cells) and tissue (tobacco hairy roots) that uses deoxyribonuclease I (DNase I)). As a proof of concept, all cultured plant cells and tissue were transformed to express recombinant enhanced green fluorescent protein (EGFP) to show that the proteins of interest could be retained within the matrices. Decellularization of lyophilized tobacco BY-2 cells with DNase for 30 min depleted the DNA content from 1503 ± 459 to 31 ± 5 ng/sample. The decellularization procedure resulted in approximately 36% total protein retention (154 ± 60 vs 424 ± 70 μg/sample) and 33% EGFP retention. Similar results for DNA removal and protein retention were observed with the rice cells and tobacco hairy root matrices. When exposed to decellularized BY-2 cell-derived matrices, monolayer cultures of human foreskin fibroblasts (hFFs) maintained or increased metabolic activity, which is an indicator of cell viability. Furthermore, hFFs were able to attach, spread, and proliferate when cultured with the decellularized BY-2 cell-derived matrices in an aggregate model. Overall, these studies demonstrate that cultured plant cells and tissue can be effectively decellularized with DNase I with substantial protein retention. The resulting material has a positive impact on hFF metabolic activity and could be employed to create a three-dimensional environment for cell growth. These results thus show the promise of using naturally derived cellulose matrices from cultured plant cells and tissues for biomedical applications.
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Affiliation(s)
- Nhi V Phan
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609-2280, United States
| | - Tristen Wright
- Department of Biological Science, Arkansas State University, Jonesboro, Arkansas 72401, United States
| | - M Masrur Rahman
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609-2280, United States
| | - Jianfeng Xu
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas 72401, United States.,College of Agriculture, Arkansas State University, Jonesboro, Arkansas 72401, United States
| | - Jeannine M Coburn
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609-2280, United States
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8
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Seifikalhor M, Aliniaeifard S, Shomali A, Azad N, Hassani B, Lastochkina O, Li T. Calcium signaling and salt tolerance are diversely entwined in plants. PLANT SIGNALING & BEHAVIOR 2019; 14:1665455. [PMID: 31564206 PMCID: PMC6804723 DOI: 10.1080/15592324.2019.1665455] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/26/2019] [Accepted: 08/28/2019] [Indexed: 05/11/2023]
Abstract
In plants dehydration imposed by salinity can invoke physical changes at the interface of the plasma membrane and cell wall. Changes in hydrostatic pressure activate ion channels and cause depolarization of the plasma membrane due to disturbance in ion transport. During the initial phases of salinity stress, the relatively high osmotic potential of the rhizosphere enforces the plant to use a diverse spectrum of strategies to optimize water and nutrient uptake. Signals of salt stress are recognized by specific root receptors that activate an osmosensing network. Plant response to hyperosmotic tension is closely linked to the calcium (Ca2+) channels and interacting proteins such as calmodulin. A rapid rise in cytosolic Ca2+ levels occurs within seconds of exposure to salt stress. Plants employ multiple sensors and signaling components to sense and respond to salinity stress, of which most are closely related to Ca2+ sensing and signaling. Several tolerance strategies such as osmoprotectant accumulation, antioxidant boosting, polyaminses and nitric oxide (NO) machineries are also coordinated by Ca2+ signaling. Substantial research has been done to discover the salt stress pathway and tolerance mechanism in plants, resulting in new insights into the perception of salt stress and the downstream signaling that happens in response. Nevertheless, the role of multifunctional components such as Ca2+ has not been sufficiently addressed in the context of salt stress. In this review, we elaborate that the salt tolerance signaling pathway converges with Ca2+ signaling in diverse pathways. We summarize knowledge related to different dimensions of salt stress signaling pathways in the cell by emphasizing the administrative role of Ca2+ signaling on salt perception, signaling, gene expression, ion homeostasis and adaptive responses.
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Affiliation(s)
- Maryam Seifikalhor
- Department of Plant Biology, College of Science, University of Tehran, Tehran, Iran
| | - Sasan Aliniaeifard
- Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Aida Shomali
- Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Nikoo Azad
- Department of Plant Biology, College of Science, University of Tehran, Tehran, Iran
| | - Batool Hassani
- Department of Plant Sciences, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Oksana Lastochkina
- Ufa Federal Research Centre, Russian Academy of Sciences, Bashkir Research Institute of Agriculture, Ufa, Russia
- Ufa Federal Research Centre, Russian Academy of Sciences, Institute of Biochemistry and Genetics, Ufa, Russia
| | - Tao Li
- Chinese Academy of Agricultural Science, Institute of Environment and Sustainable Development in Agriculture, Beijing, China
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9
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Xu N, Liu S, Xin F, Zhou J, Jia H, Xu J, Jiang M, Dong W. Biomethane Production From Lignocellulose: Biomass Recalcitrance and Its Impacts on Anaerobic Digestion. Front Bioeng Biotechnol 2019; 7:191. [PMID: 31440504 PMCID: PMC6694284 DOI: 10.3389/fbioe.2019.00191] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/24/2019] [Indexed: 11/29/2022] Open
Abstract
Anaerobic digestion using lignocellulosic material as the substrate is a cost-effective strategy for biomethane production, which provides great potential to convert biomass into renewable energy. However, the recalcitrance of native lignocellulosic biomass makes it resistant to microbial hydrolysis, which reduces the bioconversion efficiency of organic matter into biogas. Therefore, it is necessary to critically investigate the correlation between lignocellulose characteristics and bioconversion efficiency. Accordingly, this review comprehensively summarizes the anaerobic digestion process and rate-limiting step, structural and compositional properties of lignocellulosic biomass, recalcitrance and inhibitors of lignocellulose and their major effects on anaerobic digestion for biomethane production. Moreover, various type of pretreatment strategies applied to lignocellulosic biomass was discussed in detail, which would contribution to cell wall degradation and improvement of biomethane yields. In the view of current knowledge, high energy input and cost requirements are the main limitations of these pretreatment methods. In addition to optimization of fermentation process, further studies should focus much more on key structural influence factors of biomass recalcitrance and anaerobic digestion efficiency, which will contribute to improvement of biomethane production from lignocellulose.
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Affiliation(s)
- Ning Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, Huai'an, China
| | - Shixun Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Honghua Jia
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Jiming Xu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, Huai'an, China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.,Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, China
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10
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See TY, Yusoff R, Chan CH, Ngoh GC. A solid-state microwave method to disrupt biomass microstructure for natural product extraction. FOOD AND BIOPRODUCTS PROCESSING 2018. [DOI: 10.1016/j.fbp.2018.03.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Okubo-Kurihara E, Matsui M. Phenotype-Based Screening of Small Molecules to Modify Plant Cell Walls Using BY-2 Cells. Methods Mol Biol 2018; 1795:85-92. [PMID: 29846920 DOI: 10.1007/978-1-4939-7874-8_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The plant cell wall is an important and abundant biomass with great potential for use as a modern recyclable resource. For effective utilization of this cellulosic biomass, its ability to degrade efficiently is key point. With the aim of modifying the cell wall to allow easy decomposition, we used chemical biological technology to alter its structure. As a first step toward evaluating the chemicals in the cell wall we employed a phenotype-based approach using high-throughput screening. As the plant cell wall is essential in determining cell morphology, phenotype-based screening is particularly effective in identifying compounds that bring about alterations in the cell wall. For rapid and reproducible screening, tobacco BY-2 cell is an excellent system in which to observe cell morphology. In this chapter, we provide a detailed chemical biological methodology for studying cell morphology using tobacco BY-2 cells.
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Affiliation(s)
| | - Minami Matsui
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
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Dejonghe W, Russinova E. Plant Chemical Genetics: From Phenotype-Based Screens to Synthetic Biology. PLANT PHYSIOLOGY 2017; 174:5-20. [PMID: 28275150 PMCID: PMC5411137 DOI: 10.1104/pp.16.01805] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/20/2017] [Indexed: 05/21/2023]
Abstract
The treatment of a biological system with small molecules to specifically perturb cellular functions is commonly referred to as chemical biology. Small molecules are used commercially as drugs, herbicides, and fungicides in different systems, but in recent years they are increasingly exploited as tools for basic research. For instance, chemical genetics involves the discovery of small-molecule effectors of various cellular functions through screens of compound libraries. Whereas the drug discovery field has largely been driven by target-based screening approaches followed by drug optimization, chemical genetics in plant systems tends to be fueled by more general phenotype-based screens, opening the possibility to identify a wide range of small molecules that are not necessarily directly linked to the process of interest. Here, we provide an overview of the current progress in chemical genetics in plants, with a focus on the discoveries regarding small molecules identified in screens designed with a basic biology perspective. We reflect on the possibilities that lie ahead and discuss some of the potential pitfalls that might be encountered upon adopting a given chemical genetics approach.
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Affiliation(s)
- Wim Dejonghe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (W.D., E.R); and
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium (W.D., E.R.)
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (W.D., E.R); and
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium (W.D., E.R.)
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Ohtani M, Ramachandran V, Tokumoto T, Takebayashi A, Ihara A, Matsumoto T, Hiroyama R, Nishikubo N, Demura T. Identification of novel factors that increase enzymatic saccharification efficiency in Arabidopsis wood cells. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2017; 34:203-206. [PMID: 31275029 PMCID: PMC6543695 DOI: 10.5511/plantbiotechnology.17.1107a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/07/2017] [Indexed: 05/12/2023]
Abstract
Developing methods to efficiently convert lignocellulosic polymers, i.e. cellulose, hemicellulose, and lignin into user-friendly carbon resources, such as fermentable sugars, is critical for improving plant biomass utilization. Here, we report the identification of genes that increase enzymatic saccharification efficiency in cultured Arabidopsis wood cells. We overexpressed a set of genes that were upregulated during the early stages of in vitro xylem vessel cell differentiation, including transcription factor and CAZYme genes, in Arabidopsis and tested their effects on enzymatic saccharification efficiency. Of the 96 transgenic seedlings sampled, 37 and 17 lines showed significant increases and decreases in glucose yields, respectively. Further analysis of 20 overexpression lines with high glucose yields in seedling samples indicated that compared to wild type, the glucose and xylose yields from inflorescence stem samples were higher in lines overexpressing genes encoding BETA-XYLOSIDASE 2, UDP-GLUCOSYL TRANSFERASE 88A1, AT3G15350 (a class GT14 glycosyltransferase protein), and the Dof-type transcription factor Dof4.6, whose detailed molecular functions have not yet been characterized. No apparent defect in growth or inflorescence stem structure was detected in these overexpression lines. Therefore, these four genes might represent novel factors that can be used to increase saccharification efficiency in wood tissues without negatively affecting total biomass production. Furthermore, our results confirm the validity of our screening strategy for isolating factors related to the saccharification efficiency of lignocellulosic biomass.
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Affiliation(s)
- Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- E-mail: Tel: +81-743-72-5460 Fax: +81-743-72-5469
| | - Vasagi Ramachandran
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takuya Tokumoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Arika Takebayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ayumi Ihara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Tomoko Matsumoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ryoko Hiroyama
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Nobuyuki Nishikubo
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- E-mail: Tel: +81-743-72-5460 Fax: +81-743-72-5469
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Ohtani M, Ramachandran V, Tokumoto T, Takebayashi A, Ihara A, Matsumoto T, Hiroyama R, Nishikubo N, Demura T. Identification of novel factors that increase enzymatic saccharification efficiency in Arabidopsis wood cells. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2017; 34:203-206. [PMID: 31275029 DOI: 10.5511/plantbiotechnology] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Accepted: 11/07/2017] [Indexed: 05/22/2023]
Abstract
Developing methods to efficiently convert lignocellulosic polymers, i.e. cellulose, hemicellulose, and lignin into user-friendly carbon resources, such as fermentable sugars, is critical for improving plant biomass utilization. Here, we report the identification of genes that increase enzymatic saccharification efficiency in cultured Arabidopsis wood cells. We overexpressed a set of genes that were upregulated during the early stages of in vitro xylem vessel cell differentiation, including transcription factor and CAZYme genes, in Arabidopsis and tested their effects on enzymatic saccharification efficiency. Of the 96 transgenic seedlings sampled, 37 and 17 lines showed significant increases and decreases in glucose yields, respectively. Further analysis of 20 overexpression lines with high glucose yields in seedling samples indicated that compared to wild type, the glucose and xylose yields from inflorescence stem samples were higher in lines overexpressing genes encoding BETA-XYLOSIDASE 2, UDP-GLUCOSYL TRANSFERASE 88A1, AT3G15350 (a class GT14 glycosyltransferase protein), and the Dof-type transcription factor Dof4.6, whose detailed molecular functions have not yet been characterized. No apparent defect in growth or inflorescence stem structure was detected in these overexpression lines. Therefore, these four genes might represent novel factors that can be used to increase saccharification efficiency in wood tissues without negatively affecting total biomass production. Furthermore, our results confirm the validity of our screening strategy for isolating factors related to the saccharification efficiency of lignocellulosic biomass.
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Affiliation(s)
- Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Vasagi Ramachandran
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takuya Tokumoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Arika Takebayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ayumi Ihara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Tomoko Matsumoto
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ryoko Hiroyama
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Nobuyuki Nishikubo
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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