1
|
Oshikiri H, Li H, Manabe M, Yamamoto H, Yazaki K, Takanashi K. Comparative Analysis of Shikonin and Alkannin Acyltransferases Reveals Their Functional Conservation in Boraginaceae. PLANT & CELL PHYSIOLOGY 2024; 65:362-371. [PMID: 38181221 DOI: 10.1093/pcp/pcad158] [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: 02/07/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
Shikonin and its enantiomer, alkannin, are bioactive naphthoquinones produced in several plants of the family Boraginaceae. The structures of these acylated derivatives, which have various short-chain acyl moieties, differ among plant species. The acylation of shikonin and alkannin in Lithospermum erythrorhizon was previously reported to be catalyzed by two enantioselective BAHD acyltransferases, shikonin O-acyltransferase (LeSAT1) and alkannin O-acyltransferase (LeAAT1). However, the mechanisms by which various shikonin and alkannin derivatives are produced in Boraginaceae plants remain to be determined. In the present study, evaluation of six Boraginaceae plants identified 23 homologs of LeSAT1 and LeAAT1, with 15 of these enzymes found to catalyze the acylation of shikonin or alkannin, utilizing acetyl-CoA, isobutyryl-CoA or isovaleryl-CoA as an acyl donor. Analyses of substrate specificities of these enzymes for both acyl donors and acyl acceptors and determination of their subcellular localization using Nicotiana benthamiana revealed a distinct functional differentiation of BAHD acyltransferases in Boraginaceae plants. Gene expression of these acyltransferases correlated with the enantiomeric ratio of produced shikonin/alkannin derivatives in L. erythrorhizon and Echium plantagineum. These enzymes showed conserved substrate specificities for acyl donors among plant species, indicating that the diversity in acyl moieties of shikonin/alkannin derivatives involved factors other than the differentiation of acyltransferases. These findings provide insight into the chemical diversification and evolutionary processes of shikonin/alkannin derivatives.
Collapse
Affiliation(s)
- Haruka Oshikiri
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Hao Li
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
| | - Misaki Manabe
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| | - Hirobumi Yamamoto
- Department of Applied Biology, Faculty of Life Sciences, Toyo University, Izumino 1-1-1, Itakura-machi, Oru-gun, Gunma, 374-0193 Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, 611-0011 Japan
| | - Kojiro Takanashi
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano, 390-8621 Japan
| |
Collapse
|
2
|
Peng M, He H, Wang X, Wang Z, Zhuang L. Comparison of network connectivity and environmental driving factors of root-associated fungal communities of desert ephemeral plants in two habitat soils. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 332:117375. [PMID: 36716547 DOI: 10.1016/j.jenvman.2023.117375] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/04/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Root-associated microorganisms regulate plant growth and development, and their distribution is likely influenced by habitat conditions. In this study, the responses of rhizosphere and root-endophytic fungi of dominant ephemeral plants to aeolian soil (AS) and grey desert soil (DS) in the Gurbantünggüt Desert were analyzed using high-throughput sequencing. This was done to understand the adaptation strategies of this vegetation in typical habitat soils from a microbial perspective. We found that the diversity of root-associated fungi of ephemeral plants differed in the two habitat soils. The diversity of rhizosphere fungi was relatively low in AS compared to DS, whereas the diversity of root-endophytic fungi was higher in AS. The community structure of root-associated fungi and relative abundances of some dominant taxa differed between the two soils. A co-occurrence network showed that the degree of coupling and interaction between root-associated fungal taxa were closer in AS than in DS and that most of the fungal taxa were cooperative in the two habitat soils. Additionally, the network properties of the root-endophytic fungi were apparent different between the two soils. Environmental factors, including electrical conductivity, soil organic carbon, carbon/nitrogen, and carbon/phosphorus ratios, were found to be key factors affecting rhizosphere fungi in DS, whereas soil available phosphorus was the main factor in AS. Several factors affect the root-endophytic fungal community and are more influential in DS than in AS. Overall, the root-associated fungal communities of ephemeral plants had different adaptation strategies to the two soils: increasing the diversity of rhizosphere fungi and their relationship with environmental factors in DS, and increasing the diversity and network relationships of root-endophytic fungi in AS. These findings provide insight into the assemblage of ephemeral plant root-associated microbial communities and the underlying environmental factors, which allows for a deeper understanding of how to construct an artificial core root microbiota to promote plant growth and resistance.
Collapse
Affiliation(s)
- Mengwen Peng
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Hao He
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Xiushuang Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Zhongke Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Li Zhuang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China.
| |
Collapse
|
3
|
Świątczak J, Kalwasińska A, Szabó A, Swiontek Brzezinska M. Pseudomonas sivasensis 2RO45 inoculation alters the taxonomic structure and functioning of the canola rhizosphere microbial community. Front Microbiol 2023; 14:1168907. [PMID: 37213523 PMCID: PMC10196004 DOI: 10.3389/fmicb.2023.1168907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/17/2023] [Indexed: 05/23/2023] Open
Abstract
Inoculation with plant growth-promoting rhizobacteria (PGPR) is an eco-friendly sustainable strategy for improving crop productivity in diverse environments under different conditions. Our earlier study demonstrated that Pseudomonas sivasensis 2RO45 significantly stimulated canola (Brassica napus L. var. napus) growth. The aim of the present study was to investigate the structural and functional dynamics in the canola rhizosphere microbiome after inoculation with PGPR P. sivasensis 2RO45. The results based on alpha diversity metrics showed that P. sivasensis 2RO45 did not significantly alter the diversity of the native soil microbiota. However, the introduced strain modified the taxonomic structure of microbial communities, increasing the abundance of plant beneficial microorganisms, e.g., bacteria affiliated with families Comamonadaceae, Vicinamibacteraceae, genus Streptomyces, and fungi assigned to Nectriaceae, Didymellaceae, Exophiala, Cyphellophora vermispora, and Mortierella minutissima. The analysis of community level physiological profiling (CLPP) revealed that microbial communities in the P. sivasensis 2RO45 treated canola rhizospheres were more metabolically active than those in the non-treated canola rhizosphere. Four carbon sources (phenols, polymers, carboxylic acids, and amino acids) were better metabolized by the microbial communities from the rhizosphere of plants inoculated with the P. sivasensis 2RO45 than non-inoculated canola rhizospheres. Based on the community-level physiological profiles, the functional diversity of the rhizosphere microbiome was altered by the P. sivasensis 2RO45 inoculation. Substrate utilization Shannon diversity (H) index and evenness (E) index were significantly increased in the treated canola plants. The study provides new insight into PGPR-canola interactions for sustainable agriculture development.
Collapse
Affiliation(s)
- Joanna Świątczak
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Toruń, Poland
- *Correspondence: Joanna Świątczak,
| | - Agnieszka Kalwasińska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Toruń, Poland
- Agnieszka Kalwasińska,
| | - Attila Szabó
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Maria Swiontek Brzezinska
- Department of Environmental Microbiology and Biotechnology, Nicolaus Copernicus University in Toruń, Toruń, Poland
| |
Collapse
|
4
|
Ahmad M, Varela Alonso A, Koletti AE, Rodić N, Reichelt M, Rödel P, Assimopoulou AN, Paun O, Declerck S, Schneider C, Molin EM. Dynamics of alkannin/shikonin biosynthesis in response to jasmonate and salicylic acid in Lithospermum officinale. Sci Rep 2022; 12:17093. [PMID: 36224205 PMCID: PMC9554848 DOI: 10.1038/s41598-022-21322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/26/2022] [Indexed: 01/04/2023] Open
Abstract
Alkannin/shikonin and their derivatives are specialised metabolites of high pharmaceutical and ecological importance exclusively produced in the periderm of members of the plant family Boraginaceae. Previous studies have shown that their biosynthesis is induced in response to methyl jasmonate but not salicylic acid, two phytohormones that play important roles in plant defence. However, mechanistic understanding of induction and non-induction remains largely unknown. In the present study, we generated the first comprehensive transcriptomic dataset and metabolite profiles of Lithospermum officinale plants treated with methyl jasmonate and salicylic acid to shed light on the underlying mechanisms. Our results highlight the diverse biological processes activated by both phytohormones and reveal the important regulatory role of the mevalonate pathway in alkannin/shikonin biosynthesis in L. officinale. Furthermore, by modelling a coexpression network, we uncovered structural and novel regulatory candidate genes connected to alkannin/shikonin biosynthesis. Besides providing new mechanistic insights into alkannin/shikonin biosynthesis, the generated methyl jasmonate and salicylic acid elicited expression profiles together with the coexpression networks serve as important functional genomic resources for the scientific community aiming at deepening the understanding of alkannin/shikonin biosynthesis.
Collapse
Affiliation(s)
- Muhammad Ahmad
- grid.4332.60000 0000 9799 7097Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria ,grid.10420.370000 0001 2286 1424Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Alicia Varela Alonso
- grid.506382.aInstitut für Pflanzenkultur GmbH & Co. KG., Schnega, Germany ,grid.7942.80000 0001 2294 713XEarth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Antigoni E. Koletti
- grid.4793.90000000109457005Department of Chemical Engineering, Laboratory of Organic Chemistry and Center of Interdisciplinary Research and Innovation, Natural Products Research Centre of Excellence (NatPro-AUTh), Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Nebojša Rodić
- grid.4793.90000000109457005Department of Chemical Engineering, Laboratory of Organic Chemistry and Center of Interdisciplinary Research and Innovation, Natural Products Research Centre of Excellence (NatPro-AUTh), Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Michael Reichelt
- grid.418160.a0000 0004 0491 7131Department of Biochemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Philipp Rödel
- grid.506382.aInstitut für Pflanzenkultur GmbH & Co. KG., Schnega, Germany
| | - Andreana N. Assimopoulou
- grid.4793.90000000109457005Department of Chemical Engineering, Laboratory of Organic Chemistry and Center of Interdisciplinary Research and Innovation, Natural Products Research Centre of Excellence (NatPro-AUTh), Aristotle University of Thessaloniki, Thessaloníki, Greece
| | - Ovidiu Paun
- grid.10420.370000 0001 2286 1424Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Stéphane Declerck
- grid.7942.80000 0001 2294 713XEarth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Carolin Schneider
- grid.506382.aInstitut für Pflanzenkultur GmbH & Co. KG., Schnega, Germany
| | - Eva M. Molin
- grid.4332.60000 0000 9799 7097Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| |
Collapse
|
5
|
Varela Alonso A, Naranjo HD, Rat A, Rodić N, Nannou CI, Lambropoulou DA, Assimopoulou AN, Declerck S, Rödel P, Schneider C, Willems A. Root-associated bacteria modulate the specialised metabolome of Lithospermum officinale L. FRONTIERS IN PLANT SCIENCE 2022; 13:908669. [PMID: 36110355 PMCID: PMC9468582 DOI: 10.3389/fpls.2022.908669] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Bacteria influence plant growth and development and therefore are attractive resources for applications in agriculture. However, little is known about the impact of these microorganisms on secondary metabolite (SM) production by medicinal plants. Here we assessed, for the first time, the effects of bacteria on the modulation of SM production in the medicinal plant Lithospermum officinale (Boraginaceae family) with a focus on the naphthoquinones alkannin/shikonin and their derivatives (A/Sd). The study was conducted in an in vitro cultivation system developed for that purpose, as well as in a greenhouse. Targeted and non-targeted metabolomics were performed, and expression of the gene PGT encoding for a key enzyme in the A/S biosynthesis pathway was evaluated with qPCR. Three strains, Chitinophaga sp. R-73072, Xanthomonas sp. R-73098 and Pseudomonas sp. R-71838 induced a significant increase of A/Sd in L. officinale in both systems, demonstrating the strength of our approach for screening A/Sd-inducing bacteria. The bacterial treatments altered other plant metabolites derived from the shikimate pathway as well. Our results demonstrate that bacteria influence the biosynthesis of A/Sd and interact with different metabolic pathways. This work highlights the potential of bacteria to increase the production of SM in medicinal plants and reveals new patterns in the metabolome regulation of L. officinale.
Collapse
Affiliation(s)
- Alicia Varela Alonso
- Institut für Pflanzenkultur GmbH & Co. KG., Schnega, Germany
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Henry D. Naranjo
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Angélique Rat
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Nebojša Rodić
- Laboratory of Organic Chemistry, School of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Natural Products Research Center of Excellence (NatPro-AUTh), Center for Interdisciplinary Research and Innovation (CIRI-AUTh), Thessaloniki, Greece
| | - Christina I. Nannou
- Center for Interdisciplinary Research and Innovation (CIRI-AUTh), Balkan Center, Thessaloniki, Greece
- Laboratory of Environmental Pollution Control, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitra A. Lambropoulou
- Center for Interdisciplinary Research and Innovation (CIRI-AUTh), Balkan Center, Thessaloniki, Greece
- Laboratory of Environmental Pollution Control, Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreana N. Assimopoulou
- Laboratory of Organic Chemistry, School of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Natural Products Research Center of Excellence (NatPro-AUTh), Center for Interdisciplinary Research and Innovation (CIRI-AUTh), Thessaloniki, Greece
| | - Stéphane Declerck
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Philipp Rödel
- Institut für Pflanzenkultur GmbH & Co. KG., Schnega, Germany
| | | | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
6
|
Ahmad M, Varela Alonso A, Koletti AE, Assimopoulou AN, Declerck S, Schneider C, Molin EM. Transcriptional dynamics of Chitinophaga sp. strain R-73072-mediated alkannin/shikonin biosynthesis in Lithospermum officinale. Front Microbiol 2022; 13:978021. [PMID: 36071973 PMCID: PMC9441710 DOI: 10.3389/fmicb.2022.978021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 07/25/2022] [Indexed: 01/09/2023] Open
Abstract
Plants are colonized by a wide range of bacteria, several of which are known to confer benefits to their hosts such as enhancing plant growth and the biosynthesis of secondary metabolites (SMs). Recently, it has been shown that Chitinophaga sp. strain R-73072 enhances the production of alkannin/shikonin, SMs of pharmaceutical and ecological importance. However, the mechanisms by which this bacterial strain increases these SMs in plants are not yet understood. To gain insight into these mechanisms, we analyzed the molecular responses of Lithospermum officinale, an alkannin/shikonin producing member of Boraginaceae, to inoculation with R-73072 in a gnotobiotic system using comparative transcriptomics and targeted metabolite profiling of root samples. We found that R-73072 modulated the expression of 1,328 genes, of which the majority appeared to be involved in plant defense and SMs biosynthesis including alkannin/shikonin derivatives. Importantly, bacterial inoculation induced the expression of genes that predominately participate in jasmonate and ethylene biosynthesis and signaling, suggesting an important role of these phytohormones in R-73072-mediated alkannin/shikonin biosynthesis. A detached leaf bioassay further showed that R-73072 confers systemic protection against Botrytis cinerea. Finally, R-73072-mediated coregulation of genes involved in plant defense and the enhanced production of alkannin/shikonin esters further suggest that these SMs could be important components of the plant defense machinery in alkannin/shikonin producing species.
Collapse
Affiliation(s)
- Muhammad Ahmad
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria,Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Alicia Varela Alonso
- Institut für Pflanzenkultur GmbH & Co. KG., Schnega, Germany,Earth and Life Institute, Mycology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Antigoni E. Koletti
- School of Chemical Engineering, Laboratory of Organic Chemistry and Center for Interdisciplinary Research and Innovation of AUTh, Natural Products, Research Centre of Excellence (NatPro-AUTh), Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreana N. Assimopoulou
- School of Chemical Engineering, Laboratory of Organic Chemistry and Center for Interdisciplinary Research and Innovation of AUTh, Natural Products, Research Centre of Excellence (NatPro-AUTh), Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stéphane Declerck
- Earth and Life Institute, Mycology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | | | - Eva M. Molin
- Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria,*Correspondence: Eva M. Molin,
| |
Collapse
|
7
|
Ajilogba CF, Olanrewaju OS, Babalola OO. Plant Growth Stage Drives the Temporal and Spatial Dynamics of the Bacterial Microbiome in the Rhizosphere of Vigna subterranea. Front Microbiol 2022; 13:825377. [PMID: 35250941 PMCID: PMC8891599 DOI: 10.3389/fmicb.2022.825377] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/10/2022] [Indexed: 11/23/2022] Open
Abstract
Bambara groundnut (BGN) is an underutilized legume commonly found in sub-Saharan Africa. It thrives in marginal soils and is resistant to drought stress. Several studies have been carried out on the nutritional properties of BGN, but very little is known about the effects of plant growth changes and development on rhizosphere bacterial dynamics and function. This study reports on the bacterial dynamics and function in the bulk and rhizosphere soils of BGN at different growth stages (vegetative, flowering, pod-filling, and maturation stages). Aside from the maturation stage that shows distinct community structure from the other growth stages, results obtained showed no significant differences in bacterial community structure among the other growth stages. At a closer level, Actinobacteria, Proteobacteria, and Acidobacteria were dominant in rhizosphere soils at all growth stages. The bulk soil had the least average phyla abundance, while the maturity stage was characterized by the highest average phyla abundance. Rubrobacter, Acidobacterium, and Skermanella were the most predominant genus. It was observed from the analysis of operational taxonomic units that there was significant change in the bacterial structure of the rhizosphere with a higher abundance of potential plant growth-promoting rhizobacteria, at the different growth stages, which include the genera Bacillus and Acidobacterium. Biomarker analysis revealed 7 and 4 highly significant bacterial biomarkers by linear discriminant analysis effect size and random forest analysis at the maturation stage, respectively. The results obtained in this study demonstrated that the bacterial communities of BGN rhizosphere microbiome dynamics and function are influenced by the plant’s growth stages.
Collapse
Affiliation(s)
- Caroline Fadeke Ajilogba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- Agricultural Research Council, Natural Resources and Engineering, Division of Agrometeorology, Pretoria, South Africa
| | - Oluwaseyi Samuel Olanrewaju
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- *Correspondence: Olubukola Oluranti Babalola,
| |
Collapse
|