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Hu Z, Xiong Q, Wang K, Zhang L, Yan Y, Cao L, Niu F, Zhu J, Hu J, Wu S. Identification of a New Giant Emrbryo Allele, and Integrated Transcriptomics and Metabolomics Analysis of Giant Embryo Development in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:697889. [PMID: 34434206 PMCID: PMC8381154 DOI: 10.3389/fpls.2021.697889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/05/2021] [Indexed: 05/16/2023]
Abstract
Rice embryos are rich in high-quality protein, lipid, vitamins and minerals, representing the most important nutritional part of brown rice. However, the molecular mechanism of rice embryo development is poorly understood. In this study, two rice cultivars with contrasting embryo size (the giant embryo cultivar Dapeimi and the normal embryo cultivar 187R) were used to explore excellent genes controlling embryo size, and the developed near-isogenic lines (NILs) (NIL-D, which has the giant embryo phenotype, and its matching line, NIL-X) were used to explore transcript and metabolic properties in the earlier maturation stage of giant embryo development under natural conditions. The map-based cloning results demonstrated that Dapeimi is a novel allelic mutant of the rice GIANT EMBRYO (GE) gene, and the functional mutation site is a single cytosine deletion in the exon1. A total of 285 differentially accumulated metabolites (DAMs) and 677 differentially expressed genes (DEGs) were identified between NIL-D and NIL-X. The analysis of DAMs indicated that plants lacking GE mainly promoted energy metabolism, amino acid metabolism, and lipid metabolism pathways in the rice embryo. Pearson correlation coefficient showed that 300 pairs of gene-metabolites were highly correlated. Among them, OsZS_02G0528500 and OsZS_12G0013700 were considered to be key genes regulating L-Aspartic acid and L-Tryptophan content during rice giant embryo development, which are promising to be good candidate genes to improve rice nutrition. By analyzing rice embryo development through a combination of strategies, this research contributes to a greater understanding of the molecular mechanism of rice embryo development, and provides a theoretical foundation for breeding high-nutrition varieties.
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Affiliation(s)
- Zejun Hu
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agricultural Products Preservation Processing Engineering Technology Research Center, Shanghai, China
| | - Qiangqiang Xiong
- Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture, Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Kai Wang
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Lixia Zhang
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agricultural Products Preservation Processing Engineering Technology Research Center, Shanghai, China
| | - Ying Yan
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Liming Cao
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agricultural Products Preservation Processing Engineering Technology Research Center, Shanghai, China
| | - Fuan Niu
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinyan Zhu
- Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture, Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Jinlong Hu
- Innovation Center of Rice Cultivation Technology in Yangtze Valley, Ministry of Agriculture, Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Shujun Wu
- Rice Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Agricultural Products Preservation Processing Engineering Technology Research Center, Shanghai, China
- *Correspondence: Shujun Wu,
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Davis K, Gkotsi DS, Smith DRM, Goss RJM, Caputi L, O’Connor SE. Nicotiana benthamiana as a Transient Expression Host to Produce Auxin Analogs. FRONTIERS IN PLANT SCIENCE 2020; 11:581675. [PMID: 33329644 PMCID: PMC7714751 DOI: 10.3389/fpls.2020.581675] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/26/2020] [Indexed: 05/29/2023]
Abstract
Plant secondary metabolites have applications for the food, biofuel, and pharmaceutical industries. Recent advances in pathway elucidation and host expression systems now allow metabolic engineering of plant metabolic pathways to produce "new-to-nature" derivatives with novel biological activities, thereby amplifying the range of industrial uses for plant metabolites. Here we use a transient expression system in the model plant Nicotiana benthamiana to reconstitute the two-step plant-derived biosynthetic pathway for auxin (indole acetic acid) to achieve accumulation up to 500 ng/g fresh mass (FM). By expressing these plant-derived enzymes in combination with either bacterial halogenases and alternative substrates, we can produce both natural and new-to-nature halogenated auxin derivatives up to 990 ng/g FM. Proteins from the auxin synthesis pathway, tryptophan aminotransferases (TARs) and flavin-dependent monooxygenases (YUCs), could be transiently expressed in combination with four separate bacterial halogenases to generate halogenated auxin derivatives. Brominated auxin derivatives could also be observed after infiltration of the transfected N. benthamiana with potassium bromide and the halogenases. Finally, the production of additional auxin derivatives could also be achieved by co-infiltration of TAR and YUC genes with various tryptophan analogs. Given the emerging importance of transient expression in N. benthamiana for industrial scale protein and product expression, this work provides insight into the capacity of N. benthamiana to interface bacterial genes and synthetic substrates to produce novel halogenated metabolites.
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Affiliation(s)
- Katharine Davis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Danai S. Gkotsi
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Duncan R. M. Smith
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Rebecca J. M. Goss
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Lorenzo Caputi
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Sarah E. O’Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
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Oleńska E, Małek W, Wójcik M, Swiecicka I, Thijs S, Vangronsveld J. Beneficial features of plant growth-promoting rhizobacteria for improving plant growth and health in challenging conditions: A methodical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 743:140682. [PMID: 32758827 DOI: 10.1016/j.scitotenv.2020.140682] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/31/2020] [Accepted: 06/30/2020] [Indexed: 05/08/2023]
Abstract
New eco-friendly approaches are required to improve plant biomass production. Beneficial plant growth-promoting (PGP) bacteria may be exploited as excellent and efficient biotechnological tools to improve plant growth in various - including stressful - environments. We present an overview of bacterial mechanisms which contribute to plant health, growth, and development. Plant growth promoting rhizobacteria (PGPR) can interact with plants directly by increasing the availability of essential nutrients (e.g. nitrogen, phosphorus, iron), production and regulation of compounds involved in plant growth (e.g. phytohormones), and stress hormonal status (e.g. ethylene levels by ACC-deaminase). They can also indirectly affect plants by protecting them against diseases via competition with pathogens for highly limited nutrients, biocontrol of pathogens through production of aseptic-activity compounds, synthesis of fungal cell wall lysing enzymes, and induction of systemic responses in host plants. The potential of PGPR to facilitate plant growth is of fundamental importance, especially in case of abiotic stress, where bacteria can support plant fitness, stress tolerance, and/or even assist in remediation of pollutants. Providing additional evidence and better understanding of bacterial traits underlying plant growth-promotion can inspire and stir up the development of innovative solutions exploiting PGPR in times of highly variable environmental and climatological conditions.
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Affiliation(s)
- Ewa Oleńska
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Białystok, Ciołkowskiego 1J, 15-245 Białystok, Poland.
| | - Wanda Małek
- Department of Genetics and Microbiology, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Małgorzata Wójcik
- Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Faculty of Biology and Biotechnology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Izabela Swiecicka
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Białystok, Ciołkowskiego 1J, 15-245 Białystok, Poland.
| | - Sofie Thijs
- Faculty of Sciences, Centre for Environmental Sciences, Hasselt University, Agoralaan D, B-3590, Belgium.
| | - Jaco Vangronsveld
- Faculty of Sciences, Centre for Environmental Sciences, Hasselt University, Agoralaan D, B-3590, Belgium.
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Marwa N, Mishra N, Singh N, Mishra A, Saxena G, Pandey V, Singh N. Effect of rhizospheric inoculation of isolated arsenic (As) tolerant strains on growth, As-uptake and bacterial communities in association with Adiantum capillus-veneris. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 196:110498. [PMID: 32247957 DOI: 10.1016/j.ecoenv.2020.110498] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 03/05/2020] [Accepted: 03/16/2020] [Indexed: 05/03/2023]
Abstract
Two arsenic (As) hyper-tolerant bacterial strains NM01 Paracoccus versutus and NM04 Aeromonas caviae were isolated from As polluted site of West Bengal, India. The strains not only possess the potential to tolerate up to 20,000 mgl-1 As(V) and 10,000 mgl-1 As(III) but also possess plant growth promoting (PGP) traits like phosphate solubilization, siderophore production, IAA production. Greenhouse pot experiments were conducted to assess the effect of rhizospheric inoculation of both the strains individually and in consortia in As accumulation by Adiantum capillus-veneries. It was observed that the microbial inoculation significantly (p < 0.05) increased the synthesis of thiolic compounds and thus, enhanced As accumulation with translocation factor (TF) > 1. The strains regulated endogenous phytohormone up to 90% and 77.9% increase in auxin of consortia inoculated root and shoot, respectively. Interestingly, inoculation of the isolated strains augmented rhizospheric microbial diversity which was negatively affected by heavy metal. The results of high-throughput Illumina MiSeq sequencing technique to observe the composition of the bacterial community revealed 11,536 unique bacterial operational taxonomic units (OTUs) from As + S (non-inoculated), whereas 11,884 from Consortia As + S (inoculated) rhizospheric soil samples. Inoculated soil displayed higher bacterial diversity indices (ACE and Chao 1) with the dominant bacterial phyla Proteobacteria, Actinobacteria and Firmicutes. Our results highlight the innate PGP abilities of the strains and its potential to facilitate phytoextraction by enhancing As accumulation in the shoot.
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Affiliation(s)
- Naina Marwa
- Plant Ecology and Climate Change Science, National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, UP, India; Department of Botany, University of Lucknow, UP, India.
| | - Nishtha Mishra
- Division of Microbial Technology, National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, UP, India
| | - Namrata Singh
- Plant Ecology and Climate Change Science, National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, UP, India
| | - Aradhana Mishra
- Division of Microbial Technology, National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, UP, India
| | - Gauri Saxena
- Department of Botany, University of Lucknow, UP, India
| | - Vivek Pandey
- Plant Ecology and Climate Change Science, National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, UP, India
| | - Nandita Singh
- Plant Ecology and Climate Change Science, National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, UP, India.
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Zhao Y. Essential Roles of Local Auxin Biosynthesis in Plant Development and in Adaptation to Environmental Changes. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:417-435. [PMID: 29489397 DOI: 10.1146/annurev-arplant-042817-040226] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
It has been a dominant dogma in plant biology that the self-organizing polar auxin transport system is necessary and sufficient to generate auxin maxima and minima that are essential for almost all aspects of plant growth and development. However, in the past few years, it has become clear that local auxin biosynthesis is required for a suite of developmental processes, including embryogenesis, endosperm development, root development, and floral initiation and patterning. Moreover, it was discovered that local auxin biosynthesis maintains optimal plant growth in response to environmental signals, including light, temperature, pathogens, and toxic metals. In this article, I discuss the recent progress in auxin biosynthesis research and the paradigm shift in recognizing the important roles of local auxin biosynthesis in plant biology.
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Affiliation(s)
- Yunde Zhao
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093, USA;
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Liu C, Su J, Stephen GK, Wang H, Song A, Chen F, Zhu Y, Chen S, Jiang J. Overexpression of Phosphate Transporter Gene CmPht1;2 Facilitated Pi Uptake and Alternated the Metabolic Profiles of Chrysanthemum Under Phosphate Deficiency. FRONTIERS IN PLANT SCIENCE 2018; 9:686. [PMID: 30079072 PMCID: PMC6062769 DOI: 10.3389/fpls.2018.00686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/04/2018] [Indexed: 05/21/2023]
Abstract
Low availability of phosphorus (P) in the soil is the principal limiting factor for the growth of cut chrysanthemum. Plant phosphate transporters (PTs) facilitate acquisition of inorganic phosphate (Pi) and its homeostasis within the plant. In the present study, CmPht1;2 of the Pht1 family was cloned from chrysanthemum. CmPht1;2 is composed of 12 transmembrane domains and localized to the plasma membrane. Expression of CmPht1;2 in roots was induced by Pi starvation. Chrysanthemum plants with overexpression of CmPht1;2 (Oe) showed higher Pi uptake, as compared to the wild type (WT), both under Pi-starvation and Pi-sufficient conditions, and also showed a higher root biomass compared to WT in the Pi-starvation conditions. Seven days after the P-deficiency treatment, 85 distinct analytes were identified in the roots and 27 in the shoots between the Oe1 plant and WT, in which sophorose, sorbitol (sugars), hydroxybutyric acid (organic acids), and ornithine (amino acid) of CmPht1;2 overexpressing chrysanthemum are specific responses to P-starvation.
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Affiliation(s)
- Chen Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Jiangshuo Su
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Githeng’u K. Stephen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Haibin Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
| | - Yiyong Zhu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
- *Correspondence: Sumei Chen, Jiafu Jiang,
| | - Jiafu Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, Nanjing, China
- *Correspondence: Sumei Chen, Jiafu Jiang,
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Imada EL, Rolla dos Santos AADP, Oliveira ALMD, Hungria M, Rodrigues EP. Indole-3-acetic acid production via the indole-3-pyruvate pathway by plant growth promoter Rhizobium tropici CIAT 899 is strongly inhibited by ammonium. Res Microbiol 2017; 168:283-292. [DOI: 10.1016/j.resmic.2016.10.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 10/26/2016] [Accepted: 10/31/2016] [Indexed: 11/26/2022]
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Rodrigues EP, Soares CDP, Galvão PG, Imada EL, Simões-Araújo JL, Rouws LFM, de Oliveira ALM, Vidal MS, Baldani JI. Identification of Genes Involved in Indole-3-Acetic Acid Biosynthesis by Gluconacetobacter diazotrophicus PAL5 Strain Using Transposon Mutagenesis. Front Microbiol 2016; 7:1572. [PMID: 27774087 PMCID: PMC5053998 DOI: 10.3389/fmicb.2016.01572] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 09/20/2016] [Indexed: 02/03/2023] Open
Abstract
Gluconacetobacter diazotrophicus is a beneficial nitrogen-fixing endophyte found in association with sugarcane plants and other important crops. Beneficial effects of G. diazotrophicus on sugarcane growth and productivity have been attributed to biological nitrogen fixation process and production of phytohormones especially indole-3-acetic acid (IAA); however, information about the biosynthesis and function of IAA in G. diazotrophicus is still scarce. Therefore, the aim of this work was to identify genes and pathways involved in IAA biosynthesis in this bacterium. In our study, the screening of two independent Tn5 mutant libraries of PAL5T strain using the Salkowski colorimetric assay revealed two mutants (Gdiaa34 and Gdiaa01), which exhibited 95% less indolic compounds than the parental strain when grown in LGIP medium supplemented with L-tryptophan. HPLC chromatograms of the wild-type strain revealed the presence of IAA and of the biosynthetic intermediates indole-3-pyruvic acid (IPyA) and indole-3-lactate (ILA). In contrast, the HPLC profiles of both mutants showed no IAA but only a large peak of non-metabolized tryptophan and low levels of IPyA and ILA were detected. Molecular characterization revealed that Gdiaa01 and Gdiaa34 mutants had unique Tn5 insertions at different sites within the GDI2456 open read frame, which is predicted to encode a L-amino acid oxidase (LAAO). GDI2456 (lao gene) forms a cluster with GDI2455 and GDI2454 ORFs, which are predicted to encode a cytochrome C and an RidA protein, respectively. RT-qPCR showed that transcript levels of lao. cccA, and ridA genes were reduced in the Gdiaa01 as compared to PAL5T. In addition, rice plants inoculated with Gdiaa01 showed significantly smaller root development (length, surface area, number of forks and tips) than those plants inoculated with PAL5T. In conclusion, our study demonstrated that G. diazotrophicus PAL5T produces IAA via the IPyA pathway in cultures supplemented with tryptophan and provides evidence for the involvement of an L-amino acid oxidase gene cluster in the biosynthesis of IAA. Furthermore, we showed that the mutant strains with reduction in IAA biosynthesis ability, in consequence of the lower transcription levels of genes of the lao cluster, had remarkable effects on development of rice roots.
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Affiliation(s)
- Elisete P Rodrigues
- Laboratório de Genética de Microrganismos, Departamento de Biologia, Universidade Estadual de Londrina Londrina, Brazil
| | | | | | - Eddie L Imada
- Laboratório de Genética de Microrganismos, Departamento de Biologia, Universidade Estadual de Londrina Londrina, Brazil
| | | | | | - André L M de Oliveira
- Laboratório de Bioquímica Molecular, Departamento de Bioquímica e Biotecnologia, Universidade Estadual de Londrina Londrina, Brazil
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