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State-of-the-Art Molecular Plant Sciences in Japan

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 13342

Special Issue Editors


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Collection Editor

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Collection Editor
United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
Interests: plant molecular biology; plant physiology

Special Issue Information

Dear Colleagues, 

This Topical Collection aims to provide a comprehensive overview of recent advances in plant molecular science in Japan by inviting contributions from Japanese research institutes/laboratories that consolidate our understanding of this area. Potential topics regarding molecular studies in plants include, but are not limited to, biophysics, biochemistry, and molecular biology; cell biology; physiology; genomics/epigenomics; proteomics and metabolomics; bioactive phytochemicals; plant–microbe interactions; developmental biology; pests and diseases; synthetic biology; computational biology; and the development of new technologies in plant sciences. In this Topical Collection, we welcome submissions in the form of comprehensive reviews or new research advancements in all the abovementioned areas.

Prof. Dr. Setsuko Komatsu
Prof. Dr. Matsuo Uemura
Collection Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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Published Papers (7 papers)

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Editorial

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4 pages, 188 KiB  
Editorial
Special Issue “State-of-the-Art Molecular Plant Sciences in Japan”
by Setsuko Komatsu and Matsuo Uemura
Int. J. Mol. Sci. 2024, 25(4), 2365; https://doi.org/10.3390/ijms25042365 - 17 Feb 2024
Viewed by 607
Abstract
Food shortages are one of the most serious problems caused by global warming and population growth in this century [...] Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Japan)

Research

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14 pages, 1731 KiB  
Article
The Feeder Effects of Cultured Rice Cells on the Early Development of Rice Zygotes
by Yoriko Watanabe, Yuko Nobe, Masato Taoka and Takashi Okamoto
Int. J. Mol. Sci. 2023, 24(22), 16541; https://doi.org/10.3390/ijms242216541 - 20 Nov 2023
Cited by 1 | Viewed by 1050
Abstract
Feeder cells and the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) in a culture medium promote mitosis and cell division in cultured cells. These are also added to nutrient medium for the cultivation of highly active in mitosis and dividing zygotes, produced in vitro or [...] Read more.
Feeder cells and the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) in a culture medium promote mitosis and cell division in cultured cells. These are also added to nutrient medium for the cultivation of highly active in mitosis and dividing zygotes, produced in vitro or isolated from pollinated ovaries. In the study, an in vitro fertilization (IVF) system was used to study the precise effects of feeder cells and 2,4-D on the growth and development of rice (Oryza sativa L.) zygote. The elimination of 2,4-D from the culture medium did not affect the early developmental profiles of the zygotes, but decreased the division rates of multicellular embryos. The omission of feeder cells resulted in defective karyogamy, fusion between male and female nuclei, and the subsequent first division of the cultured zygotes. The culture of zygotes in a conditioned medium corrected developmental disorders. Proteome analyses of the conditioned medium revealed the presence of abundant hydrolases possibly released from the feeder cells. Exogenously applied α-amylase ameliorated karyogamy and promoted zygote development. It is suggested that hydrolytic enzymes, including α-amylase, released from feeder cells may be involved in the progression of zygotic development. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Japan)
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15 pages, 3372 KiB  
Article
Changes in the Endophytic Bacterial Community of Brassica rapa after Application of Systemic Insecticides
by Md. Tareq Bin Salam and Ryota Kataoka
Int. J. Mol. Sci. 2023, 24(20), 15306; https://doi.org/10.3390/ijms242015306 - 18 Oct 2023
Cited by 3 | Viewed by 878
Abstract
Insecticides not only control target pests but also adversely affect non-target communities including humans, animals, and microbial communities in host plants and soils. The effect of insecticides on non-target communities, especially endophytic bacterial communities, remains poorly understood. Two phases of treatments were conducted [...] Read more.
Insecticides not only control target pests but also adversely affect non-target communities including humans, animals, and microbial communities in host plants and soils. The effect of insecticides on non-target communities, especially endophytic bacterial communities, remains poorly understood. Two phases of treatments were conducted to compare the trends in endophytic bacterial response after insecticide application. Endophytic bacteria were isolated at 2 and 4 weeks after germination. Most insecticide treatments showed a declining trend in bacterial diversity and abundance, whereas an increasing trend was observed in the control. Therefore, insecticide use negatively affected non-target endophytic bacterial communities. Bacillus spp. was mostly dominant in the early stage in both insecticide treatment and control groups. Nevertheless, in the matured stage, mostly bacteria including Pseudomonas spp., Priestia spp. were dominant in groups treated with high insecticide concentrations. Therefore, plants can regulate and moderate their microbiome during their lifecycle depending on surrounding environmental conditions. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Japan)
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27 pages, 5714 KiB  
Article
Effect of Light Quality on Metabolomic, Ionomic, and Transcriptomic Profiles in Tomato Fruit
by Lingran Xiao, Tomoki Shibuya, Toshihiro Watanabe, Kazuhisa Kato and Yoshinori Kanayama
Int. J. Mol. Sci. 2022, 23(21), 13288; https://doi.org/10.3390/ijms232113288 - 31 Oct 2022
Cited by 1 | Viewed by 2162
Abstract
Light quality affects plant growth and the functional component accumulation of fruits. However, there is little knowledge of the effects of light quality based on multiomics profiles. This study combined transcriptomic, ionomic, and metabolomic analyses to elucidate the effects of light quality on [...] Read more.
Light quality affects plant growth and the functional component accumulation of fruits. However, there is little knowledge of the effects of light quality based on multiomics profiles. This study combined transcriptomic, ionomic, and metabolomic analyses to elucidate the effects of light quality on metabolism and gene expression in tomato fruit. Micro-Tom plants were grown under blue or red light-emitting diode light for 16 h daily after anthesis. White fluorescent light was used as a reference. The metabolite and element concentrations and the expression of genes markedly changed in response to blue and red light. Based on the metabolomic analysis, amino acid metabolism and secondary metabolite biosynthesis were active in blue light treatment. According to transcriptomic analysis, differentially expressed genes in blue and red light treatments were enriched in the pathways of secondary metabolite biosynthesis, carbon fixation, and glycine, serine, and threonine metabolism, supporting the results of the metabolomic analysis. Ionomic analysis indicated that the element levels in fruits were more susceptible to changes in light quality than in leaves. The concentration of some ions containing Fe in fruits increased under red light compared to under blue light. The altered expression level of genes encoding metal ion-binding proteins, metal tolerance proteins, and metal transporters in response to blue and red light in the transcriptomic analysis contributes to changes in the ionomic profiles of tomato fruit. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Japan)
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17 pages, 3437 KiB  
Article
De Novo Transcriptome Analysis Reveals Flowering-Related Genes That Potentially Contribute to Flowering-Time Control in the Japanese Cultivated Gentian Gentiana triflora
by Tomoyuki Takase, Motoki Shimizu, Shigekazu Takahashi, Keiichirou Nemoto, Fumina Goto, Chiharu Yoshida, Akira Abe and Masahiro Nishihara
Int. J. Mol. Sci. 2022, 23(19), 11754; https://doi.org/10.3390/ijms231911754 - 4 Oct 2022
Cited by 1 | Viewed by 1612
Abstract
Japanese cultivated gentians are perennial plants that flower in early summer to late autumn in Japan, depending on the cultivar. Several flowering-related genes, including GtFT1 and GtTFL1, are known to be involved in regulating flowering time, but many such genes [...] Read more.
Japanese cultivated gentians are perennial plants that flower in early summer to late autumn in Japan, depending on the cultivar. Several flowering-related genes, including GtFT1 and GtTFL1, are known to be involved in regulating flowering time, but many such genes remain unidentified. In this study, we obtained transcriptome profiling data using the Gentiana triflora cultivar ‘Maciry’, which typically flowers in late July. We conducted deep RNA sequencing analysis using gentian plants grown under natural field conditions for three months before flowering. To investigate diurnal changes, the plants were sampled at 4 h intervals over 24 h. Using these transcriptome data, we determined the expression profiles of leaves based on homology searches against the Flowering-Interactive Database of Arabidopsis. In particular, we focused on transcription factor genes, belonging to the BBX and MADS-box families, and analyzed their developmental and diurnal variation. The expression levels of representative BBX genes were also analyzed under long- and short-day conditions using in-vitro-grown seedlings, and the expression patterns of some BBX genes differed. Clustering analysis revealed that the transcription factor genes were coexpressed with GtFT1. Overall, these expression profiles will facilitate further analysis of the molecular mechanisms underlying the control of flowering time in gentians. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Japan)
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16 pages, 1445 KiB  
Article
Morphological and Proteomic Analyses of Soybean Seedling Interaction Mechanism Affected by Fiber Crosslinked with Zinc-Oxide Nanoparticles
by Setsuko Komatsu, Kazuki Murata, Sayuri Yakeishi, Kazuyuki Shimada, Hisateru Yamaguchi, Keisuke Hitachi, Kunihiro Tsuchida, Rumina Obi, Shoichi Akita and Ryo Fukuda
Int. J. Mol. Sci. 2022, 23(13), 7415; https://doi.org/10.3390/ijms23137415 - 3 Jul 2022
Cited by 3 | Viewed by 1531
Abstract
Nanoparticles (NPs) enhance soybean growth; however, their precise mechanism is not clearly understood. To develop a more effective method using NPs for the enhancement of soybean growth, fiber crosslinked with zinc oxide (ZnO) NPs was prepared. The solution of ZnO NPs with 200 [...] Read more.
Nanoparticles (NPs) enhance soybean growth; however, their precise mechanism is not clearly understood. To develop a more effective method using NPs for the enhancement of soybean growth, fiber crosslinked with zinc oxide (ZnO) NPs was prepared. The solution of ZnO NPs with 200 nm promoted soybean growth at the concentration of 10 ppm, while fibers crosslinked with ZnO NPs promoted growth at a 1 ppm concentration. Soybeans grown on fiber cross-linked with ZnO NPs had higher Zn content in their roots than those grown in ZnO NPs solution. To study the positive mechanism of fiber crosslinked with ZnO NPs on soybean growth, a proteomic technique was used. Proteins categorized in photosynthesis and secondary metabolism accumulated more in soybeans grown on fiber crosslinked with ZnO NPs than in those grown in ZnO NPs solution. Furthermore, significantly accumulated proteins, which were NADPH oxidoreductase and tubulins, were confirmed using immunoblot analysis. The abundance of NADPH oxidoreductase increased in soybean by ZnO NPs application. These results suggest that fiber crosslinked with ZnO NPs enhances soybean growth through the increase of photosynthesis and secondary metabolism. Additionally, the accumulation of NADPH oxidoreductase might relate to the effect of auxin with fiber crosslinked with ZnO NPs on soybean growth. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Japan)
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Review

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23 pages, 1212 KiB  
Review
Fine Tuning of ROS, Redox and Energy Regulatory Systems Associated with the Functions of Chloroplasts and Mitochondria in Plants under Heat Stress
by Nobuhiro Suzuki
Int. J. Mol. Sci. 2023, 24(2), 1356; https://doi.org/10.3390/ijms24021356 - 10 Jan 2023
Cited by 14 | Viewed by 4143
Abstract
Heat stress severely affects plant growth and crop production. It is therefore urgent to uncover the mechanisms underlying heat stress responses of plants and establish the strategies to enhance heat tolerance of crops. The chloroplasts and mitochondria are known to be highly sensitive [...] Read more.
Heat stress severely affects plant growth and crop production. It is therefore urgent to uncover the mechanisms underlying heat stress responses of plants and establish the strategies to enhance heat tolerance of crops. The chloroplasts and mitochondria are known to be highly sensitive to heat stress. Heat stress negatively impacts on the electron transport chains, leading to increased production of reactive oxygen species (ROS) that can cause damages on the chloroplasts and mitochondria. Disruptions of photosynthetic and respiratory metabolisms under heat stress also trigger increase in ROS and alterations in redox status in the chloroplasts and mitochondria. However, ROS and altered redox status in these organelles also activate important mechanisms that maintain functions of these organelles under heat stress, which include HSP-dependent pathways, ROS scavenging systems and retrograde signaling. To discuss heat responses associated with energy regulating organelles, we should not neglect the energy regulatory hub involving TARGET OF RAPAMYCIN (TOR) and SNF-RELATED PROTEIN KINASE 1 (SnRK1). Although roles of TOR and SnRK1 in the regulation of heat responses are still unknown, contributions of these proteins to the regulation of the functions of energy producing organelles implicate the possible involvement of this energy regulatory hub in heat acclimation of plants. Full article
(This article belongs to the Special Issue State-of-the-Art Molecular Plant Sciences in Japan)
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