International Journal of Molecular Sciences

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14 pages, 3259 KiB

Open AccessArticle

The Rice CHD3/Mi-2 Chromatin Remodeling Factor Rolled Fine Striped Promotes Flowering Independent of Photoperiod

by Hyeryung Yoon, Yejin Shim, Soo-Cheul Yoo, Kiyoon Kang and Nam-Chon Paek

Int. J. Mol. Sci. 2021, 22(3), 1303; https://doi.org/10.3390/ijms22031303 - 28 Jan 2021

Cited by 2 | Viewed by 2131

Abstract

Genetic studies have revealed that chromatin modifications affect flowering time, but the underlying mechanisms by which chromatin remodeling factors alter flowering remain largely unknown in rice (Oryza sativa). Here, we show that Rolled Fine Striped (RFS), a chromodomain helicase DNA-binding 3 [...] Read more.

Genetic studies have revealed that chromatin modifications affect flowering time, but the underlying mechanisms by which chromatin remodeling factors alter flowering remain largely unknown in rice (Oryza sativa). Here, we show that Rolled Fine Striped (RFS), a chromodomain helicase DNA-binding 3 (CHD3)/Mi-2 subfamily ATP-dependent chromatin remodeling factor, promotes flowering in rice. Diurnal expression of RFS peaked at night under short-day (SD) conditions and at dawn under long-day (LD) conditions. The rfs-1 and rfs-2 mutants (derived from different genetic backgrounds) displayed a late-flowering phenotype under SD and LD conditions. Reverse transcription-quantitative PCR analysis revealed that among the flowering time-related genes, the expression of the major floral repressor Grain number and heading date 7 (Ghd7) was mainly upregulated in rfs mutants, resulting in downregulation of its downstream floral inducers, including Early heading date 1 (Ehd1), Heading date 3a (Hd3a), and Rice FLOWERING LOCUS T 1 (RFT1). The rfs mutation had pleiotropic negative effects on rice grain yield and yield components, such as plant height and fertility. Taking these observations together, we propose that RFS participates in multiple aspects of rice development, including the promotion of flowering independent of photoperiod. Full article

(This article belongs to the Special Issue Regional Adaptation of Crop Plant in Response to Environmental Stress)

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23 pages, 5150 KiB

Open AccessArticle

Phenolic Metabolites from Barley in Contribution to Phenome in soil Moisture Deficit

by Anna Piasecka, Aneta Sawikowska, Anetta Kuczyńska, Piotr Ogrodowicz, Krzysztof Mikołajczak, Paweł Krajewski and Piotr Kachlicki

Int. J. Mol. Sci. 2020, 21(17), 6032; https://doi.org/10.3390/ijms21176032 - 21 Aug 2020

Cited by 5 | Viewed by 3218

Abstract

Eight barley varieties from Europe and Asia were subjected to moisture deficit at various development stages. At the seedling stage and the flag leaf stage combined stress was applied. The experiment was designed for visualization of the correlation between the dynamics of changes [...] Read more.

Eight barley varieties from Europe and Asia were subjected to moisture deficit at various development stages. At the seedling stage and the flag leaf stage combined stress was applied. The experiment was designed for visualization of the correlation between the dynamics of changes in phenolic compound profiles and the external phenome. The most significant increase of compound content in water deficiency was observed for chrysoeriol and apigenin glycoconjugates acylated with methoxylated hydroxycinnamic acids that enhanced the UV-protection effectiveness. Moreover, other good antioxidants such as derivatives of luteolin and hordatines were also induced by moisture deficit. The structural diversity of metabolites of the contents changed in response to water deficiency in barley indicates their multipath activities under stress. Plants exposed to moisture deficit at the seedling stage mobilized twice as many metabolites as plants exposed to this stress at the flag leaf stage. Specific metabolites such as methoxyhydroxycinnamic acids participated in the long-term acclimation. In addition, differences in phenolome mobilization in response to moisture deficit applied at the vegetative and generative phases were correlated with the phenotypical consequences. Observations of plant yield and biomass gave us the possibility to discuss the developmentally related consequences of moisture deficit for plants’ fitness. Full article

(This article belongs to the Special Issue Regional Adaptation of Crop Plant in Response to Environmental Stress)

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21 pages, 5282 KiB

Open AccessArticle

Wild and Cultivated Species of Rice Have Distinctive Proteomic Responses to Drought

by Sara Hamzelou, Karthik Shantharam Kamath, Farhad Masoomi-Aladizgeh, Matthew M. Johnsen, Brian J. Atwell and Paul A. Haynes

Int. J. Mol. Sci. 2020, 21(17), 5980; https://doi.org/10.3390/ijms21175980 - 19 Aug 2020

Cited by 11 | Viewed by 3797

Abstract

Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial [...] Read more.

Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial Australian wild species (Oryza australiensis) were grown in soil at 40% field capacity for 7 d (drought). The hypothesis was that the natural tolerance of O. australiensis to erratic water supply would be reflected in a unique proteomic profile. Leaves from droughted plants and well-watered controls were harvested for label-free quantitative shotgun proteomics. Physiological and gene ontology analysis confirmed that O. australiensis responded uniquely to drought, with superior leaf water status and enhanced levels of photosynthetic proteins. Distinctive patterns of protein accumulation in drought were observed across the O. australiensis proteome. Photosynthetic and stress-response proteins were more abundant in drought-affected O. glaberrima than O. sativa, and were further enriched in O. australiensis. In contrast, the level of accumulation of photosynthetic proteins decreased when O. sativa underwent drought, while a narrower range of stress-responsive proteins showed increased levels of accumulation. Distinctive proteomic profiles and the accumulated levels of individual proteins with specific functions in response to drought in O. australiensis indicate the importance of this species as a source of stress tolerance genes. Full article

(This article belongs to the Special Issue Regional Adaptation of Crop Plant in Response to Environmental Stress)

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23 pages, 4154 KiB

Open AccessArticle

Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture

by Prasanta K. Subudhi, Richard S. Garcia, Sapphire Coronejo and Ronald Tapia

Int. J. Mol. Sci. 2020, 21(16), 5759; https://doi.org/10.3390/ijms21165759 - 11 Aug 2020

Cited by 28 | Viewed by 3377

Abstract

The indiscriminate use of nitrogenous fertilizers continues unabated for commercial crop production, resulting in air and water pollution. The development of rice varieties with enhanced nitrogen use efficiency (NUE) will require a thorough understanding of the molecular basis of a plant’s response to [...] Read more.

The indiscriminate use of nitrogenous fertilizers continues unabated for commercial crop production, resulting in air and water pollution. The development of rice varieties with enhanced nitrogen use efficiency (NUE) will require a thorough understanding of the molecular basis of a plant’s response to low nitrogen (N) availability. The global expression profiles of root tissues collected from low and high N treatments at different time points in two rice genotypes, Pokkali and Bengal, with contrasting responses to N stress and contrasting root architectures were examined. Overall, the number of differentially expressed genes (DEGs) in Pokkali (indica) was higher than in Bengal (japonica) during low N and early N recovery treatments. Most low N DEGs in both genotypes were downregulated whereas early N recovery DEGs were upregulated. Of these, 148 Pokkali-specific DEGs might contribute to Pokkali’s advantage under N stress. These DEGs included transcription factors and transporters and were involved in stress responses, growth and development, regulation, and metabolism. Many DEGs are co-localized with quantitative trait loci (QTL) related to root growth and development, chlorate-resistance, and NUE. Our findings suggest that the superior growth performance of Pokkali under low N conditions could be due to the genetic differences in a diverse set of genes influencing N uptake through the regulation of root architecture. Full article

(This article belongs to the Special Issue Regional Adaptation of Crop Plant in Response to Environmental Stress)

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14 pages, 2277 KiB

Open AccessArticle

The N-Terminal Region of Soybean PM1 Protein Protects Liposomes during Freeze-Thaw

by Liyi Chen, Yajun Sun, Yun Liu, Yongdong Zou, Jianzi Huang, Yizhi Zheng and Guobao Liu

Int. J. Mol. Sci. 2020, 21(15), 5552; https://doi.org/10.3390/ijms21155552 - 3 Aug 2020

Cited by 4 | Viewed by 2674

Abstract

Late embryogenesis abundant (LEA) group 1 (LEA_1) proteins are intrinsically disordered proteins (IDPs) that play important roles in protecting plants from abiotic stress. Their protective function, at a molecular level, has not yet been fully elucidated, but several studies suggest their involvement in [...] Read more.

Late embryogenesis abundant (LEA) group 1 (LEA_1) proteins are intrinsically disordered proteins (IDPs) that play important roles in protecting plants from abiotic stress. Their protective function, at a molecular level, has not yet been fully elucidated, but several studies suggest their involvement in membrane stabilization under stress conditions. In this paper, the soybean LEA_1 protein PM1 and its truncated forms (PM1-N: N-terminal half; PM1-C: C-terminal half) were tested for the ability to protect liposomes against damage induced by freeze-thaw stress. Turbidity measurement and light microscopy showed that full-length PM1 and PM1-N, but not PM1-C, can prevent freeze-thaw-induced aggregation of POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) liposomes and native thylakoid membranes, isolated from spinach leaves (Spinacia oleracea). Particle size distribution analysis by dynamic light scattering (DLS) further confirmed that PM1 and PM1-N can prevent liposome aggregation during freeze-thaw. Furthermore, PM1 or PM1-N could significantly inhibit membrane fusion of liposomes, but not reduce the leakage of their contents following freezing stress. The results of proteolytic digestion and circular dichroism experiments suggest that PM1 and PM1-N proteins bind mainly on the surface of the POPC liposome. We propose that, through its N-terminal region, PM1 functions as a membrane-stabilizing protein during abiotic stress, and might inhibit membrane fusion and aggregation of vesicles or other endomembrane structures within the plant cell. Full article

(This article belongs to the Special Issue Regional Adaptation of Crop Plant in Response to Environmental Stress)

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14 pages, 1699 KiB

Open AccessArticle

Crop Enhancement of Cucumber Plants under Heat Stress by Shungite Carbon

by Tae Yoon Kim, Hara Ku and Seung-Yop Lee

Int. J. Mol. Sci. 2020, 21(14), 4858; https://doi.org/10.3390/ijms21144858 - 9 Jul 2020

Cited by 16 | Viewed by 4011

Abstract

Heat stress negatively impacts plant growth and yield. The effects of carbon materials on plants in response to abiotic stress and antioxidant activity are poorly understood. In this study, we propose a new method for improving heat tolerance in cucumber (Cucumis sativus [...] Read more.

Heat stress negatively impacts plant growth and yield. The effects of carbon materials on plants in response to abiotic stress and antioxidant activity are poorly understood. In this study, we propose a new method for improving heat tolerance in cucumber (Cucumis sativus L.) using a natural carbon material, shungite, which can be easily mixed into any soil. We analyzed the phenotype and physiological changes in cucumber plants maintained at 35 °C or 40 °C for 1 week. Our results show that shungite-treated cucumber plants had a healthier phenotype, exhibiting dark green leaves, compared to the plants in the control soil group. Furthermore, in the shungite-treated plants, the monodehydroascorbate content (a marker of oxidative damage) of the leaf was 34% lower than that in the control group. In addition, scavengers against reactive oxygen species, such as superoxide dismutase, catalase, and peroxidase were significantly upregulated. These results indicate that the successive pre-treatment of soil with a low-cost natural carbon material can improve the tolerance of cucumber plants to heat stress, as well as improve the corresponding antioxidant activity. Full article

(This article belongs to the Special Issue Regional Adaptation of Crop Plant in Response to Environmental Stress)

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14 pages, 4405 KiB

Open AccessArticle

Integrated RNA-seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

by Weilong Kong, Chenhao Zhang, Yalin Qiang, Hua Zhong, Gangqing Zhao and Yangsheng Li

Int. J. Mol. Sci. 2020, 21(13), 4615; https://doi.org/10.3390/ijms21134615 - 29 Jun 2020

Cited by 23 | Viewed by 3773

Abstract

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular [...] Read more.

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice. Full article

(This article belongs to the Special Issue Regional Adaptation of Crop Plant in Response to Environmental Stress)

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13 pages, 2726 KiB

Open AccessArticle

Two Chalcone Synthase Isozymes Participate Redundantly in UV-Induced Sakuranetin Synthesis in Rice

by Hye Lin Park, Youngchul Yoo, Seong Hee Bhoo, Tae-Hoon Lee, Sang-Won Lee and Man-Ho Cho

Int. J. Mol. Sci. 2020, 21(11), 3777; https://doi.org/10.3390/ijms21113777 - 27 May 2020

Cited by 18 | Viewed by 2591

Abstract

Chalcone synthase (CHS) is a key enzyme in the flavonoid pathway, participating in the production of phenolic phytoalexins. The rice genome contains 31 CHS family genes (OsCHSs). The molecular characterization of OsCHSs suggests that OsCHS8 and OsCHS24 belong in the [...] Read more.

Chalcone synthase (CHS) is a key enzyme in the flavonoid pathway, participating in the production of phenolic phytoalexins. The rice genome contains 31 CHS family genes (OsCHSs). The molecular characterization of OsCHSs suggests that OsCHS8 and OsCHS24 belong in the bona fide CHSs, while the other members are categorized in the non-CHS group of type III polyketide synthases (PKSs). Biochemical analyses of recombinant OsCHSs also showed that OsCHS24 and OsCHS8 catalyze the formation of naringenin chalcone from p-coumaroyl-CoA and malonyl-CoA, while the other OsCHSs had no detectable CHS activity. OsCHS24 is kinetically more efficient than OsCHS8. Of the OsCHSs, OsCHS24 also showed the highest expression levels in different tissues and developmental stages, suggesting that it is the major CHS isoform in rice. In oschs24 mutant leaves, sakuranetin content decreased to 64.6% and 80.2% of those in wild-type leaves at 2 and 4 days after UV irradiation, respectively, even though OsCHS24 expression was mostly suppressed. Instead, the OsCHS8 expression was markedly increased in the oschs24 mutant under UV stress conditions compared to that in the wild-type, which likely supports the UV-induced production of sakuranetin in oschs24. These results suggest that OsCHS24 acts as the main CHS isozyme and OsCHS8 redundantly contributes to the UV-induced production of sakuranetin in rice leaves. Full article

(This article belongs to the Special Issue Regional Adaptation of Crop Plant in Response to Environmental Stress)

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Review

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15 pages, 891 KiB

Open AccessReview

Environmental Signal-Dependent Regulation of Flowering Time in Rice

by Jae Sung Shim and Geupil Jang

Int. J. Mol. Sci. 2020, 21(17), 6155; https://doi.org/10.3390/ijms21176155 - 26 Aug 2020

Cited by 19 | Viewed by 4622

Abstract

The transition from the vegetative to the reproductive stage of growth is a critical event in the lifecycle of a plant and is required for the plant’s reproductive success. Flowering time is tightly regulated by an internal time-keeping system and external light conditions, [...] Read more.

The transition from the vegetative to the reproductive stage of growth is a critical event in the lifecycle of a plant and is required for the plant’s reproductive success. Flowering time is tightly regulated by an internal time-keeping system and external light conditions, including photoperiod, light quality, and light quantity. Other environmental factors, such as drought and temperature, also participate in the regulation of flowering time. Thus, flexibility in flowering time in response to environmental factors is required for the successful adaptation of plants to the environment. In this review, we summarize our current understanding of the molecular mechanisms by which internal and environmental signals are integrated to regulate flowering time in Arabidopsis thaliana and rice (Oryza sativa). Full article

(This article belongs to the Special Issue Regional Adaptation of Crop Plant in Response to Environmental Stress)

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