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Molecular and Structural Research Advances in Model Plants
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Molecular and Structural Research Advances in Model Plants

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 (20 December 2024) | Viewed by 14662

Special Issue Editor

Dr. Ioannis-Dimosthenis Adamakis

E-Mail Website
Guest Editor
Section of Botany, Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
Interests: abiotic/biotic stress effects on plants; plant cell biology; phytomorphogenesis; plant biomass utilization; innovative ecological quality monitoring systems
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Model plants, grown from seed as well as tissue or cellular culture, help researchers to study key biological phenomena, processes, and characteristics that are useful for understanding the consequences of natural mutations, adaptation of plants to the harsh environment or changing climate, plant ecology and evolution as well as polyploidization. Following the adoption of Arabidopsis thaliana as the primary plant model, plant science entered the era of molecular biology and genetics, in which traits could be studied at the molecular level. With the availability of new ‘omics’ tools, new plant models are added to our collection at an unprecedented speed, and old non-model plant models are, in many regards, elevated to proper model system status. Emerging new candidate model plant species will be widely used to simulate various morphological, physiological, and molecular processes in plants, allowing a more accurate understanding of the mechanisms explaining the plant ontogenesis and in general plant function. Some examples such plants could be: Marchantia polymorpha (common liverwort), Physcomitrella patens (earthmoss), Brachypodium distachyon (stiff brome), Setaria viridis (green foxtail), Phragmites australis (common reed), Cardamine hirsuta (hairy bittercress), Pisum sativum (pea), Zea mays (corn), Antirrhinum sp. (snapdragon), Populus sp. (poplar), algal models etc. Thererofere this Special Issue focuses on the research advances using model plants, with an emphasis on elucidating molecular/cellular/physiological mechanisms governing key processes or even morphological/anatomical adaptations. We encourage novices and experienced scientists to contribute original research papers and reviews on the above subject. Contributions at the organism, cellular, molecular, and -omic level are highly welcome.

Dr. Ioannis-Dimosthenis Adamakis
Guest Editor

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Keywords

  • A. thaliana
  • plant biology
  • model organisms
  • plant models
  • non-model plant models

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Published Papers (8 papers)

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Research

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14 pages, 2215 KiB  
Article
DNA Methylation of the Autonomous Pathway Is Associated with Flowering Time Variations in Arabidopsis thaliana
by Hongjie Xie, Xinchen Li, Yuli Sun, Lei Lin, Keke Xu, Huan Lu, Biao Cheng, Siming Xue, Dan Cheng and Sheng Qiang
Int. J. Mol. Sci. 2024, 25(13), 7478; https://doi.org/10.3390/ijms25137478 - 8 Jul 2024
Cited by 2 | Viewed by 1415
Abstract
Plant flowering time is affected by endogenous and exogenous factors, but its variation patterns among different populations of a species has not been fully established. In this study, 27 Arabidopsis thaliana accessions were used to investigate the relationship between autonomous pathway gene methylation, [...] Read more.
Plant flowering time is affected by endogenous and exogenous factors, but its variation patterns among different populations of a species has not been fully established. In this study, 27 Arabidopsis thaliana accessions were used to investigate the relationship between autonomous pathway gene methylation, gene expression and flowering time variation. DNA methylation analysis, RT-qPCR and transgenic verification showed that variation in the flowering time among the Arabidopsis populations ranged from 19 to 55 days and was significantly correlated with methylation of the coding regions of six upstream genes in the autonomous pathway, FLOWERING LOCUS VE (FVE), FLOWERING LOCUS Y (FY), FLOWERING LOCUS D (FLD), PEPPER (PEP), HISTONE DEACETYLASE 5 (HAD5) and Pre-mRNA Processing Protein 39-1 (PRP39-1), as well as their relative expression levels. The expression of FVE and FVE(CS) was modified separately through degenerate codon substitution of cytosine and led to earlier flowering of transgenic plants by 8 days and 25 days, respectively. An accurate determination of methylated sites in FVE and FVE(CS) among those transgenic plants and the recipient Col-0 verified the close relationship between the number of methylation sites, expression and flowering time. Our findings suggest that the methylation variation of these six key upstream transcription factors was associated with the gene expression level of the autonomous pathway and flowering time in Arabidopsis. The FVE(CS) and FVE genes in transgenic plants tended to be hypermethylated, which could be a protective mechanism for plants. However, modification of gene sequences through degenerate codon substitution to reduce cytosine can avoid hypermethylated transferred genes in transgenic plants. It may be possible to partially regulate the flowering of plants by modified trans-epigenetic technology. Full article
(This article belongs to the Special Issue Molecular and Structural Research Advances in Model Plants)
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20 pages, 7295 KiB  
Article
Establishment of a Homologous Silencing System with Intact-Plant Infiltration and Minimized Operation for Studying Gene Function in Herbaceous Peonies
by Kaijing Zhang, Xiaobin Wang, Xiaoxuan Chen, Runlong Zhang, Junhong Guo, Qiyao Wang, Danqing Li, Lingmei Shao, Xiaohua Shi, Jingtong Han, Zhiyang Liu, Yiping Xia and Jiaping Zhang
Int. J. Mol. Sci. 2024, 25(8), 4412; https://doi.org/10.3390/ijms25084412 - 17 Apr 2024
Cited by 2 | Viewed by 1212
Abstract
Gene function verification is a crucial step in studying the molecular mechanisms regulating various plant life activities. However, a stable and efficient homologous genetic transgenic system for herbaceous peonies has not been established. In this study, using virus-induced gene silencing technology (VIGS), a [...] Read more.
Gene function verification is a crucial step in studying the molecular mechanisms regulating various plant life activities. However, a stable and efficient homologous genetic transgenic system for herbaceous peonies has not been established. In this study, using virus-induced gene silencing technology (VIGS), a highly efficient homologous transient verification system with distinctive advantages was proposed, which not only achieves true “intact-plant” infiltration but also minimizes the operation. One-year-old roots of the representative species, Paeonia lactiflora Pall., were used as the materials; prechilling (4 °C) treatment for 3–5 weeks was applied as a critical precondition for P. lactiflora to acquire a certain chilling accumulation. A dormancy-related gene named HOMEOBOX PROTEIN 31 (PlHB31), believed to negatively regulate bud endodormancy release (BER), was chosen as the target gene in this study. GFP fluorescence was detected in directly infiltrated and newly developed roots and buds; the transgenic plantlets exhibited remarkably earlier budbreak, and PlHB31 was significantly downregulated in silenced plantlets. This study established a homologous transient silencing system featuring intact-plant infiltration and minimized manipulation for gene function research, and also offers technical support and serves as a theoretical basis for gene function discovery in numerous other geophytes. Full article
(This article belongs to the Special Issue Molecular and Structural Research Advances in Model Plants)
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14 pages, 1914 KiB  
Article
Knocking Out Chloroplastic Aldolases/Rubisco Lysine Methyltransferase Enhances Biomass Accumulation in Nannochloropsis oceanica under High-Light Stress
by Wensi Liang, Li Wei, Qintao Wang, Wuxin You, Ansgar Poetsch, Xuefeng Du, Nana Lv and Jian Xu
Int. J. Mol. Sci. 2024, 25(7), 3756; https://doi.org/10.3390/ijms25073756 - 28 Mar 2024
Cited by 2 | Viewed by 1484
Abstract
Rubisco large-subunit methyltransferase (LSMT), a SET-domain protein lysine methyltransferase, catalyzes the formation of trimethyl-lysine in the large subunit of Rubisco or in fructose-1,6-bisphosphate aldolases (FBAs). Rubisco and FBAs are both vital proteins involved in CO2 fixation in chloroplasts; however, the physiological effect [...] Read more.
Rubisco large-subunit methyltransferase (LSMT), a SET-domain protein lysine methyltransferase, catalyzes the formation of trimethyl-lysine in the large subunit of Rubisco or in fructose-1,6-bisphosphate aldolases (FBAs). Rubisco and FBAs are both vital proteins involved in CO2 fixation in chloroplasts; however, the physiological effect of their trimethylation remains unknown. In Nannochloropsis oceanica, a homolog of LSMT (NoLSMT) is found. Phylogenetic analysis indicates that NoLSMT and other algae LSMTs are clustered in a basal position, suggesting that algal species are the origin of LSMT. As NoLSMT lacks the His-Ala/ProTrp triad, it is predicted to have FBAs as its substrate instead of Rubisco. The 18–20% reduced abundance of FBA methylation in NoLSMT-defective mutants further confirms this observation. Moreover, this gene (nolsmt) can be induced by low-CO2 conditions. Intriguingly, NoLSMT-knockout N. oceanica mutants exhibit a 9.7–13.8% increase in dry weight and enhanced growth, which is attributed to the alleviation of photoinhibition under high-light stress. This suggests that the elimination of FBA trimethylation facilitates carbon fixation under high-light stress conditions. These findings have implications in engineering carbon fixation to improve microalgae biomass production. Full article
(This article belongs to the Special Issue Molecular and Structural Research Advances in Model Plants)
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18 pages, 9589 KiB  
Article
Silencing an ATP-Dependent Caseinolytic Protease Proteolytic Subunit Gene Enhances the Resistance of Rice to Nilaparvata lugens
by Shuting Chen, Miaofen Ye, Peng Kuai, Lin Chen and Yonggen Lou
Int. J. Mol. Sci. 2024, 25(7), 3699; https://doi.org/10.3390/ijms25073699 - 26 Mar 2024
Cited by 1 | Viewed by 1086
Abstract
The ATP-dependent caseinolytic protease (Clp) system has been reported to play an important role in plant growth, development, and defense against pathogens. However, whether the Clp system is involved in plant defense against herbivores remains largely unclear. We explore the role of the [...] Read more.
The ATP-dependent caseinolytic protease (Clp) system has been reported to play an important role in plant growth, development, and defense against pathogens. However, whether the Clp system is involved in plant defense against herbivores remains largely unclear. We explore the role of the Clp system in rice defenses against brown planthopper (BPH) Nilaparvata lugens by combining chemical analysis, transcriptome, and molecular analyses, as well as insect bioassays. We found the expression of a rice Clp proteolytic subunit gene, OsClpP6, was suppressed by infestation of BPH gravid females and mechanical wounding. Silencing OsClpP6 enhanced the level of BPH-induced jasmonic acid (JA), JA-isoleucine (JA-Ile), and ABA, which in turn promoted the production of BPH-elicited rice volatiles and increased the resistance of rice to BPH. Field trials showed that silencing OsClpP6 decreased the population densities of BPH and WBPH. We also observed that silencing OsClpP6 decreased chlorophyll content in rice leaves at early developmental stages and impaired rice root growth and seed setting rate. These findings demonstrate that an OsClpP6-mediated Clp system in rice was involved in plant growth-defense trade-offs by affecting the biosynthesis of defense-related signaling molecules in chloroplasts. Moreover, rice plants, after recognizing BPH infestation, can enhance rice resistance to BPH by decreasing the Clp system activity. The work might provide a new way to breed rice varieties that are resistant to herbivores. Full article
(This article belongs to the Special Issue Molecular and Structural Research Advances in Model Plants)
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15 pages, 2056 KiB  
Article
Brassica oleracea L. var. italica Aquaporin Reconstituted Proteoliposomes as Nanosystems for Resveratrol Encapsulation
by Lucia Yepes-Molina, José A. Teruel, Urban Johanson and Micaela Carvajal
Int. J. Mol. Sci. 2024, 25(4), 1987; https://doi.org/10.3390/ijms25041987 - 6 Feb 2024
Viewed by 1306
Abstract
Aquaporins (AQPs), membrane proteins responsible for facilitating water transport, found in plant membrane vesicles (MV), have been related to the functionality and stability of MV. We focused on AQPs obtained from broccoli, as they show potential for biotechnological applications. To gain further insight [...] Read more.
Aquaporins (AQPs), membrane proteins responsible for facilitating water transport, found in plant membrane vesicles (MV), have been related to the functionality and stability of MV. We focused on AQPs obtained from broccoli, as they show potential for biotechnological applications. To gain further insight into the role of AQPs in MV, we describe the heterologous overexpression of two broccoli AQPs (BoPIP1;2 and BoPIP2;2) in Pichia pastoris, resulting in their purification with high yield (0.14 and 0.99 mg per gram cells for BoPIP1;2 and BoPIP2;2). We reconstituted AQPs in liposomes to study their functionality, and the size of proteoliposomes did not change concerning liposomes. BoPIP2;2 facilitated water transport, which was preserved for seven days at 4 °C and at room temperature but not at 37 °C. BoPIP2;2 was incorporated into liposomes to encapsulate a resveratrol extract, resulting in increased entrapment efficiency (EE) compared to conventional liposomes. Molecular docking was utilized to identify binding sites in PIP2s for resveratrol, highlighting the role of aquaporins in the improved EE. Moreover, interactions between plant AQP and human integrin were shown, which may increase internalization by the human target cells. Our results suggest AQP-based alternative encapsulation systems can be used in specifically targeted biotechnological applications. Full article
(This article belongs to the Special Issue Molecular and Structural Research Advances in Model Plants)
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Review

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25 pages, 1647 KiB  
Review
Insight into Rice Resistance to the Brown Planthopper: Gene Cloning, Functional Analysis, and Breeding Applications
by Yangdong Ye, Shangye Xiong, Xin Guan, Tianxin Tang, Zhihong Zhu, Xiao Zhu, Jie Hu, Jianguo Wu and Shuai Zhang
Int. J. Mol. Sci. 2024, 25(24), 13397; https://doi.org/10.3390/ijms252413397 - 13 Dec 2024
Viewed by 794
Abstract
This review provides a comprehensive overview of the current understanding of rice resistance to the brown planthopper (BPH), a major pest that poses significant threats to rice production through direct feeding damage and by transmitting viruses such as Rice grassy stunt virus (RGSV) [...] Read more.
This review provides a comprehensive overview of the current understanding of rice resistance to the brown planthopper (BPH), a major pest that poses significant threats to rice production through direct feeding damage and by transmitting viruses such as Rice grassy stunt virus (RGSV) and Rice ragged stunt virus (RRSV). We highlight the emergence of various BPH biotypes that have overcome specific resistance genes in rice. Advances in genetic mapping and cloning have identified 17 BPH resistance genes, classified into typical R genes encoding nucleotide-binding leucine-rich repeat (NLR) proteins and atypical R genes such as lectin receptor kinases and proteins affecting cell wall composition. The molecular mechanisms of these genes involve the activation of plant defense pathways mediated by phytohormones like jasmonic acid (JA), salicylic acid (SA), and ethylene, as well as the production of defensive metabolites. We also examine the complex interactions between BPH salivary proteins and rice defense responses, noting how salivary effectors can both suppress and trigger plant immunity. The development and improvement of BPH-resistant rice varieties through conventional breeding and molecular marker-assisted selection are discussed, including strategies like gene pyramiding to enhance resistance durability. Finally, we outline the challenges and future directions in breeding for durable BPH resistance, emphasizing the need for continued research on resistance mechanisms and the development of rice varieties with broad-spectrum and long-lasting resistance. Full article
(This article belongs to the Special Issue Molecular and Structural Research Advances in Model Plants)
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12 pages, 1354 KiB  
Review
Molecular Mechanisms of Heterosis and Its Applications in Tree Breeding: Progress and Perspectives
by Zeyu Li, Yan Zhao and Keming Luo
Int. J. Mol. Sci. 2024, 25(22), 12344; https://doi.org/10.3390/ijms252212344 - 17 Nov 2024
Viewed by 1373
Abstract
Heterosis, or hybrid vigor, refers to the phenomenon where hybrid progenies outperform their parents in traits such as yield and resistance. This phenomenon has been widely applied in plant breeding. Recent advances in high-throughput genomics have significantly advanced our understanding of heterosis. This [...] Read more.
Heterosis, or hybrid vigor, refers to the phenomenon where hybrid progenies outperform their parents in traits such as yield and resistance. This phenomenon has been widely applied in plant breeding. Recent advances in high-throughput genomics have significantly advanced our understanding of heterosis. This review systematically summarizes the genetic, molecular, and epigenetic mechanisms underlying heterosis. Furthermore, we discuss recent advances in predictive methods for heterosis and their applications in improving growth rate, resistance to abiotic stresses, and wood yield in tree species. We also explore the role of tree genomics in unraveling the mechanisms underlying heterosis, emphasizing the potential of integrating high-resolution genomics, single-cell sequencing, and spatial transcriptomics to achieve a comprehensive understanding of heterosis from the molecular to spatial levels. Building on this, CRISPR-based gene-editing technologies can be employed to precisely edit heterotic loci, enabling the study of allele function. Additionally, molecular marker-assisted selection (MAS) can be utilized to identify heterotic loci in parental lines, facilitating the selection of optimal hybrid combinations and significantly reducing the labor and time costs of hybrid breeding. Finally, we review the utilization of heterosis in tree breeding and provide a forward-looking perspective on future research directions, highlighting the potential of integrating multi-omics approaches and emerging gene-editing tools to revolutionize tree hybrid breeding. Full article
(This article belongs to the Special Issue Molecular and Structural Research Advances in Model Plants)
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33 pages, 2023 KiB  
Review
Recent Advances in Studying the Regulation of Fruit Ripening in Tomato Using Genetic Engineering Approaches
by Denis Baranov and Vadim Timerbaev
Int. J. Mol. Sci. 2024, 25(2), 760; https://doi.org/10.3390/ijms25020760 - 7 Jan 2024
Cited by 4 | Viewed by 4833
Abstract
Tomato (Solanum lycopersicum L.) is one of the most commercially essential vegetable crops cultivated worldwide. In addition to the nutritional value, tomato is an excellent model for studying climacteric fruits’ ripening processes. Despite this, the available natural pool of genes that allows [...] Read more.
Tomato (Solanum lycopersicum L.) is one of the most commercially essential vegetable crops cultivated worldwide. In addition to the nutritional value, tomato is an excellent model for studying climacteric fruits’ ripening processes. Despite this, the available natural pool of genes that allows expanding phenotypic diversity is limited, and the difficulties of crossing using classical selection methods when stacking traits increase proportionally with each additional feature. Modern methods of the genetic engineering of tomatoes have extensive potential applications, such as enhancing the expression of existing gene(s), integrating artificial and heterologous gene(s), pointing changes in target gene sequences while keeping allelic combinations characteristic of successful commercial varieties, and many others. However, it is necessary to understand the fundamental principles of the gene molecular regulation involved in tomato fruit ripening for its successful use in creating new varieties. Although the candidate genes mediate ripening have been identified, a complete picture of their relationship has yet to be formed. This review summarizes the latest (2017–2023) achievements related to studying the ripening processes of tomato fruits. This work attempts to systematize the results of various research articles and display the interaction pattern of genes regulating the process of tomato fruit ripening. Full article
(This article belongs to the Special Issue Molecular and Structural Research Advances in Model Plants)
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