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Plant Omics: Sensing, Signaling, Regulation and Homeostasis
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Plant Omics: Sensing, Signaling, Regulation and Homeostasis

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: 31 May 2024 | Viewed by 3973

Special Issue Editor

Dr. Margherita-Gabriella De Biasi

E-Mail Website
Guest Editor
Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
Interests: plant secondary metabolites; antimicrobial effects of phytochemical components; biochemistry and biotechnology; plant-derived antibiotics; plant responses to stresses; phytoremediation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are pleased to announce a Special Issue, entitled “Plant Omics: Sensing, Signaling, Regulation and Homeostasis”, in the International Journal of Molecular Sciences. This Special Issue aims to provide a comprehensive understanding of the complex regulatory mechanisms underlying plant homeostasis by exploring the latest advances in omics technologies, including metabolomics, ionomics, transcriptomics, proteomics, and genomics.

Plant homeostasis is a complex phenomenon that involves a delicate balance of metabolic and regulatory networks that enable plants to adapt and thrive in a changing environment. Recent advancements in omics technologies have provided powerful tools for the comprehensive analysis of these networks and have significantly advanced our understanding of plant homeostasis.

We welcome original research articles, reviews, and perspectives that address the following topics:

  • Emerging omics technologies for the study of plant homeostasis;
  • Omics-based approaches to understanding metabolic regulation of plants;
  • Genomics and plant homeostasis: from genes to biological functions;
  • Omics-based approaches to understanding plant responses to environmental stress;
  • Emerging omics technologies and their application to unravel the complexity of plant homeostasis;
  • Metabolomics and plant homeostasis: recent developments and future directions;
  • Integrating ionomics and genetics to unravel the basis of plant ion homeostasis.

We invite colleges in the field of plant science to contribute their research to this Special Issue, which will provide a comprehensive understanding of the intricate mechanisms underlying plant homeostasis and their regulation.

Prof. Dr. Margherita-Gabriella De Biasi
Guest Editor

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.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant homeostasis
  • omics
  • transcriptomics
  • metabolomics
  • proteomics
  • genomics
  • ionomics
  • environmental stress
  • regulatory mechanisms
  • metabolic processes
  • systems biology

Published Papers (4 papers)

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Research

14 pages, 3322 KiB  
Article
A Fruit-Expressed MYB Transcription Factor Regulates Anthocyanin Biosynthesis in Atropa belladonna
by Xiaoqiang Liu, Tengfei Zhao, Lina Yuan, Fei Qiu, Yueli Tang, Dan Li, Fangyuan Zhang, Lingjiang Zeng, Chunxian Yang, Mohammad Mahmoud Nagdy, Zun Lai Lai Htun, Xiaozhong Lan, Min Chen, Zhihua Liao and Yan Li
Int. J. Mol. Sci. 2024, 25(9), 4963; https://doi.org/10.3390/ijms25094963 - 2 May 2024
Viewed by 311
Abstract
Anthocyanins are water-soluble flavonoid pigments that play a crucial role in plant growth and metabolism. They serve as attractants for animals by providing plants with red, blue, and purple pigments, facilitating pollination and seed dispersal. The fruits of solanaceous plants, tomato (Solanum [...] Read more.
Anthocyanins are water-soluble flavonoid pigments that play a crucial role in plant growth and metabolism. They serve as attractants for animals by providing plants with red, blue, and purple pigments, facilitating pollination and seed dispersal. The fruits of solanaceous plants, tomato (Solanum lycopersicum) and eggplant (Solanum melongena), primarily accumulate anthocyanins in the fruit peels, while the ripe fruits of Atropa belladonna (Ab) have a dark purple flesh due to anthocyanin accumulation. In this study, an R2R3-MYB transcription factor (TF), AbMYB1, was identified through association analysis of gene expression and anthocyanin accumulation in different tissues of A. belladonna. Its role in regulating anthocyanin biosynthesis was investigated through gene overexpression and RNA interference (RNAi). Overexpression of AbMYB1 significantly enhanced the expression of anthocyanin biosynthesis genes, such as AbF3H, AbF3′5′H, AbDFR, AbANS, and Ab3GT, leading to increased anthocyanin production. Conversely, RNAi-mediated suppression of AbMYB1 resulted in decreased expression of most anthocyanin biosynthesis genes, as well as reduced anthocyanin contents in A. belladonna. Overall, AbMYB1 was identified as a fruit-expressed R2R3-MYB TF that positively regulated anthocyanin biosynthesis in A. belladonna. This study provides valuable insights into the regulation of anthocyanin biosynthesis in Solanaceae plants, laying the foundation for understanding anthocyanin accumulation especially in the whole fruits of solanaceous plants. Full article
(This article belongs to the Special Issue Plant Omics: Sensing, Signaling, Regulation and Homeostasis)
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17 pages, 7747 KiB  
Article
Responsive Alternative Splicing Events of Opisthopappus Species against Salt Stress
by Mian Han, Mengfan Niu, Ting Gao, Yuexin Shen, Xiaojuan Zhou, Yimeng Zhang, Li Liu, Min Chai, Genlou Sun and Yiling Wang
Int. J. Mol. Sci. 2024, 25(2), 1227; https://doi.org/10.3390/ijms25021227 - 19 Jan 2024
Cited by 3 | Viewed by 775
Abstract
Salt stress profoundly affects plant growth, prompting intricate molecular responses, such as alternative splicing (AS), for environmental adaptation. However, the response of AS events to salt stress in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear, which is a Taihang Mountain [...] Read more.
Salt stress profoundly affects plant growth, prompting intricate molecular responses, such as alternative splicing (AS), for environmental adaptation. However, the response of AS events to salt stress in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear, which is a Taihang Mountain cliff-dwelling species. Using RNA-seq data, differentially expressed genes (DEGs) were identified under time and concentration gradients of salt stress. Two types of AS, skipped exon (SE) and mutually exclusive exons (MXE), were found. Differentially alternative splicing (DAS) genes in both species were significantly enriched in “protein phosphorylation”, “starch and sucrose metabolism”, and “plant hormone signal transduction” pathways. Meanwhile, distinct GO terms and KEGG pathways of DAS occurred between two species. Only a small subset of DAS genes overlapped with DEGs under salt stress. Although both species likely adopted protein phosphorylation to enhance salt stress tolerance, they exhibited distinct responses. The results indicated that the salt stress mechanisms of both Opisthopappus species exhibited similarities and differences in response to salt stress, which suggested that adaptive divergence might have occurred between them. This study initially provides a comprehensive description of salt responsive AS events in Opisthopappus and conveys some insights into the molecular mechanisms behind species tolerance on the Taihang Mountains. Full article
(This article belongs to the Special Issue Plant Omics: Sensing, Signaling, Regulation and Homeostasis)
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19 pages, 4291 KiB  
Article
Proteomic and Low-Polar Metabolite Profiling Reveal Unique Dynamics in Fatty Acid Metabolism during Flower and Berry Development of Table Grapes
by Patricio Olmedo, Juan Vidal, Excequel Ponce, Bruno G. Defilippi, Alonso G. Pérez-Donoso, Claudio Meneses, Sebastien Carpentier, Romina Pedreschi and Reinaldo Campos-Vargas
Int. J. Mol. Sci. 2023, 24(20), 15360; https://doi.org/10.3390/ijms242015360 - 19 Oct 2023
Viewed by 975
Abstract
Grapevine development and ripening are complex processes that involve several biochemical pathways, including fatty acid and lipid metabolism. Fatty acids are essential components of lipids, which play crucial roles in fruit maturation and flavor development. However, the dynamics of fatty acid metabolism in [...] Read more.
Grapevine development and ripening are complex processes that involve several biochemical pathways, including fatty acid and lipid metabolism. Fatty acids are essential components of lipids, which play crucial roles in fruit maturation and flavor development. However, the dynamics of fatty acid metabolism in grape flowers and berries are poorly understood. In this study, we present those dynamics and investigate the mechanisms of fatty acid homeostasis on ‘Thompson Seedless’ berries using metabolomic and proteomic analyses. Low-polar metabolite profiling indicated a higher abundance of fatty acids at the pre-flowering and pre-veraison stages. Proteomic analyses revealed that grape flowers and berries display unique profiles of proteins involved in fatty acid biosynthesis, triacylglycerol assembly, fatty acid β-oxidation, and lipid signaling. These findings show, for the first time, that fatty acid metabolism also plays an important role in the development of non-oil-rich tissues, opening new perspectives about lipid function and its relation to berry quality. Full article
(This article belongs to the Special Issue Plant Omics: Sensing, Signaling, Regulation and Homeostasis)
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18 pages, 2472 KiB  
Article
A Switch from Latent to Typical Infection during Pectobacterium atrosepticum—Tobacco Interactions: Predicted and True Molecular Players
by Ivan Tsers, Olga Parfirova, Varvara Moruzhenkova, Olga Petrova, Natalia Gogoleva, Vladimir Vorob’ev, Yuri Gogolev and Vladimir Gorshkov
Int. J. Mol. Sci. 2023, 24(17), 13283; https://doi.org/10.3390/ijms241713283 - 27 Aug 2023
Cited by 3 | Viewed by 881
Abstract
Phytopathogenic microorganisms, being able to cause plant diseases, usually interact with hosts asymptomatically, resulting in the development of latent infections. Knowledge of the mechanisms that trigger a switch from latent to typical, symptomatic infection is of great importance from the perspectives of both [...] Read more.
Phytopathogenic microorganisms, being able to cause plant diseases, usually interact with hosts asymptomatically, resulting in the development of latent infections. Knowledge of the mechanisms that trigger a switch from latent to typical, symptomatic infection is of great importance from the perspectives of both fundamental science and disease management. No studies to date have compared, at the systemic molecular level, the physiological portraits of plants when different infection types (typical and latent) are developed. The only phytopathogenic bacterium for which latent infections were not only widely described but also at least fluently characterized at the molecular level is Pectobacterium atrosepticum (Pba). The present study aimed at the comparison of plant transcriptome responses during typical and latent infections caused by Pba in order to identify and then experimentally verify the key molecular players that act as switchers, turning peaceful plant-Pba coexistence into a typical infection. Based on RNA-Seq, we predicted plant cell wall-, secondary metabolism-, and phytohormone-related genes whose products contributed to the development of the disease or provided asymptomatic plant—Pba interactions. By treatment tests, we confirmed that a switch from latent to typical Pba-caused infection is determined by the plant susceptible responses mediated by the joint action of ethylene and jasmonates. Full article
(This article belongs to the Special Issue Plant Omics: Sensing, Signaling, Regulation and Homeostasis)
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