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Omics Study to Uncover Signalling and Gene Regulation in Plants 2.0

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

Deadline for manuscript submissions: closed (20 February 2024) | Viewed by 7441

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Dr. Maria G. Samsonova

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Mathematical Biology and Bioinformatics Laboratory, Institute of Physics and Mechanics, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia
Interests: systems biology and mechanisms of the development; gene regulation; multi-omics approaches; abiotic and biotic stress response
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Dear Colleagues,

As sessile organisms, plants are exposed to dynamically changing environmental conditions throughout their life span. To ensure survival and reproductive success, plants have evolved the ability to perceive multiple stimuli and then transmit this information into appropriate responses. This is achieved by the coordinated action of signaling cascades and communication networks that broadcast signals throughout the plant body to orchestrate the expression of the genes controlling plant physiology and development. Numerous molecules are involved in these processes, ranging from mobile hormones and peptides to metabolites and RNAs. Recently, information has begun to emerge about the involvement of reactive oxygen species, ion fluxes and electrical signaling as a parallel systemic signal.

Omics studies are at the cornerstone of deciphering signaling and communication networks in plants. These studies are based on a plethora of technologies, including DNA sequencing and genotyping, as well as transcriptome, epigenome, proteome and metabolome analysis. All these technologies rely on large numbers of comparisons and tailored statistical analyses. Recent advances in the integration of different omics technologies has led to a greater understanding of the functional consequences of signalling and gene regulation in plants.

This Special Issue aims to present the latest research in the application of omics technologies, as well as statistical and bioinformatic approaches, to decipher signalling, gene regulation and systemic communication pathways in plants. Both original research articles and comprehensive reviews are welcomed.

Dr. Maria G. Samsonova
Guest Editor

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Keywords

signalling
gene regulation
hormones
systemic response
abiotic and biotic stress response
multi-omics approaches

Published Papers (6 papers)

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Research

14 pages, 6874 KiB

Open AccessArticle

PgDDS Changes the Plant Growth of Transgenic Aralia elata and Improves the Production of Re and Rg₃ in Its Leaves

by Wenhua Guo, Yue Zhao, Honghao Xu, Yuxin Xia, Lei Tao and Xiangling You

Int. J. Mol. Sci. 2024, 25(3), 1945; https://doi.org/10.3390/ijms25031945 - 5 Feb 2024

Viewed by 773

Abstract

Aralia elata (Miq.) Seem is a medicinal plant that shares a common pathway for the biosynthesis of triterpenoid saponins with Panax ginseng. Here, we transferred the dammarenediol-II synthase gene from P. ginseng (PgDDS; GenBank: AB122080.1) to A. elata. The growth of 2-year-old transgenic plants (L27; 9.63 cm) was significantly decreased compared with wild-type plants (WT; 74.97 cm), and the leaflet shapes and sizes of the transgenic plants differed from those of the WT plants. Based on a terpene metabolome analysis of leaf extracts from WT, L13, and L27 plants, a new structural skeleton for ursane-type triterpenoid saponins was identified. Six upregulated differentially accumulated metabolites (DAMs) were detected, and the average levels of Rg3 and Re in the leaves of the L27 plants were 42.64 and 386.81 μg/g, respectively, increased significantly compared with the WT plants (15.48 and 316.96 μg/g, respectively). Thus, the expression of PgDDS in A. elata improved its medicinal value. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants 2.0)

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16 pages, 3210 KiB

Open AccessArticle

The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice

by Ranran Huang, Yilong Feng, Zhicheng Gao, Asgar Ahmed and Wenli Zhang

Int. J. Mol. Sci. 2024, 25(1), 634; https://doi.org/10.3390/ijms25010634 - 4 Jan 2024

Cited by 1 | Viewed by 1449

Abstract

A G-quadruplex (G4) is a typical non-B DNA structure and involved in various DNA-templated events in eukaryotic genomes. PEG and PDS chemicals have been widely applied for promoting the folding of in vivo or in vitro G4s. However, how PEG and PDS preferentially affect a subset of G4 formation genome-wide is still largely unknown. We here conducted a BG4-based IP-seq in vitro under K⁺+PEG or K⁺+PDS conditions in the rice genome. We found that PEG-favored IP-G4s⁺ have distinct sequence features, distinct genomic distributions and distinct associations with TEGs, non-TEGs and subtypes of TEs compared to PDS-favored ones. Strikingly, PEG-specific IP-G4s⁺ are associated with euchromatin with less enrichment levels of DNA methylation but with more enriched active histone marks, while PDS-specific IP-G4s⁺ are associated with heterochromatin with higher enrichment levels of DNA methylation and repressive marks. Moreover, we found that genes with PEG-specific IP-G4s⁺ are more expressed than those with PDS-specific IP-G4s⁺, suggesting that PEG/PDS-specific IP-G4s⁺ alone or coordinating with epigenetic marks are involved in the regulation of the differential expression of related genes, therefore functioning in distinct biological processes. Thus, our study provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants 2.0)

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15 pages, 6576 KiB

Open AccessArticle

The R2R3-MYB Transcriptional Repressor TgMYB4 Negatively Regulates Anthocyanin Biosynthesis in Tulips (Tulipa gesneriana L.)

by Xianmei Hu, Zehui Liang, Tianxiao Sun, Ling Huang, Yanping Wang, Zhulong Chan and Lin Xiang

Int. J. Mol. Sci. 2024, 25(1), 563; https://doi.org/10.3390/ijms25010563 - 1 Jan 2024

Cited by 2 | Viewed by 1132

Abstract

Anthocyanins play a paramount role in color variation and significantly contribute to the economic value of ornamental plants. The conserved activation complex MYB-bHLH-WD40 (MBW; MYB: v-myb avian myeloblastosis viral oncogene homolog; bHLH: basic helix–loop–helix protein; WD40:WD-repeat protein) involved in anthocyanin biosynthesis has been thoroughly researched, but there have been limited investigations into the function of repressor factors. In this study, we characterized TgMYB4, an R2R3-MYB transcriptional repressor which is highly expressed during petal coloration in red petal cultivars. TgMYB4-overexpressing tobaccos exhibited white or light pink petals with less anthocyanin accumulation compared to control plants. TgMYB4 was found to inhibit the transcription of ANTHOCYANIDIN SYNTHASE (TfANS1) and DIHYDRO-FLAVONOL-4-REDUCTASE (AtDFR), although it did not bind to their promoters. Moreover, the TgMYB4 protein was able to compete with the MYB activator to bind to the :bHLHprotein, thereby suppressing the function of the activator MBW complex. These findings demonstrate that TgMYB4 plays a suppressive role in the regulation of anthocyanin synthesis during flower pigmentation. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants 2.0)

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15 pages, 4030 KiB

Open AccessArticle

Integrative Metabolomic and Transcriptomic Landscape during Akebia trifoliata Fruit Ripening and Cracking

by Yongli Jiang, Yanlin Du, Chongyang Chen, Danfeng Wang, Yu Zhong and Yun Deng

Int. J. Mol. Sci. 2023, 24(23), 16732; https://doi.org/10.3390/ijms242316732 - 24 Nov 2023

Viewed by 827

Abstract

Akebia trifoliata fruit is prone to crack after ripening, but little is known about the mechanism underlying the cracking process. This study integrated transcriptomic and metabolomic data, revealing significant changes in 398 metabolites and 8414 genes during ripening and cracking, mainly impacting cell-wall metabolism. Multi-omics joint analysis indicated that genes related to polygalacturonase, pectate lyase, α-amylase, and glycogen phosphorylase were up-regulated after cracking, degrading cell wall and starch. Concurrently, diminished photosynthetic metabolism and heightened phenylpropanoid metabolism suggested alterations in cuticle structure, potentially impacting cell-wall robustness. Numerous auxin and abscisic acid signaling-related genes were expressed, and we assume that they contributed to the promoting peel growth. These alterations collectively might compromise peel strength and elevate expanding pressure, potentially leading to A. trifoliata cracking. Transcription factors, predominantly ethylene response factors and helix-loop-helix family members, appeared to regulate these metabolic shifts. These findings provide valuable insights into A. trifoliata cracking mechanisms; however, direct experimental validation of these assumptions is necessary to strengthen these conclusions and expedite their commercial utilization. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants 2.0)

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18 pages, 6007 KiB

Open AccessArticle

Overexpression of a Grape MYB Transcription Factor Gene VhMYB2 Increases Salinity and Drought Tolerance in Arabidopsis thaliana

by Chuankun Ren, Zhenghao Li, Penghui Song, Yu Wang, Wanda Liu, Lihua Zhang, Xingguo Li, Wenhui Li and Deguo Han

Int. J. Mol. Sci. 2023, 24(13), 10743; https://doi.org/10.3390/ijms241310743 - 28 Jun 2023

Cited by 3 | Viewed by 1252

Abstract

In viticulture, the highly resistant rootstock ‘Beta’ is widely used in Chinese grape production to avoid the effects of soil salinization and drought on grape growth. However, the mechanism of high resistance to abiotic stress in the ‘Beta’ rootstock is not clear. In this study, we demonstrated that VhMYB2 as a transcription factor made a significant contribution to salinity and drought stress, which was isolated from the ‘Beta’ rootstock. The coding sequence of the VhMYB2 gene was 858 bp, encoding 285 amino acids. The subcellular localization of VhMYB2 was located in the nucleus of tobacco epidermal cells. Moreover, RT-qPCR found that VhMYB2 was predominantly expressed in the mature leaf and root of the grape. Under salinity and drought stress, overexpressing VhMYB2 showed a higher resistant phenotype and survival rates in A. thaliana while the transgenic lines had a survival advantage by measuring the contents of proline, chlorophyll, and MDA, and activities of POD, SOD, and CAT, and expression levels of related stress response genes. The results reveal that VhMYB2 may be an important transcription factor regulating ‘Beta’ resistance in response to abiotic stress. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants 2.0)

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22 pages, 3206 KiB

Open AccessArticle

Elucidating the Mesocarp Drupe Transcriptome of Açai (Euterpe oleracea Mart.): An Amazonian Tree Palm Producer of Bioactive Compounds

by Elaine Darnet, Bruno Teixeira, Hubert Schaller, Hervé Rogez and Sylvain Darnet

Int. J. Mol. Sci. 2023, 24(11), 9315; https://doi.org/10.3390/ijms24119315 - 26 May 2023

Viewed by 1392

Abstract

Euterpe oleracea palm, endemic to the Amazon region, is well known for açai, a fruit violet beverage with nutritional and medicinal properties. During E. oleracea fruit ripening, anthocyanin accumulation is not related to sugar production, contrarily to grape and blueberry. Ripened fruits have a high content of anthocyanins, isoprenoids, fibers, and proteins, and are poor in sugars. E. oleracea is proposed as a new genetic model for metabolism partitioning in the fruit. Approximately 255 million single-end-oriented reads were generated on an Ion Proton NGS platform combining fruit cDNA libraries at four ripening stages. The de novo transcriptome assembly was tested using six assemblers and 46 different combinations of parameters, a pre-processing and a post-processing step. The multiple k-mer approach with TransABySS as an assembler and Evidential Gene as a post-processer have shown the best results, with an N50 of 959 bp, a read coverage mean of 70x, a BUSCO complete sequence recovery of 36% and an RBMT of 61%. The fruit transcriptome dataset included 22,486 transcripts representing 18 Mbp, of which a proportion of 87% had significant homology with other plant sequences. Approximately 904 new EST-SSRs were described, and were common and transferable to Phoenix dactylifera and Elaeis guineensis, two other palm trees. The global GO classification of transcripts showed similar categories to that in P. dactylifera and E. guineensis fruit transcriptomes. For an accurate annotation and functional description of metabolism genes, a bioinformatic pipeline was developed to precisely identify orthologs, such as one-to-one orthologs between species, and to infer multigenic family evolution. The phylogenetic inference confirmed an occurrence of duplication events in the Arecaceae lineage and the presence of orphan genes in E. oleracea. Anthocyanin and tocopherol pathways were annotated entirely. Interestingly, the anthocyanin pathway showed a high number of paralogs, similar to in grape, whereas the tocopherol pathway exhibited a low and conserved gene number and the prediction of several splicing forms. The release of this exhaustively annotated molecular dataset of E. oleracea constitutes a valuable tool for further studies in metabolism partitioning and opens new great perspectives to study fruit physiology with açai as a model. Full article

(This article belongs to the Special Issue Omics Study to Uncover Signalling and Gene Regulation in Plants 2.0)

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