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Integrative Biology in Plants: From Molecular Stress Response to Systems...
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Integrative Biology in Plants: From Molecular Stress Response to Systems Biology

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (30 May 2023) | Viewed by 15755

Special Issue Editors

Dr. Mónica Escandón

E-Mail Website
Guest Editor
Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
Interests: forest species; molecular biology; stress; system biology; omics; plant physiology
Dr. Jesús Pascual

E-Mail Website
Guest Editor
Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, ‎Asturias‎, Spain
Interests: plant physiology; stress response; UV-B; signaling pathways; proteomics; bioinformatics

Special Issue Information

Dear Colleagues, 

Stress response in plants has been widely studied from a physiological perspective, having been most commonly combined with classical biochemical and molecular analysis of different complexity. In this regard, the complexity of molecular analysis has increased particularly in the last decade due to methodological breakthroughs in high-throughput omic techniques and their increased accessibility and affordability. This has contributed to their popularization in plant sciences. These technical advancements have allowed for a more global or system-level analysis of stress response processes in plants and have brought along higher complexity when it comes to data analysis and result interpretation. The current trend in the field in that regard is to go one step further from mere analysis of single and independent omic layers by performing a global integration of different ones as well as with biochemical, physiological or phenotypic data. This approach potentially exposes the existing interconnection between different molecular levels, providing a more complete (or real) view of stress response in plants. The integration of different layers of information (for example: physiological, metabolomic, and proteomic layers) is not an easy or direct task, and its potential for the generation of novel knowledge is not always fully noticed by the plant science community. Therefore, an overview of the application of different representative and state-of-the-art methods and approaches used in the field of plant integrative biology for the study of stress response is needed. In this Special Issue, we are looking at how the integration of different molecular layers allows us to obtain a more complete view of the stress response processes and how it could increase the potential applicability of the obtained results by paving the way for systems biology modeling.

Dr. Mónica Escandón
Dr. Jesús Pascual
Guest 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.

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. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). 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

  • integrative molecular research
  • omics layers and physiological parameters
  • plants stress

Published Papers (6 papers)

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Research

15 pages, 1625 KiB  
Article
The Integration of Data from Different Long-Read Sequencing Platforms Enhances Proteoform Characterization in Arabidopsis
by Lara García-Campa, Luis Valledor and Jesús Pascual
Plants 2023, 12(3), 511; https://doi.org/10.3390/plants12030511 - 22 Jan 2023
Cited by 1 | Viewed by 1677
Abstract
The increasing availability of massive omics data requires improving the quality of reference databases and their annotations. The combination of full-length isoform sequencing (Iso-Seq) with short-read transcriptomics and proteomics has been successfully used for increasing proteoform characterization, which is a main ongoing goal [...] Read more.
The increasing availability of massive omics data requires improving the quality of reference databases and their annotations. The combination of full-length isoform sequencing (Iso-Seq) with short-read transcriptomics and proteomics has been successfully used for increasing proteoform characterization, which is a main ongoing goal in biology. However, the potential of including Oxford Nanopore Technologies Direct RNA Sequencing (ONT-DRS) data has not been explored. In this paper, we analyzed the impact of combining Iso-Seq- and ONT-DRS-derived data on the identification of proteoforms in Arabidopsis MS proteomics data. To this end, we selected a proteomics dataset corresponding to senescent leaves and we performed protein searches using three different protein databases: AtRTD2 and AtRTD3, built from the homonymous transcriptomes, regarded as the most complete and up-to-date available for the species; and a custom hybrid database combining AtRTD3 with publicly available ONT-DRS transcriptomics data generated from Arabidopsis leaves. Our results show that the inclusion and combination of long-read sequencing data from Iso-Seq and ONT-DRS into a proteogenomic workflow enhances proteoform characterization and discovery in bottom-up proteomics studies. This represents a great opportunity to further investigate biological systems at an unprecedented scale, although it brings challenges to current protein searching algorithms. Full article
(This article belongs to the Special Issue Integrative Biology in Plants: From Molecular Stress Response to Systems Biology)
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17 pages, 17099 KiB  
Article
Multiomic Data Integration in the Analysis of Drought-Responsive Mechanisms in Quercus ilex Seedlings
by Víctor M. Guerrero-Sánchez, Cristina López-Hidalgo, María-Dolores Rey, María Ángeles Castillejo, Jesús V. Jorrín-Novo and Mónica Escandón
Plants 2022, 11(22), 3067; https://doi.org/10.3390/plants11223067 - 12 Nov 2022
Cited by 9 | Viewed by 1726
Abstract
The integrated analysis of different omic layers can provide new knowledge not provided by their individual analysis. This approach is also necessary to validate data and reveal post-transcriptional and post-translational mechanisms of gene expression regulation. In this work, we validated the possibility of [...] Read more.
The integrated analysis of different omic layers can provide new knowledge not provided by their individual analysis. This approach is also necessary to validate data and reveal post-transcriptional and post-translational mechanisms of gene expression regulation. In this work, we validated the possibility of applying this approach to non-model species such as Quercus ilex. Transcriptomics, proteomics, and metabolomics from Q. ilex seedlings subjected to drought-like conditions under the typical summer conditions in southern Spain were integrated using a non-targeted approach. Two integrative approaches, PCA and DIABLO, were used and compared. Both approaches seek to reduce dimensionality, preserving the maximum information. DIABLO also allows one to infer interconnections between the different omic layers. For easy visualization and analysis, these interconnections were analyzed using functional and statistical networks. We were able to validate results obtained by analyzing the omic layers separately. We identified the importance of protein homeostasis with numerous protease and chaperones in the networks. We also discovered new key processes, such as transcriptional control, and identified the key function of transcription factors, such as DREB2A, WRKY65, and CONSTANS, in the early response to drought. Full article
(This article belongs to the Special Issue Integrative Biology in Plants: From Molecular Stress Response to Systems Biology)
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20 pages, 15426 KiB  
Article
Investigation of Roles of TaTALE Genes during Development and Stress Response in Bread Wheat
by Meenakshi Rathour, Shumayla, Anshu Alok and Santosh Kumar Upadhyay
Plants 2022, 11(5), 587; https://doi.org/10.3390/plants11050587 - 22 Feb 2022
Cited by 12 | Viewed by 2298
Abstract
The three amino acid loop extension (TALE) genes of the homeobox superfamily are responsible for numerous biological functions in plants. Herein, we identified a total of 72 TaTALE genes in the allohexaploid genome of bread wheat (Triticum aestivum L.) and [...] Read more.
The three amino acid loop extension (TALE) genes of the homeobox superfamily are responsible for numerous biological functions in plants. Herein, we identified a total of 72 TaTALE genes in the allohexaploid genome of bread wheat (Triticum aestivum L.) and performed a comprehensive investigation for gene and protein structural properties, phylogeny, expression patterns, and multilevel gene regulations. The identified TaTALE proteins were further classified into two groups, TaBLHs and TaKNOXs, which were tightly clustered into the phylogeny. The negative Ka/Ks ratio of duplicated genes suggested purifying selection pressure with confined functional divergence. Various signature domains and motifs were found conserved in both groups of proteins. The occurrence of diverse cis-regulatory elements and modulated expression during various developmental stages and in the presence of abiotic (heat, drought, salt) and two different fungal stresses suggested their roles in development and stress response, as well. The interaction of TaTALEs with the miRNAs and other development-related homeobox proteins also suggested their roles in growth and development and stress response. The present study revealed several important aspects of TaTALEs that will be useful in further functional validation of these genes in future studies. Full article
(This article belongs to the Special Issue Integrative Biology in Plants: From Molecular Stress Response to Systems Biology)
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17 pages, 4471 KiB  
Article
The Omics Hunt for Novel Molecular Markers of Resistance to Phytophthora infestans
by Hana Dufková, Miroslav Berka, Marie Greplová, Šarlota Shejbalová, Romana Hampejsová, Markéta Luklová, Jaroslava Domkářová, Jan Novák, Viktor Kopačka, Břetislav Brzobohatý and Martin Černý
Plants 2022, 11(1), 61; https://doi.org/10.3390/plants11010061 - 25 Dec 2021
Cited by 8 | Viewed by 3559
Abstract
Wild Solanum accessions are a treasured source of resistance against pathogens, including oomycete Phytophthora infestans, causing late blight disease. Here, Solanum pinnatisectum, Solanum tuberosum, and the somatic hybrid between these two lines were analyzed, representing resistant, susceptible, and moderately resistant [...] Read more.
Wild Solanum accessions are a treasured source of resistance against pathogens, including oomycete Phytophthora infestans, causing late blight disease. Here, Solanum pinnatisectum, Solanum tuberosum, and the somatic hybrid between these two lines were analyzed, representing resistant, susceptible, and moderately resistant genotypes, respectively. Proteome and metabolome analyses showed that the infection had the highest impact on leaves of the resistant plant and indicated, among others, an extensive remodeling of the leaf lipidome. The lipidome profiling confirmed an accumulation of glycerolipids, a depletion in the total pool of glycerophospholipids, and showed considerable differences between the lipidome composition of resistant and susceptible genotypes. The analysis of putative resistance markers pinpointed more than 100 molecules that positively correlated with resistance including phenolics and cysteamine, a compound with known antimicrobial activity. Putative resistance protein markers were targeted in an additional 12 genotypes with contrasting resistance to P. infestans. At least 27 proteins showed a negative correlation with the susceptibility including HSP70-2, endochitinase B, WPP domain-containing protein, and cyclase 3. In summary, these findings provide insights into molecular mechanisms of resistance against P. infestans and present novel targets for selective breeding. Full article
(This article belongs to the Special Issue Integrative Biology in Plants: From Molecular Stress Response to Systems Biology)
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22 pages, 6688 KiB  
Article
Investigation and Computational Analysis of the Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum): Insights into Sulfur Adjustment for Proper Development and Stimuli Responses
by Sahar Faraji, Parviz Heidari, Hoorieh Amouei, Ertugrul Filiz, Abdullah and Peter Poczai
Plants 2021, 10(12), 2597; https://doi.org/10.3390/plants10122597 - 26 Nov 2021
Cited by 36 | Viewed by 3030
Abstract
Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the [...] Read more.
Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the significant nutritional crop potato (Solanum tuberosum L.). Twenty-nine putative StSOT genes were identified in the potato genome and were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure revealed two highly conserved 5′-phosphosulfate-binding (5′ PSB) regions and a 3′-phosphate-binding (3′ PB) motif that are essential for sulfotransferase activities. The protein–protein interaction networks also revealed an interesting interaction between SOTs and other proteins, such as PRTase, APS-kinase, protein phosphatase, and APRs, involved in sulfur compound biosynthesis and the regulation of flavonoid and brassinosteroid metabolic processes. This suggests the importance of sulfotransferases for proper potato growth and development and stress responses. Notably, homology modeling of StSOT proteins and docking analysis of their ligand-binding sites revealed the presence of proline, glycine, serine, and lysine in their active sites. An expression essay of StSOT genes via potato RNA-Seq data suggested engagement of these gene family members in plants’ growth and extension and responses to various hormones and biotic or abiotic stimuli. Our predictions may be informative for the functional characterization of the SOT genes in potato and other nutritional crops. Full article
(This article belongs to the Special Issue Integrative Biology in Plants: From Molecular Stress Response to Systems Biology)
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26 pages, 4012 KiB  
Article
Proteomics and Interspecies Interaction Analysis Revealed Abscisic Acid Signalling to Be the Primary Driver for Oil Palm’s Response against Red Palm Weevil Infestation
by Nazmi Harith-Fadzilah, Su Datt Lam, Mohammad Haris-Hussain, Idris Abd Ghani, Zamri Zainal, Johari Jalinas and Maizom Hassan
Plants 2021, 10(12), 2574; https://doi.org/10.3390/plants10122574 - 25 Nov 2021
Cited by 5 | Viewed by 2337
Abstract
The red palm weevil (RPW; Rhynchophorus ferrugineus Olivier (Coleoptera Curculionidae)) is an invasive insect pest that is difficult to manage due to its nature of infesting the host palm trees from within. A holistic, molecular-based approach to identify proteins that correlate with RPW [...] Read more.
The red palm weevil (RPW; Rhynchophorus ferrugineus Olivier (Coleoptera Curculionidae)) is an invasive insect pest that is difficult to manage due to its nature of infesting the host palm trees from within. A holistic, molecular-based approach to identify proteins that correlate with RPW infestation could give useful insights into the vital processes that are prevalent to the host’s infestation response and identify the potential biomarkers for an early detection technique. Here, a shotgun proteomic analysis was performed on oil palm (Elaeis guineensis; OP) under untreated (control), wounding by drilling (wounded), and artificial larval infestation (infested) conditions at three different time points to characterise the RPW infestation response at three different stages. KEGG pathway enrichment analysis revealed many overlapping pathways between the control, wounded, and infested groups. Further analysis via literature searches narrowed down biologically relevant proteins into categories, which were photosynthesis, growth, and stress response. Overall, the patterns of protein expression suggested abscisic acid (ABA) hormone signalling to be the primary driver of insect herbivory response. Interspecies molecular docking analysis between RPW ligands and OP receptor proteins provided putative interactions that result in ABA signalling activation. Seven proteins were selected as candidate biomarkers for early infestation detection based on their relevance and association with ABA signalling. The MS data are available via ProteomeXchange with identifier PXD028986. This study provided a deeper insight into the mechanism of stress response in OP in order to develop a novel detection method or improve crop management. Full article
(This article belongs to the Special Issue Integrative Biology in Plants: From Molecular Stress Response to Systems Biology)
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