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Special Issue "Selected Papers from International Conference on Plant Systems Biology and Biotechnology 2020"

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 (31 July 2021) | Viewed by 10386

Special Issue Editors

Prof. Dr. Tsanko S. Gechev
E-Mail Website
Guest Editor
Center of Plant Systems Biology and Biotechnology, Plovdiv University “Paisii Hilendarski”, 40000 Plovdiv, Bulgaria
Interests: abiotic stress; desiccation tolerance; drought; oxidative stress; resurrection plants
Special Issues, Collections and Topics in MDPI journals
Dr. Veselin Petrov
E-Mail
Guest Editor
1. Department of Plant Physiology, Biochemistry and Genetics, Agricultural University,12 Mendeleev Str., 4000 Plovdiv, Bulgaria
2. Center of Plant Systems Biology and Biotechnology (CPSBB), 139 Ruski Blvd., 4000 Plovdiv, Bulgaria
Interests: abiotic stresses; plant biochemistry; signal transduction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Due to their inherent complexity, analyzing only certain aspects of organisms is often insufficient for elucidating status, functions, and behavior. Modern technologies provide the opportunity to use holistic omics approaches to study living objects at the system level.

Plant systems biology has revolutionized our view on how plants grow, develop, and respond to the environment. Nowadays, the use of high-throughput genomics, transcriptomics, proteomics, and metabolomics technologies combined with bioinformatics analysis and mathematical modeling allows us to take an in-depth look into the most intimate molecular mechanisms that govern a plant’s life. Plant systems biology together with plant biotechnology now give us endless opportunities to not only study the biological processes in a complex manner but also improve our utilization of plants as important sources of food and valuable metabolites.

This Special Issue will publish selected papers from scientists who attended the International Conference on Plant Systems Biology and Biotechnology 2020 (ICPSBB 2020). We encourage the submission of experimental articles, but review articles are also possible. Contributions will be initially screened by the Editors for suitability/quality and then sent for peer review.

The deadline for submissions to the ICPSBB 2020 Special Issue is 31 July 2021.

Prof. Dr. Tsanko S. Gechev
Dr. Veselin Petrov
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

  • genomics;
  • abiotic and oxidative stress;
  • plant development;
  • plant biotechnology;
  • molecular biology;
  • evolutionary biology;
  • molecular breeding;
  • plant systems biology;
  • bioinformatics and computational modeling

Published Papers (8 papers)

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Editorial

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Editorial
Plant Systems Biology in 2022 and Beyond
Int. J. Mol. Sci. 2022, 23(8), 4159; https://doi.org/10.3390/ijms23084159 - 09 Apr 2022
Viewed by 285
Abstract
Plants have remarkable plasticity due to their vast genetic potential which interacts with many external factors and developmental signals to govern development and adaptation to changing environments [...] Full article

Research

Jump to: Editorial

Article
Hormonomic Changes Driving the Negative Impact of Broomrape on Plant Host Interactions with Arbuscular Mycorrhizal Fungi
Int. J. Mol. Sci. 2021, 22(24), 13677; https://doi.org/10.3390/ijms222413677 - 20 Dec 2021
Cited by 2 | Viewed by 980
Abstract
Belowground interactions of plants with other organisms in the rhizosphere rely on extensive small-molecule communication. Chemical signals released from host plant roots ensure the development of beneficial arbuscular mycorrhizal (AM) fungi which in turn modulate host plant growth and stress tolerance. However, parasitic [...] Read more.
Belowground interactions of plants with other organisms in the rhizosphere rely on extensive small-molecule communication. Chemical signals released from host plant roots ensure the development of beneficial arbuscular mycorrhizal (AM) fungi which in turn modulate host plant growth and stress tolerance. However, parasitic plants have adopted the capacity to sense the same signaling molecules and to trigger their own seed germination in the immediate vicinity of host roots. The contribution of AM fungi and parasitic plants to the regulation of phytohormone levels in host plant roots and root exudates remains largely obscure. Here, we studied the hormonome in the model system comprising tobacco as a host plant, Phelipanche spp. as a holoparasitic plant, and the AM fungus Rhizophagus irregularis. Co-cultivation of tobacco with broomrape and AM fungi alone or in combination led to characteristic changes in the levels of endogenous and exuded abscisic acid, indole-3-acetic acid, cytokinins, salicylic acid, and orobanchol-type strigolactones. The hormonal content in exudates of broomrape-infested mycorrhizal roots resembled that in exudates of infested non-mycorrhizal roots and differed from that observed in exudates of non-infested mycorrhizal roots. Moreover, we observed a significant reduction in AM colonization of infested tobacco plants, pointing to a dominant role of the holoparasite within the tripartite system. Full article
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Article
Genotyping by Sequencing Reveals Genetic Relatedness of Southwestern U.S. Blue Maize Landraces
Int. J. Mol. Sci. 2021, 22(7), 3436; https://doi.org/10.3390/ijms22073436 - 26 Mar 2021
Cited by 1 | Viewed by 775
Abstract
Maize has played a key role in the sustenance and cultural traditions of the inhabitants of the southwestern USA for many centuries. Blue maize is an important component of the diverse landraces still cultivated in the region but the degree to which they [...] Read more.
Maize has played a key role in the sustenance and cultural traditions of the inhabitants of the southwestern USA for many centuries. Blue maize is an important component of the diverse landraces still cultivated in the region but the degree to which they are related is unknown. This research was designed to ascertain the genotypic, morphological, and phenotypic diversity of six representative southwestern blue maize landraces. Their genotypic diversity was examined using tunable genotyping-by-sequencing (tGBS™). A total of 81,038 high quality SNPs were identified and obtained through tGBS. A total of 45 morphological and biochemical traits were evaluated at two locations in New Mexico. The varieties Los Lunas High and Flor del Rio were genetically less related with other southwestern landraces whereas diffusion between Navajo Blue, Hopi Blue, Yoeme Blue, and Taos Blue demonstrated that these landraces were genetically related. Phenotypic variability was highest for kernel traits and least for plant traits. Plant, ear, and kernel traits were fairly consistent within and across locations. Principal component analysis and tGBS showed that Corn Belt variety ‘Ohio Blue’ was distinctly different from southwestern landraces. Genotypic analysis displayed that southwestern landraces are genetically closely related, but selection has resulted in differing phenotypes. This study has provided additional insight into the genetic relatedness of southwestern blue maize landraces. Full article
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Article
Biotechnologically-Produced Myconoside and Calceolarioside E Induce Nrf2 Expression in Neutrophils
Int. J. Mol. Sci. 2021, 22(4), 1759; https://doi.org/10.3390/ijms22041759 - 10 Feb 2021
Cited by 2 | Viewed by 1434
Abstract
The pathological manifestation of various diseases can be suppressed by the activation of nuclear factor erythroid 2 p45-related factor 2 (Nrf2), a transcriptional regulator of the cellular redox balance. Haberlea rhodopensis Friv. is a resurrection plant species endemic for Bulgaria, containing biologically active [...] Read more.
The pathological manifestation of various diseases can be suppressed by the activation of nuclear factor erythroid 2 p45-related factor 2 (Nrf2), a transcriptional regulator of the cellular redox balance. Haberlea rhodopensis Friv. is a resurrection plant species endemic for Bulgaria, containing biologically active phenylethanoid glycosides that might possess antioxidant or redox activity. This study aimed to analyze the metabolic profile of in vitro cultured H. rhodopensis and to identify molecules that increase Nrf2 expression in bone marrow neutrophils. Fractions B, D, and E containing myconoside, or myconoside and calceolarioside E in ratios 1:0.6 and 0.25:1 were found to be the most active ones. Fraction B (200 µg/mL) improved neutrophil survival and strongly increased the Nrf2 intracellular level, while D and E, as well as, myconoside and calceolarioside E at the same ratios had a superior effect. Calceolarioside E (32 µg/mL) had stronger activity than myconoside, the effect of which was very similar to that of 2-cyano-3,12-dioxo-oleana-1,9(11)-dien-28-oic acid methyl ester (CDDO-Me), used as a positive control. These data indicate that both molecules, used alone or in combination have stimulatory activity on the endogenous Nrf2 level, indicating their therapeutic potential to regulate the cellular redox homeostasis oxidative stress-associated pathologies. Full article
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Article
Priming with a Seaweed Extract Strongly Improves Drought Tolerance in Arabidopsis
Int. J. Mol. Sci. 2021, 22(3), 1469; https://doi.org/10.3390/ijms22031469 - 02 Feb 2021
Cited by 6 | Viewed by 1585
Abstract
Drought represents a major threat to plants in natural ecosystems and agricultural settings. The biostimulant Super Fifty (SF), produced from the brown alga Ascophyllum nodosum, enables ecologically friendly stress mitigation. We investigated the physiological and whole-genome transcriptome responses of Arabidopsis thaliana to [...] Read more.
Drought represents a major threat to plants in natural ecosystems and agricultural settings. The biostimulant Super Fifty (SF), produced from the brown alga Ascophyllum nodosum, enables ecologically friendly stress mitigation. We investigated the physiological and whole-genome transcriptome responses of Arabidopsis thaliana to drought stress after a treatment with SF. SF strongly decreased drought-induced damage. Accumulation of reactive oxygen species (ROS), which typically stifle plant growth during drought, was reduced in SF-primed plants. Relative water content remained high in SF-treated plants, whilst ion leakage, a measure of cell damage, was reduced compared to controls. Plant growth requires a functional shoot apical meristem (SAM). Expression of a stress-responsive negative growth regulator, RESPONSIVE TO DESICCATION 26 (RD26), was repressed by SF treatment at the SAM, consistent with the model that SF priming maintains the function of the SAM during drought stress. Accordingly, expression of the cell cycle marker gene HISTONE H4 (HIS4) was maintained at the SAMs of SF-primed plants, revealing active cell cycle progression after SF priming during drought. In accordance with this, CYCP2;1, which promotes meristem cell division, was repressed by drought but enhanced by SF. SF also positively affected stomatal behavior to support the tolerance to drought stress. Collectively, our data show that SF priming mitigates multiple cellular processes that otherwise impair plant growth under drought stress, thereby providing a knowledge basis for future research on crops. Full article
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Article
Caffeic and Chlorogenic Acids Synergistically Activate Browning Program in Human Adipocytes: Implications of AMPK- and PPAR-Mediated Pathways
Int. J. Mol. Sci. 2020, 21(24), 9740; https://doi.org/10.3390/ijms21249740 - 21 Dec 2020
Cited by 15 | Viewed by 1905
Abstract
Caffeic acid (CA) and chlorogenic acid (CGA) are phenolic compounds claimed to be responsible for the metabolic effects of coffee and tea consumption. Along with their structural similarities, they share common mechanisms such as activation of the AMP-activated protein kinase (AMPK) signaling. The [...] Read more.
Caffeic acid (CA) and chlorogenic acid (CGA) are phenolic compounds claimed to be responsible for the metabolic effects of coffee and tea consumption. Along with their structural similarities, they share common mechanisms such as activation of the AMP-activated protein kinase (AMPK) signaling. The present study aimed to investigate the anti-obesity potential of CA and CGA as co-treatment in human adipocytes. The molecular interactions of CA and CGA with key adipogenic transcription factors were simulated through an in silico molecular docking approach. The expression levels of white and brown adipocyte markers, as well as genes related to lipid metabolism, were analyzed by real-time quantitative PCR and Western blot analyses. Mechanistically, the CA/CGA combination induced lipolysis, upregulated AMPK and browning gene expression and downregulated peroxisome proliferator-activated receptor γ (PPARγ) at both transcriptional and protein levels. The gene expression profiles of the CA/CGA-co-treated adipocytes strongly resembled brown-like signatures. Major pathways identified included the AMPK- and PPAR-related signaling pathways. Collectively, these findings indicated that CA/CGA co-stimulation exerted a browning-inducing potential superior to that of either compound used alone which merits implementation in obesity management. Further, the obtained data provide additional insights on how CA and CGA modify adipocyte function, differentiation and lipid metabolism. Full article
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Article
Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes
Int. J. Mol. Sci. 2020, 21(23), 9131; https://doi.org/10.3390/ijms21239131 - 30 Nov 2020
Cited by 6 | Viewed by 1264
Abstract
The reactive oxygen species (ROS) gene network, consisting of both ROS-generating and detoxifying enzymes, adjusts ROS levels in response to various stimuli. We performed a cross-kingdom comparison of ROS gene networks to investigate how they have evolved across all Eukaryotes, including protists, fungi, [...] Read more.
The reactive oxygen species (ROS) gene network, consisting of both ROS-generating and detoxifying enzymes, adjusts ROS levels in response to various stimuli. We performed a cross-kingdom comparison of ROS gene networks to investigate how they have evolved across all Eukaryotes, including protists, fungi, plants and animals. We included the genomes of 16 extremotolerant Eukaryotes to gain insight into ROS gene evolution in organisms that experience extreme stress conditions. Our analysis focused on ROS genes found in all Eukaryotes (such as catalases, superoxide dismutases, glutathione reductases, peroxidases and glutathione peroxidase/peroxiredoxins) as well as those specific to certain groups, such as ascorbate peroxidases, dehydroascorbate/monodehydroascorbate reductases in plants and other photosynthetic organisms. ROS-producing NADPH oxidases (NOX) were found in most multicellular organisms, although several NOX-like genes were identified in unicellular or filamentous species. However, despite the extreme conditions experienced by extremophile species, we found no evidence for expansion of ROS-related gene families in these species compared to other Eukaryotes. Tardigrades and rotifers do show ROS gene expansions that could be related to their extreme lifestyles, although a high rate of lineage-specific horizontal gene transfer events, coupled with recent tetraploidy in rotifers, could explain this observation. This suggests that the basal Eukaryotic ROS scavenging systems are sufficient to maintain ROS homeostasis even under the most extreme conditions. Full article
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Article
Integrated Proteomic and Metabolomic Profiling of Phytophthora cinnamomi Attack on Sweet Chestnut (Castanea sativa) Reveals Distinct Molecular Reprogramming Proximal to the Infection Site and Away from It
Int. J. Mol. Sci. 2020, 21(22), 8525; https://doi.org/10.3390/ijms21228525 - 12 Nov 2020
Cited by 10 | Viewed by 1333
Abstract
Phytophthora cinnamomi is one of the most invasive tree pathogens that devastates wild and cultivated forests. Due to its wide host range, knowledge of the infection process at the molecular level is lacking for most of its tree hosts. To expand the repertoire [...] Read more.
Phytophthora cinnamomi is one of the most invasive tree pathogens that devastates wild and cultivated forests. Due to its wide host range, knowledge of the infection process at the molecular level is lacking for most of its tree hosts. To expand the repertoire of studied Phytophthora–woody plant interactions and identify molecular mechanisms that can facilitate discovery of novel ways to control its spread and damaging effects, we focused on the interaction between P. cinnamomi and sweet chestnut (Castanea sativa), an economically important tree for the wood processing industry. By using a combination of proteomics, metabolomics, and targeted hormonal analysis, we mapped the effects of P. cinnamomi attack on stem tissues immediately bordering the infection site and away from it. P. cinnamomi led to a massive reprogramming of the chestnut proteome and accumulation of the stress-related hormones salicylic acid (SA) and jasmonic acid (JA), indicating that stem inoculation can be used as an easily accessible model system to identify novel molecular players in P. cinnamomi pathogenicity. Full article
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