International Journal of Molecular Sciences

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5 pages, 205 KiB

Open AccessEditorial

Plant Systems Biology in 2022 and Beyond

by Tsanko Gechev and Veselin Petrov

Int. J. Mol. Sci. 2022, 23(8), 4159; https://doi.org/10.3390/ijms23084159 - 9 Apr 2022

Cited by 2 | Viewed by 2282

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

(This article belongs to the Special Issue Selected Papers from International Conference on Plant Systems Biology and Biotechnology 2020)

Research

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17 pages, 2700 KiB

Open AccessArticle

Hormonomic Changes Driving the Negative Impact of Broomrape on Plant Host Interactions with Arbuscular Mycorrhizal Fungi

by Kiril Mishev, Petre I. Dobrev, Jozef Lacek, Roberta Filepová, Bistra Yuperlieva-Mateeva, Anelia Kostadinova and Tsveta Hristeva

Int. J. Mol. Sci. 2021, 22(24), 13677; https://doi.org/10.3390/ijms222413677 - 20 Dec 2021

Cited by 15 | Viewed by 3603

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

(This article belongs to the Special Issue Selected Papers from International Conference on Plant Systems Biology and Biotechnology 2020)

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23 pages, 6538 KiB

Open AccessArticle

Genotyping by Sequencing Reveals Genetic Relatedness of Southwestern U.S. Blue Maize Landraces

by Amol N. Nankar and Richard C. Pratt

Int. J. Mol. Sci. 2021, 22(7), 3436; https://doi.org/10.3390/ijms22073436 - 26 Mar 2021

Cited by 5 | Viewed by 2745

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

(This article belongs to the Special Issue Selected Papers from International Conference on Plant Systems Biology and Biotechnology 2020)

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15 pages, 1923 KiB

Open AccessArticle

Biotechnologically-Produced Myconoside and Calceolarioside E Induce Nrf2 Expression in Neutrophils

by Kristiana M. Amirova, Petya A. Dimitrova, Andrey S. Marchev, Slaveya V. Krustanova, Svetlana D. Simova, Kalina I. Alipieva and Milen I. Georgiev

Int. J. Mol. Sci. 2021, 22(4), 1759; https://doi.org/10.3390/ijms22041759 - 10 Feb 2021

Cited by 12 | Viewed by 3925

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

(This article belongs to the Special Issue Selected Papers from International Conference on Plant Systems Biology and Biotechnology 2020)

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28 pages, 4727 KiB

Open AccessArticle

Priming with a Seaweed Extract Strongly Improves Drought Tolerance in Arabidopsis

by Fiaz Rasul, Saurabh Gupta, Justyna Jadwiga Olas, Tsanko Gechev, Neerakkal Sujeeth and Bernd Mueller-Roeber

Int. J. Mol. Sci. 2021, 22(3), 1469; https://doi.org/10.3390/ijms22031469 - 2 Feb 2021

Cited by 46 | Viewed by 6634

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

(This article belongs to the Special Issue Selected Papers from International Conference on Plant Systems Biology and Biotechnology 2020)

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16 pages, 3092 KiB

Open AccessArticle

Caffeic and Chlorogenic Acids Synergistically Activate Browning Program in Human Adipocytes: Implications of AMPK- and PPAR-Mediated Pathways

by Liliya V. Vasileva, Martina S. Savova, Kristiana M. Amirova, Zhivka Balcheva-Sivenova, Claudio Ferrante, Giustino Orlando, Martin Wabitsch and Milen I. Georgiev

Int. J. Mol. Sci. 2020, 21(24), 9740; https://doi.org/10.3390/ijms21249740 - 21 Dec 2020

Cited by 43 | Viewed by 5231

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

(This article belongs to the Special Issue Selected Papers from International Conference on Plant Systems Biology and Biotechnology 2020)

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27 pages, 9049 KiB

Open AccessArticle

Comparative Analysis of ROS Network Genes in Extremophile Eukaryotes

by Rafe Lyall, Zoran Nikoloski and Tsanko Gechev

Int. J. Mol. Sci. 2020, 21(23), 9131; https://doi.org/10.3390/ijms21239131 - 30 Nov 2020

Cited by 12 | Viewed by 4139

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

(This article belongs to the Special Issue Selected Papers from International Conference on Plant Systems Biology and Biotechnology 2020)

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19 pages, 3331 KiB

Open AccessArticle

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

by Iñigo Saiz-Fernández, Ivan Milenković, Miroslav Berka, Martin Černý, Michal Tomšovský, Břetislav Brzobohatý and Pavel Kerchev

Int. J. Mol. Sci. 2020, 21(22), 8525; https://doi.org/10.3390/ijms21228525 - 12 Nov 2020

Cited by 22 | Viewed by 3991

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

(This article belongs to the Special Issue Selected Papers from International Conference on Plant Systems Biology and Biotechnology 2020)

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