TY  - JOUR
AU  - Pantelić, Ana
AU  - Stevanović, Strahinja
AU  - Milić Komić, Sonja
AU  - Kilibarda, Nataša
AU  - Vidović, Marija
PY  - 2022
UR  - http://rimsi.imsi.bg.ac.rs/handle/123456789/1575
AB  - Ramonda serbica Panc. is an ancient resurrection plant able to survive a long desiccation period and recover metabolic functions upon watering. The accumulation of protective late embryogenesis abundant proteins (LEAPs) is a desiccation tolerance hallmark. To propose their role in R. serbica desiccation tolerance, we structurally characterised LEAPs and evaluated LEA gene expression levels in hydrated and desiccated leaves. By integrating de novo transcriptomics and homologues LEAP domains, 318 R. serbica LEAPs were identified and classified according to their conserved motifs and phylogeny. The in silico analysis revealed that hydrophilic LEA4 proteins exhibited an exceptionally high tendency to form amphipathic α‐helices. The most abundant, atypical LEA2 group contained more hydrophobic proteins predicted to fold into the defined globular domains. Within the desiccation‐upregulated LEA genes, the majority encoded highly disordered DEH1, LEA1, LEA4.2, and LEA4.3 proteins, while the greatest portion of downregulated genes encoded LEA2.3 and LEA2.5 proteins. While dehydrins might chelate metals and bind DNA under water deficit, other intrinsically disordered LEAPs might participate in forming intracellular proteinaceous condensates or adopt amphipathic α‐helical conformation, enabling them to stabilise desiccation‐sensitive proteins and membranes. This comprehensive LEAPs structural characterisation is essential to understanding their function and regulation during desiccation aiming at crop drought tolerance improvement.
PB  - MDPI
T2  - International Journal of Molecular Sciences
T1  - In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc.
IS  - 7
SP  - 3547
VL  - 23
DO  - 10.3390/ijms23073547
ER  - 

@article{
author = "Pantelić, Ana and Stevanović, Strahinja and Milić Komić, Sonja and Kilibarda, Nataša and Vidović, Marija",
year = "2022",
abstract = "Ramonda serbica Panc. is an ancient resurrection plant able to survive a long desiccation period and recover metabolic functions upon watering. The accumulation of protective late embryogenesis abundant proteins (LEAPs) is a desiccation tolerance hallmark. To propose their role in R. serbica desiccation tolerance, we structurally characterised LEAPs and evaluated LEA gene expression levels in hydrated and desiccated leaves. By integrating de novo transcriptomics and homologues LEAP domains, 318 R. serbica LEAPs were identified and classified according to their conserved motifs and phylogeny. The in silico analysis revealed that hydrophilic LEA4 proteins exhibited an exceptionally high tendency to form amphipathic α‐helices. The most abundant, atypical LEA2 group contained more hydrophobic proteins predicted to fold into the defined globular domains. Within the desiccation‐upregulated LEA genes, the majority encoded highly disordered DEH1, LEA1, LEA4.2, and LEA4.3 proteins, while the greatest portion of downregulated genes encoded LEA2.3 and LEA2.5 proteins. While dehydrins might chelate metals and bind DNA under water deficit, other intrinsically disordered LEAPs might participate in forming intracellular proteinaceous condensates or adopt amphipathic α‐helical conformation, enabling them to stabilise desiccation‐sensitive proteins and membranes. This comprehensive LEAPs structural characterisation is essential to understanding their function and regulation during desiccation aiming at crop drought tolerance improvement.",
publisher = "MDPI",
journal = "International Journal of Molecular Sciences",
title = "In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc.",
number = "7",
pages = "3547",
volume = "23",
doi = "10.3390/ijms23073547"
}

Pantelić, A., Stevanović, S., Milić Komić, S., Kilibarda, N.,& Vidović, M.. (2022). In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc.. in International Journal of Molecular Sciences
MDPI., 23(7), 3547.
https://doi.org/10.3390/ijms23073547

Pantelić A, Stevanović S, Milić Komić S, Kilibarda N, Vidović M. In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc.. in International Journal of Molecular Sciences. 2022;23(7):3547.
doi:10.3390/ijms23073547 .

Pantelić, Ana, Stevanović, Strahinja, Milić Komić, Sonja, Kilibarda, Nataša, Vidović, Marija, "In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc." in International Journal of Molecular Sciences, 23, no. 7 (2022):3547,
https://doi.org/10.3390/ijms23073547 . .

TY  - CONF
AU  - Milić Komić, Sonja
AU  - Stevanović, Strahinja
AU  - Vidović, Marija
PY  - 2021
UR  - http://rimsi.imsi.bg.ac.rs/handle/123456789/1491
AB  - Ramonda serbica Panc. is a resurrection plant that can survive long desiccation
periods (extreme loss of cellular water). The accumulation of late embryogenesis abundant
proteins (LEAPs) is a crucial step in desiccation tolerance mechanism. Based on in vitro studies,
LEAPs can be involved in antioxidative defense, ion sequestration, structural stabilization
of both membranes and enzymes during freezing or drying, while by forming intracellular
proteinaceous condensates they increase structural integrity and intracellular viscosity of cells
during desiccation. Here we investigated the antioxidative potential of LEAPs identified by de
novo transcriptomics of R. serbica, based on their primary and secondary confirmation. In our
previous work [1], we displayed the antioxidative capacity of 20 free proteogenic amino acids
(FAA) through determining their hydroxyl radical (•
OH, generated in Fenton reaction) scavenging
rate by using electron paramagnetic resonance. These results served as a basis for generating
a model for prediction of •
OH scavenging activity for selected proteins. In addition, the model
was built based on protein primary sequences, hydrophobicity, 3D structure and predicted
solvent accessible area. Manually curated data for peptides and proteins with experimentally
determined •
OH scavenging rate were used for training and testing. The model was fed into
machine learning algorithm and •
OH scavenging potential scale was created using IC50 values.
By applying our model, we classified 164 LEAPs according to their potential for •
OH scavenging.
Further work will focus on the experimental evaluation of the obtained model by measuring of
the rate of •
OH scavenging in the presence of recombinantly produced LEAPs.
PB  - Elsevier Science Inc, New York
C3  - Free Radical Biology and Medicine
T1  - Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica - in silico approach
VL  - 177
UR  - https://hdl.handle.net/21.15107/rcub_rimsi_1491
ER  - 

@conference{
author = "Milić Komić, Sonja and Stevanović, Strahinja and Vidović, Marija",
year = "2021",
abstract = "Ramonda serbica Panc. is a resurrection plant that can survive long desiccation
periods (extreme loss of cellular water). The accumulation of late embryogenesis abundant
proteins (LEAPs) is a crucial step in desiccation tolerance mechanism. Based on in vitro studies,
LEAPs can be involved in antioxidative defense, ion sequestration, structural stabilization
of both membranes and enzymes during freezing or drying, while by forming intracellular
proteinaceous condensates they increase structural integrity and intracellular viscosity of cells
during desiccation. Here we investigated the antioxidative potential of LEAPs identified by de
novo transcriptomics of R. serbica, based on their primary and secondary confirmation. In our
previous work [1], we displayed the antioxidative capacity of 20 free proteogenic amino acids
(FAA) through determining their hydroxyl radical (•
OH, generated in Fenton reaction) scavenging
rate by using electron paramagnetic resonance. These results served as a basis for generating
a model for prediction of •
OH scavenging activity for selected proteins. In addition, the model
was built based on protein primary sequences, hydrophobicity, 3D structure and predicted
solvent accessible area. Manually curated data for peptides and proteins with experimentally
determined •
OH scavenging rate were used for training and testing. The model was fed into
machine learning algorithm and •
OH scavenging potential scale was created using IC50 values.
By applying our model, we classified 164 LEAPs according to their potential for •
OH scavenging.
Further work will focus on the experimental evaluation of the obtained model by measuring of
the rate of •
OH scavenging in the presence of recombinantly produced LEAPs.",
publisher = "Elsevier Science Inc, New York",
journal = "Free Radical Biology and Medicine",
title = "Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica - in silico approach",
volume = "177",
url = "https://hdl.handle.net/21.15107/rcub_rimsi_1491"
}

Milić Komić, S., Stevanović, S.,& Vidović, M.. (2021). Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica - in silico approach. in Free Radical Biology and Medicine
Elsevier Science Inc, New York., 177.
https://hdl.handle.net/21.15107/rcub_rimsi_1491

Milić Komić S, Stevanović S, Vidović M. Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica - in silico approach. in Free Radical Biology and Medicine. 2021;177.
https://hdl.handle.net/21.15107/rcub_rimsi_1491 .

Milić Komić, Sonja, Stevanović, Strahinja, Vidović, Marija, "Hydroxyl radical scavenging potential of the late embryogenesis abundant proteins (LEA) proteins from Ramonda serbica - in silico approach" in Free Radical Biology and Medicine, 177 (2021),
https://hdl.handle.net/21.15107/rcub_rimsi_1491 .