TY  - JOUR
AU  - Nikolić, Ivana
AU  - Samardžić, Jelena
AU  - Stevanović, Strahinja
AU  - Miljuš-Đukić, Jovanka
AU  - Milisavljević, Mira
AU  - Timotijević, Gordana
PY  - 2023
UR  - https://www.mdpi.com/1422-0067/24/3/2442
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1883
AB  - Global climate change has a detrimental effect on plant growth and health, causing serious losses in agriculture. Investigation of the molecular mechanisms of plant responses to various environmental pressures and the generation of plants tolerant to abiotic stress are imperative to modern plant science. In this paper, we focus on the application of the well-established technology CRISPR/Cas9 genome editing to better understand the functioning of the intrinsically disordered protein DSS1 in plant response to oxidative stress. The Arabidopsis genome contains two highly homologous DSS1 genes, AtDSS1(I) and AtDSS1(V). This study was designed to identify the functional differences between AtDSS1s, focusing on their potential roles in oxidative stress. We generated single dss1(I) and dss1(V) mutant lines of both Arabidopsis DSS1 genes using CRISPR/Cas9 technology. The homozygous mutant lines with large indels (dss1(I)del25 and dss1(V)ins18) were phenotypically characterized during plant development and their sensitivity to oxidative stress was analyzed. The characterization of mutant lines revealed differences in root and stem lengths, and rosette area size. Plants with a disrupted AtDSS1(V) gene exhibited lower survival rates and increased levels of oxidized proteins in comparison to WT plants exposed to oxidative stress induced by hydrogen peroxide. In this work, the dss1 double mutant was not obtained due to embryonic lethality. These results suggest that the DSS1(V) protein could be an important molecular component in plant abiotic stress response
T2  - International Journal of Molecular Sciences
T2  - International Journal of Molecular Sciences
T1  - CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response
IS  - 3
SP  - 2442
VL  - 24
DO  - 10.3390/ijms24032442
ER  - 

@article{
author = "Nikolić, Ivana and Samardžić, Jelena and Stevanović, Strahinja and Miljuš-Đukić, Jovanka and Milisavljević, Mira and Timotijević, Gordana",
year = "2023",
abstract = "Global climate change has a detrimental effect on plant growth and health, causing serious losses in agriculture. Investigation of the molecular mechanisms of plant responses to various environmental pressures and the generation of plants tolerant to abiotic stress are imperative to modern plant science. In this paper, we focus on the application of the well-established technology CRISPR/Cas9 genome editing to better understand the functioning of the intrinsically disordered protein DSS1 in plant response to oxidative stress. The Arabidopsis genome contains two highly homologous DSS1 genes, AtDSS1(I) and AtDSS1(V). This study was designed to identify the functional differences between AtDSS1s, focusing on their potential roles in oxidative stress. We generated single dss1(I) and dss1(V) mutant lines of both Arabidopsis DSS1 genes using CRISPR/Cas9 technology. The homozygous mutant lines with large indels (dss1(I)del25 and dss1(V)ins18) were phenotypically characterized during plant development and their sensitivity to oxidative stress was analyzed. The characterization of mutant lines revealed differences in root and stem lengths, and rosette area size. Plants with a disrupted AtDSS1(V) gene exhibited lower survival rates and increased levels of oxidized proteins in comparison to WT plants exposed to oxidative stress induced by hydrogen peroxide. In this work, the dss1 double mutant was not obtained due to embryonic lethality. These results suggest that the DSS1(V) protein could be an important molecular component in plant abiotic stress response",
journal = "International Journal of Molecular Sciences, International Journal of Molecular Sciences",
title = "CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response",
number = "3",
pages = "2442",
volume = "24",
doi = "10.3390/ijms24032442"
}

Nikolić, I., Samardžić, J., Stevanović, S., Miljuš-Đukić, J., Milisavljević, M.,& Timotijević, G.. (2023). CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response. in International Journal of Molecular Sciences, 24(3), 2442.
https://doi.org/10.3390/ijms24032442

Nikolić I, Samardžić J, Stevanović S, Miljuš-Đukić J, Milisavljević M, Timotijević G. CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response. in International Journal of Molecular Sciences. 2023;24(3):2442.
doi:10.3390/ijms24032442 .

Nikolić, Ivana, Samardžić, Jelena, Stevanović, Strahinja, Miljuš-Đukić, Jovanka, Milisavljević, Mira, Timotijević, Gordana, "CRISPR/Cas9-Targeted Disruption of Two Highly Homologous Arabidopsis thaliana DSS1 Genes with Roles in Development and the Oxidative Stress Response" in International Journal of Molecular Sciences, 24, no. 3 (2023):2442,
https://doi.org/10.3390/ijms24032442 . .

TY  - CONF
AU  - Pantelić, Ana
AU  - Stevanović, Strahinja
AU  - Milić Komić, Sonja
AU  - Kilibarda, Nataša
AU  - Vidović, Marija
PY  - 2023
UR  - https://belbi.bg.ac.rs/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/2008
AB  - Ramonda serbica Panc. is an ancient resurrection plant, that survives a long desiccation period
and fully recovers metabolic functions upon watering. The main characteristic of desiccationtolerant
plant species is their ability to accumulate protective late embryogenesis abounded
protein (LEAPs). To propose their role in R. serbica desiccation tolerance we structurally
analysed LEAPs in hydrated and desiccated leaves.
According to transcriptomics, 318 LEAPs were identified and classified into seven family
groups based on protein BLAST analysis and conserved motifs (Pfam). The largest LEAPs
belonged to the LEA2 and LEA4 protein family groups. We employed online tools to analyse
physicochemical characteristics (Expasy, ProtParam, BioPython, GRAVY calculator), disorder
propensity, and characterization protein structures (FELLS, JPred, SOPMA, PsiPred, Phyre2,
Espritz-DisProt, Espritz-X, Iupred, TMHMM, +Heliquest).
The most abundant, atypical LEA2 group containing 127, mostly hydrophobic proteins, was
divided into five subgroups. Members of this group were predicted to fold into globular
domains, β-barrel at the C-terminus, followed by transmembrane hydrophobic-helices and
disordered N-terminal regions. Results indicated the possible involvement in the protection
of the chloroplastic membranes.
The LEA4 group exhibited an exceptionally high tendency to form amphipathic α-helices and
simultaneously had a high disorder propensity. This group is made of 96 proteins, classified into 3
subgroups. The high content of polar and charged amino acids (lysine, glutamate, and aspartate) is
characteristic of this group. Motifs corresponding to the R. serbica LEA4 protein family group folded
into A-type α-helices that contained positive, negative, and hydrophobic surfaces. Based on previous
knowledge, the possible functions of the LEA2 and LEA4 groups are discussed with significant
implications on cell preservation technology and the improvement of crop drought tolerance.
PB  - Belgrade : Institute of molecular genetics and genetic engineering
C3  - 4th Belgrade Bioinformatics Conference
T1  - Two contrasting late embryogenesis abounded protein family groups of Ramonda serbica Panc.
EP  - 68
SP  - 68
VL  - 4
UR  - https://hdl.handle.net/21.15107/rcub_imagine_2008
ER  - 

@conference{
author = "Pantelić, Ana and Stevanović, Strahinja and Milić Komić, Sonja and Kilibarda, Nataša and Vidović, Marija",
year = "2023",
abstract = "Ramonda serbica Panc. is an ancient resurrection plant, that survives a long desiccation period
and fully recovers metabolic functions upon watering. The main characteristic of desiccationtolerant
plant species is their ability to accumulate protective late embryogenesis abounded
protein (LEAPs). To propose their role in R. serbica desiccation tolerance we structurally
analysed LEAPs in hydrated and desiccated leaves.
According to transcriptomics, 318 LEAPs were identified and classified into seven family
groups based on protein BLAST analysis and conserved motifs (Pfam). The largest LEAPs
belonged to the LEA2 and LEA4 protein family groups. We employed online tools to analyse
physicochemical characteristics (Expasy, ProtParam, BioPython, GRAVY calculator), disorder
propensity, and characterization protein structures (FELLS, JPred, SOPMA, PsiPred, Phyre2,
Espritz-DisProt, Espritz-X, Iupred, TMHMM, +Heliquest).
The most abundant, atypical LEA2 group containing 127, mostly hydrophobic proteins, was
divided into five subgroups. Members of this group were predicted to fold into globular
domains, β-barrel at the C-terminus, followed by transmembrane hydrophobic-helices and
disordered N-terminal regions. Results indicated the possible involvement in the protection
of the chloroplastic membranes.
The LEA4 group exhibited an exceptionally high tendency to form amphipathic α-helices and
simultaneously had a high disorder propensity. This group is made of 96 proteins, classified into 3
subgroups. The high content of polar and charged amino acids (lysine, glutamate, and aspartate) is
characteristic of this group. Motifs corresponding to the R. serbica LEA4 protein family group folded
into A-type α-helices that contained positive, negative, and hydrophobic surfaces. Based on previous
knowledge, the possible functions of the LEA2 and LEA4 groups are discussed with significant
implications on cell preservation technology and the improvement of crop drought tolerance.",
publisher = "Belgrade : Institute of molecular genetics and genetic engineering",
journal = "4th Belgrade Bioinformatics Conference",
title = "Two contrasting late embryogenesis abounded protein family groups of Ramonda serbica Panc.",
pages = "68-68",
volume = "4",
url = "https://hdl.handle.net/21.15107/rcub_imagine_2008"
}

Pantelić, A., Stevanović, S., Milić Komić, S., Kilibarda, N.,& Vidović, M.. (2023). Two contrasting late embryogenesis abounded protein family groups of Ramonda serbica Panc.. in 4th Belgrade Bioinformatics Conference
Belgrade : Institute of molecular genetics and genetic engineering., 4, 68-68.
https://hdl.handle.net/21.15107/rcub_imagine_2008

Pantelić A, Stevanović S, Milić Komić S, Kilibarda N, Vidović M. Two contrasting late embryogenesis abounded protein family groups of Ramonda serbica Panc.. in 4th Belgrade Bioinformatics Conference. 2023;4:68-68.
https://hdl.handle.net/21.15107/rcub_imagine_2008 .

Pantelić, Ana, Stevanović, Strahinja, Milić Komić, Sonja, Kilibarda, Nataša, Vidović, Marija, "Two contrasting late embryogenesis abounded protein family groups of Ramonda serbica Panc." in 4th Belgrade Bioinformatics Conference, 4 (2023):68-68,
https://hdl.handle.net/21.15107/rcub_imagine_2008 .

TY  - CONF
AU  - Pantelić, Ana
AU  - Stevanović, Strahinja
AU  - Milić, Dejana
AU  - Milić Komić, Sonja
AU  - Kilibarda, Nataša
AU  - Vidović, Marija
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1846
AB  - An ancient resurrection plant Ramonda serbica Panc. is able to survive a long desiccation period
and reestablish metabolic activity upon watering. A hallmark of desiccation tolerance in the resurrection
species is the accumulation of protective late embryogenesis abundant proteins (LEAPs).
These intrinsically disordered proteins (IDPs) may stabilize the correct structure of proteins and
membranes during cellular dehydration. The aim of our study was to assess LEA genes’ expression
levels in hydrated (HL) and desiccated leaves (DL) and to identify, characterise, and estimate
the potential role of R. serbica LEAPs in desiccation tolerance. In total, 318 LEAPs from HL and DL
were identified and classified into the seven LEA protein family groups ranging from LEA1-LEA5,
seed maturation proteins (SMPs), and dehydrins (DEH). Analysis of the physicochemical properties,
motif architecture, secondary structure, homology, and phylogenetic relationships demonstrated
that R. serbica LEAPs greatly differed among the LEA family groups. The most abundant LEA2
proteins (mostly downregulated upon desiccation) exhibited lower hydrophilicity and propensity
to fold into organised globular domains. Oppositely, hydrophilic LEA4 proteins tended to form
amphipathic, A-type, α-helices. Most of desiccation-upregulated LEA genes encoded highly disordered
DEH1, LEA1, LEA4.2, and LEA4.3 proteins. While dehydrins might chelate metals and bind
DNA under water deficit, other ID LEAPs (e.g. LEA1, LEA3, LEA4) might participate in forming intracellular
proteinaceous condensates or adopt amphipathic α-helical conformation, enabling them
to stabilise desiccation-sensitive proteins and membranes. Taken together, possible functions of
LEAPs are discussed with significant implications on drought tolerance improvement of crops
grown in arid areas.
PB  - Serbian Plant Physiology Society Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade Faculty of Biology, University of Belgrade
C3  - 4th International Conference on Plant Biology and 23rd SPPS Meeting
T1  - Late embryogenesis abundant (LEA) proteins in Ramonda serbica Panc identification, classification and structural characterization
SP  - 95
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1846
ER  - 

@conference{
author = "Pantelić, Ana and Stevanović, Strahinja and Milić, Dejana and Milić Komić, Sonja and Kilibarda, Nataša and Vidović, Marija",
year = "2022",
abstract = "An ancient resurrection plant Ramonda serbica Panc. is able to survive a long desiccation period
and reestablish metabolic activity upon watering. A hallmark of desiccation tolerance in the resurrection
species is the accumulation of protective late embryogenesis abundant proteins (LEAPs).
These intrinsically disordered proteins (IDPs) may stabilize the correct structure of proteins and
membranes during cellular dehydration. The aim of our study was to assess LEA genes’ expression
levels in hydrated (HL) and desiccated leaves (DL) and to identify, characterise, and estimate
the potential role of R. serbica LEAPs in desiccation tolerance. In total, 318 LEAPs from HL and DL
were identified and classified into the seven LEA protein family groups ranging from LEA1-LEA5,
seed maturation proteins (SMPs), and dehydrins (DEH). Analysis of the physicochemical properties,
motif architecture, secondary structure, homology, and phylogenetic relationships demonstrated
that R. serbica LEAPs greatly differed among the LEA family groups. The most abundant LEA2
proteins (mostly downregulated upon desiccation) exhibited lower hydrophilicity and propensity
to fold into organised globular domains. Oppositely, hydrophilic LEA4 proteins tended to form
amphipathic, A-type, α-helices. Most of desiccation-upregulated LEA genes encoded highly disordered
DEH1, LEA1, LEA4.2, and LEA4.3 proteins. While dehydrins might chelate metals and bind
DNA under water deficit, other ID LEAPs (e.g. LEA1, LEA3, LEA4) might participate in forming intracellular
proteinaceous condensates or adopt amphipathic α-helical conformation, enabling them
to stabilise desiccation-sensitive proteins and membranes. Taken together, possible functions of
LEAPs are discussed with significant implications on drought tolerance improvement of crops
grown in arid areas.",
publisher = "Serbian Plant Physiology Society Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade Faculty of Biology, University of Belgrade",
journal = "4th International Conference on Plant Biology and 23rd SPPS Meeting",
title = "Late embryogenesis abundant (LEA) proteins in Ramonda serbica Panc identification, classification and structural characterization",
pages = "95",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1846"
}

Pantelić, A., Stevanović, S., Milić, D., Milić Komić, S., Kilibarda, N.,& Vidović, M.. (2022). Late embryogenesis abundant (LEA) proteins in Ramonda serbica Panc identification, classification and structural characterization. in 4th International Conference on Plant Biology and 23rd SPPS Meeting
Serbian Plant Physiology Society Institute for Biological Research “Siniša Stanković” – National Institute of Republic of Serbia, University of Belgrade Faculty of Biology, University of Belgrade., 95.
https://hdl.handle.net/21.15107/rcub_imagine_1846

Pantelić A, Stevanović S, Milić D, Milić Komić S, Kilibarda N, Vidović M. Late embryogenesis abundant (LEA) proteins in Ramonda serbica Panc identification, classification and structural characterization. in 4th International Conference on Plant Biology and 23rd SPPS Meeting. 2022;:95.
https://hdl.handle.net/21.15107/rcub_imagine_1846 .

Pantelić, Ana, Stevanović, Strahinja, Milić, Dejana, Milić Komić, Sonja, Kilibarda, Nataša, Vidović, Marija, "Late embryogenesis abundant (LEA) proteins in Ramonda serbica Panc identification, classification and structural characterization" in 4th International Conference on Plant Biology and 23rd SPPS Meeting (2022):95,
https://hdl.handle.net/21.15107/rcub_imagine_1846 .

TY  - JOUR
AU  - Pantelić, Ana
AU  - Stevanović, Strahinja
AU  - Komić, Sonja Milic
AU  - Kilibarda, Nataša
AU  - Vidović, Marija
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1560
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 alpha-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 alpha-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, Basel
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
VL  - 23
DO  - 10.3390/ijms23073547
ER  - 

@article{
author = "Pantelić, Ana and Stevanović, Strahinja and Komić, Sonja Milic 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 alpha-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 alpha-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, Basel",
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",
volume = "23",
doi = "10.3390/ijms23073547"
}

Pantelić, A., Stevanović, S., Komić, S. M., 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, Basel., 23(7).
https://doi.org/10.3390/ijms23073547

Pantelić A, Stevanović S, Komić SM, 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).
doi:10.3390/ijms23073547 .

Pantelić, Ana, Stevanović, Strahinja, Komić, Sonja Milic, 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),
https://doi.org/10.3390/ijms23073547 . .

TY  - DATA
AU  - Pantelić, Ana
AU  - Stevanović, Strahinja
AU  - Milić-Komić, Sonja
AU  - Kilibarda, Nataša
AU  - Vidović, Marija
PY  - 2022
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1853
AB  - Ramonda serbica de novo transcriptome database
PB  - MDPI
T2  - International Journal of Molecular Science
T1  - Ramonda serbica de novo transcriptome database related to the article: Pantelic, A.; Stevanović, S.; Milic-Komic, S.; Kilibarda, N.; Vidovic, M. Characterization and expression analysis of the late embryogenesis abundant (LEA) proteins family in hydrated and desiccated Ramonda serbica Panc. leaves
VL  - n/a
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1853
ER  - 

@misc{
author = "Pantelić, Ana and Stevanović, Strahinja and Milić-Komić, Sonja and Kilibarda, Nataša and Vidović, Marija",
year = "2022",
abstract = "Ramonda serbica de novo transcriptome database",
publisher = "MDPI",
journal = "International Journal of Molecular Science",
title = "Ramonda serbica de novo transcriptome database related to the article: Pantelic, A.; Stevanović, S.; Milic-Komic, S.; Kilibarda, N.; Vidovic, M. Characterization and expression analysis of the late embryogenesis abundant (LEA) proteins family in hydrated and desiccated Ramonda serbica Panc. leaves",
volume = "n/a",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1853"
}

Pantelić, A., Stevanović, S., Milić-Komić, S., Kilibarda, N.,& Vidović, M.. (2022). Ramonda serbica de novo transcriptome database related to the article: Pantelic, A.; Stevanović, S.; Milic-Komic, S.; Kilibarda, N.; Vidovic, M. Characterization and expression analysis of the late embryogenesis abundant (LEA) proteins family in hydrated and desiccated Ramonda serbica Panc. leaves. in International Journal of Molecular Science
MDPI., n/a.
https://hdl.handle.net/21.15107/rcub_imagine_1853

Pantelić A, Stevanović S, Milić-Komić S, Kilibarda N, Vidović M. Ramonda serbica de novo transcriptome database related to the article: Pantelic, A.; Stevanović, S.; Milic-Komic, S.; Kilibarda, N.; Vidovic, M. Characterization and expression analysis of the late embryogenesis abundant (LEA) proteins family in hydrated and desiccated Ramonda serbica Panc. leaves. in International Journal of Molecular Science. 2022;n/a.
https://hdl.handle.net/21.15107/rcub_imagine_1853 .

Pantelić, Ana, Stevanović, Strahinja, Milić-Komić, Sonja, Kilibarda, Nataša, Vidović, Marija, "Ramonda serbica de novo transcriptome database related to the article: Pantelic, A.; Stevanović, S.; Milic-Komic, S.; Kilibarda, N.; Vidovic, M. Characterization and expression analysis of the late embryogenesis abundant (LEA) proteins family in hydrated and desiccated Ramonda serbica Panc. leaves" in International Journal of Molecular Science, n/a (2022),
https://hdl.handle.net/21.15107/rcub_imagine_1853 .

TY  - CONF
AU  - Pantelić, Ana
AU  - Stevanović, Strahinja
AU  - Kilibarda, Nataša
AU  - Vidović, Marija
PY  - 2021
UR  - http://ojs.pmf.uns.ac.rs/index.php/dbe_serbica/index
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1856
AB  - An extreme loss of cellular water or desiccation (5-10% of relative water content) leads to protein denaturation, aggregation and degradation, and affects the fluidity of membrane lipids resulting in loss of membrane integrity [1]. The essential constituents of vegetative desiccation tolerance in so-called resurrection plants are late embryogenesis abundant proteins (LEAPs). This heterogeneous group of anhydrobiosis-related intrinsically disordered proteins forms mostly random conformation when fully hydrated, turning into compact α-helices during desiccation [2]. Based on in vitro studies, LEAPs can be involved in water binding, ion sequestration, stabilization of both membrane 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 identify 164 members of LEA gene family in endemic and relict resurrection species Ramonda serbica by integrating previously done de novo transcriptome and homologues protein motifs. Identified LEAPs were classification into six groups according to Protein family (PFAM) database and the most populated group was LEA4 containing 47% of total identified LEAPs. By using four secondary structure predictors, we showed that this group exhibited a high propensity to form amphipathic α-helices (81% of total sequence length is predicted to form α-helical structure). This implies that charged residues might be exposed to the solvent, while hydrophobic amino acids might interact with lipid bilayers or with other target proteins in the cell. In addition, as predicted by several bioinformatic tools, more than 70% of identified LEAPs were found to be highly disordered (~64%). Structural characterization of LEAPs is a key to understand their function and regulation of their intrinsic structural disorder-to-order transition during desiccation. These findings will promote transformative advancements in various fields, such as the development of new strategies in neurodegenerative disorders, cell preservation technology and the improvement of crop drought tolerance.
PB  - Novi Sad : Faculty of Sciences, Department of Biology and Ecology
C3  - Biologia Serbica
T1  - De Novo Transcriptome Sequencing of Ramonda serbica: Identification of Late Embryogenesis Abundant Proteins
EP  - 65
IS  - 1 (spec. ed.)
SP  - 65
VL  - 43
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1856
ER  - 

@conference{
author = "Pantelić, Ana and Stevanović, Strahinja and Kilibarda, Nataša and Vidović, Marija",
year = "2021",
abstract = "An extreme loss of cellular water or desiccation (5-10% of relative water content) leads to protein denaturation, aggregation and degradation, and affects the fluidity of membrane lipids resulting in loss of membrane integrity [1]. The essential constituents of vegetative desiccation tolerance in so-called resurrection plants are late embryogenesis abundant proteins (LEAPs). This heterogeneous group of anhydrobiosis-related intrinsically disordered proteins forms mostly random conformation when fully hydrated, turning into compact α-helices during desiccation [2]. Based on in vitro studies, LEAPs can be involved in water binding, ion sequestration, stabilization of both membrane 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 identify 164 members of LEA gene family in endemic and relict resurrection species Ramonda serbica by integrating previously done de novo transcriptome and homologues protein motifs. Identified LEAPs were classification into six groups according to Protein family (PFAM) database and the most populated group was LEA4 containing 47% of total identified LEAPs. By using four secondary structure predictors, we showed that this group exhibited a high propensity to form amphipathic α-helices (81% of total sequence length is predicted to form α-helical structure). This implies that charged residues might be exposed to the solvent, while hydrophobic amino acids might interact with lipid bilayers or with other target proteins in the cell. In addition, as predicted by several bioinformatic tools, more than 70% of identified LEAPs were found to be highly disordered (~64%). Structural characterization of LEAPs is a key to understand their function and regulation of their intrinsic structural disorder-to-order transition during desiccation. These findings will promote transformative advancements in various fields, such as the development of new strategies in neurodegenerative disorders, cell preservation technology and the improvement of crop drought tolerance.",
publisher = "Novi Sad : Faculty of Sciences, Department of Biology and Ecology",
journal = "Biologia Serbica",
title = "De Novo Transcriptome Sequencing of Ramonda serbica: Identification of Late Embryogenesis Abundant Proteins",
pages = "65-65",
number = "1 (spec. ed.)",
volume = "43",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1856"
}

Pantelić, A., Stevanović, S., Kilibarda, N.,& Vidović, M.. (2021). De Novo Transcriptome Sequencing of Ramonda serbica: Identification of Late Embryogenesis Abundant Proteins. in Biologia Serbica
Novi Sad : Faculty of Sciences, Department of Biology and Ecology., 43(1 (spec. ed.)), 65-65.
https://hdl.handle.net/21.15107/rcub_imagine_1856

Pantelić A, Stevanović S, Kilibarda N, Vidović M. De Novo Transcriptome Sequencing of Ramonda serbica: Identification of Late Embryogenesis Abundant Proteins. in Biologia Serbica. 2021;43(1 (spec. ed.)):65-65.
https://hdl.handle.net/21.15107/rcub_imagine_1856 .

Pantelić, Ana, Stevanović, Strahinja, Kilibarda, Nataša, Vidović, Marija, "De Novo Transcriptome Sequencing of Ramonda serbica: Identification of Late Embryogenesis Abundant Proteins" in Biologia Serbica, 43, no. 1 (spec. ed.) (2021):65-65,
https://hdl.handle.net/21.15107/rcub_imagine_1856 .

TY  - CONF
AU  - Vidović, Marija
AU  - Stevanović, Strahinja
AU  - Pantelić, Ana
AU  - Veljović-Jovanović, Sonja
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1855
AB  - Ramonda serbica Panc. is a resurrection plant that can survive a long period of severe dehydrationdesiccation.Desiccation induces cellular membrane integrity loss, protein aggregation, and denaturation, as well asaccelerated generation of reactive oxygen species. However, R. serbica can fully recover its metabolic functionsalready one day upon watering [1].Aim: to obtain more insight into the mechanisms of desiccation tolerance in R. serbica by differential de novotranscriptomics of hydrated (HL) and desiccated leaves (DL).
C3  - Belgrade BioInformatics Conference 2021, 21-25 June, Vinča, Serbia
T1  - De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1855
ER  - 

@conference{
author = "Vidović, Marija and Stevanović, Strahinja and Pantelić, Ana and Veljović-Jovanović, Sonja",
year = "2021",
abstract = "Ramonda serbica Panc. is a resurrection plant that can survive a long period of severe dehydrationdesiccation.Desiccation induces cellular membrane integrity loss, protein aggregation, and denaturation, as well asaccelerated generation of reactive oxygen species. However, R. serbica can fully recover its metabolic functionsalready one day upon watering [1].Aim: to obtain more insight into the mechanisms of desiccation tolerance in R. serbica by differential de novotranscriptomics of hydrated (HL) and desiccated leaves (DL).",
journal = "Belgrade BioInformatics Conference 2021, 21-25 June, Vinča, Serbia",
title = "De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1855"
}

Vidović, M., Stevanović, S., Pantelić, A.,& Veljović-Jovanović, S.. (2021). De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance. in Belgrade BioInformatics Conference 2021, 21-25 June, Vinča, Serbia.
https://hdl.handle.net/21.15107/rcub_imagine_1855

Vidović M, Stevanović S, Pantelić A, Veljović-Jovanović S. De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance. in Belgrade BioInformatics Conference 2021, 21-25 June, Vinča, Serbia. 2021;.
https://hdl.handle.net/21.15107/rcub_imagine_1855 .

Vidović, Marija, Stevanović, Strahinja, Pantelić, Ana, Veljović-Jovanović, Sonja, "De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance" in Belgrade BioInformatics Conference 2021, 21-25 June, Vinča, Serbia (2021),
https://hdl.handle.net/21.15107/rcub_imagine_1855 .

TY  - CONF
AU  - Stevanović, Strahinja
AU  - Vidović, Marija
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1836
AB  - Desiccation or extreme water loss leads to protein denaturation, aggregation, and degradation and impairs membrane lipid fluidity, resulting in loss of membrane integrity at the cellular level. The induction of late embryogenesis abundant proteins (LEAPs) is considered an essential component of desiccation tolerance strategy in so-called resurrection plants. This heterogeneous group of hydrophilic, non-globular proteins is characterized by a high structural plasticity that allows them to adopt a random conformation in aqueous solutions that transforms into α-helices during dehydration [1]. Therefore, LEAPs can interact with various ligands and partners, including ion sequestration and stabilization of membranes and enzymes during freezing or drying [2]. Our new transcriptome database of an endemic resurrection species Ramonda serbica allowed us to identify 153 members of the LEA gene family. LEAPs of this sample data have an average primary sequence similarity and identity of 10% and 6%, respectively, but with a high variance (141 and 108), which means that the sample proteins can be classified based on domain homology. The averaging is based on multiple sequence alignment and the variance is estimated using pairwise sequence alignment scores. Accordingly, all identified LEAPs were clustered into six groups based on protein families (PFAM). Among these groups, LEAPs differ significantly in their secondary structure, disorder propensity and aggregation potential. Furthermore, we built homology models using Protein Data Bank structure information as templates. For each group, an ensemble of superimposed 3D homology models was analyzed. The information obtained from the representative structural models is key to understanding the function of LEAPs and the regulation of their intrinsic structural disorder-to-order transition during desiccation. This will pave the way for the identification of LEAPs endogenous partners and their targets in the cell and provide further insights into the protective mechanisms of desiccation tolerance.
C3  - Virtual symposium celebrating the 50th anniversary of the Protein Data Bank, May 4–5
T1  - In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1836
ER  - 

@conference{
author = "Stevanović, Strahinja and Vidović, Marija",
year = "2021",
abstract = "Desiccation or extreme water loss leads to protein denaturation, aggregation, and degradation and impairs membrane lipid fluidity, resulting in loss of membrane integrity at the cellular level. The induction of late embryogenesis abundant proteins (LEAPs) is considered an essential component of desiccation tolerance strategy in so-called resurrection plants. This heterogeneous group of hydrophilic, non-globular proteins is characterized by a high structural plasticity that allows them to adopt a random conformation in aqueous solutions that transforms into α-helices during dehydration [1]. Therefore, LEAPs can interact with various ligands and partners, including ion sequestration and stabilization of membranes and enzymes during freezing or drying [2]. Our new transcriptome database of an endemic resurrection species Ramonda serbica allowed us to identify 153 members of the LEA gene family. LEAPs of this sample data have an average primary sequence similarity and identity of 10% and 6%, respectively, but with a high variance (141 and 108), which means that the sample proteins can be classified based on domain homology. The averaging is based on multiple sequence alignment and the variance is estimated using pairwise sequence alignment scores. Accordingly, all identified LEAPs were clustered into six groups based on protein families (PFAM). Among these groups, LEAPs differ significantly in their secondary structure, disorder propensity and aggregation potential. Furthermore, we built homology models using Protein Data Bank structure information as templates. For each group, an ensemble of superimposed 3D homology models was analyzed. The information obtained from the representative structural models is key to understanding the function of LEAPs and the regulation of their intrinsic structural disorder-to-order transition during desiccation. This will pave the way for the identification of LEAPs endogenous partners and their targets in the cell and provide further insights into the protective mechanisms of desiccation tolerance.",
journal = "Virtual symposium celebrating the 50th anniversary of the Protein Data Bank, May 4–5",
title = "In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1836"
}

Stevanović, S.,& Vidović, M.. (2021). In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship. in Virtual symposium celebrating the 50th anniversary of the Protein Data Bank, May 4–5.
https://hdl.handle.net/21.15107/rcub_imagine_1836

Stevanović S, Vidović M. In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship. in Virtual symposium celebrating the 50th anniversary of the Protein Data Bank, May 4–5. 2021;.
https://hdl.handle.net/21.15107/rcub_imagine_1836 .

Stevanović, Strahinja, Vidović, Marija, "In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship" in Virtual symposium celebrating the 50th anniversary of the Protein Data Bank, May 4–5 (2021),
https://hdl.handle.net/21.15107/rcub_imagine_1836 .

TY  - CONF
AU  - Pantelić, Ana
AU  - Stevanović, Strahinja
AU  - Kilibarda, Nataša
AU  - Milić Komić, Sonja
AU  - Radosavljevic, Jelena
AU  - Vidović, Marija
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1882
AB  - Endemic plant species, Ramonda serbica is a resurrection plant that can tolerate extreme
dehydration (desiccation, loss of 95% of cellular water) even over months. The
accumulation of late embryogenesis abundant proteins (LEAPs) is a crucial step in the
mechanism of desiccation tolerance. The role of LEAPs is not completely resolved, but
they are accepted as intrinsically disordered proteins (IDPs). Based on previously
established de novo transcriptome database of R. serbica leaves we identify around 160
members of LEA gene family. Identified LEAPs were classified into six groups: LEA 1-5
and seed maturation proteins (SMPs) according to protein family (Pfam) database. Based
on multiple sequence alignment, secondary structure prediction and 3D structure modeling,
we conducted LEA protein structure analysis. We showed that more than 50% of identified
LEAPs exhibited a high propensity to form α-helices. As predicted by several
bioinformatic tools, more than 70% of identified LEAPs were found to be highly
disordered. Thus, these proteins are predicted to be disordered in solution, but they acquire
a secondary, predominantly α-helical structure during drying, in contrast to globular
proteins, which most often causes the loss of structure upon dehydration. By using
molecular dynamic simulations, we identified the most favorable conformations of
representative LEAPs and we have studied conformational transitions driven by the water
scarcity. Structural characterization of LEAPs is a key to understand their function and
regulation of their intrinsic structural disorder-to-order transition during desiccation as a
requirement for biological function, in order to promote development of new therapeutic
strategies in neurodegenerative disorders, cell preservation technology and the
improvement of crop drought tolerance.
PB  - Belgrade : Serbian Biochemical Society
C3  - Biochemical Insights into Molecular Mechanisms
T1  - Characterization of the late embryogenesis abundant (LEA) proteins family in hydrated and desiccated Ramonda serbica Panc. leaves
SP  - 117
SP  - 118
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1882
ER  - 

@conference{
author = "Pantelić, Ana and Stevanović, Strahinja and Kilibarda, Nataša and Milić Komić, Sonja and Radosavljevic, Jelena and Vidović, Marija",
year = "2021",
abstract = "Endemic plant species, Ramonda serbica is a resurrection plant that can tolerate extreme
dehydration (desiccation, loss of 95% of cellular water) even over months. The
accumulation of late embryogenesis abundant proteins (LEAPs) is a crucial step in the
mechanism of desiccation tolerance. The role of LEAPs is not completely resolved, but
they are accepted as intrinsically disordered proteins (IDPs). Based on previously
established de novo transcriptome database of R. serbica leaves we identify around 160
members of LEA gene family. Identified LEAPs were classified into six groups: LEA 1-5
and seed maturation proteins (SMPs) according to protein family (Pfam) database. Based
on multiple sequence alignment, secondary structure prediction and 3D structure modeling,
we conducted LEA protein structure analysis. We showed that more than 50% of identified
LEAPs exhibited a high propensity to form α-helices. As predicted by several
bioinformatic tools, more than 70% of identified LEAPs were found to be highly
disordered. Thus, these proteins are predicted to be disordered in solution, but they acquire
a secondary, predominantly α-helical structure during drying, in contrast to globular
proteins, which most often causes the loss of structure upon dehydration. By using
molecular dynamic simulations, we identified the most favorable conformations of
representative LEAPs and we have studied conformational transitions driven by the water
scarcity. Structural characterization of LEAPs is a key to understand their function and
regulation of their intrinsic structural disorder-to-order transition during desiccation as a
requirement for biological function, in order to promote development of new therapeutic
strategies in neurodegenerative disorders, cell preservation technology and the
improvement of crop drought tolerance.",
publisher = "Belgrade : Serbian Biochemical Society",
journal = "Biochemical Insights into Molecular Mechanisms",
title = "Characterization of the late embryogenesis abundant (LEA) proteins family in hydrated and desiccated Ramonda serbica Panc. leaves",
pages = "117-118",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1882"
}

Pantelić, A., Stevanović, S., Kilibarda, N., Milić Komić, S., Radosavljevic, J.,& Vidović, M.. (2021). Characterization of the late embryogenesis abundant (LEA) proteins family in hydrated and desiccated Ramonda serbica Panc. leaves. in Biochemical Insights into Molecular Mechanisms
Belgrade : Serbian Biochemical Society., 117.
https://hdl.handle.net/21.15107/rcub_imagine_1882

Pantelić A, Stevanović S, Kilibarda N, Milić Komić S, Radosavljevic J, Vidović M. Characterization of the late embryogenesis abundant (LEA) proteins family in hydrated and desiccated Ramonda serbica Panc. leaves. in Biochemical Insights into Molecular Mechanisms. 2021;:117.
https://hdl.handle.net/21.15107/rcub_imagine_1882 .

Pantelić, Ana, Stevanović, Strahinja, Kilibarda, Nataša, Milić Komić, Sonja, Radosavljevic, Jelena, Vidović, Marija, "Characterization of the late embryogenesis abundant (LEA) proteins family in hydrated and desiccated Ramonda serbica Panc. leaves" in Biochemical Insights into Molecular Mechanisms (2021):117,
https://hdl.handle.net/21.15107/rcub_imagine_1882 .

TY  - CONF
AU  - Vidović, Marija
AU  - Stevanović, Strahinja
AU  - Franchin, Cinzia
AU  - Battisti, Ilaria
AU  - Arrigoni, Giorgio
AU  - Masi, Antonio
AU  - Veljović Jovanović, Sonja
PY  - 2021
UR  - https://inppo.org/inppo2020/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1835
AB  - Resurrection plant Ramonda serbica Panc. survives desiccation for a long period and fully recovers metabolic functions already within one day upon watering [1]. Besides osmotic stress, desiccation provokes the accelerated generation of reactive oxygen species. The aim of our study was obtaining more insight into the mechanisms of desiccation tolerance in R. serbica by TMT labelled comparative quantitative proteomics of hydrated (HL) and desiccated leaves (DL). After de novo transcriptome analysis, 189456 transcripts with 189003 unigenes were annotated with seven common databases. Proteomic analysis allowed for the relative quantification of 895 different protein groups, 321 with a statistically significant difference in abundance between FL and DL. Among them, 25% referred to chloroplast and almost the same percentage were associated with desiccation and oxidative stress. Almost all differentially abundant proteins related to photosynthetic processes were down-regulated in DL, while those required for protein translation were more abundant in HL. Within differentially abundant proteins involved in antioxidative defence, the levels of enzymes involved in ascorbate-glutathione cycle, peroxiredoxins, Fe and Mn superoxide dismutase (SOD) were all reduced in DL, while germin-like proteins, three Cu/Zn SOD isoforms and polyphenol oxidases were more abundant in DL compared with HL. The protein family with the highest number of members showing the greatest accumulation upon desiccation comprised twenty different late embryogenesis abundant proteins (LEAPs), similarly as found by differential transcriptomic analysis. Taken together, our results imply a key role of LEAPs and Cu/Zn SOD in protective mechanism against desiccation in R. serbica, that may have significant implications on drought-related studies of crops grown in arid areas. This work was supported by the Science Fund of the Republic of Serbia (PROMIS project LEAPSyn-SCI, grant number 6039663). M.V. wishes to acknowledge the support of COST Action BM1405 for approving STSM in Padua during 2017 and 2018.
PB  - International Plant Proteomics Organization
C3  - The Fourth Conference of the International Plant Proteomics Organization
T1  - Twenty different late embryogenesis abundant proteins (LEAPs) accumulate in desiccated Ramonda serbica leaves
EP  - 44
SP  - 43
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1835
ER  - 

@conference{
author = "Vidović, Marija and Stevanović, Strahinja and Franchin, Cinzia and Battisti, Ilaria and Arrigoni, Giorgio and Masi, Antonio and Veljović Jovanović, Sonja",
year = "2021",
abstract = "Resurrection plant Ramonda serbica Panc. survives desiccation for a long period and fully recovers metabolic functions already within one day upon watering [1]. Besides osmotic stress, desiccation provokes the accelerated generation of reactive oxygen species. The aim of our study was obtaining more insight into the mechanisms of desiccation tolerance in R. serbica by TMT labelled comparative quantitative proteomics of hydrated (HL) and desiccated leaves (DL). After de novo transcriptome analysis, 189456 transcripts with 189003 unigenes were annotated with seven common databases. Proteomic analysis allowed for the relative quantification of 895 different protein groups, 321 with a statistically significant difference in abundance between FL and DL. Among them, 25% referred to chloroplast and almost the same percentage were associated with desiccation and oxidative stress. Almost all differentially abundant proteins related to photosynthetic processes were down-regulated in DL, while those required for protein translation were more abundant in HL. Within differentially abundant proteins involved in antioxidative defence, the levels of enzymes involved in ascorbate-glutathione cycle, peroxiredoxins, Fe and Mn superoxide dismutase (SOD) were all reduced in DL, while germin-like proteins, three Cu/Zn SOD isoforms and polyphenol oxidases were more abundant in DL compared with HL. The protein family with the highest number of members showing the greatest accumulation upon desiccation comprised twenty different late embryogenesis abundant proteins (LEAPs), similarly as found by differential transcriptomic analysis. Taken together, our results imply a key role of LEAPs and Cu/Zn SOD in protective mechanism against desiccation in R. serbica, that may have significant implications on drought-related studies of crops grown in arid areas. This work was supported by the Science Fund of the Republic of Serbia (PROMIS project LEAPSyn-SCI, grant number 6039663). M.V. wishes to acknowledge the support of COST Action BM1405 for approving STSM in Padua during 2017 and 2018.",
publisher = "International Plant Proteomics Organization",
journal = "The Fourth Conference of the International Plant Proteomics Organization",
title = "Twenty different late embryogenesis abundant proteins (LEAPs) accumulate in desiccated Ramonda serbica leaves",
pages = "44-43",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1835"
}

Vidović, M., Stevanović, S., Franchin, C., Battisti, I., Arrigoni, G., Masi, A.,& Veljović Jovanović, S.. (2021). Twenty different late embryogenesis abundant proteins (LEAPs) accumulate in desiccated Ramonda serbica leaves. in The Fourth Conference of the International Plant Proteomics Organization
International Plant Proteomics Organization., 43-44.
https://hdl.handle.net/21.15107/rcub_imagine_1835

Vidović M, Stevanović S, Franchin C, Battisti I, Arrigoni G, Masi A, Veljović Jovanović S. Twenty different late embryogenesis abundant proteins (LEAPs) accumulate in desiccated Ramonda serbica leaves. in The Fourth Conference of the International Plant Proteomics Organization. 2021;:43-44.
https://hdl.handle.net/21.15107/rcub_imagine_1835 .

Vidović, Marija, Stevanović, Strahinja, Franchin, Cinzia, Battisti, Ilaria, Arrigoni, Giorgio, Masi, Antonio, Veljović Jovanović, Sonja, "Twenty different late embryogenesis abundant proteins (LEAPs) accumulate in desiccated Ramonda serbica leaves" in The Fourth Conference of the International Plant Proteomics Organization (2021):43-44,
https://hdl.handle.net/21.15107/rcub_imagine_1835 .

TY  - CONF
AU  - Vidović, Marija
AU  - Stevanović, Strahinja
AU  - Veljović-Jovanović, Sonja
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1834
AB  - Ramonda serbica Panc. is a resurrection plant that can survive a long period of severe dehydration-desiccation. Desiccation induces cellular membrane integrity loss, protein aggregation, and denaturation, as well as accelerated generation of reactive oxygen species. However, R. serbica can fully recover its metabolic functions already one day upon watering [1]. The aim of our study was to obtain more insight into the desiccation tolerance mechanisms by differential de novo transcriptomics of hydrated (HL) and desiccated leaves (DL). For R. serbica transcriptome construction, the total high-quality RNA from HL and DL was extracted according to our previously optimised protocol [2]. Highly purified cDNA libraries were sequenced on an Illumina Hi-Seq platform. The ambiguous nucleotides, adapter sequences, and low-quality sequences were trimmed, and the quality of the reads was checked before and after the trimming. In total, 39608813 (with Q30=94%) and 37482969 (with Q30=94.1%) clean reads were obtained in HL and DL, respectively, and used to perform transcriptome assembly by Trinity software. After removing the redundancy, 189456 transcripts with 189003 unigenes were obtained (32.6% with the length between 500-1kbp).Comparative analysis revealed that a large portion of R. serbica sequences (49.1%) was similar to sequences found in the genome of another resurrection plant Boea hygrometrica. Furthermore, among obtained unigenes, 64.6% and 42.3% were annotated by NCBI non-redundant protein and nucleotide sequences database (db), 23% by PFAM db, 22.5% by Clusters of Orthologous Groups of proteins db, 48.02% by Swiss-Prot db, 23 % KEGG db and 13.73 by Gene Ontology db. The majority of annotated genes were associated with translation, ribosomal structure, posttranslational modifications, protein turnover, signalling pathways and cytoskeleton and encoded chaperonins and late embryogenesis abundant (LEA) proteins. Aiming to provide a list of candidates involved in the desiccation tolerance in R. serbica we analysed differentially expressed genes in HL and DL. Genes associated with transmembrane transport, reproduction, cell proliferation, and protein folding were up-regulated in HL compared with DL. On the other hand, genes encoding proteins involved in cell wall architecture, LEA proteins and antioxidative defence were up-regulated in DL.
C3  - Biologia Serbica
T1  - De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance
EP  - 76
IS  - 1 (spec. ed.)
SP  - 75
VL  - 43
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1834
ER  - 

@conference{
author = "Vidović, Marija and Stevanović, Strahinja and Veljović-Jovanović, Sonja",
year = "2021",
abstract = "Ramonda serbica Panc. is a resurrection plant that can survive a long period of severe dehydration-desiccation. Desiccation induces cellular membrane integrity loss, protein aggregation, and denaturation, as well as accelerated generation of reactive oxygen species. However, R. serbica can fully recover its metabolic functions already one day upon watering [1]. The aim of our study was to obtain more insight into the desiccation tolerance mechanisms by differential de novo transcriptomics of hydrated (HL) and desiccated leaves (DL). For R. serbica transcriptome construction, the total high-quality RNA from HL and DL was extracted according to our previously optimised protocol [2]. Highly purified cDNA libraries were sequenced on an Illumina Hi-Seq platform. The ambiguous nucleotides, adapter sequences, and low-quality sequences were trimmed, and the quality of the reads was checked before and after the trimming. In total, 39608813 (with Q30=94%) and 37482969 (with Q30=94.1%) clean reads were obtained in HL and DL, respectively, and used to perform transcriptome assembly by Trinity software. After removing the redundancy, 189456 transcripts with 189003 unigenes were obtained (32.6% with the length between 500-1kbp).Comparative analysis revealed that a large portion of R. serbica sequences (49.1%) was similar to sequences found in the genome of another resurrection plant Boea hygrometrica. Furthermore, among obtained unigenes, 64.6% and 42.3% were annotated by NCBI non-redundant protein and nucleotide sequences database (db), 23% by PFAM db, 22.5% by Clusters of Orthologous Groups of proteins db, 48.02% by Swiss-Prot db, 23 % KEGG db and 13.73 by Gene Ontology db. The majority of annotated genes were associated with translation, ribosomal structure, posttranslational modifications, protein turnover, signalling pathways and cytoskeleton and encoded chaperonins and late embryogenesis abundant (LEA) proteins. Aiming to provide a list of candidates involved in the desiccation tolerance in R. serbica we analysed differentially expressed genes in HL and DL. Genes associated with transmembrane transport, reproduction, cell proliferation, and protein folding were up-regulated in HL compared with DL. On the other hand, genes encoding proteins involved in cell wall architecture, LEA proteins and antioxidative defence were up-regulated in DL.",
journal = "Biologia Serbica",
title = "De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance",
pages = "76-75",
number = "1 (spec. ed.)",
volume = "43",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1834"
}

Vidović, M., Stevanović, S.,& Veljović-Jovanović, S.. (2021). De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance. in Biologia Serbica, 43(1 (spec. ed.)), 75-76.
https://hdl.handle.net/21.15107/rcub_imagine_1834

Vidović M, Stevanović S, Veljović-Jovanović S. De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance. in Biologia Serbica. 2021;43(1 (spec. ed.)):75-76.
https://hdl.handle.net/21.15107/rcub_imagine_1834 .

Vidović, Marija, Stevanović, Strahinja, Veljović-Jovanović, Sonja, "De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance" in Biologia Serbica, 43, no. 1 (spec. ed.) (2021):75-76,
https://hdl.handle.net/21.15107/rcub_imagine_1834 .

TY  - GEN
AU  - Pantelić, Ana
AU  - Stevanović, Strahinja
AU  - Kilibarda, Nataša
AU  - Vidović, Marija
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1852
AB  - Resurrection plant Ramonda serbica Panc. survives
desiccation for a long period and fully recovers
metabolic functions already within one day upon
watering. Desiccation (extreme dehydration) induces protein
unfolding and aggregation, destabilization or loss of
cellular membrane integrity. Besides, desiccation
provokes the accelerated generation of reactive
oxygen species.
HL
DL

Aim: To identify Late Embryogenesis Abundant Proteins
(LEAPs) that contribute to desiccation tolerance in
R. serbica by comparative transcriptomics of
hydrated (HL) and desiccated leaves (DL).
PB  - Belgrade BioInformatics
T2  - Belgrade BioInformatics Conference 2021
T1  - De Novo Transcriptome Sequencing of Ramonda serbica : Identification of Late Embryogenesis Abundant Proteins
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1852
ER  - 

@misc{
author = "Pantelić, Ana and Stevanović, Strahinja and Kilibarda, Nataša and Vidović, Marija",
year = "2021",
abstract = "Resurrection plant Ramonda serbica Panc. survives
desiccation for a long period and fully recovers
metabolic functions already within one day upon
watering. Desiccation (extreme dehydration) induces protein
unfolding and aggregation, destabilization or loss of
cellular membrane integrity. Besides, desiccation
provokes the accelerated generation of reactive
oxygen species.
HL
DL

Aim: To identify Late Embryogenesis Abundant Proteins
(LEAPs) that contribute to desiccation tolerance in
R. serbica by comparative transcriptomics of
hydrated (HL) and desiccated leaves (DL).",
publisher = "Belgrade BioInformatics",
journal = "Belgrade BioInformatics Conference 2021",
title = "De Novo Transcriptome Sequencing of Ramonda serbica : Identification of Late Embryogenesis Abundant Proteins",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1852"
}

Pantelić, A., Stevanović, S., Kilibarda, N.,& Vidović, M.. (2021). De Novo Transcriptome Sequencing of Ramonda serbica : Identification of Late Embryogenesis Abundant Proteins. in Belgrade BioInformatics Conference 2021
Belgrade BioInformatics..
https://hdl.handle.net/21.15107/rcub_imagine_1852

Pantelić A, Stevanović S, Kilibarda N, Vidović M. De Novo Transcriptome Sequencing of Ramonda serbica : Identification of Late Embryogenesis Abundant Proteins. in Belgrade BioInformatics Conference 2021. 2021;.
https://hdl.handle.net/21.15107/rcub_imagine_1852 .

Pantelić, Ana, Stevanović, Strahinja, Kilibarda, Nataša, Vidović, Marija, "De Novo Transcriptome Sequencing of Ramonda serbica : Identification of Late Embryogenesis Abundant Proteins" in Belgrade BioInformatics Conference 2021 (2021),
https://hdl.handle.net/21.15107/rcub_imagine_1852 .

TY  - CONF
AU  - Vidović, Marija
AU  - Pantelić, Ana
AU  - Stevanović, Strahinja
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1881
AB  - Ramonda serbica is an endemic and resurrection plant species that can survive
extreme dehydration even over months. Desiccation (loss of >95% of cellular water) leads to
protein denaturation, aggregation, and degradation and impairs membrane lipid fluidity, resulting in
loss of membrane integrity at the cellular level. The induction of late embryogenesis abundant
proteins (LEAPs) is considered an essential component of desiccation tolerance strategy in so-called
resurrection plants. This heterogeneous group of anhydrobiosis-related intrinsically
disordered proteins (IDPs) is characterized by high structural plasticity enabling them to interact
with various ligands and partners, including ion sequestration and stabilization of membranes and
enzymes during freezing or drying. the aim of our research is to assess the potential of selected
RsLEAPs to inhibit the aggregation of α-synuclein, paving the way for new therapeutic
strategies against neurodegenerative disorders, such as Parkinson’s disease.
Our new transcriptome database of R. serbica leaves allowed us to identify around 165
members of LEA protein family. Based on multiple sequence alignment, secondary structure
prediction and 3D structure modelling we classified identified LEAPs into six groups
(according to the Pfam database) and showed that more than 50% of identified LEAPs
exhibited a high propensity to form α-helices. As predicted by several bioinformatic tools,
more than 70% of identified LEAPs were found to be highly disordered. By using molecular
dynamic simulations, we identified the most favourable conformations of representative
LEAPs and showed the loss of the secondary, α-helical structure in water, in contrast to
globular proteins.
Structural characterization of LEAPs is a key to understand their function and
regulation of their intrinsic structural disorder-to-order transition during desiccation. These
findings will promote transformative advancements in various fields, such as the
development of new strategies in neurodegenerative disorders, cell preservation technology
and the improvement of crop drought tolerance.
AB  - Ramonda serbica endemska vrsta, i biljka vaskrsnica, sposobna da preživi u uslovima
ekstremne dehidratacije tokom perioda dužeg od mesec dana. Desikacija (gubitak preko 95
% vode u ćeliji) dovodi do denaturacije, agregacije i degradacije proteina, i utiče na fluidnost
membrana, što finalno dovodi do gubitka integriteta ćelije. Prisustvo proteina zastupljenih u
kasnoj fazi embriogeneze (late embryogenesis abundant proteins – LEAPs) se smatra esencijalnim
delom strategije tolerancije na desikaciju kod vaskrsnica. Ovu heterogenu grupu prirodno neuređenih
proteina, povezanih sa anhidrobiozom, odlikuje visoka strukturna plastičnost koja im omogućava
interakciju sa brojnim ligandima i partnerima. LEA proteini su uključeni u heliranje jona, stabilizaciju
membrana i enzima tokom zamrzavanja ili suše. Cilj našeg istraživanja je procena potencijala
izabranog LEA proteina iz ramonde da inhibira agregaciju α-sinukleina, otvarajući put ka razvoju
novih terapija za lečenje neurodegenerativnih poremećaja poput Parkinskonove bolesti.
Analiziranjem transkriptoma listova R. serbica i formiranjem baze podataka
identifikovano je oko 165 proteina koji pripadaju LEA proteinskoj familiji. Na osnovu
višestrukog poravnjanja aminokiselinskih sekvenci, predviđanja sekundarne strukture i 3D
strukturnog modelinga, identifikovani LEA proteini su podeljeni u šest grupa (prema Pfam
bazi podataka) i pokazano je sa velikom verovatnoćom da je više od 50 % LEA proteina u
mogućnosti da formira α-helikse. Pomoću nekoliko bioinformatičkih alata predviđeno je da
više od 70 % identifikovanih LEA proteina formira visoko neuređenu strukturu. Korišćenjem
simulacije molekularne dinamike, identifikovane su najpovoljnije konformacije
reprezentativnih LEA proteina. Tom prilikom je kod LEA proteina uočen gubitak sekundarne
α-heliksne strukture u vodi, za razliku od globularnih proteina kada je ova struktura
favorizovana.
Strukturna karakterizacija LEA proteina je ključna za razumevanje njihove funkcije i
regulaciju njihovog prelaska iz neuređene u uređenu konformaciju tokom desikacije. Ova
saznanja bi trebalo da omoguće značajna napredovanja na različitim poljima, kao što je
razvoj novih strategija u borbi protiv neurodegenerativnih poremećaja, tehnologija čuvanja
zamrznutih ćelija, kao i na povećanje otpornosti useva na sušu.
PB  - Beograd : Savez farmaceutskih udruženja Srbije
C3  - Archives of Pharmacy -  2nd Scientific symposium SFUS
T1  - Structural characterisation of Late Embryogenesis Abundant Proteins from Ramonda Serbica: potential to inhibit α-synuclein aggregation
T1  - Strukturna karakterizacija proteina zastupljenih u kasnoj fazi embriogeneze iz biljke Ramonda Serbica : Potencijalni inhibitor agregacije  α‐ sinukleina
EP  - 31
IS  - Suppl. 5
SP  - 30
VL  - 71
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1881
ER  - 

@conference{
author = "Vidović, Marija and Pantelić, Ana and Stevanović, Strahinja",
year = "2021",
abstract = "Ramonda serbica is an endemic and resurrection plant species that can survive
extreme dehydration even over months. Desiccation (loss of >95% of cellular water) leads to
protein denaturation, aggregation, and degradation and impairs membrane lipid fluidity, resulting in
loss of membrane integrity at the cellular level. The induction of late embryogenesis abundant
proteins (LEAPs) is considered an essential component of desiccation tolerance strategy in so-called
resurrection plants. This heterogeneous group of anhydrobiosis-related intrinsically
disordered proteins (IDPs) is characterized by high structural plasticity enabling them to interact
with various ligands and partners, including ion sequestration and stabilization of membranes and
enzymes during freezing or drying. the aim of our research is to assess the potential of selected
RsLEAPs to inhibit the aggregation of α-synuclein, paving the way for new therapeutic
strategies against neurodegenerative disorders, such as Parkinson’s disease.
Our new transcriptome database of R. serbica leaves allowed us to identify around 165
members of LEA protein family. Based on multiple sequence alignment, secondary structure
prediction and 3D structure modelling we classified identified LEAPs into six groups
(according to the Pfam database) and showed that more than 50% of identified LEAPs
exhibited a high propensity to form α-helices. As predicted by several bioinformatic tools,
more than 70% of identified LEAPs were found to be highly disordered. By using molecular
dynamic simulations, we identified the most favourable conformations of representative
LEAPs and showed the loss of the secondary, α-helical structure in water, in contrast to
globular proteins.
Structural characterization of LEAPs is a key to understand their function and
regulation of their intrinsic structural disorder-to-order transition during desiccation. These
findings will promote transformative advancements in various fields, such as the
development of new strategies in neurodegenerative disorders, cell preservation technology
and the improvement of crop drought tolerance., Ramonda serbica endemska vrsta, i biljka vaskrsnica, sposobna da preživi u uslovima
ekstremne dehidratacije tokom perioda dužeg od mesec dana. Desikacija (gubitak preko 95
% vode u ćeliji) dovodi do denaturacije, agregacije i degradacije proteina, i utiče na fluidnost
membrana, što finalno dovodi do gubitka integriteta ćelije. Prisustvo proteina zastupljenih u
kasnoj fazi embriogeneze (late embryogenesis abundant proteins – LEAPs) se smatra esencijalnim
delom strategije tolerancije na desikaciju kod vaskrsnica. Ovu heterogenu grupu prirodno neuređenih
proteina, povezanih sa anhidrobiozom, odlikuje visoka strukturna plastičnost koja im omogućava
interakciju sa brojnim ligandima i partnerima. LEA proteini su uključeni u heliranje jona, stabilizaciju
membrana i enzima tokom zamrzavanja ili suše. Cilj našeg istraživanja je procena potencijala
izabranog LEA proteina iz ramonde da inhibira agregaciju α-sinukleina, otvarajući put ka razvoju
novih terapija za lečenje neurodegenerativnih poremećaja poput Parkinskonove bolesti.
Analiziranjem transkriptoma listova R. serbica i formiranjem baze podataka
identifikovano je oko 165 proteina koji pripadaju LEA proteinskoj familiji. Na osnovu
višestrukog poravnjanja aminokiselinskih sekvenci, predviđanja sekundarne strukture i 3D
strukturnog modelinga, identifikovani LEA proteini su podeljeni u šest grupa (prema Pfam
bazi podataka) i pokazano je sa velikom verovatnoćom da je više od 50 % LEA proteina u
mogućnosti da formira α-helikse. Pomoću nekoliko bioinformatičkih alata predviđeno je da
više od 70 % identifikovanih LEA proteina formira visoko neuređenu strukturu. Korišćenjem
simulacije molekularne dinamike, identifikovane su najpovoljnije konformacije
reprezentativnih LEA proteina. Tom prilikom je kod LEA proteina uočen gubitak sekundarne
α-heliksne strukture u vodi, za razliku od globularnih proteina kada je ova struktura
favorizovana.
Strukturna karakterizacija LEA proteina je ključna za razumevanje njihove funkcije i
regulaciju njihovog prelaska iz neuređene u uređenu konformaciju tokom desikacije. Ova
saznanja bi trebalo da omoguće značajna napredovanja na različitim poljima, kao što je
razvoj novih strategija u borbi protiv neurodegenerativnih poremećaja, tehnologija čuvanja
zamrznutih ćelija, kao i na povećanje otpornosti useva na sušu.",
publisher = "Beograd : Savez farmaceutskih udruženja Srbije",
journal = "Archives of Pharmacy -  2nd Scientific symposium SFUS",
title = "Structural characterisation of Late Embryogenesis Abundant Proteins from Ramonda Serbica: potential to inhibit α-synuclein aggregation, Strukturna karakterizacija proteina zastupljenih u kasnoj fazi embriogeneze iz biljke Ramonda Serbica : Potencijalni inhibitor agregacije  α‐ sinukleina",
pages = "31-30",
number = "Suppl. 5",
volume = "71",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1881"
}

Vidović, M., Pantelić, A.,& Stevanović, S.. (2021). Structural characterisation of Late Embryogenesis Abundant Proteins from Ramonda Serbica: potential to inhibit α-synuclein aggregation. in Archives of Pharmacy -  2nd Scientific symposium SFUS
Beograd : Savez farmaceutskih udruženja Srbije., 71(Suppl. 5), 30-31.
https://hdl.handle.net/21.15107/rcub_imagine_1881

Vidović M, Pantelić A, Stevanović S. Structural characterisation of Late Embryogenesis Abundant Proteins from Ramonda Serbica: potential to inhibit α-synuclein aggregation. in Archives of Pharmacy -  2nd Scientific symposium SFUS. 2021;71(Suppl. 5):30-31.
https://hdl.handle.net/21.15107/rcub_imagine_1881 .

Vidović, Marija, Pantelić, Ana, Stevanović, Strahinja, "Structural characterisation of Late Embryogenesis Abundant Proteins from Ramonda Serbica: potential to inhibit α-synuclein aggregation" in Archives of Pharmacy -  2nd Scientific symposium SFUS, 71, no. Suppl. 5 (2021):30-31,
https://hdl.handle.net/21.15107/rcub_imagine_1881 .

TY  - CONF
AU  - Vidović, Marija
AU  - Stevanović, Strahinja
AU  - Veljović-Jovanović, Sonja
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1876
AB  - Ramonda serbica Panc. is a resurrection plant that can survive a long period of severe dehydration-desiccation.
Desiccation induces cellular membrane integrity loss, protein aggregation, and denaturation, as well as
accelerated generation of reactive oxygen species. However, R. serbica can fully recover its metabolic functions
already one day upon watering [1]. The aim of our study was to obtain more insight into the desiccation
tolerance mechanisms by differential de novo transcriptomics of hydrated (HL) and desiccated leaves (DL).
For R. serbica transcriptome construction, the total high-quality RNA from mixed samples of five biological
replicates of HL and of DL separately, was extracted according to our previously optimised protocol [2].
Highly purified cDNA libraries were sequenced on an Illumina Hi-Seq platform. The ambiguous nucleotides,
adapter sequences, and low-quality sequences were trimmed, and the quality of the reads was checked before
and after the trimming. In total, 39608813 (with Q30=94%) and 37482969 (with Q30=94.1%) clean reads
were obtained in HL and DL, respectively, and used to perform transcriptome assembly by Trinity software.
After removing the redundancy, 189456 transcripts with 189003 unigenes were obtained (32.6% with the
length between 500-1kbp).
Comparative analysis revealed that a large portion of R. serbica sequences (49.1%) exhibited high homology
(according to obtained blast hits, e-value = 1e-5) with sequences found in the genome of another resurrection
plant Boea hygrometrica. Furthermore, among the obtained unigenes (merged data for HL and DL),
64.6% and 42.3% were annotated by NCBI non-redundant protein and nucleotide sequences database (db),
23% by PFAM db, 22.5% by Clusters of Orthologous Groups of proteins db, 48.02% by Swiss-Prot db, 23 %
KEGG db and 13.73 by Gene Ontology db. According to Blast2go analysis, the majority of annotated genes
of R. serbica were associated with translation, ribosomal structure, posttranslational modifications, protein
turnover, signalling pathways and cytoskeleton and encoded chaperonins and late embryogenesis abundant
(LEA) proteins.
Aiming to provide a list of candidates involved in the desiccation tolerance in R. serbica we analysed differentially
expressed genes in HL and DL. Genes associated with transmembrane transport, reproduction,
cell proliferation, and protein folding were up-regulated in HL compared with DL. On the other hand, genes
encoding proteins involved in cell wall architecture, LEA proteins and antioxidative defence were up-regulated
in DL. Taken together, our results imply a key role of genes responsible for leaf morphological changes
(wrapping and curling), and those encoding antioxidative enzymes (polyphenol oxidases and superoxide
dismutases), as well as LEA proteins, known to be a hallmark of desiccation tolerance in resurrection plants.
PB  - Novi Sad : Faculty of Sciences, Department of Biology and Ecology
C3  - Biologia Serbica
T1  - De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance
EP  - 76
IS  - 1 (Special Edition)
SP  - 75
VL  - 43
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1876
ER  - 

@conference{
author = "Vidović, Marija and Stevanović, Strahinja and Veljović-Jovanović, Sonja",
year = "2021",
abstract = "Ramonda serbica Panc. is a resurrection plant that can survive a long period of severe dehydration-desiccation.
Desiccation induces cellular membrane integrity loss, protein aggregation, and denaturation, as well as
accelerated generation of reactive oxygen species. However, R. serbica can fully recover its metabolic functions
already one day upon watering [1]. The aim of our study was to obtain more insight into the desiccation
tolerance mechanisms by differential de novo transcriptomics of hydrated (HL) and desiccated leaves (DL).
For R. serbica transcriptome construction, the total high-quality RNA from mixed samples of five biological
replicates of HL and of DL separately, was extracted according to our previously optimised protocol [2].
Highly purified cDNA libraries were sequenced on an Illumina Hi-Seq platform. The ambiguous nucleotides,
adapter sequences, and low-quality sequences were trimmed, and the quality of the reads was checked before
and after the trimming. In total, 39608813 (with Q30=94%) and 37482969 (with Q30=94.1%) clean reads
were obtained in HL and DL, respectively, and used to perform transcriptome assembly by Trinity software.
After removing the redundancy, 189456 transcripts with 189003 unigenes were obtained (32.6% with the
length between 500-1kbp).
Comparative analysis revealed that a large portion of R. serbica sequences (49.1%) exhibited high homology
(according to obtained blast hits, e-value = 1e-5) with sequences found in the genome of another resurrection
plant Boea hygrometrica. Furthermore, among the obtained unigenes (merged data for HL and DL),
64.6% and 42.3% were annotated by NCBI non-redundant protein and nucleotide sequences database (db),
23% by PFAM db, 22.5% by Clusters of Orthologous Groups of proteins db, 48.02% by Swiss-Prot db, 23 %
KEGG db and 13.73 by Gene Ontology db. According to Blast2go analysis, the majority of annotated genes
of R. serbica were associated with translation, ribosomal structure, posttranslational modifications, protein
turnover, signalling pathways and cytoskeleton and encoded chaperonins and late embryogenesis abundant
(LEA) proteins.
Aiming to provide a list of candidates involved in the desiccation tolerance in R. serbica we analysed differentially
expressed genes in HL and DL. Genes associated with transmembrane transport, reproduction,
cell proliferation, and protein folding were up-regulated in HL compared with DL. On the other hand, genes
encoding proteins involved in cell wall architecture, LEA proteins and antioxidative defence were up-regulated
in DL. Taken together, our results imply a key role of genes responsible for leaf morphological changes
(wrapping and curling), and those encoding antioxidative enzymes (polyphenol oxidases and superoxide
dismutases), as well as LEA proteins, known to be a hallmark of desiccation tolerance in resurrection plants.",
publisher = "Novi Sad : Faculty of Sciences, Department of Biology and Ecology",
journal = "Biologia Serbica",
title = "De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance",
pages = "76-75",
number = "1 (Special Edition)",
volume = "43",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1876"
}

Vidović, M., Stevanović, S.,& Veljović-Jovanović, S.. (2021). De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance. in Biologia Serbica
Novi Sad : Faculty of Sciences, Department of Biology and Ecology., 43(1 (Special Edition)), 75-76.
https://hdl.handle.net/21.15107/rcub_imagine_1876

Vidović M, Stevanović S, Veljović-Jovanović S. De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance. in Biologia Serbica. 2021;43(1 (Special Edition)):75-76.
https://hdl.handle.net/21.15107/rcub_imagine_1876 .

Vidović, Marija, Stevanović, Strahinja, Veljović-Jovanović, Sonja, "De Novo Transcriptome Sequencing of Ramonda serbica: Identification of the Candidate Genes Involved in the Desiccation Tolerance" in Biologia Serbica, 43, no. 1 (Special Edition) (2021):75-76,
https://hdl.handle.net/21.15107/rcub_imagine_1876 .

TY  - CONF
AU  - Milić Komić, Sonja
AU  - Stevanović, Strahinja
AU  - Vidović, Marija
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1438
UR  - https://www.sciencedirect.com/science/article/pii/S0891584921006778
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.
Keywords: desiccation tolerance; electron paramagnetic resonance (EPR); intrinsically disordered
proteins; machine learning; resurrection plants; secondary structure.
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
EP  - S130
IS  - Supplement 1
SP  - S129
VL  - 177
VL  - 177
DO  - 10.1016/j.freeradbiomed.2021.08.216
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.
Keywords: desiccation tolerance; electron paramagnetic resonance (EPR); intrinsically disordered
proteins; machine learning; resurrection plants; secondary structure.",
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",
pages = "S130-S129",
number = "Supplement 1",
volume = "177, 177",
doi = "10.1016/j.freeradbiomed.2021.08.216"
}

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(Supplement 1), S129-S130.
https://doi.org/10.1016/j.freeradbiomed.2021.08.216

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(Supplement 1):S129-S130.
doi:10.1016/j.freeradbiomed.2021.08.216 .

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, no. Supplement 1 (2021):S129-S130,
https://doi.org/10.1016/j.freeradbiomed.2021.08.216 . .

TY  - CONF
AU  - Stevanović, Strahinja
AU  - Vidović, Marija
PY  - 2021
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1858
AB  - Desiccation or extreme water loss leads to protein denaturation, aggregation, and degradation and impairs membrane lipid fluidity, resulting in loss of membrane integrity at the cellular level. The induction of late embryogenesis abundant proteins (LEAPs) is considered an essential component of desiccation tolerance strategy in so-called resurrection plants. This heterogeneous group of hydrophilic, non-globular proteins is characterised by a high structural plasticity that allows them to adopt a random conformation in aqueous solutions that transforms into α-helices during dehydration [1]. Therefore, LEAPs can interact with various ligands and partners, including ion sequestration and stabilisation of membranes and enzymes during freezing or drying [2].Our new transcriptome database of an endemic resurrection species Ramonda serbica allowed us to identify 164 members of the LEA gene family. LEAPs of this sample data have an average primary sequence similarity and identity of 10% and 6%, respectively, but with a high variance (141 and 108), which means that the sample proteins can be classified based on domain homology. The averaging is based on multiple sequence alignment and the variance is estimated using pairwise sequence alignment scores. Accordingly, all identified LEAPs were clustered into six groups based on protein families (PFAM). Among these groups, LEAPs differ significantly in their secondary structure, disorder propensity and aggregation potential. Furthermore, we built homology models using PDB structures as templates. For each group, an ensemble of superimposed 3D homology models was analyzed. The information obtained from the representative structural models is key to understanding the function of LEAPs and the regulation of their intrinsic structural disorder-to-order transition during desiccation. This will pave the way for the identification of LEAPs endogenous partners and their targets in the cell and provide further insights into the protective mechanisms of desiccation tolerance.
C3  - Virtual symposium celebrating the 50th anniversary of the Protein Data Bank, May 4–5
T1  - In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1858
ER  - 

@conference{
author = "Stevanović, Strahinja and Vidović, Marija",
year = "2021",
abstract = "Desiccation or extreme water loss leads to protein denaturation, aggregation, and degradation and impairs membrane lipid fluidity, resulting in loss of membrane integrity at the cellular level. The induction of late embryogenesis abundant proteins (LEAPs) is considered an essential component of desiccation tolerance strategy in so-called resurrection plants. This heterogeneous group of hydrophilic, non-globular proteins is characterised by a high structural plasticity that allows them to adopt a random conformation in aqueous solutions that transforms into α-helices during dehydration [1]. Therefore, LEAPs can interact with various ligands and partners, including ion sequestration and stabilisation of membranes and enzymes during freezing or drying [2].Our new transcriptome database of an endemic resurrection species Ramonda serbica allowed us to identify 164 members of the LEA gene family. LEAPs of this sample data have an average primary sequence similarity and identity of 10% and 6%, respectively, but with a high variance (141 and 108), which means that the sample proteins can be classified based on domain homology. The averaging is based on multiple sequence alignment and the variance is estimated using pairwise sequence alignment scores. Accordingly, all identified LEAPs were clustered into six groups based on protein families (PFAM). Among these groups, LEAPs differ significantly in their secondary structure, disorder propensity and aggregation potential. Furthermore, we built homology models using PDB structures as templates. For each group, an ensemble of superimposed 3D homology models was analyzed. The information obtained from the representative structural models is key to understanding the function of LEAPs and the regulation of their intrinsic structural disorder-to-order transition during desiccation. This will pave the way for the identification of LEAPs endogenous partners and their targets in the cell and provide further insights into the protective mechanisms of desiccation tolerance.",
journal = "Virtual symposium celebrating the 50th anniversary of the Protein Data Bank, May 4–5",
title = "In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1858"
}

Stevanović, S.,& Vidović, M.. (2021). In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship. in Virtual symposium celebrating the 50th anniversary of the Protein Data Bank, May 4–5.
https://hdl.handle.net/21.15107/rcub_imagine_1858

Stevanović S, Vidović M. In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship. in Virtual symposium celebrating the 50th anniversary of the Protein Data Bank, May 4–5. 2021;.
https://hdl.handle.net/21.15107/rcub_imagine_1858 .

Stevanović, Strahinja, Vidović, Marija, "In silico structural survey of newly identified late embryogenesis abundant proteins (LEAPs) from Ramonda serbica and their structure - function relationship" in Virtual symposium celebrating the 50th anniversary of the Protein Data Bank, May 4–5 (2021),
https://hdl.handle.net/21.15107/rcub_imagine_1858 .

TY  - CONF
AU  - Stevanović, Strahinja
AU  - Franchin, Cinzia
AU  - Battisti, Ilaria
AU  - Arrigoni, Giorgio
AU  - Masi, Antonio
AU  - Veljović Jovanović, Sonja
PY  - 2021
UR  - https://inppo.org/inppo2020/
UR  - https://imagine.imgge.bg.ac.rs/handle/123456789/1857
AB  - Resurrection plant Ramonda serbica Panc. survives desiccation for a long period and fully recovers metabolic functions already within one day upon watering [1]. Besides osmotic stress, desiccation provokes the accelerated generation of reactive oxygen species. The aim of our study was obtaining more insight into the mechanisms of desiccation tolerance in R. serbica by TMT labelled comparative quantitative proteomics of hydrated (HL) and desiccated leaves (DL). After de novo transcriptome analysis, 189456 transcripts with 189003 unigenes were annotated with seven common databases. Proteomic analysis allowed for the relative quantification of 895 different protein groups, 321 with a statistically significant difference in abundance between FL and DL. Among them, 25% referred to chloroplast and almost the same percentage were associated with desiccation and oxidative stress. Almost all differentially abundant proteins related to photosynthetic processes were down-regulated in DL, while those required for protein translation were more abundant in HL. Within differentially abundant proteins involved in antioxidative defence, the levels of enzymes involved in ascorbate-glutathione cycle, peroxiredoxins, Fe and Mn superoxide dismutase (SOD) were all reduced in DL, while germin-like proteins, three Cu/Zn SOD isoforms and polyphenol oxidases were more abundant in DL compared with HL. The protein family with the highest number of members showing the greatest accumulation upon desiccation comprised twenty different late embryogenesis abundant proteins (LEAPs), similarly as found by differential transcriptomic analysis. Taken together, our results imply a key role of LEAPs and Cu/Zn SOD in protective mechanism against desiccation in R. serbica, that may have significant implications on drought-related studies of crops grown in arid areas. This work was supported by the Science Fund of the Republic of Serbia (PROMIS project LEAPSyn-SCI, grant number 6039663). M.V. wishes to acknowledge the support of COST Action BM1405 for approving STSM in Padua during 2017 and 2018.
PB  - International Plant Proteomics Organization
C3  - The Fourth Conference of the International Plant Proteomics Organization
T1  - Twenty different late embryogenesis abundant proteins (LEAPs) accumulate in desiccated Ramonda serbica leaves
UR  - https://hdl.handle.net/21.15107/rcub_imagine_1857
ER  - 

@conference{
author = "Stevanović, Strahinja and Franchin, Cinzia and Battisti, Ilaria and Arrigoni, Giorgio and Masi, Antonio and Veljović Jovanović, Sonja",
year = "2021",
abstract = "Resurrection plant Ramonda serbica Panc. survives desiccation for a long period and fully recovers metabolic functions already within one day upon watering [1]. Besides osmotic stress, desiccation provokes the accelerated generation of reactive oxygen species. The aim of our study was obtaining more insight into the mechanisms of desiccation tolerance in R. serbica by TMT labelled comparative quantitative proteomics of hydrated (HL) and desiccated leaves (DL). After de novo transcriptome analysis, 189456 transcripts with 189003 unigenes were annotated with seven common databases. Proteomic analysis allowed for the relative quantification of 895 different protein groups, 321 with a statistically significant difference in abundance between FL and DL. Among them, 25% referred to chloroplast and almost the same percentage were associated with desiccation and oxidative stress. Almost all differentially abundant proteins related to photosynthetic processes were down-regulated in DL, while those required for protein translation were more abundant in HL. Within differentially abundant proteins involved in antioxidative defence, the levels of enzymes involved in ascorbate-glutathione cycle, peroxiredoxins, Fe and Mn superoxide dismutase (SOD) were all reduced in DL, while germin-like proteins, three Cu/Zn SOD isoforms and polyphenol oxidases were more abundant in DL compared with HL. The protein family with the highest number of members showing the greatest accumulation upon desiccation comprised twenty different late embryogenesis abundant proteins (LEAPs), similarly as found by differential transcriptomic analysis. Taken together, our results imply a key role of LEAPs and Cu/Zn SOD in protective mechanism against desiccation in R. serbica, that may have significant implications on drought-related studies of crops grown in arid areas. This work was supported by the Science Fund of the Republic of Serbia (PROMIS project LEAPSyn-SCI, grant number 6039663). M.V. wishes to acknowledge the support of COST Action BM1405 for approving STSM in Padua during 2017 and 2018.",
publisher = "International Plant Proteomics Organization",
journal = "The Fourth Conference of the International Plant Proteomics Organization",
title = "Twenty different late embryogenesis abundant proteins (LEAPs) accumulate in desiccated Ramonda serbica leaves",
url = "https://hdl.handle.net/21.15107/rcub_imagine_1857"
}

Stevanović, S., Franchin, C., Battisti, I., Arrigoni, G., Masi, A.,& Veljović Jovanović, S.. (2021). Twenty different late embryogenesis abundant proteins (LEAPs) accumulate in desiccated Ramonda serbica leaves. in The Fourth Conference of the International Plant Proteomics Organization
International Plant Proteomics Organization..
https://hdl.handle.net/21.15107/rcub_imagine_1857

Stevanović S, Franchin C, Battisti I, Arrigoni G, Masi A, Veljović Jovanović S. Twenty different late embryogenesis abundant proteins (LEAPs) accumulate in desiccated Ramonda serbica leaves. in The Fourth Conference of the International Plant Proteomics Organization. 2021;.
https://hdl.handle.net/21.15107/rcub_imagine_1857 .

Stevanović, Strahinja, Franchin, Cinzia, Battisti, Ilaria, Arrigoni, Giorgio, Masi, Antonio, Veljović Jovanović, Sonja, "Twenty different late embryogenesis abundant proteins (LEAPs) accumulate in desiccated Ramonda serbica leaves" in The Fourth Conference of the International Plant Proteomics Organization (2021),
https://hdl.handle.net/21.15107/rcub_imagine_1857 .