De Novo Transcriptome Sequencing of Ramonda serbica: Identification of Late Embryogenesis Abundant Proteins
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 pr...eviously 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.
Keywords:
desiccation tolerance / intrinsically disordered proteins / liquid-liquid phase separation / resurrection plants / secondary structure prediction / water stressSource:
Biologia Serbica, 2021, 43, 1 (spec. ed.), 65-65Publisher:
- Novi Sad : Faculty of Sciences, Department of Biology and Ecology
Funding / projects:
- LEAPSyn-SCI - Late Embryogenesis Abundant Proteins: Structural Characterisation and Interaction With Α-Synuclein (RS-ScienceFundRS-Promis-6039663)
- Ministry of Science, Technological Development and Innovation of the Republic of Serbia, institutional funding - 200042 (University of Belgrade, Institute of Molecular Genetics and Genetic Engineering) (RS-MESTD-inst-2020-200042)
Note:
- Book of Abstracts; Belgrade BioInformatics Conference 2021, 21-25 June 2021, Vinča, Serbia
URI
http://ojs.pmf.uns.ac.rs/index.php/dbe_serbica/indexhttps://imagine.imgge.bg.ac.rs/handle/123456789/1856
Collections
Institution/Community
Institut za molekularnu genetiku i genetičko inženjerstvoTY - 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 .