Label-Free Quantitative Proteomics of Pelargonium zonale: Tissue-Specific Differences
Autori
Milić, DejanaBalliau, Thierry
Davanture, Marlène
Blein-Nicolas, Melisande
Vidović, Marija
Ostala autorstva
Morić, IvanaĐorđević, Valentina
Konferencijski prilog (Objavljena verzija)
Metapodaci
Prikaz svih podataka o dokumentuApstrakt
Variegated Pelargonium zonale plants present excellent model for studying metabolite
fluxes and photosynthesis-related processes between the photosynthetically active
(green, vG) and inactive (white, vW) tissues within the same leaf under the same
microenvironmental conditions. We aimed to investigate the proteomic differences
between these two metabolically contrasting tissue types, as well as between vG and
plain morphs (G) to gain more insight into the evolutionary benefits of variegation.
Label-free proteomics was performed using liquid chromatography coupled to tandem
mass spectrometry. The data were searched against the newly expanded RNAseq
database for P. zonale leaves. Analysis was done with X!Tandem, using 10 ppm precursor
mass precision and fragment 0.02 Th mass tolerance. The identified proteins were filtered
using X!TandemPipeline, requiring at least two peptides with E-values lower than 0.01
and a protein E-value<10-5. Peptide ions, and their parental proteins,... were quantified by
integrating signal intensities from extracted ion currents (XIC) using MassChroQ software.
A total of 2707 protein groups were identified. After removing dubious data and peptides
with missing values, we obtained 2009 protein group. We annotated 564 and 79
differentially abundant proteins in vG vs. vW and vG vs. G, respectively. The differentially
abundant proteins were mapped into metabolic pathways using the modified MapMan
3.6.0RC1 software. Proteins related to photosynthesis and carbohydrate metabolism
were more abundant in vG compared with vW, while proteins related to oxidative stress
and protein degradation were more abundant in vW than in vG. Compared to vG, G tissue
contained more proteins involved in energy production and protein synthesis. Briefly,
this study has paved the way to uncover the evolutionary advantages of the variegated
phenotype.
Ključne reči:
differential proteomic analysis / variegated Pelargonium zonale / metabolic pathwaysIzvor:
5th Belgrade Bioinformatics Conference, 2024, 52-52Izdavač:
- Belgrade : Institute of Molecular Genetics and Genetic Engineering
Finansiranje / projekti:
- Ministarstvo nauke, tehnološkog razvoja i inovacija Republike Srbije, institucionalno finansiranje - 200042 (Univerzitet u Beogradu, Institut za molekularnu genetiku i genetičko inženjerstvo) (RS-MESTD-inst-2020-200042)
- Bilateral project with Republic of France (no. 337-00-93/2023-05/3).
Napomena:
- Book of abstracts: 5th Belgrade Bioinformatics Conference, Serbia, Belgrade,17-20 june 2024.
Kolekcije
Institucija/grupa
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Milić, Dejana AU - Balliau, Thierry AU - Davanture, Marlène AU - Blein-Nicolas, Melisande AU - Vidović, Marija PY - 2024 UR - www.belbi.bg.ac.rs UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2455 AB - Variegated Pelargonium zonale plants present excellent model for studying metabolite fluxes and photosynthesis-related processes between the photosynthetically active (green, vG) and inactive (white, vW) tissues within the same leaf under the same microenvironmental conditions. We aimed to investigate the proteomic differences between these two metabolically contrasting tissue types, as well as between vG and plain morphs (G) to gain more insight into the evolutionary benefits of variegation. Label-free proteomics was performed using liquid chromatography coupled to tandem mass spectrometry. The data were searched against the newly expanded RNAseq database for P. zonale leaves. Analysis was done with X!Tandem, using 10 ppm precursor mass precision and fragment 0.02 Th mass tolerance. The identified proteins were filtered using X!TandemPipeline, requiring at least two peptides with E-values lower than 0.01 and a protein E-value<10-5. Peptide ions, and their parental proteins, were quantified by integrating signal intensities from extracted ion currents (XIC) using MassChroQ software. A total of 2707 protein groups were identified. After removing dubious data and peptides with missing values, we obtained 2009 protein group. We annotated 564 and 79 differentially abundant proteins in vG vs. vW and vG vs. G, respectively. The differentially abundant proteins were mapped into metabolic pathways using the modified MapMan 3.6.0RC1 software. Proteins related to photosynthesis and carbohydrate metabolism were more abundant in vG compared with vW, while proteins related to oxidative stress and protein degradation were more abundant in vW than in vG. Compared to vG, G tissue contained more proteins involved in energy production and protein synthesis. Briefly, this study has paved the way to uncover the evolutionary advantages of the variegated phenotype. PB - Belgrade : Institute of Molecular Genetics and Genetic Engineering C3 - 5th Belgrade Bioinformatics Conference T1 - Label-Free Quantitative Proteomics of Pelargonium zonale: Tissue-Specific Differences EP - 52 SP - 52 UR - https://hdl.handle.net/21.15107/rcub_imagine_2455 ER -
@conference{ author = "Milić, Dejana and Balliau, Thierry and Davanture, Marlène and Blein-Nicolas, Melisande and Vidović, Marija", year = "2024", abstract = "Variegated Pelargonium zonale plants present excellent model for studying metabolite fluxes and photosynthesis-related processes between the photosynthetically active (green, vG) and inactive (white, vW) tissues within the same leaf under the same microenvironmental conditions. We aimed to investigate the proteomic differences between these two metabolically contrasting tissue types, as well as between vG and plain morphs (G) to gain more insight into the evolutionary benefits of variegation. Label-free proteomics was performed using liquid chromatography coupled to tandem mass spectrometry. The data were searched against the newly expanded RNAseq database for P. zonale leaves. Analysis was done with X!Tandem, using 10 ppm precursor mass precision and fragment 0.02 Th mass tolerance. The identified proteins were filtered using X!TandemPipeline, requiring at least two peptides with E-values lower than 0.01 and a protein E-value<10-5. Peptide ions, and their parental proteins, were quantified by integrating signal intensities from extracted ion currents (XIC) using MassChroQ software. A total of 2707 protein groups were identified. After removing dubious data and peptides with missing values, we obtained 2009 protein group. We annotated 564 and 79 differentially abundant proteins in vG vs. vW and vG vs. G, respectively. The differentially abundant proteins were mapped into metabolic pathways using the modified MapMan 3.6.0RC1 software. Proteins related to photosynthesis and carbohydrate metabolism were more abundant in vG compared with vW, while proteins related to oxidative stress and protein degradation were more abundant in vW than in vG. Compared to vG, G tissue contained more proteins involved in energy production and protein synthesis. Briefly, this study has paved the way to uncover the evolutionary advantages of the variegated phenotype.", publisher = "Belgrade : Institute of Molecular Genetics and Genetic Engineering", journal = "5th Belgrade Bioinformatics Conference", title = "Label-Free Quantitative Proteomics of Pelargonium zonale: Tissue-Specific Differences", pages = "52-52", url = "https://hdl.handle.net/21.15107/rcub_imagine_2455" }
Milić, D., Balliau, T., Davanture, M., Blein-Nicolas, M.,& Vidović, M.. (2024). Label-Free Quantitative Proteomics of Pelargonium zonale: Tissue-Specific Differences. in 5th Belgrade Bioinformatics Conference Belgrade : Institute of Molecular Genetics and Genetic Engineering., 52-52. https://hdl.handle.net/21.15107/rcub_imagine_2455
Milić D, Balliau T, Davanture M, Blein-Nicolas M, Vidović M. Label-Free Quantitative Proteomics of Pelargonium zonale: Tissue-Specific Differences. in 5th Belgrade Bioinformatics Conference. 2024;:52-52. https://hdl.handle.net/21.15107/rcub_imagine_2455 .
Milić, Dejana, Balliau, Thierry, Davanture, Marlène, Blein-Nicolas, Melisande, Vidović, Marija, "Label-Free Quantitative Proteomics of Pelargonium zonale: Tissue-Specific Differences" in 5th Belgrade Bioinformatics Conference (2024):52-52, https://hdl.handle.net/21.15107/rcub_imagine_2455 .