Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Outros Autores: | , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.cpb.2023.100286 http://hdl.handle.net/11449/247378 |
Resumo: | Climate change is escalating the frequency and intensity of warming and drought periods around the globe, currently representing a threat to many plant species. Understanding how plants cope with such abiotic stresses is crucial.We investigate how Eucalyptus grandis, a plant species with several industry applications, copes with seasonal variation and water restriction imposition at the proteomic level under field conditions. Therefore, we attempted to identify known proteins and novel peptides associated with the effect of seasonality and water restriction impositions, as well as to provide insights into how novel peptides behave under such conditions. The leaf proteome of E. grandis plants was studied under both a conventional proteomic workflow and a dedicated proteogenomics approach. The highest proteomic variability was identified in the summer season and the most abundant known proteins associated with seasonal variation were related to photosynthesis. Post-translational modifications, protein turnover, and chaperones were the main functional classifications identified among biological treatments. Furthermore, 144 novel peptides not predicted by current proteomics pipelines, were identified by both spectral correlations against modified databases (43) and a de novo peptide sequencing approach (101). It is predicted that most single amino acid substituted (SAS) peptides, mainly associated with the photosynthesis process, decrease protein stability by altering the quantitative change upon ΔΔG values and non-covalent interactions. Multiple reaction monitoring validation assays were performed for selected novel peptide identifications demonstrating that it is a very robust mass spectrometry-based method of validation. Data are available via ProteomeXchange with identifier PXD031100. |
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Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteomeDrought stressMRMProteogenomicsProteomicsClimate change is escalating the frequency and intensity of warming and drought periods around the globe, currently representing a threat to many plant species. Understanding how plants cope with such abiotic stresses is crucial.We investigate how Eucalyptus grandis, a plant species with several industry applications, copes with seasonal variation and water restriction imposition at the proteomic level under field conditions. Therefore, we attempted to identify known proteins and novel peptides associated with the effect of seasonality and water restriction impositions, as well as to provide insights into how novel peptides behave under such conditions. The leaf proteome of E. grandis plants was studied under both a conventional proteomic workflow and a dedicated proteogenomics approach. The highest proteomic variability was identified in the summer season and the most abundant known proteins associated with seasonal variation were related to photosynthesis. Post-translational modifications, protein turnover, and chaperones were the main functional classifications identified among biological treatments. Furthermore, 144 novel peptides not predicted by current proteomics pipelines, were identified by both spectral correlations against modified databases (43) and a de novo peptide sequencing approach (101). It is predicted that most single amino acid substituted (SAS) peptides, mainly associated with the photosynthesis process, decrease protein stability by altering the quantitative change upon ΔΔG values and non-covalent interactions. Multiple reaction monitoring validation assays were performed for selected novel peptide identifications demonstrating that it is a very robust mass spectrometry-based method of validation. Data are available via ProteomeXchange with identifier PXD031100.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)School of Agriculture and Veterinary Sciences São Paulo State University (UNESP), SPChristopher S. Bond Life Sciences Center University of MissouriDepartment of Biochemistry University of MissouriSchool of Agriculture and Veterinary Sciences São Paulo State University (UNESP), SPCNPq: n° 140809/2018-0CNPq: n° 200872/2020-6FAPESP: n° 2018/15035-8CNPq: n° 304479/2020-9CNPq: n° 400459/2016-7Universidade Estadual Paulista (UNESP)University of MissouriJorge, Gabriel L. [UNESP]de Paula, Rinaldo C. [UNESP]Mooney, BrianThelen, Jay J.Balbuena, Tiago S. [UNESP]2023-07-29T13:14:24Z2023-07-29T13:14:24Z2023-06-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1016/j.cpb.2023.100286Current Plant Biology, v. 34.2214-6628http://hdl.handle.net/11449/24737810.1016/j.cpb.2023.1002862-s2.0-85159320808Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengCurrent Plant Biologyinfo:eu-repo/semantics/openAccess2023-07-29T13:14:24Zoai:repositorio.unesp.br:11449/247378Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-07-29T13:14:24Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome |
title |
Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome |
spellingShingle |
Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome Jorge, Gabriel L. [UNESP] Drought stress MRM Proteogenomics Proteomics |
title_short |
Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome |
title_full |
Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome |
title_fullStr |
Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome |
title_full_unstemmed |
Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome |
title_sort |
Seasonal and water restriction-related changes in Eucalyptus grandis leaf proteins: Shedding light on the dark proteome |
author |
Jorge, Gabriel L. [UNESP] |
author_facet |
Jorge, Gabriel L. [UNESP] de Paula, Rinaldo C. [UNESP] Mooney, Brian Thelen, Jay J. Balbuena, Tiago S. [UNESP] |
author_role |
author |
author2 |
de Paula, Rinaldo C. [UNESP] Mooney, Brian Thelen, Jay J. Balbuena, Tiago S. [UNESP] |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (UNESP) University of Missouri |
dc.contributor.author.fl_str_mv |
Jorge, Gabriel L. [UNESP] de Paula, Rinaldo C. [UNESP] Mooney, Brian Thelen, Jay J. Balbuena, Tiago S. [UNESP] |
dc.subject.por.fl_str_mv |
Drought stress MRM Proteogenomics Proteomics |
topic |
Drought stress MRM Proteogenomics Proteomics |
description |
Climate change is escalating the frequency and intensity of warming and drought periods around the globe, currently representing a threat to many plant species. Understanding how plants cope with such abiotic stresses is crucial.We investigate how Eucalyptus grandis, a plant species with several industry applications, copes with seasonal variation and water restriction imposition at the proteomic level under field conditions. Therefore, we attempted to identify known proteins and novel peptides associated with the effect of seasonality and water restriction impositions, as well as to provide insights into how novel peptides behave under such conditions. The leaf proteome of E. grandis plants was studied under both a conventional proteomic workflow and a dedicated proteogenomics approach. The highest proteomic variability was identified in the summer season and the most abundant known proteins associated with seasonal variation were related to photosynthesis. Post-translational modifications, protein turnover, and chaperones were the main functional classifications identified among biological treatments. Furthermore, 144 novel peptides not predicted by current proteomics pipelines, were identified by both spectral correlations against modified databases (43) and a de novo peptide sequencing approach (101). It is predicted that most single amino acid substituted (SAS) peptides, mainly associated with the photosynthesis process, decrease protein stability by altering the quantitative change upon ΔΔG values and non-covalent interactions. Multiple reaction monitoring validation assays were performed for selected novel peptide identifications demonstrating that it is a very robust mass spectrometry-based method of validation. Data are available via ProteomeXchange with identifier PXD031100. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-07-29T13:14:24Z 2023-07-29T13:14:24Z 2023-06-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1016/j.cpb.2023.100286 Current Plant Biology, v. 34. 2214-6628 http://hdl.handle.net/11449/247378 10.1016/j.cpb.2023.100286 2-s2.0-85159320808 |
url |
http://dx.doi.org/10.1016/j.cpb.2023.100286 http://hdl.handle.net/11449/247378 |
identifier_str_mv |
Current Plant Biology, v. 34. 2214-6628 10.1016/j.cpb.2023.100286 2-s2.0-85159320808 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Current Plant Biology |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1799964844387991552 |