Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants.

Proteogenomics Genome Proteome / genetics Transcriptome
proteogenomics single-cell omics spatial omics

Journal

Trends in biotechnology
ISSN: 1879-3096
Titre abrégé: Trends Biotechnol
Pays: England
ID NLM: 8310903

Informations de publication

Date de publication:
12 2023
Historique:
received: 17 03 2023
revised: 17 05 2023
accepted: 30 05 2023
medline: 13 11 2023
pubmed: 27 6 2023
entrez: 26 6 2023
Statut: ppublish

Résumé

Proteogenomics (PG) integrates the proteome with the genome and transcriptome to refine gene models and annotation. Coupled with single-cell (SC) assays, PG effectively distinguishes heterogeneity among cell groups. Affiliating spatial information to PG reveals the high-resolution circuitry within SC atlases. Additionally, PG can investigate dynamic changes in protein-coding genes in plants across growth and development as well as stress and external stimulation, significantly contributing to the functional genome. Here we summarize existing PG research in plants and introduce the technical features of various methods. Combining PG with other omics, such as metabolomics and peptidomics, can offer even deeper insights into gene functions. We argue that the application of PG will represent an important font of foundational knowledge for plants.

Identifiants

DOI: 10.1016/j.tibtech.2023.05.010 PMID: 37365082
pubmed: 37365082
pii: S0167-7799(23)00157-9
doi: 10.1016/j.tibtech.2023.05.010
pii:
doi:

Substances chimiques

Proteome 0

Types de publication

Journal Article Review Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1532-1548

Informations de copyright

Copyright © 2023 Elsevier Ltd. All rights reserved.

Déclaration de conflit d'intérêts

Declaration of interests No interests are declared by the authors.

Auteurs

Yu-Chen Song (YC)

State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China.

Debatosh Das (D)

College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences and Technology, 52 Agricultural Building, University of Missouri-Columbia, MO 65201, USA.

Youjun Zhang (Y)

Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.

Mo-Xian Chen (MX)

State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China. Electronic address: cmx2009920734@gmail.com.

Alisdair R Fernie (AR)

Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria. Electronic address: Fernie@mpimp-golm.mpg.de.

Fu-Yuan Zhu (FY)

State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China. Electronic address: fyzhu@njfu.edu.cn.

Jiangang Han (J)

State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; College of Biology and Environment, Nanjing Forestry University, Nanjing 210037, China. Electronic address: hjg@njfu.edu.cn.

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Classifications MeSH

questionsmedicales.fr › Disciplines des sciences naturelles › Chimie › Biochimie › Protéomique › Protéogénomique › Proteogenomics-based functional genome...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Proteogenomics-based functional genome...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Protéome › Proteogenomics-based functional genome...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Transcriptome › Proteogenomics-based functional genome...