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

Yu-Chen Song; Debatosh Das; Youjun Zhang; Mo-Xian Chen; Alisdair R Fernie; Fu-Yuan Zhu; Jiangang Han

doi:10.1016/j.tibtech.2023.05.010

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

Trends Biotechnol. 2023 Dec;41(12):1532-1548. doi: 10.1016/j.tibtech.2023.05.010. Epub 2023 Jun 24.

Authors

Yu-Chen Song¹, Debatosh Das², Youjun Zhang³, Mo-Xian Chen⁴, Alisdair R Fernie⁵, Fu-Yuan Zhu⁶, Jiangang Han⁷

Affiliations

¹ 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.
² College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences and Technology, 52 Agricultural Building, University of Missouri-Columbia, MO 65201, USA.
³ Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria.
⁴ 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.
⁵ 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.
⁶ 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.
⁷ 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.

PMID: 37365082
DOI: 10.1016/j.tibtech.2023.05.010

Abstract

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.

Keywords: proteogenomics; single-cell omics; spatial omics.

Publication types

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

MeSH terms

Genome
Proteogenomics*
Proteome / genetics
Transcriptome

Substances

Proteome