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Ubiquitylome analysis reveals the involvement of ubiquitination in the bast fiber growth of ramie

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Abstract

Main conclusion

A total of 249 sites from 197 proteins showed a differential ubiquitination level in the fiber development of ramie barks. The function of two differentially ubiquitinated proteins for fiber growth was demonstrated.

Abstract

Ubiquitination is one of the most common post-translational modifications of proteins, and it plays essential roles in plant growth and development. However, the involvement of ubiquitination in the growth of plant fibers remains largely unknown. We compared the ubiquitylome of the top and middle stems of ramie bark, with different fiber growth stages. We identified 249 differentially ubiquitinated sites in 197 proteins in fiber-developing barks in the stems and found that seven were homologs of Arabidopsis proteins associated with fiber growth. Overexpression of the differentially ubiquitinated proteins, RWA3 homolog whole_GLEAN_10024150 and MYB protein whole_GLEAN_10015497, significantly promoted fiber growth in transgenic Arabidopsis, indicating their involvement in this process. We also found that the abundance of these proteins decreased when their ubiquitination levels increased and vice versa in the fiber-developing bark. These results indicated that the abundance of these two proteins was adjusted through ubiquitin-dependent degradation. Collectively, our findings provide important insights into the involvement of ubiquitination in the growth of ramie fibers.

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Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the iProX partner repository with the data set identifier PXD024923.

Abbreviations

GO:

Gene Ontology

MPS:

Bast in middle part of stem

PTM:

Post-translational modification

TPS:

Bast in top part of stem

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (31871678, 32001512), the Agricultural Science and Technology Innovation Program of China (CAAS-ASTIP-IBFC), and the National Modern Agroindustry Technology Research System of China (nycytx-19-E16).

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Authors and Affiliations

  1. Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China

    Qiaoyun He, Zheng Zeng, Fu Li, Yanzhou Wang & Touming Liu

  2. Hunan Institute of Plant Protection, Changsha, 410125, China

    Renyan Huang

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  1. Qiaoyun He
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Contributions

HQ analyzed the ubiquitylome. ZZ performed the overexpression analysis of two genes. LF collected tissue samples and extracted proteins. HR conducted the bioinformatic analysis. WY managed the project and contributed novel reagents. LT designed this study and wrote the manuscript.

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Correspondence to Touming Liu.

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425_2021_3652_MOESM1_ESM.docx

Supplementary file 1 (DOCX 1244 KB) Table S1. Primer sequences for DNA amplification. Fig. S1. Microscopy findings of fiber cells from ramie stem barks (from Chen et al. 2014, BMC Genomics 15:919). We analyzed ubiquitylomes in bark from top (TPS) and from middle (MPS) portions of stems, where growth of secondary cellular walls had, respectively, not started and had thickened. Red arrows indicate the differential thickness in the cell wall of fibers from two tissues. Bars in the microscopic section of TPS and MPS is 20 μm long, and in the figure of whole-plant plant is 10 cm long. Fig. S2. Evaluation of repeatability among replicates based on principal component correlation analysis. Blue and red dots, replicate bark samples from top (TPS) and middle (MPS) parts of stems. Fig. S3. Expression of seven fiber growth-related candidates in the bark from the top part of the stem (TPS) and the middle part of the stem (MPS), where the fiber growth is under different stage. The y-axis represents the value of fragments per kilobase per million reads (FPKM).

Supplementary file 2 (XLSX 55 KB) Table S2. Differentially ubiquitinated sites in 197 proteins.

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He, Q., Zeng, Z., Li, F. et al. Ubiquitylome analysis reveals the involvement of ubiquitination in the bast fiber growth of ramie. Planta 254, 1 (2021). https://doi.org/10.1007/s00425-021-03652-x

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