TMT proteomics analysis of a pseudocereal crop, quinoa (Chenopodium quinoa Willd.), during seed maturation

Zhi-Jun Shen; Su-Xia Xu; Qing-Yun Huang; Zi-Yang Li; Yi-Ding Xu; Chun-Song Lin; Yi-Jin Huang

doi:10.3389/fpls.2022.975073

TMT proteomics analysis of a pseudocereal crop, quinoa (Chenopodium quinoa Willd.), during seed maturation

Front Plant Sci. 2022 Nov 8:13:975073. doi: 10.3389/fpls.2022.975073. eCollection 2022.

Authors

Zhi-Jun Shen¹, Su-Xia Xu¹, Qing-Yun Huang¹, Zi-Yang Li², Yi-Ding Xu³, Chun-Song Lin¹, Yi-Jin Huang⁴

Affiliations

¹ Fujian Key Laboratory of Subtropical Plant Physiology and Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, China.
² Institute of Gene Science for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China.
³ Landscape Architecture and Landscape Research Branch, China Academy of Urban Planning and Design, Beijing, China.
⁴ Department of Dermatology, The First Affiliated Hospital of Xiamen University, Xiamen, China.

Abstract

Quinoa (Chenopodium quinoa Willd.), an Andean native crop, is increasingly popular around the world due to its high nutritional content and stress tolerance. The production and the popularity of this strategic global food are greatly restricted by many limiting factors, such as seed pre-harvest sprouting, bitter saponin, etc. To solve these problems, the underlying mechanism of seed maturation in quinoa needs to be investigated. In this study, based on the investigation of morphological characteristics, a quantitative analysis of its global proteome was conducted using the combinational proteomics of tandem mass tag (TMT) labeling and parallel reaction monitoring (PRM). The proteome changes related to quinoa seed maturation conversion were monitored to aid its genetic improvement. Typical changes of morphological characteristics were discovered during seed maturation, including mean grain diameter, mean grain thickness, mean hundred-grain weight, palea, episperm color, etc. With TMT proteomics analysis, 581 differentially accumulated proteins (DAPs) were identified. Functional classification analysis and Gene Ontology enrichment analysis showed that most DAPs involved in photosynthesis were downregulated, indicating low levels of photosynthesis. DAPs that participated in glycolysis, such as glyceraldehyde-3-phosphate dehydrogenase, pyruvate decarboxylase, and alcohol dehydrogenase, were upregulated to fulfill the increasing requirement of energy consumption during maturation conversion. The storage proteins, such as globulins, legumins, vicilins, and oleosin, were also increased significantly during maturation conversion. Protein-protein interaction analysis and function annotation revealed that the upregulation of oleosin, oil body-associated proteins, and acyl-coenzyme A oxidase 2 resulted in the accumulation of oil in quinoa seeds. The downregulation of β-amyrin 28-oxidase was observed, indicating the decreasing saponin content, during maturation, which makes the quinoa "sweet". By the PRM and qRT-PCR analysis, the expression patterns of most selected DAPs were consistent with the result of TMT proteomics. Our study enhanced the understanding of the maturation conversion in quinoa. This might be the first and most important step toward the genetic improvement of quinoa.

Keywords: PRM; TMT proteomics; quinoa; regulation mechanism; seed maturation.