Proteome characterization of cassava (Manihot esculenta Crantz) somatic embryos, plantlets and tuberous roots

Abstract

Background: Proteomics is increasingly becoming an important tool for the study of many different aspects of plant functions, such as investigating the molecular processes underlying in plant physiology, development, differentiation and their interaction with the environments. To investigate the cassava (Manihot esculenta Crantz) proteome, we extracted proteins from somatic embryos, plantlets and tuberous roots of cultivar SC8 and separated them by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE).

Results: Analysis by liquid chromatography-electrospray ionisation-tandem mass spectrometry (LC-ESI-MS/MS) yielded a total of 383 proteins including isoforms, classified into 14 functional groups. The majority of these were carbohydrate and energy metabolism associated proteins (27.2%), followed by those involved in protein biosynthesis (14.4%). Subsequent analysis has revealed that 54, 59, 74 and 102 identified proteins are unique to the somatic embryos, shoots, adventitious roots and tuberous roots, respectively. Some of these proteins may serve as signatures for the physiological and developmental stages of somatic embryos, shoots, adventitious roots and tuberous root. Western blotting results have shown high expression levels of Rubisco in shoots and its absence in the somatic embryos. In addition, high-level expression of alpha-tubulin was found in tuberous roots, and a low-level one in somatic embryos. This extensive study effectively provides a huge data set of dynamic protein-related information to better understand the molecular basis underlying cassava growth, development, and physiological functions.

Conclusion: This work paves the way towards a comprehensive, system-wide analysis of the cassava. Integration with transcriptomics, metabolomics and other large scale "-omics" data with systems biology approaches can open new avenues towards engineering cassava to enhance yields, improve nutritional value and overcome the problem of post-harvest physiological deterioration.

Figure 1

Different developmental stages of cassava cultivar SC8. A, The pure somatic embryos (SE). The framed region is a single SE. B, Plantlets. Protein extracts are from adventitious roots and shoots of plantlets, respectively; and C, Tuberous root. The framed region presents the place of protein extracts.

Figure 2

Results of Rubisco in cassava cultivar SC8 tuberous roots as a representation using LC-ESI-MS/MS. A and B, Output of the database searching by the MSCOT program using MS/MS data in the identification of Rubisco. The matched peptides were shown in bold red and sequence coverage was 26%. C. MS/MS spectrum of ions with m/z values of 725.96 in panel A covered with circle.

Figure 3

The functional classification and distribution of all 383 identified proteins from cassava cultivar SC8. Unknown proteins include those whose functions have not been described.

Figure 4

The functional classification and distribution of identified proteins from somatic embryos, adventitious roots, shoots and tuberous roots.

Figure 5

Western blotting of Rubisco and α-tubulan. Rubisco and α-tubulan in the somatic embryos, plantlets and tuberous roots of cassava cultivar SC8 were detected by Western blotting using antiRubisco-polyclonal antibody from Agrisera (AS07218) and anti-α-tubulin-monoclonal antibody from Sigma-Aldrich (T9026). ARs, adventitious roots.