Calculation of enrichment factors identifies low abundant lipid droplet-associated proteins from Arabidopsis thaliana seeds and seedlings

ABSTRACT: The developmental program of seed formation and seedling development requires not only tight regulation of cell division and metabolism but also the adaption of organelles in structure and function. Therefore, changes in organellar protein composition is one crucial factor in development. Of particular interest in plants is the switch to photoautotrophic growth, for which biosynthesis and degradation of lipid droplets (LDs) play a critical role. We present here a bottom-up proteomics study analyzing eight different developmental phases during silique development, seed germination and seedling establishment. We investigated both total protein fractions and LD-enriched fractions for each time point. The overall changes in the seed and seedling proteome during germination and seedling establishment monitored in this study present a rich resource for researchers interested in different questions of early seedling biology. The analysis of the proteome of LDs using LD-enrichment factors allowed the identification of four LD-associated protein families, which were subsequently confirmed by a cell biological approach. In addition to protein discovery, our dataset allows for the study of the dynamics of LD proteins throughout the developmental phases analyzed. We found that the relative levels of oleosin stay stable, while many other proteins accumulate on LDs at later stages of seedling establishment. The methodology described here is shown to be well suited for describing a comprehensive and quantitative view of the Arabidopsis proteome across time, with a particular focus on proteins associated with LDs.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Seedling, Seed, Silique

SUBMITTER: Till Ischebeck  

LAB HEAD: Till Ischebeck

PROVIDER: PXD015091 | Pride | 2019-12-18

REPOSITORIES: Pride