Plant organelle proteomics: Collaborating for optimal cell function

Abstract

Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.

Plastid Proteomics in Higher Plants: Current State and Future Goals

“…However, this is challenging for Arabidopsis, since its seeds and flowers are small and it does not develop storage organs. Thus, organelle isolation is often impractical, and proteome analyses are better performed at the level of the entire organ, as illustrated by the analysis of plastids in seeds (Chen et al, 2009 (Agrawal et al, 2010). However, so far, this has not significantly increased the number of identified plastid proteins, in part due to the lack of complete genome sequence information.…”

“…The spatial distribution of proteins within chloroplasts has been the target of several proteome analyses, originally starting with the thylakoid lumen and peripheral soluble thylakoid proteins (Peltier et al, 2000), followed by systematic analyses of the thylakoid and envelope membrane proteomes, the soluble stroma proteome, specialized thylakoid-associated lipoprotein particles, assigned plastoglobules, and proteins associated with the plastid chromosome (Baginsky, 2009;Agrawal et al, 2010). A recent study separated the Arabidopsis chloroplast proteome into soluble proteins and thylakoid and envelope membrane proteins .…”

“…prabi.fr/at_chloro/). Because of space constraints in this update, we refer the reader to the most recent and comprehensive review with extensive literature citations (Agrawal et al, 2010) instead of discussing the original literature in this report.…”

“…Thus, analyses of the protein composition of cell organelles were reported for virtually all plant cell organelles or membranes (Baginsky, 2009;Agrawal et al, 2010). At present, plant modeling and systems analysis approaches with subcellular organelles suffer from incomplete proteome identification and annotation.…”

“…should ultimately be able to answer. For more exhaustive overviews on proteomics of plastids, we refer to two recent review articles and the references therein (Baginsky, 2009;Agrawal et al, 2010); space restrictions do not allow us to cite recent literature more extensively.…”