Plastid Proteomic Analysis in Tomato Fruit Development

Abstract

To better understand the mechanism of plastid differentiation from chloroplast to chromoplast, we examined proteome and plastid changes over four distinct developmental stages of ‘Micro-Tom’ fruit. Additionally, to discover more about the relationship between fruit color and plastid differentiation, we also analyzed and compared ‘Micro-Tom’ results with those from two other varieties, ‘Black’ and ‘White Beauty’. We confirmed that proteins related to photosynthesis remain through the orange maturity stage of ‘Micro-Tom’, and also learned that thylakoids no longer exist at this stage. These results suggest that at a minimum there are changes in plastid morphology occurring before all related proteins change. We also compared ‘Micro-Tom’ fruits with ‘Black’ and ‘White Beauty’ using two-dimensional gel electrophoresis. We found a decrease of CHRC (plastid-lipid-associated protein) and HrBP1 (harpin binding protein-1) in the ‘Black’ and ‘White Beauty’ varieties. CHRC is involved in carotenoid accumulation and stabilization. HrBP1 in Arabidopsis has a sequence similar to proteins in the PAP/fibrillin family. These proteins have characteristics and functions similar to lipocalin, an example of which is the transport of hydrophobic molecules. We detected spots of TIL (temperature-induced lipocalin) in 2D-PAGE results, however the number of spots and their isoelectric points differed between ‘Micro-Tom’ and ‘Black’/‘White Beauty’. Lipocalin has various functions including those related to environmental stress response, apoptosis induction, membrane formation and fixation, regulation of immune response, cell growth, and metabolism adjustment. Lipocalin related proteins such as TIL and HrBP1 could be related to the accumulation of carotenoids, fruit color and the differentiation of chromoplast.

Multi-Omics Driven Assembly and Annotation of the Sandalwood (Santalum album) Genome

“…Proteins with dominant expression in fruits include an uncharacterized protein containing a ubiquitin domain (SaT16667-R1), another uncharacterized protein containing a conserved thioredoxin domain (SaT05074-R1), and fatty acid desaturase (SaT02659-R1). The differential regulation of thioredoxin protein has been reported during fruit ripening in apple (Malus domestica) and tomato (Solanum lycopersicum 'Micro-Tom'; Shi et al, 2014;Suzuki et al, 2015). Proteins abundant in leaves include proteins related to photosynthesis and glycolytic enzymes such as conserved PSII 10-kD polypeptide PsbR domaincontaining protein (SaT05917-R1), chlorophyll a/bbinding protein (SaT03975-R1 and SaT07418-R1), manganese-stabilizing protein/PSII polypeptide (SaT04497-R1), and Fru-bisphosphate aldolase class I (SaT02900-R1 and SaT02144-R1).…”

The proteOMIC era: a useful tool to gain deeper insights into plastid physiology

“…All the knowledge exposed here show how useful proteomic strategies are to obtain information not only about the protein of interest but also about protein interactors, their substrates, or processes directly/ indirectly related with the function of the protein of interest (Li et al 2012;Nishimura et al 2013;Gayen et al 2016). Moreover, proteomics can provide extensive information about the proteome in a specific developmental stage of the plant and explain which changes could have an impact in plastid or plant physiology (Barsan et al 2010(Barsan et al , 2012Suzuki et al 2015). It is important to mention that the value of proteomics can be enhanced by combination with other techniques (e.g.…”

“…1). The most commonly used protocol is the trypsin digestion which allows the generation of thousands of peptides for further quantification by mass spectrometry (Faurobert et al 2007; Barsan et al 2010;Suzuki et al 2015). There are also gel-free approaches such as label-free and labelbased techniques.…”

“…2). At early stages of the proteomic era all the efforts were placed in the proteome of chloroplast but recently more and more reports have been published about chromoplast proteomics in order to understand the physiology of the fruit by characterization of plastid differentiation during fruit ripening (Barsan et al 2010(Barsan et al , 2012Wang et al 2013;Suzuki et al 2015). One of the first reports using proteomics to characterize chromoplast biogenesis during tomato (cherry) development is the work published by Faurobert et al (Faurobert et al 2007).…”

“…This correlates with the disruption of the photosynthetic machinery for thylakoids and photosystem biogenesis and the loss of the plastid division machinery. A more recent and extensive analysis conducted by Suzuki et al (Suzuki et al 2015) in which they compared four distinct stages of Micro-Tom fruit development and two different varieties-Black and White Beauty provided new insights into specific proteins related with tomato fruit development. Interestingly, they could confirm that proteins related to photosynthesis remain through the orange maturity stage of Micro-Tom while thylakoids showed to no longer exist in this stage suggesting that at least some morphological changes occur before the protein content change (Suzuki et al 2015).…”