iTRAQ-Based Proteomic Analysis of the Metabolism Mechanism Associated with Silicon Response in the Marine Diatom Thalassiosira pseudonana

Abstract

Silicon is a critical element for diatom growth; however our understanding of the molecular mechanisms involved in intracellular silicon responses are limited. In this study, an iTRAQ-LC-MS/MS quantitative proteomic approach was coupled with an established synchrony technique to reveal the global metabolic silicon-response in the model diatom Thalassiosira pseudonana subject to silicon starvation and readdition. Four samples, which corresponded to the time of silicon starvation, girdle band synthesis, valve formation, and right after daughter cell separation (0, 1, 5, 7 h), were collected for the proteomic analysis. The results indicated that a total of 1,831 proteins, representing 16% of the predicted proteins encoded by the T. pseudonana genome, could be identified. Of the identified proteins, 165 were defined as being differentially expressed proteins, and these proteins could be linked to multiple biochemical pathways. In particular, a number of proteins related to silicon transport, cell wall synthesis, and cell-cycle progress could be identified. In addition, other proteins that are potentially involved in amino acid synthesis, protein metabolism, and energy generation may have roles in the cellular response to silicon. Our findings provide a range of valuable information that will be of use for further studies of this important physiological response that is unique to diatoms.

Dynamic responses to silicon in Thalasiossira pseudonana - Identification, characterisation and classification of signature genes and their corresponding protein motifs

“…While the correlation between transcript and protein abundance is not absolute 46, 47 , components of protein complexes such as the ribosome or the proteasome generally show a high degree of co-expression 43, 48–50 . Frustule synthesis in diatom cultures is strongly correlated with the cell cycle; furthermore, synthesis of the valve and girdle bands is partly separated in time 20, 38, 51 . It is likely that the expression of proteins involved in frustule biosynthesis needs to be coordinated, and that substructures of the frustule need different subsets of proteins.…”

“…Recent research has revealed large clusters of genes with expression that is correlated with central Si metabolism genes such as Si transporters or silaffins 35, 36 . Proteomic studies of diatom frustules 16, 37 and responses to Si replenishment 38 have provided another layer of information regarding Si metabolism and frustule synthesis.…”

The involvement and possible mechanism of pro-inflammatory tumor necrosis factor alpha (TNF-α) in thoracic ossification of the ligamentum flavum

“…In order to acquire a comprehensive and quantitative protein profile, the isobaric tags for relative and absolute quantitation (iTRAQ) has been developed to become an approach appropriate for investigating proteomic changes during various developmental stages [28]. …”

Comparative analyses of transcriptome and proteome in response to cotton bollworm between a resistant wild soybean and a susceptible soybean cultivar

“…Subsequently, the labeled peptide mixtures were pooled and pre-separated by strong cation exchange chromatography with the LC-20AB HPLC pump system (Shimadzu, Kyoto, Japan). iTRAQ analysis was performed on a TripleTOF 5600 system (AB SCIEX, Concord, ON, Canada) combined with a Famos autosampler (LC Packings) and LC20-AD Nano HPLC (Shimadzu, Kyoto, Japan), according to a previously reported study (Du et al 2014). Proteome Discoverer software (ver.1.2.0.339; Thermo Fisher Scientific, San Jose, CA, USA) was used to transform raw data files into MGF files.…”