Chapter 6 : The Proteome

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The Proteome, Page 1 of 2

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Proteome-wide studies of malaria have also lent a great deal of insight into protein-protein and protein-drug interactions, subcellular localization, functional characterization of unknown genes, and mechanisms of posttranscriptional regulation through comparisons with mRNA expression profiles. The work outlined in this chapter focuses on bottom-up approaches to study the malaria proteome. In October 2002, the genome sequence of was released, paving the way not only for genome-wide studies of mRNA but also for protein profiling. The accumulation of data collected from large-scale profiling experiments has also demonstrated ways that proteome data can aid the annotation of recently sequenced genomes. The genome showed markedly different properties from any other organism, namely, that it is the most A-T-rich genome sequenced to date, making the bioinformatic prediction of gene products from the genome sequence difficult based heavily on knowledge from other organisms. While proteome-wide studies of whole-cell lysates lend a great deal of information about an organism from a holistic perspective, it is equally informative to combine cell fractionation methods with high-throughput protein identifications to define the proteome of a particular subcellular location or organelle. Most significantly, correlating mRNA and protein expression profiles for individual genes revealed particular genes and families of functionally related genes that appeared to observe similar patterns of mRNA and protein accumulation.

Citation: Johnson J, Yates J. 2005. The Proteome, p 85-94. In Sherman I (ed), Molecular Approaches to Malaria. ASM Press, Washington, DC. doi: 10.1128/9781555817558.ch6

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Liquid Chromatography-Tandem Mass Spectrometry
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Image of FIGURE 1

Subtractive analysis of rhoptry-enriched proteins. Plotted is the percent difference in sequence coverage between proteome analyses of rhoptry-enriched proteins and whole cell extracts of asexual blood stages. Transmembrane domains and signal peptides are indicated, as are proteins representative of the rhoptry-enriched fraction.

Citation: Johnson J, Yates J. 2005. The Proteome, p 85-94. In Sherman I (ed), Molecular Approaches to Malaria. ASM Press, Washington, DC. doi: 10.1128/9781555817558.ch6
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Image of FIGURE 2

Scatterplots of mRNA and protein fold changes during trophozoite-to-schizont transitions. Quadrants are indicated by Roman numerals. Data points falling into quadrants I and III are shown by open squares, and data points falling into quadrants II and IV are shown by closed squares. Data points that fell into quadrants II and IV were replotted (inset) as the mRNA fold change of the transition indicated versus the protein fold change of the following transition (i.e., the inset is a plot of the fold change in mRNA abundance for the trophozoite-toschizont versus the fold change in protein abundance for the schizont-to-merozoite transition).

Citation: Johnson J, Yates J. 2005. The Proteome, p 85-94. In Sherman I (ed), Molecular Approaches to Malaria. ASM Press, Washington, DC. doi: 10.1128/9781555817558.ch6
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