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Post-translational regulation and the evolution of eukaryotic genomes

Ying He (UGent)
(2011)
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Abstract
With the advent of phosphoproteomics in the past decade, high-throughput detection of phosphorylation sites, at the genome scale, became available. Therefore, it provides a great opportunity to study the general properties of the phosphoproteome and the impact of protein phosphorylation, probably the most abundant post-translational modifications, on the evolution of the genome, by using computational and evolutionary analyses. A large number of phosphoproteomics experiments have been performed with Saccharomyces cerevisiae, under a reasonably wide range of conditions. With a wealth of relevant functional genomic information available for this organism, all of these factors should assist in an in-depth bioinformatics analysis of the yeast phosphoproteome. Observations from the yeast phosphoproteome may help draw general conclusions and formulate new questions about phosphorylation and understand certain biological processes in other eukaryotes. In Chapter 2, general properties of the yeast phosphoproteome have been investigated. A high-quality curated phosphoproteomic dataset is assembled from 12 publicly available phosphoproteomic datasets. Recently, concerns have been raised about the possibility of detecting non-functional phosphorylation sites that are technical false-positives or of low-stoichiometry within the cell. The HQ dataset we have provided in Chapter 2 is considered to be filtered of such noise and has been used to study the general properties of the yeast phosphoproteome in a comprehensive way. The impact of post-translational regulation, in particular phosphorylation, on eukaryotic genome evolution has been studied in Chapter 3. Interestingly, we reported for the first time in literature that phosphorylation affects the retention of duplicated genes (especially after genome duplication) in the fungal lineages. This finding may help better understand the basic mechanisms of gene retention and genome evolution. In addition, the general properties (amino acid substitution) of phosphorylation sites have been investigated in Chapter 4. It has been observed in this study that phosphorylated serines, compared to their non-modified counterparts, tend to substitute more frequently to amino acids (aspartic acid, glutamic acid) that shared similar (phosphomimetic) properties and less frequently to alanine which resembles non-phosphorylation status.
Keywords
yeast phosphoproteome, gene regulation, whole genome duplication, phosphorylation, post-translational modification, gene retention, genome evolution

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Citation

Please use this url to cite or link to this publication:

Chicago
He, Ying. 2011. “Post-translational Regulation and the Evolution of Eukaryotic Genomes”. Ghent, Belgium: Ghent University. Faculty of Sciences.
APA
He, Ying. (2011). Post-translational regulation and the evolution of eukaryotic genomes. Ghent University. Faculty of Sciences, Ghent, Belgium.
Vancouver
1.
He Y. Post-translational regulation and the evolution of eukaryotic genomes. [Ghent, Belgium]: Ghent University. Faculty of Sciences; 2011.
MLA
He, Ying. “Post-translational Regulation and the Evolution of Eukaryotic Genomes.” 2011 : n. pag. Print.
@phdthesis{1969560,
  abstract     = {With the advent of phosphoproteomics in the past decade, high-throughput detection of phosphorylation sites, at the genome scale, became available. Therefore, it provides a great opportunity to study the general properties of the phosphoproteome and the impact of protein phosphorylation, probably the most abundant post-translational modifications, on the evolution of the genome, by using computational and evolutionary analyses. 
A large number of phosphoproteomics experiments have been performed with Saccharomyces cerevisiae, under a reasonably wide range of conditions. With a wealth of relevant functional genomic information available for this organism, all of these factors should assist in an in-depth bioinformatics analysis of the yeast phosphoproteome. Observations from the yeast phosphoproteome may help draw general conclusions and formulate new questions about phosphorylation and understand certain biological processes in other eukaryotes. 
In Chapter 2, general properties of the yeast phosphoproteome have been investigated. A high-quality curated phosphoproteomic dataset is assembled from 12 publicly available phosphoproteomic datasets. Recently, concerns have been raised about the possibility of detecting non-functional phosphorylation sites that are technical false-positives or of low-stoichiometry within the cell. The HQ dataset we have provided in Chapter 2 is considered to be filtered of such noise and has been used to study the general properties of the yeast phosphoproteome in a comprehensive way.
The impact of post-translational regulation, in particular phosphorylation, on eukaryotic genome evolution has been studied in Chapter 3. Interestingly, we reported for the first time in literature that phosphorylation affects the retention of duplicated genes (especially after genome duplication) in the fungal lineages. This finding may help better understand the basic mechanisms of gene retention and genome evolution.
In addition, the general properties (amino acid substitution) of phosphorylation sites have been investigated in Chapter 4. It has been observed in this study that phosphorylated serines, compared to their non-modified counterparts, tend to substitute more frequently to amino acids (aspartic acid, glutamic acid) that shared similar (phosphomimetic) properties and less frequently to alanine which resembles non-phosphorylation status.},
  author       = {He, Ying},
  keyword      = {yeast phosphoproteome,gene regulation,whole genome duplication,phosphorylation,post-translational modification,gene retention,genome evolution},
  language     = {eng},
  pages        = {XVI, 136},
  publisher    = {Ghent University. Faculty of Sciences},
  school       = {Ghent University},
  title        = {Post-translational regulation and the evolution of eukaryotic genomes},
  year         = {2011},
}