Vijayendran, Chandran: Proteome, transcriptome and metabolome plasticity in closely related strains of Escherichia coli - K12 and its diversity during molecular evolution pr [...]. 2007
Inhalt
- Prologue
- I The plasticity of global proteome and genome expression analyzed in closely related W3110 and MG1655 strains of a well studied model organism, Escherichia coli - K12.
- Introduction (I)
- Materials and Methods (I)
- Strains and medium
- Two-dimensional SDS-PAGE gel electrophoresis
- In-gel tryptic digestion and mass spectrometry
- Microarray experiments
- DNA microarray analysis
- Microarray data analysis
- Real-time RT-PCR
- Determination of siderophores
- Cloning and sequencing of rpoS
- Results and Discussion (I)
- Expression of RpoS-dependent genes
- Expression of energy metabolism genes
- Expression of iron-related genes
- Verification of microarray results
- Effect of rpoS gene amber mutation in gene expression
- Expression of cellular proteins
- Conclusion (I)
- II Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling.
- Introduction (II)
- Materials and Methods (II)
- Strains and culture conditions
- Metabolite profiling
- Gene expression profiling
- Microarray data analysis
- Network analysis
- Network functional analysis
- Outer-membrane protein analysis
- Results (II)
- Metabolome profiling
- Gene expression profiling
- Extent of changes
- Direction of the observed extent of changes
- Metabolite to gene correlation network analysis
- Evaluation of evolution specific networks
- Evolution specific intersection networks
- Parallelism and functional relevance of molecular evolution
- Parallelism in outer-membrane protein expression
- Discussion (II)
- Conclusion (II)
- III Integration of proteome with transcriptome and metabolome profile during molecular evolution processes in Escherichia coli.
- Introduction (III)
- Materials and Methods (III)
- Strain and culture conditions
- Two-dimensional SDS-PAGE gel electrophoresis
- In-gel tryptic digestion and mass spectrometry
- Analysis of two-dimensional protein gels
- Network analysis
- Results (III)
- Proteome profiles of ancestral and evolved lines
- Changes in transcript and metabolite levels
- Changes in protein expression levels in experimental evolutionary conditions
- Direction of the observed protein expression changes
- Protein correlation network analysis
- Comparison of transcript, metabolite and protein levels
- Comparison of parallelism in the three functional levels
- Discussion (III)
- Conclusion (III)
- IV 2DBase: 2D-PAGE Database of Escherichia coli.