Gene and Protein Evolution

Cover......Page 1
Contents......Page 6
Preface......Page 8
Abstract......Page 10
Correlated Patterns......Page 11
Correlated Processes......Page 13
Incorporating Functional Information......Page 15
Within Genes: Proteins......Page 16
Discussion......Page 18
References......Page 20
Protein-Protein Interaction Network as a Typical Example of Biological Networks......Page 22
Evolutionary Studies of Protein-Protein Interaction Networks......Page 24
Differential Evolutionary Rates of Duplicated Genes in Protein Interaction Network......Page 25
Losses of PPIs for Proteins Encoded by Duplicated Genes......Page 26
Functional Divergence through Changes in PPIs......Page 27
Tendency of PPI Divergence for Duplicated Pair in Different Functional Classes......Page 29
The Evolutionary Rate of a Protein is Influenced by F atures of the Interacting Partners......Page 31
SF vs. DF Proteins......Page 32
Comparison of Evolutionary Rates among SF-DP, SF-SP, DF-DP and DF-SP Proteins......Page 33
Prospect of Studies in PPI Network Evolution......Page 35
References......Page 36
Type III Secretion......Page 39
An Evolutionary Conundrum?......Page 41
Modularity......Page 42
Gene Duplication......Page 43
Recombination......Page 44
Molecular Phylogenies and Arguments from Cladistics......Page 45
‘Difficulties on Theory’: EspA and FliK......Page 47
Is FliJ Homologue of YscO?......Page 49
Origins of the Flagellar Motor: From Ion Channel to Rotor?......Page 51
Case Study 3: The Search for Outliers......Page 53
References......Page 54
Abstract......Page 57
The Demography of Packaging ATPases in Large DNA Viruses......Page 59
Multiple Origins for Different Packaging ATPases within the P-loop NTPase Fold......Page 61
Diversity of the Terminase-Dependent Packaging Systems: A Common Origin for Portal Proteins of All Tailed Bacteriophages......Page 64
Contextual Information and Inference of Novel Components of the Terminase Portal Systems......Page 65
Evolutionary Considerations and General Conclusions......Page 69
References......Page 71
Abstract......Page 75
Evolution of Transcription Factors and Target Genes......Page 78
Evolution of the Local Network Structure......Page 80
Evolution of the Global Network Structure......Page 83
Conclusion......Page 85
Acknowledgements......Page 86
References......Page 87
Abstract......Page 90
Identification of Suitable Data Sets......Page 91
Search for Regulatory Motifs Conserved in Each of the Gene Sets......Page 92
Identifying Motifs Supporting Subfunctionalization......Page 95
Results......Page 97
Identification of Motifs Supporting Subfunctionalization......Page 98
Detailed Description of the Datasets with Subfunctionalized Motifs......Page 100
Discussion......Page 106
References......Page 107
Origin of Sex Chromosomes......Page 110
Theoretical Predictions for Molecular Evolution of X-linked and Autosomal Genes......Page 112
Patterns of In Situ Evolution of X-linked and Autosomal Genes......Page 115
Gene Complements of the X Chromosome Versus the Autosomes......Page 119
Patterns of Gene Traffic on the X and the Autosomes......Page 120
Summary......Page 122
References......Page 124
Abstract......Page 128
Distribution of Coding Repeats and Homopeptides......Page 129
Coding Repeats and Protein Function......Page 131
Structure of polyA and polyQ Repeats......Page 132
Formation of Aggregates by Homopeptides......Page 133
Coding Repeats and Evolution......Page 135
References......Page 137
Abstract......Page 140
Molecular Mechanisms Leading to Chimeric Genes......Page 141
Transposable Elements as ‘Fragment Joiners’......Page 142
Nonhomologous Recombination: Ancient Chimeras......Page 144
Nonhomologous Recombination – Evolutionarily Recent Chimeras......Page 146
A Recent Example: Insights from Hun, a Young Gene Generated by NHR......Page 147
Transposable Elements as ‘Fragment Joiners’......Page 150
Chimeric Genes Generated by Gene Fusions......Page 151
References......Page 152
Transposable Elements Defined......Page 156
Selfish DNA Theory of TEs......Page 159
Molecular Domestication......Page 160
Host CDSs from TEs......Page 162
Genome Wide Analyses......Page 163
A New Framework is Needed......Page 165
References......Page 168
Abstract......Page 172
Class I Transposons......Page 173
Class II elements......Page 175
TE Cassettes in mRNAs......Page 176
TE Sequences in Promoter Regions......Page 179
Final Remarks......Page 180
References......Page 181
Abstract......Page 184
Protein-Coding Genes Derived from Retroelements......Page 185
Protein-Coding Retrogenes......Page 187
Neuronal BC1 RNA in Rodents......Page 188
Alu-Derived Neuronal npcRNAs in Primates......Page 190
Retroposed Copies of snoRNAs and Pre-miRNAs......Page 193
The Tip of the Iceberg......Page 194
References......Page 196
Author Index......Page 200
H......Page 201
T......Page 202
Y......Page 203