微信扫一扫,移动浏览光盘
简介
Summary:
Publisher Summary 1
Volff notes in his preface to this volume that the genomics era has completely altered our understanding of evolution, particularly through the emergence of comparative genomics, which allows analysis of complete genomes and biological processes over huge periods of time. In this collection of monographs, internationally-recognized experts discuss an update of the evolutionary processes at the basis of organismal diversification and complexity, and review the mechanisms that lead to the acquisition of new traits and functions. Different levels of evolution are considered, from internal modules in genes and proteins to interactomes and biological networks. Topics also include the origin of novel genes and gene functions and the evolutionary impact of the duplication of genetic information, and several chapters focus on transposable elements. The volume contains several color and black-and-white illustrations. Annotation 漏2008 Book News, Inc., Portland, OR (booknews.com)
目录
Cover 1
Contents 6
Preface 8
Coevolution within and between Genes 10
Abstract 10
Methods of Coevolution Detection 11
Correlated Patterns 11
Correlated Processes 13
Incorporating Functional Information 15
Lessons from Molecular Coevolution Studies 16
Within Genes: RNAs 16
Within Genes: Proteins 16
Between Genes 18
Discussion 18
References 20
Evolution of Protein-Protein Interaction Network 22
Abstract 22
Protein-Protein Interaction Network as a Typical Example of Biological Networks 22
Evolutionary Studies of Protein-Protein Interaction Networks 24
Differential Evolutionary Rates of Duplicated Genes in Protein Interaction Network 25
Losses of PPIs for Proteins Encoded by Duplicated Genes 26
Functional Divergence through Changes in PPIs 27
Tendency of PPI Divergence for Duplicated Pair in Different Functional Classes 29
The Evolutionary Rate of a Protein is Influenced by F atures of the Interacting Partners 31
SF vs. DF Proteins 32
DP vs. SP Proteins 33
Comparison of Evolutionary Rates among SF-DP, SF-SP, DF-DP and DF-SP Proteins 33
Prospect of Studies in PPI Network Evolution 35
Acknowledgements 36
References 36
Bacterial Flagella and Type III Secretion: Case Studies in the Evolution of Complexity 39
Abstract 39
Type III Secretion 39
An Evolutionary Conundrum? 41
From Simplicity to Complexity 42
Repetition and Self-assembly 42
Modularity 42
Molecular Bricolage 43
Gene Duplication 43
Recombination 44
Case Study 1: Chickens, Eggs and Trees 45
Molecular Phylogenies and Arguments from Cladistics 45
\u2018Difficulties on Theory\u2019: EspA and FliK 47
Case Study 2: New Homologies? 49
Is FliJ Homologue of YscO? 49
Origins of the Flagellar Motor: From Ion Channel to Rotor? 51
Case Study 3: The Search for Outliers 53
Conclusions 54
Note Added in Proof 54
References 54
Comparative Genomics and Evolutionary Trajectories of Viral ATP Dependent DNA-Packaging Systems 57
Abstract 57
Results and Discussion 59
The Demography of Packaging ATPases in Large DNA Viruses 59
Multiple Origins for Different Packaging ATPases within the P-loop NTPase Fold 61
Ancilliary Components of DNA Packaging Systems 64
Diversity of the Terminase-Dependent Packaging Systems: A Common Origin for Portal Proteins of All Tailed Bacteriophages 64
Contextual Information and Inference of Novel Components of the Terminase Portal Systems 65
In Situ Gene Displacement in Terminase Portal Gene Neighborhoods 69
Evolutionary Considerations and General Conclusions 69
Acknowledgements 71
Supplementary Material 71
Note Added in Proof 71
References 71
General Trends in the Evolution of Prokaryotic Transcriptional Regulatory Networks 75
Abstract 75
Evolution of Transcription Factors and Target Genes 78
Evolution of the Local Network Structure 80
Evolution of the Global Network Structure 83
Conclusion 85
Supplementary URL 86
Acknowledgements 86
References 87
Divergence of Regulatory Sequences in Duplicated Fish Genes 90
Abstract 90
Methodology 91
Identification of Suitable Data Sets 91
Pairwise Alignment of Paralogous Intergenic Sequences 92
Search for Regulatory Motifs Conserved in Each of the Gene Sets 92
Assessing the Statistical Significance of Detected Motifs 95
Identifying Motifs Supporting Subfunctionalization 95
Results 97
Identifying Gene Sets Containing Duplicated Fish Genes 98
Determining the Overall Homology Between Paralogous Intergenic Regions 98
Identification of Motifs Supporting Subfunctionalization 98
Detailed Description of the Datasets with Subfunctionalized Motifs 100
Discussion 106
Acknowledgements 107
References 107
Evolution of Gene Function on the X Chromosome Versus the Autosomes 110
Abstract 110
Origin of Sex Chromosomes 110
Theoretical Predictions for Molecular Evolution of X-linked and Autosomal Genes 112
Patterns of In Situ Evolution of X-linked and Autosomal Genes 115
Gene Complements of the X Chromosome Versus the Autosomes 119
Patterns of Gene Traffic on the X and the Autosomes 120
Summary 122
References 124
Amino Acid Repeats and the Structure and Evolution of Proteins 128
Abstract 128
Distribution of Coding Repeats and Homopeptides 129
Relationship between GC Content and Repeat Content 131
Coding Repeats and Protein Function 131
Structure of polyA and polyQ Repeats 132
Structure of other Homopolymers and Nearly Perfect Repeats 133
Formation of Aggregates by Homopeptides 133
Structure of Amyloid 135
Coding Repeats and Evolution 135
References 137
Origination of Chimeric Genes through DNA-Level Recombination 140
Abstract 140
Molecular Mechanisms Leading to Chimeric Genes 141
Nonhomologous Recombination 142
Nondallelic Homologous Recombination 142
Transposable Elements as \u2018Fragment Joiners\u2019 142
Gene Fusions 144
Evidence for Chimeric Proteins 144
Nonhomologous Recombination: Ancient Chimeras 144
Nonhomologous Recombination \u2013 Evolutionarily Recent Chimeras 146
A Recent Example: Insights from Hun, a Young Gene Generated by NHR 147
HR As a Way of Generating Chimeric Proteins \u2013 NAHR 150
Transposable Elements as \u2018Fragment Joiners\u2019 150
Chimeric Genes Generated by Gene Fusions 151
Conclusion 152
Acknowledgement 152
References 152
Exaptation of Protein Coding Sequences from Transposable Elements 156
Abstract 156
Transposable Elements Defined 156
Selfish DNA Theory of TEs 159
Molecular Domestication 160
Host CDSs from TEs 162
Genome Wide Analyses 163
A New Framework is Needed 165
References 168
Modulation of Host Genes by Mammalian Transposable Elements 172
Abstract 172
Transposable Elements 173
Class I Transposons 173
Class II elements 175
Exaptation of Sequences Originated in Transposable Elements (TEs) 176
TE Cassettes in mRNAs 176
TE Sequences in Promoter Regions 179
Transposable Elements and microRNAs 180
Final Remarks 180
References 181
Modern Genomes with Retro-Look: Retrotransposed Elements, Retroposition and the Origin of New Genes 184
Abstract 184
Protein-Coding Genes Derived from Retroelements 185
Protein-Coding Retrogenes 187
RNA Genes 188
Neuronal BC1 RNA in Rodents 188
Alu-Derived Neuronal npcRNAs in Primates 190
Retroposed Copies of snoRNAs and Pre-miRNAs 193
The Tip of the Iceberg 194
Acknowledgements 196
References 196
Author Index 200
Subject Index 201
A 201
B 201
C 201
D 201
E 201
F 201
G 201
H 201
I 202
J 202
L 202
M 202
N 202
O 202
P 202
R 202
S 202
T 202
V 203
W 203
X 203
Y 203
Contents 6
Preface 8
Coevolution within and between Genes 10
Abstract 10
Methods of Coevolution Detection 11
Correlated Patterns 11
Correlated Processes 13
Incorporating Functional Information 15
Lessons from Molecular Coevolution Studies 16
Within Genes: RNAs 16
Within Genes: Proteins 16
Between Genes 18
Discussion 18
References 20
Evolution of Protein-Protein Interaction Network 22
Abstract 22
Protein-Protein Interaction Network as a Typical Example of Biological Networks 22
Evolutionary Studies of Protein-Protein Interaction Networks 24
Differential Evolutionary Rates of Duplicated Genes in Protein Interaction Network 25
Losses of PPIs for Proteins Encoded by Duplicated Genes 26
Functional Divergence through Changes in PPIs 27
Tendency of PPI Divergence for Duplicated Pair in Different Functional Classes 29
The Evolutionary Rate of a Protein is Influenced by F atures of the Interacting Partners 31
SF vs. DF Proteins 32
DP vs. SP Proteins 33
Comparison of Evolutionary Rates among SF-DP, SF-SP, DF-DP and DF-SP Proteins 33
Prospect of Studies in PPI Network Evolution 35
Acknowledgements 36
References 36
Bacterial Flagella and Type III Secretion: Case Studies in the Evolution of Complexity 39
Abstract 39
Type III Secretion 39
An Evolutionary Conundrum? 41
From Simplicity to Complexity 42
Repetition and Self-assembly 42
Modularity 42
Molecular Bricolage 43
Gene Duplication 43
Recombination 44
Case Study 1: Chickens, Eggs and Trees 45
Molecular Phylogenies and Arguments from Cladistics 45
\u2018Difficulties on Theory\u2019: EspA and FliK 47
Case Study 2: New Homologies? 49
Is FliJ Homologue of YscO? 49
Origins of the Flagellar Motor: From Ion Channel to Rotor? 51
Case Study 3: The Search for Outliers 53
Conclusions 54
Note Added in Proof 54
References 54
Comparative Genomics and Evolutionary Trajectories of Viral ATP Dependent DNA-Packaging Systems 57
Abstract 57
Results and Discussion 59
The Demography of Packaging ATPases in Large DNA Viruses 59
Multiple Origins for Different Packaging ATPases within the P-loop NTPase Fold 61
Ancilliary Components of DNA Packaging Systems 64
Diversity of the Terminase-Dependent Packaging Systems: A Common Origin for Portal Proteins of All Tailed Bacteriophages 64
Contextual Information and Inference of Novel Components of the Terminase Portal Systems 65
In Situ Gene Displacement in Terminase Portal Gene Neighborhoods 69
Evolutionary Considerations and General Conclusions 69
Acknowledgements 71
Supplementary Material 71
Note Added in Proof 71
References 71
General Trends in the Evolution of Prokaryotic Transcriptional Regulatory Networks 75
Abstract 75
Evolution of Transcription Factors and Target Genes 78
Evolution of the Local Network Structure 80
Evolution of the Global Network Structure 83
Conclusion 85
Supplementary URL 86
Acknowledgements 86
References 87
Divergence of Regulatory Sequences in Duplicated Fish Genes 90
Abstract 90
Methodology 91
Identification of Suitable Data Sets 91
Pairwise Alignment of Paralogous Intergenic Sequences 92
Search for Regulatory Motifs Conserved in Each of the Gene Sets 92
Assessing the Statistical Significance of Detected Motifs 95
Identifying Motifs Supporting Subfunctionalization 95
Results 97
Identifying Gene Sets Containing Duplicated Fish Genes 98
Determining the Overall Homology Between Paralogous Intergenic Regions 98
Identification of Motifs Supporting Subfunctionalization 98
Detailed Description of the Datasets with Subfunctionalized Motifs 100
Discussion 106
Acknowledgements 107
References 107
Evolution of Gene Function on the X Chromosome Versus the Autosomes 110
Abstract 110
Origin of Sex Chromosomes 110
Theoretical Predictions for Molecular Evolution of X-linked and Autosomal Genes 112
Patterns of In Situ Evolution of X-linked and Autosomal Genes 115
Gene Complements of the X Chromosome Versus the Autosomes 119
Patterns of Gene Traffic on the X and the Autosomes 120
Summary 122
References 124
Amino Acid Repeats and the Structure and Evolution of Proteins 128
Abstract 128
Distribution of Coding Repeats and Homopeptides 129
Relationship between GC Content and Repeat Content 131
Coding Repeats and Protein Function 131
Structure of polyA and polyQ Repeats 132
Structure of other Homopolymers and Nearly Perfect Repeats 133
Formation of Aggregates by Homopeptides 133
Structure of Amyloid 135
Coding Repeats and Evolution 135
References 137
Origination of Chimeric Genes through DNA-Level Recombination 140
Abstract 140
Molecular Mechanisms Leading to Chimeric Genes 141
Nonhomologous Recombination 142
Nondallelic Homologous Recombination 142
Transposable Elements as \u2018Fragment Joiners\u2019 142
Gene Fusions 144
Evidence for Chimeric Proteins 144
Nonhomologous Recombination: Ancient Chimeras 144
Nonhomologous Recombination \u2013 Evolutionarily Recent Chimeras 146
A Recent Example: Insights from Hun, a Young Gene Generated by NHR 147
HR As a Way of Generating Chimeric Proteins \u2013 NAHR 150
Transposable Elements as \u2018Fragment Joiners\u2019 150
Chimeric Genes Generated by Gene Fusions 151
Conclusion 152
Acknowledgement 152
References 152
Exaptation of Protein Coding Sequences from Transposable Elements 156
Abstract 156
Transposable Elements Defined 156
Selfish DNA Theory of TEs 159
Molecular Domestication 160
Host CDSs from TEs 162
Genome Wide Analyses 163
A New Framework is Needed 165
References 168
Modulation of Host Genes by Mammalian Transposable Elements 172
Abstract 172
Transposable Elements 173
Class I Transposons 173
Class II elements 175
Exaptation of Sequences Originated in Transposable Elements (TEs) 176
TE Cassettes in mRNAs 176
TE Sequences in Promoter Regions 179
Transposable Elements and microRNAs 180
Final Remarks 180
References 181
Modern Genomes with Retro-Look: Retrotransposed Elements, Retroposition and the Origin of New Genes 184
Abstract 184
Protein-Coding Genes Derived from Retroelements 185
Protein-Coding Retrogenes 187
RNA Genes 188
Neuronal BC1 RNA in Rodents 188
Alu-Derived Neuronal npcRNAs in Primates 190
Retroposed Copies of snoRNAs and Pre-miRNAs 193
The Tip of the Iceberg 194
Acknowledgements 196
References 196
Author Index 200
Subject Index 201
A 201
B 201
C 201
D 201
E 201
F 201
G 201
H 201
I 202
J 202
L 202
M 202
N 202
O 202
P 202
R 202
S 202
T 202
V 203
W 203
X 203
Y 203
Gene and protein evolution /
- 名称
- 类型
- 大小
光盘服务联系方式: 020-38250260 客服QQ：4006604884
云图客服：
用户发送的提问，这种方式就需要有位在线客服来回答用户的问题，这种 就属于对话式的,问题是这种提问是否需要用户登录才能提问
Video Player
×
Audio Player
×
pdf Player
×
