Evolutionary genomics and systems biology

Evolutionary Genomics and Systems Biology......Page 5
Contents......Page 7
Preface......Page 15
Contributors......Page 19
Part I Evolution of Life......Page 23
1.1 Introduction......Page 25
1.2 Evolution and the Power of Genomes......Page 26
1.3 The Problem of Deep Phylogeny and “The Tree”......Page 27
1.4 Fred, the Last Common Ancestor of Modern Eukaryotes......Page 29
1.5 Eukaryote Origins: Continuity from the RNA World?......Page 32
1.6 Minimal Genomes and Reductive Evolution......Page 34
1.7 Evolutionary Genomics for the Future......Page 35
References......Page 36
2.1 Phylogenomics and Supermatrices......Page 39
2.2 Phylogenetic Signal Versus Nonphylogenetic Signal......Page 41
2.3.1 Homogeneous Models......Page 44
2.3.2 Handling of Rate Signal......Page 45
2.3.3 Handling of Compositional Signal......Page 46
2.3.4 Other Model Violations......Page 48
2.3.5 Future Developments......Page 49
2.4.1 Variations in Taxon Sampling......Page 50
2.4.2 Recoding and Removal of Offending Data......Page 52
2.5 CAT Model......Page 53
2.6 Case Study: Cambrian Explosion......Page 55
2.7 Conclusion......Page 57
References......Page 58
3.1 Introduction......Page 65
3.2 The Woesian Revolution......Page 67
3.3 A Rampant “Prokaryotic” Counterrevolution......Page 69
3.4 How to Polarize Characters Without a Robust Root?......Page 72
3.5 The Hidden Root: When the Weather Became Cloudy......Page 73
3.7 The Problem of Horizontal Gene Transfer and Ancient Phylogenies: Trees Versus Gene Webs......Page 76
3.8 The Nature of the RNA World......Page 77
3.9 The DNA Replication Paradox and the Nature of LUCA......Page 78
3.10 When Viruses Find Their Way into the Universal Tree of Life......Page 80
3.11 Future Directions......Page 81
References......Page 82
4.1.1 What is Significant About the Origin of the Eukaryote Cell?......Page 85
4.2 Interpreting Trees......Page 90
4.3 Moving Beyond the Deep Roots of Eukaryotes......Page 92
4.3.1 Origin of the Mitochondrion......Page 93
4.3.2 Stepwise Development of Mitochondria......Page 94
4.3.3 Intron Proliferation and Eukaryote Origins......Page 96
4.4 Concluding Remarks......Page 98
References......Page 99
5.1 Introduction......Page 103
5.2 Revisiting Information......Page 105
5.3 Ubiquitous Functions for Life......Page 106
5.4 The Cenome and the Paleome......Page 109
5.6 A Ubiquitous Information-Gaining Process: Making a Young Organism from an Aged One......Page 111
5.7 Provisional Conclusion......Page 113
References......Page 114
6.1 Introduction......Page 117
6.2 A Brief History of Hemiascomycetous Yeast Genomics......Page 118
6.3.1 Functional Genomics......Page 120
6.3.3 A Bunch of Fermentative Engines......Page 124
6.3.4 Speciation and Species Definition......Page 125
6.4.1 Distinct and Specific Genome Organization of Three Major Evolutionary Subdivisions of Hemiascomycetes......Page 126
6.4.3 Genome Redundancy and Paralogues......Page 128
6.4.4 Conservation of Synteny......Page 129
6.4.5 Genes for Noncoding RNAs, Introns, and Genetic Code Variation......Page 130
6.4.6 Sex, Transposons, Plasmids, Inteins, and Horizontal Gene Transfer......Page 131
6.4.7 Mitochondrial Genomes and NUMTs......Page 132
6.5 Surprises......Page 133
6.6 What Next?......Page 135
References......Page 137
Part II Evolution of Molecular Repertoires......Page 143
7.1 The Landscape Paradigm......Page 145
7.2 Molecular Phenotypes......Page 147
7.2.1 Protein Structures......Page 148
7.2.2 Nucleic Acid Structures......Page 151
7.3 The RNA Model......Page 154
7.3.1 RNA Replication and Mutation......Page 155
7.3.2 RNA Secondary Structures......Page 160
7.3.3 Neutrality and Its Consequences......Page 161
7.3.4 Stochastic Effects in RNA Evolution......Page 163
7.3.5 Beyond the One Sequence–One Structure Paradigm......Page 167
7.4 Conclusions and Outlook......Page 170
References......Page 171
8.1 Introduction......Page 175
8.2 Structural Granularity and Its Implications......Page 178
8.3 Protein Domains in the Study of Genome Rearrangements......Page 180
8.4 Protein Domain Gain and Loss......Page 182
8.6 But Let Us Not Forget the Influence of the Environment......Page 183
8.7 Conclusions......Page 184
References......Page 185
9.1 Introduction......Page 187
9.2 Genome Representation......Page 188
9.3 Constructing Genome Permutations from Sequence Data......Page 189
9.4 Genomic Distances......Page 190
9.4.1 Model-Free Distances......Page 191
9.4.2 Rearrangement-Based Distances......Page 192
9.5 Reconstruction of Ancestors and Evolutionary Scenarios......Page 196
9.5.1 Model-Free Reconstruction Algorithms......Page 197
9.5.2 Rearrangement-Based Reconstruction Algorithms......Page 198
9.6 Recent Applications on Large Genomes......Page 199
9.7 Challenges and Promising New Approaches......Page 200
References......Page 201
10.1 Introduction......Page 205
10.2 Overview of Considerations in Studying Protein Evolution......Page 206
10.3.1 Deciphering Complexities of Protein Evolution......Page 208
10.3.2 The Future of Modeling Protein Evolution: Merging Realism with Tractability......Page 210
10.3.3 The Effect of Increasing Taxon Sampling and Sequence Biodiversity......Page 211
10.3.4 Removing the Mutational Noise and Context-Dependent Biases from Protein Evolution......Page 212
10.3.5 Where is Protein Evolution Going?......Page 213
10.3.6 Detecting Adaptation and Functional Innovation......Page 215
10.4.1 Snake Metabolic Proteins—Integration of Inferences for Adaptation......Page 216
10.4.3 Changes at Conserved Sites and Coevolutionary Signal......Page 217
10.4.4 Integrating Evolutionary Inferences with Structure and Function Information......Page 219
10.4.5 Further Evidence of Adaptation from Molecular Convergence......Page 220
10.4.6 Integrating Inferences with Possible Causal Factors......Page 221
References......Page 222
11.1 Introduction......Page 225
11.2 Protein Material Costs......Page 226
11.4 Episodic Nutrient Scarcity Can Shape Protein Material Costs......Page 227
11.5 Highly Expressed Gene Products Often Exhibit Reduced Material Costs......Page 228
11.6 Material Costs and the Evolution of Genomes......Page 229
11.7 Material Costs and Other Costs of Making Proteins......Page 230
References......Page 231
12.1 Modular Protein Evolution......Page 235
12.2 Domain-Based Homology Identification......Page 237
12.2.1 Domain Architecture Similarity......Page 238
12.2.2 Domain Resources and Domain-Based Search......Page 241
12.2.3 Deciphering Circular Permutations with Domains......Page 243
12.3 Domains in Genomics and Proteomics......Page 244
12.3.1 Building Domain Trees......Page 245
12.4 The Coverage Problem......Page 247
12.5 Conclusion......Page 249
References......Page 250
13.1 Introduction......Page 253
13.2 Universal Domain Structure Families Identified in the Last Universal Common Ancestor......Page 254
13.4 Correlation of Structural Diversity in Superfamilies with Functional Diversity......Page 256
13.5.1 Phylogenetic Analysis of Protein Families......Page 260
13.5.3 Evolution of (COGs) Function Within CATH Superfamilies......Page 262
13.5.4 Resolving Ambiguous Evolutionary Scenarios Between Parent and Child COGs in a CATH Superfamily......Page 263
13.5.5 Relationship Between Domain Architecture Rearrangement and Functional Divergence Within CATH Superfamilies......Page 264
13.6 How Safely Can Function Be Inherited Between Homologues?......Page 267
13.7 How Are Domain Families Distributed in Protein Complexes?......Page 269
References......Page 270
14.1 Introduction......Page 273
14.2.2 Signal Recognition Particle RNA......Page 276
14.2.3 snoRNAs......Page 278
14.3.1 Telomerase RNA......Page 281
14.3.2 Spliceosomal snRNAs......Page 282
14.3.4 tmRNA......Page 284
14.3.5 6S RNA......Page 287
14.4.3 7SK RNA......Page 289
14.4.5 Bacterial RNAs......Page 292
14.4.6 A Zoo of Diverse Examples......Page 296
14.5 ncRNAs from Repeats and Pseudogenes......Page 298
14.6 mRNA-like ncRNAs......Page 299
14.6.1 Dosage Compensation......Page 301
14.6.4 Transcriptional Regulators......Page 302
14.7.2 SgrS......Page 303
14.8 Concluding Remarks......Page 304
References......Page 305
15.1 Introduction......Page 317
15.2.1 Endogenous siRNAs......Page 318
15.2.4 “Exotic” Small RNA Species......Page 319
15.3.1 Components of the Small RNA Processing Machinery......Page 320
15.3.2 MicroRNA Biogenesis......Page 321
15.3.4 Three Main Mechanisms, Same Global Effect on Gene Expression......Page 322
15.4 Computational microRNA Prediction......Page 324
15.5.1 How Many Targets?......Page 326
15.5.2 Target Prediction......Page 327
15.5.3 Targets and Polymorphisms......Page 328
15.6.1 Animal microRNAs......Page 329
15.6.2 Plant microRNAs......Page 332
15.6.3 MicroRNAs and Viruses......Page 333
15.7.1 Metazoa......Page 335
15.7.3 microRNAs and Transposable Elements......Page 336
15.7.4 Are Animal and Plant microRNAs Homologous?......Page 337
15.8.1 Clusters and Families......Page 338
15.8.2 Regulation of microRNA Expression......Page 340
15.9 Summary and Outlook......Page 342
References......Page 343
16.1 Introduction......Page 351
16.1.1 A Novel Phylogenetic Approach Based on Macromolecular Structure......Page 353
16.2 Structural Characters and Derived Phylogenetic Trees......Page 355
16.2.1 Character Coding......Page 356
16.2.2 Character Polarization......Page 357
16.2.3 Phylogenetic Analysis of RNA Structural Characters......Page 360
16.2.4 Character State Change Frequency in RNA Structural Evidence......Page 361
16.2.5 Major Properties of Phylogenetic Trees Derived from RNA Structure......Page 362
16.2.6 Potential Limitations of the Methodology......Page 365
16.3.1 tRNA......Page 366
16.3.2 5S rRNA......Page 368
16.3.3 RNase P RNA......Page 370
16.3.4 SINE RNA......Page 373
16.3.5 rRNA......Page 374
16.4 Conclusions......Page 375
References......Page 376
Part III Evolution of Biological Networks......Page 383
17.1 Introduction......Page 385
17.1.1 Mere Words?......Page 386
17.1.3 One Man’s Glitch......Page 387
17.1.4 Three Challenges......Page 388
17.2.1 The Rosetta Stone......Page 389
17.2.3 Phylogeny by Any Other Name......Page 390
17.2.4 The Emperor’s Blast Search......Page 392
17.3.1 Nip and Tuck......Page 393
17.3.2 Fold Selection......Page 394
17.3.3 Higher Order Structural Networks......Page 395
17.4 Optimal Networks......Page 396
17.4.1 Optimality Not Maximality......Page 397
17.4.2 Patchy Environments, Patchy Genomes......Page 399
17.4.3 Fixation of Novel Sequences......Page 400
17.4.4 Selfish Operons......Page 402
17.5 The Emperor’s BLAST Search Revisited......Page 403
17.5.1 Ecological Settings......Page 406
17.5.2 The Way Forward......Page 408
17.5.3 Less May be More......Page 409
17.6 Will the Real Missing Link Please Stand Up?......Page 410
17.7 All’s Well......Page 411
References......Page 413
18.1 Introduction......Page 419
18.2 Metabolic Network Properties......Page 420
18.3 Network Models For Metabolic Evolution......Page 425
18.4 Dynamic Models Of Genome-Level Metabolic Function......Page 429
References......Page 432
19.1 Introduction......Page 435
19.2 Evolution of PINs......Page 436
19.5 Diploidization Phase......Page 438
19.7 Types of Interactions......Page 439
19.8 WGDs, Transient Interactions, and Organismal Complexity......Page 440
19.9 Studies on PPIs of Ohnologues......Page 441
19.10 Concerns About the Methods of Analysis and the Quality of the Data......Page 442
19.11 The Importance of Medium-Scale Studies: the Case of Dimerization......Page 444
19.12 Evolution of Dimerization Networks......Page 446
Acknowledgment......Page 448
References......Page 449
20.1 Introduction......Page 453
20.2 Biological Structure as an Emergent Property of Dissipative Systems......Page 454
20.3 Information and Its Dissipation......Page 457
20.4 Time, Thermodynamic Irreversibility, and Growth of Order in the Universe......Page 459
20.5 Information Dissipation and Modularity Pervade Structure in Biology......Page 462
20.6 Modularity and Dissipation in Protein Evolution......Page 465
20.7 Conclusions......Page 469
References......Page 470
Index......Page 473