Evolution after Gene Duplication E-Book

Katharina Dittmar

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 735

Veröffentlichungsjahr: 2011

Beschreibung

Gene duplication has long been believed to have played a major role in the rise of biological novelty through evolution of new function and gene expression patterns. The first book to examine gene duplication across all levels of biological organization, Evolution after Gene Duplication presents a comprehensive picture of the mechanistic process by which gene duplication may have played a role in generating biodiversity.

Key Features:

• Explores comparative genomics, genome evolution studies and analysis of multi-gene families such as Hox, globins, olfactory receptors and MHC (immune system)
• A complete post-genome treatment of the topic originally covered by Ohno's 1970 classic, this volume extends coverage to include the fate of associated regulatory pathways
• Taps the significant increase in multi-gene family data that has resulted from comparative genomics
• Comprehensive coverage that includes opposing theoretical viewpoints, comparative genomics data, theoretical and empirical evidence and the role of bioinformatics in the study of gene duplication

This up-to-date overview of theory and mathematical models along with practical examples is suitable for scientists across various levels of biology as well as instructors and graduate students.

Leseprobe

Table of Contents

Title Page

Copyright

Preface

Contributors

Chapter 1: Understanding Gene Duplication Through Biochemistry and Population Genetics

1.1 Introduction

1.2 Systems Biology and Higher-Level Organization

1.3 Mutational Dynamics and Substitutions

1.4 Evolution of Enzyme Active Centers After Duplication

1.5 Mutational Opportunities After Duplicate Gene Birth

1.6 Evolutionary Mechanisms

1.7 Expectations for Retention Profile and for Substitution Profile

1.8 Role of Protein Function and Protein Fold

1.9 Species-Specific Details

1.10 Conclusions and Larger-Scale Effects

Chapter 2: Functional Divergence of Duplicated Genes

2.1 Introduction

2.2 Protein–Protein Interaction Divergence

2.3 Expression Divergence

2.4 Divergence of Splice Variants of Duplicated Genes

2.5 Concluding Remarks

Chapter 3: Duplicate Retention After Small- and Large-Scale Duplications

3.1 Introduction

3.2 Modes of duplication

3.3 Duplicate retention mechanisms

3.4 Discussion

Chapter 4: Gene Dosage and Duplication

4.1 Introduction

4.2 Gene duplications and functional redundancy

4.3 Redundancy of gene duplications

4.4 Defining the concept of genetic redundancy

4.5 Gene dosage: evidence from nature

4.6 Environmental interaction as the basis of the adaptive response

4.7 Dosage and genetic dominance

4.8 Dosage theory and gene duplications

Chapter 5: Myths and Realities of Gene Duplication

5.1 Introduction

5.2 Hypotheses of New Gene Function

5.3 Role of Natural Selection

5.4 Expression Differentiation

5.5 Segmental Duplication and Its Aftermath

5.6 Duplicate Genes in Networks

5.7 Conclusions

Chapter 6: Evolution After and Before Gene Duplication?

6.1 Introduction

6.2 Stability of protein structures

6.3 Structural promiscuity of proteins

6.4 Evolutionary transitions between protein phenotypes

6.5 Functional promiscuity of enzymes

6.6 Gene duplications and phenotypic transitions at the population level

6.7 Evolution of ribozyme structures

6.8 Conclusions

Chapter 7: Protein Products of Tandem Gene Duplication: A Structural View

7.1 Introduction

7.2 Genetic Mechanisms

7.3 Duplicated proteins

7.4 Entangled domains

7.5 Intrinsic Protein Symmetries

7.6 Duplicate and destroy

Chapter 8: Statistical Methods for Detecting Functional Divergence of Gene Families

8.1 Introduction

8.2 Two-State Model for Functional Divergence

8.3 Testing Type I Functional Divergence after Gene Duplication

8.4 Predicting Critical Residues for Type I Functional Divergence

8.5 Implementation and Case Study

Chapter 9: Mapping Gene Gains and Losses Among Metazoan Full Genomes Using an Integrated Phylogenetic Framework

9.1 Introduction

9.2 Data Mining

9.3 Character mapping

9.4 Comparisons with other databases for the localization of gains and losses

9.5 Reanalysis of previously investigated gene families

9.6 Conclusions

Chapter 10: Reconciling Phylogenetic Trees

10.1 Introduction

10.2 Basic Definitions and Notation

10.3 Gene Duplication Model

10.4 Apparent Polytomies

10.5 Unrooted Trees

10.6 Episodes of Gene Duplications

10.7 Supertrees based on Tree Reconciliation

10.8 Model-based Approaches

10.9 Conclusions

Chapter 11: On the Energy and Material Cost of Gene Duplication

11.1 Introduction

11.2 Costs visible to natural selection

11.3 Energy cost of gene expression in the yeast Saccharomyces cerevisiae

11.4 Material cost of gene expression in the yeast Saccharomyces cerevisiae

11.5 The lac operon as an experimental system to study expression costs

11.6 Evolutionary cost signatures

11.7 Conclusions

Chapter 12: Fate of a Duplicate in a Network Context

12.1 Introduction

12.2 Genes as Part of a Larger System

12.3 Studying Dynamics and Evolution at the Network Level

12.4 Reconsidering Fitness Effects of Duplications in the Context of Networks

12.5 Fate of a Gene Duplicate in a Network Context

12.6 Duplicate Retention and Robustness

12.7 Toward a Complete Model of Gene Duplication

Chapter 13: Evolutionary and Functional Aspects of Genetic Redundancy

13.1 Introduction

13.2 Genetic Redundancy: A Working Definition

13.3 Dispensability of Duplicated Genes

13.4 Dispensability of Duplicates: Redundancy or Unimportant Functions?

13.5 Evolution of Redundant Duplicates: Contrasting Theory and Observations

13.6 Explaining the Conservation of Redundant Duplicates

13.7 Conditional Coregulation and the Maintenance of Metabolic Fluxes

13.8 Redundancies of Developmental Regulators

13.9 Redundancies and Regulation

13.10 Functions of Responsive Backup Circuits

13.11 Methodologies: Inferring Redundant Interactions

Chapter 14: Phylogenomic Approach to the Evolutionary Dynamics of Gene Duplication in Birds

14.1 Introduction

14.2 Methodology and Computational Approach

14.3 Results: Dynamics of Chicken-Specific Gene Duplication

14.4 Examples of families with chicken-specific duplications

14.5 Prospects and Conclusions

Chapter 15: Gene and Genome Duplications in Plants

15.1 Introduction

15.2 Whole-Genome Duplication (Polyploidy) in Plants

15.3 Fates and Consequences of Gene Duplication in Plants

15.4 Duplications in the MADS-Box Gene Family and Their Roles in Floral Development

15.5 Conclusions

Chapter 16: Whole Genome Duplications and the Radiation of Vertebrates

16.1 Introduction

16.2 Teleost-Specific Genome Duplication

16.3 1R/2R Genome Duplication

16.4 Concluding remarks

Index

Copyright © 2010 by John Wiley & Sons, Inc. All rights reserved.

Published by John Wiley & Sons, Inc., Hoboken, New Jersey.

Published simultaneously in Canada.

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Library of Congress Cataloging-in-Publication Data:

Dittmar, Katharina.

Evolution after gene duplication / Katharina Dittmar and David Liberles. p. cm.

Includes bibliographical references and index.

Summary: ``Gene duplication has long been believed to have played a major role in the rise of biological novelty through evolution of new function and gene expression patterns. The first book to examine gene duplication across all levels of biological organization, Evolution after Gene Duplication presents a comprehensive picture of the mechanistic process by which gene duplication may have played a role in generating biodiversity. Key Features: Explores comparative genomics, genome evolution studies and analysis of multi-gene families such as Hox, globins, olfactory receptors and MHC (immune system). A complete post-genome treatment of the topic originally covered by Ohno's 1970 classic, this volume extends coverage to include the fate of associated regulatory pathways. Taps the significant increase in multi-gene family data that has resulted from comparative genomics. Comprehensive coverage that includes opposing theoretical viewpoints, comparative genomics data, theoretical and empirical evidence and the role of bioinformatics in the study of gene duplication. This up-to-date overview of theory and mathematical models along with practical examples is suitable for scientists across various levels of biology as well as instructors and graduate students'' -Provided by publisher.

ISBN 978-0-470-59382-0 (hardback)

1. Evolutionary genetics. 2. Mutation (Biology) 3. Variation (Biology) I. Liberles, David II. Title.

[DNLM: 1. Tissue Engineering-methods. QY 95 K92a 2010]

QH390.D58 2010

572.8′38–dc22

2010031097

Preface

The duplication of genes and genomes was postulated to be an important process for the evolution of functional and organismal diversity long before we entered the genome sequencing era. Many of the groundbreaking intellectual concepts for this hypothesis come from the work of Susumu Ohno. However, only with the recent availability of many genome sequences are we able to gather supporting data to develop hypotheses and test them on a large scale. Current research on the topic spans scientific disciplines from bioinformatics to organismal biology and touches on different aspects of gene and genome duplication, ranging from the molecular mechanics of the duplication process to the fate of duplicated genomes. Naturally, a variety of approaches goes hand in hand with differences in opinion, and presently, a prolific and at times overwhelming body of research has accumulated. Thus, it was our idea to provide a systematic examination of current thought on gene duplication and its importance to biological diversification across multiple levels.

This edited volume began with a review article published in the Journal of Experimental Zoology. With the expansion of concepts into full book chapters, we hoped to cover approaches from a range of fields, starting with molecular and structural biology, leading to computer science and statistics to cellular and, ultimately, organismal-level biology. It is our intention to lay out a hierarchy of chapters extending from evolutionary principles and molecular details out to increasingly higher levels of biological organization. This setup is designed to make the reader appreciate the interconnectedness of these levels.

It is important to us to present this work as a platform for diverse scientific approaches and reasoning. One clear point that will emerge in reading the book is that chapters come from authors in diverse disciplines, some of whom disagree with each other on underlying evolutionary forces, on experimental procedures, and on data interpretation. Occasionally, authors use terms in different ways. In particular, concepts of redundancy (and its maintenance) differ: Genes that one set of authors consider to have been selected for retention due to redundant function others consider to have diverged and to no longer be redundant.

The first section of the book deals with models of gene duplication and retention. Five chapters provide an overview (with some overlap in description, but involving different interpretations) of the mechanisms for the retention of duplicate genes. This includes diverse perspectives on mutational opportunities, dosage compensation, evolutionary processes, and their interrelationship with molecular processes and resulting selection. These fine-scale aspects of interpreting genomic data lay the foundation for the cell/systems level of biology of duplication as well as effects on speciation and biodiversity.

The second section, on gene/protein structure and duplication, includes two chapters. Chapter 6 links the evolutionary process associated with gene duplication through structure to function, paying particular attention to adaptive processes in proteins that have not yet undergone duplication. Chapter 7 describes the link between the process of gene duplication and protein structure, concentrating on a review of the genetic mechanisms creating fused tandem duplicates.

Comparative genomic methodologies for characterizing gene duplicates are treated in the third section. Chapter 8 overviews methodology for characterizing the functional divergence of duplicate genes, Chapter 9 presents a procedure for linking changes in gene copy number through evolution to functional and gene expression evolution, and Chapter 10 presents an overview of model and parsimony-based approaches for gene tree/species tree reconciliation coupled to a detailed presentation of most parsimonious reconciliation.

The fourth section, involving systems biology considerations of gene duplication, includes three chapters. Chapter 11 describes the energetic costs of gene duplication, arguing for a nonneutral process of fixation. The next two chapters describe the interplay between systems-level constraints and duplicate gene retention as well as the complementary interplay between duplication and the structure of biological networks.

The last section builds up to species-level characterizations of gene duplication. The first two chapters in this section treat research on duplication in birds and plants, addressing their roles in the speciation process, as well as developmental and morphological novelty. Chapter 16 concludes this work with a portrayal of the role of duplication in vertebrate speciation.

As editors, we would like to extend our thanks to all the researchers who contributed to this volume. First and foremost, we thank them for their timely delivered scientific insights, but also for their good humor and patience as we worked through the publishing process. We also thank all the colleagues, students, and friends who joined our discussions on this topic. Finally, we would like to thank Karen Chambers, at John Wiley, who was enthusiastic and supportive of our idea, and thankfully, a very patient editor in the long and at times exhausting process of assembling this volume.

We hope the book will be a useful tool for researchers and students alike to learn about current research on duplication and inspire continued discussion about this important topic.

David Liberles

Katharina Dittmar

Contributors

Maude W. Baldwin, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts

Erich Bornberg-Bauer, Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany

J. Gordon Burleigh, Department of Biology, University of Florida, Gainesville, Florida

Andre Chanderbali, Florida Museum of Natural History, University of Florida, Gainesville, Florida; Department of Biology, University of Florida, Gainesville, Florida

Katharina Dittmar, Department of Biological Sciences, SUNY at Buffalo, Buffalo, New York

Scott V. Edwards, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts

Oliver Eulenstein, Department of Computer Science, Iowa State University, Ames, Iowa

Robert Friedman, Department of Biological Sciences, University of South Carolina, Columbia, South Carolina

Xun Gu, Department of Genetics, Development and Cell Biology, Center for Bioinformatics and Biological Studies, Iowa State University, Ames, Iowa

Raphaul Helaers, Department of Biology, Facultes Universitaires Notre-Dame de la Paix, Namur, Belgium

Austin L. Hughes, Department of Biological Sciences, University of South Carolina, Columbia, South Carolina

Snehalata Huzurbazar, Department of Statistics, University of Wyoming, Laramie, Wyoming

Ran Kafri, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts

Manolis Kellis, Computer Science and Artificial Intelligence, Massachusetts Institute of Technology, Cambridge, Massachusetts

David G. Knowles, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland

Grigory Kolesov, Department of Molecular Biology, University of Wyoming, Laramie, Wyoming

Fyodor A. Kondrashov, Center for Genomic Regulation, Barcelona, Spain

Shigehiro Kuraku, Evolutionary Biology and Zoology, Department of Biology, University of Konstanz, Konstanz, Germany

David A. Liberles, Department of Molecular Biology, University of Wyoming, Laramie, Wyoming

Steven Maere, Department of Plant Systems Biology, VIB, Ghent, Belgium; Department of Molecular Genetics, Ghent University, Ghent, Belgium

Takashi Makino, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland

Aoife Mc Lysaght, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland

Axel Meyer, Evolutionary Biology and Zoology, Department of Biology, University of Konstanz, Konstanz, Germany

Michel C. Milinkovitch, Department of Genetics and Evolution, Laboratory of Natural and Artificial Evolution, Sciences III, Geneva, Switzerland

Chris L. Organ, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts

Tzachi Pilpel, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel

Matthew D. Rasmussen, Computer Science and Artificial Intelligence, Massachusetts Institute of Technology, Cambridge, Massachusetts

Michael A. Sadowski, Division of Mathematical Biology, MRC National Institute for Medical Research, London, UK

Tobias Sikosek, Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany

Douglas E. Soltis, Department of Biology, University of Florida, Gainesville, Florida

Pamela S. Soltis, Florida Museum of Natural History, University of Florida, Gainesville, Florida

Orkun S. Soyer, Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, UK

William R. Taylor, Division of Mathematical Biology, MRC National Institute for Medical Research, London, UK

Athanasia C. Tzika, Laboratory of Natural and Artificial Evolution, Department of Genetics and Evolution, Sciences III, Geneva, Switzerland; Evolutionary Biology and Ecology, Universite de Bruxelles, Brussels, Belgium

Yves Van de Peer, Department of Plant Systems Biology, VIB, Ghent, Belgium; Department of Molecular Genetics, Ghent University, Ghent, Belgium

Andreas Wagner, Department of Biochemistry, University of Zurich, Zurich, Switzerland

Mi-Jeong Yoo, Florida Museum of Natural History, University of Florida, Gainesville, Florida; Department of Biology, University of Florida, Gainesville, Florida

Chapter 1

Understanding Gene Duplication Through Biochemistry and Population Genetics

David A. Liberles and Grigory Kolesov

Department of Molecular Biology, University of Wyoming, Laramie, Wyoming

Katharina Dittmar

Department of Biological Sciences, SUNY at Buffalo, Buffalo, New York

1.1 Introduction

Gene duplication has emerged as an important process supporting the functional diversification of genes. Since publication of the seminal book Evolution by Gene Duplication by Ohno (1970), the hypothesis regarding the importance of gene duplication in the generation of evolutionary novelty has steadily gained support as we have entered the genome-sequencing era. It is through the link to functional biology that an ultimate understanding of the preservation and diversification of duplicate genes will be accomplished.

Genes can diverge in function through accumulation (fixation) of coding sequence changes, which may influence binding interactions and/or catalysis, through the evolution of splice variants, and through spatial, temporal, and concentration-level changes in the expression of the protein product. Governing these processes is an interplay among mutational opportunity, population dynamics, protein biochemistry, and systems and organismal biology. This interplay is described systematically in this chapter.

1.2 Systems Biology and Higher-Level Organization

At the level of biological systems, two early but still relevant views suggested a role for gene duplication in constructing pathways. These views are both dependent on a new function emerging in one of the duplicates, but differ in the manner in which it occurs. One view, patchwork evolution, involved a conservation of catalytic activity coupled with the evolution of a new substrate after duplication (Jensen, 1976). An alternative view, retrograde evolution, suggested that pathways are built up backward, with product becoming substrate based on recognition of the transition state in the active site, with the evolution of a new catalytic activity to generate the substrate for the downstream reaction after duplication (Horowitz, 1945). In a systematic analysis in Escherichia coli, Light and Kraulis found some evidence for the retrograde evolution model, but found the patchwork model to be much more common, possibly because it is easier to gain new binding specificity than to evolve a new catalytic activity (Light and Kraulis, 2004). Relatedly, it has been suggested that (also in bacteria) there are secondary (moonlighting) functions where enzymes with a given catalytic activity carry it out on multiple substrates with different specificities (Copley, 2003). This nature of enzymatic activities might generally lead to quick differential optimization after duplication, especially easily if maintained with different specificities in different alleles by balancing selection before duplication. Further (as discussed in detail below), specificity is chemically and evolutionarily difficult to attain, and nonspecific binding activities may arise easily when there is no selective pressure against them. Whereas selective pressures are ultimately at the systems level, divergence occurs gene by gene and mutation by mutation. This process will be dissected.

1.3 Mutational Dynamics and Substitutions

Both intramolecular and intermolecular coevolution of sites affects the probability of fixation of any individual mutation, where genetic background (the sequence at genetically interacting positions) determines the phenotype of any given mutation. The evolutionary accessibility of different mutations from a given genetic background is therefore dictated partly by the mutation rate and the frequency of multiple segregating mutations as well as the population size as a dictator of strength of selection. The same evolutionary properties affect both intramolecular and intermolecular interaction, only with differing degrees of sensitivity to mutation, due to the entropic differences between the two types of interresidue interaction. For these entropic reasons, it is easier to knock out a binding interaction than to knock out proper protein folding (although this happens, too) with a single mutation. This is because although there are a greater number of sites that influence proper folding, covalent attachment means that there will also be a greater local effective concentration of intramolecularly interacting residues requiring a lower affinity interaction to generate the same levels of bound state. If one views two residues as interacting or not interacting, the probability of interaction at any given time is dependent on their affinity for each other and how many opportunities they have to interact (their concentration about each other).

So far, we have focused on the coding properties of a gene. Gene expression is another important process that is subject to phenotypic divergence through mutation. The typical gene has approximately 12 transcription factor binding sites [the distribution of this across genomes is not well characterized, and this number is given with an approximation of six to eight base pairs (Harbison et al., 2004; Hughes and Liberles, 2007)]. The specificity of binding typically enables transcription factors to discriminate among many sites with single-base-pair mutations (Lusk and Eisen, 2008). Because of the small size of transcription factor–binding sites, site loss and de novo site evolution are reasonably common, and this is explored further below. Due to the periodicity of standard B-form DNA of about 10 bp, as well as changes in effective local concentration of transcription factors about each other and about the initiation site, it might be expected that spacing between sites is important in gene regulation, but evidence generated so far seems to downplay the role of these effects (Shultzaberger et al., 2007), leading to a focus on the evolution of the sites themselves.