Gene Sharing and Evolution: The Diversity of Protein Functions

Gene Sharing and Evolution: The Diversity of Protein Functions

by Joram Piatigorsky
ISBN-10:
0674023412
ISBN-13:
9780674023413
Pub. Date:
02/15/2007
Publisher:
Harvard

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Overview

Gene Sharing and Evolution: The Diversity of Protein Functions

"Gene sharing" means that the different functions of a protein may share the same gene--that is, a protein produced by a gene evolved to fulfill a specialized function for one biological role may also perform alternate functions for other biological roles.

In the 1980s and early 1990s, Joram Piatigorsky and colleagues coined the term "gene sharing" to describe the use of multifunctional proteins as crystallins in the eye lens. In Gene Sharing and Evolution Piatigorsky explores the generality and implications of gene sharing throughout evolution and argues that most if not all proteins perform a variety of functions in the same and in different species, and that this is a fundamental necessity for evolution.

How is a gene identified, by its structure or its function? Do the boundaries of a gene include its regulatory elements? What is the influence of gene expression on natural selection of protein functions, and how is variation in gene expression selected in evolution? These are neither new nor resolved questions. Piatigorsky shows us that the extensiveness of gene sharing and protein multifunctionality offers a way of responding to these questions that sheds light on the complex interrelationships among genes, proteins, and evolution.

Product Details

ISBN-13: 9780674023413
Publisher: Harvard
Publication date: 02/15/2007
Pages: 336
Product dimensions: 6.12(w) x 9.25(h) x (d)

About the Author

Joram Piatigorsky is a molecular biologist in Bethesda, Maryland.

Table of Contents

List of Illustrations

Preface

1. What Is "Gene Sharing"?

New Functions for Old Proteins and the Question of Gene Duplication

Origin of the Term "Gene Sharing"

Gene Sharing: General Definition and Implications

Protein Location and Gene Regulation

Why the Term "Gene Sharing"?

Mechanisms for Diversifying Gene Functions

Posttranslational Modifications

Conditions for Initiating Gene Sharing

Contrasting Phenotype with Protein Function

Take-Home Message

2. Multifunctions and Functional Shifts: Echos from the Past

Preadaptation, Prospective Adaptation, and Hopeful Monsters

Quirky Functional Shifts and Exaptation

Spandrels and Gene Sharing

Gene Regulation and Tinkering

Take-Home Message

3. The Elusive Concept of a "Gene"

The Classical Gene Concept

The Mendel-Morgan Chromosomal Theory of the Gene

Later Developments: One Gene/One Enzyme/One Polypeptide

The Molecular Era of the Gene: So Much Data, So Many Possibilities

Quantifying Genes before the Molecular Era

Quantifying Genes in the Molecular Era: Fewer than Expected

Noncoding Regulatory Genes

Protein Diversity

The Ambiguous Gene

The "Molecular Gene" Concept

The "Molecular Process Gene" Concept

The "Evolutionary Gene" Concept

Two Concepts for One Gene: Gene-P/Gene-D

Gene Sharing: A Concept Incorporating an "Open Gene"

Take-Home Message

4. Eyes and Lenses: Gene Sharing by Crystallins

Eye Diversity: Many Forms to Perform a Function

The Lens

Crystallins and the Optical Properties of the Lens

Diversity and Taxon-Specificity of Lens Crystallins

Crystallins Are Borrowed Proteins

The bg-Crystallins: A Superfamily with Distant Stress Connections

The Enzyme-Crystallins of Vertebrates

Crystallins of Invertebrates

Crystallin Gene Regulation in Vertebrates: A Similar Cast of Transcription Factors

Convergent Evolution of Crystallin Gene Expression

Evolutionary Dynamism of shsp/aB-Crystallin Gene Expression

Convergent Evolution of Invertebrate and Vertebrate Crystallin Promoters

Potential for Lens-Specific Promoter Activity

Convergent Evolution and Relaxed Stringency for Crystallins

Take-Home Message

5. The Enigmatic "Corneal Crystallins": Putative Cases of Gene Sharing

The Cornea

Aldehyde Dehydrogenase: A Candidate Corneal Crystallin

Other Candidate Corneal Crystallins: Transketolase, Isocitrate Dehydrogenase, and Cyclophilin

Adseverin: A Corneal Crystallin in Zebrafish

A Signaling Role for Adseverin

Corneal Gene Expression

The Refracton Hypothesis: Implications for Gene Sharing

Take-Home Message

6. Gene Sharing As a Common Event: Many Multifunctional Proteins

Glycolytic Enzymes and the Versatile Hexokinases

Citrate Synthase: An Enzyme and a Cytoskeletal Structure

Lactate Dehydrogenase: An Enzyme for All Seasons

Regulation of mRNA Translation by Enzyme Binding

Glyceraldehye-3-phosphate Dehydrogenase: Constant Surprises

Enolase: Another Versatile Protein

Bacterial Surface Enzymes

Xanthine Oxidoreductase: Enzyme and Envelope

The Thioredoxin/Ribonucleotide Reductase System and Thioredoxin Family Members: From Redox to Morphogenesis

Serum Albumin: Transport Protein, Enzymatic Vasodilator and Detoxifier

Gelsolin: Roles in Cytoskeletal Structure, Gene Expression, Cell Death, and Signal Transduction

Cytochrome c: Roles in Electron Transport, Cell Death, and Light Filtration

Take-Home Message

7. Gene Sharing during Gene Expression

Complexity of Transcription

Nuclear Receptors

Metabolic Enzymes and Gene Expression

Y-Box Proteins

Transcription Factors as Translational Regulators: Bicoid

Translation Factors for RNA Export: eIF4

Homeoproteins, Chromosomal Proteins and Actin

The Dynamic Flux of Nuclear Proteins

Take-Home Message

8. Gene Sharing As a Dynamic Evolutionary Process: Antifreeze Proteins and Hemoglobins

Antifreeze Proteins

Hemoglobins

Take-Home Message

9. Gene Duplication and the Evolution of New Functions

Gene Duplication and Retention of Redundant Genes

Birth and Death of Duplicated Genes

Adaptive Evolution by Positive Selection: New Functions after Gene Duplication

Subfunctionalization and Gene Sharing

Rapid Subfunctionalization with Slow Neofunctionalization

Gene Sharing Is Independent of Gene Duplication

Lens Crystallins: Gene Sharing at Different Stages of Duplication

Take-Home Message

10. Gene Sharing and Systems Biology: Implications and Speculations

Networks

Evolvability

Selective Pressure Affecting Gene Regulation

Functional Switching and the Notion of Functional "Trespassing"

Functional Noise

Genetic Differences in Levels of Gene Expression

The Molecular Clock

Gene Knockout Experiments

Gene Deletion of b-Catenin

Horizontal Gene Transfer

Take-Home Message

11. Recapitulations: Ambiguities and Possibilities

Ambiguity of Cause and Effect

Natural Selection Versus Random Drift

Gene Sharing and Robustness: When Is a Mutation Neutral?

Inconsistency with Design

Naming Is Not Knowing

The Question of Tissue Homology

Phylogenetic Trees: The Complication of Function

Defining and Counting Genes

Definition of Polypeptide Function: The Ambiguity of Molecular Mechanism

Between Genotype and Phenotype

Gene Sharing and the Importance of Research on Diverse Species

Medical Implications

Glossary

References

Index

What People are Saying About This

I have not encountered such an interesting, intellectually stimulating and exciting biological monograph in many years. Piatigorsky discusses the phenomenon of gene sharing on all levels, the molecular and cellular, as well as in the context of ìsystem biologyî and finally its ramifications on our views on evolution. He manages to concentrate a tremendous amount of information in this book and whatever he says has experimental backing. His precise and detailed technical descriptions are presented in a very readable style that also projects a sense of wonder and surprise. This is an extraordinary book that I hope will have an important impact on future biological thinking.

Austin Hughes

It has been a dogma of evolutionary biology that gene duplication precedes the evolution of new gene and protein function. Joram Piatigorsky stands this scenario on its head by showing that, in the case of lens crystallins and probably other protein families, functional diversity can precede gene duplication. His revolutionary perspective provides unexpected insight into how biological systems evolve.
Austin Hughes, Professor of Biological Sciences, University of South Carolina

Jianzhi George Zhang

Every textbook of molecular evolution has a section on gene sharing but this is the first book entirely devoted to the topic. Piatigorsky considers almost all aspects of gene sharing, provides numerous examples, and discusses the importance and contribution of gene sharing to evolution. He argues forcefully that gene sharing is widespread in many genomes. His arguments will likely alter the prevailing view of gene sharing as a unique phenomenon to crystallins.
Jianzhi George Zhang, Associate Professor of Ecology and Evolutionary Biology at the University of Michigan

Dr. Alex Keynan

I have not encountered such an interesting, intellectually stimulating and exciting biological monograph in many years. Piatigorsky discusses the phenomenon of gene sharing on all levels, the molecular and cellular, as well as in the context of ìsystem biologyî and finally its ramifications on our views on evolution. He manages to concentrate a tremendous amount of information in this book and whatever he says has experimental backing. His precise and detailed technical descriptions are presented in a very readable style that also projects a sense of wonder and surprise. This is an extraordinary book that I hope will have an important impact on future biological thinking.

Dr. Alex Keynan, Professor at Hebrew University and Special Adviser to the President of the Israeli National Academy of Sciences

Russell D. Fernald

This book introduces, explains and elaborates on the very interesting fact that some genes produce proteins that serve different (and important) functions in the same organism. This is a remarkable story well told and interesting from both evolutionary and functional perspectives.
Russell D. Fernald, Benjamin Scott Crocker Professor of Biological Sciences at Stanford University

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