Gene Sharing and Evolution

Joram Piatigorsky is a molecular biologist in Bethesda, Maryland.

• 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

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.