Molecular Evolution: Evidence for Monophyly of Metazoa

Transition from Protozoa to Metazoa: An Experimental Approach.- 1 Introduction.- 2 Proteins Present in All Biotic Regna.- 2.1 Reproduction.- 2.2 Growth and Development.- 2.3 Energy Utilization.- 2.4 Response to the Environment.- 2.5 Homeostasis.- 2.6 Evolutionary Adaptation.- 3 Monophyly of Metazoa.- 4 Origin of Metazoan Genes and Proteins.- 4.1 Introns.- 4.2 Protein Modules.- 5 Evolution of Metazoan Genes.- 5.1 Sponge: Receptor Tyrosine Kinase.- 5.2 Tunicate: Immunolectin — Antigen Receptor.- 5.2.1 Immunolectin.- 5.2.2 Antigen Receptor.- 5.3 Protein Kinases.- 5.3.1 Ser/Thr Kinases.- 5.3.2 Tyr Kinases.- 5.3.3 Relationship Between Ser/Thr and Tyr Kinases.- 6 Directed Evolution?.- References.- Individuality in Early Eukaryotes and the Consequences for Matazoan Development.- 1 Introduction.- 2 The Evolution of Metabolism and Development.- 2.1 Metabolism and Development, Revisited.- 2.1.1 Mitochondria Make Waves.- 2.1.2 Oxygen Radicals and Cell Signaling.- 2.1.3 Oxygen Radicals and Cell Signaling, Continued.- 2.1.4 Metabolism and Development in the Basal Metazoa.- 2.1.5 Summary.- 2.2 The Logic of the Metabolic Control of Development.- 2.2.1 Simple to Complex Cells.- 2.2.2 Single Cells to Multicellular Organisms.- 2.2.3 Summary: The Logic of Metabolic Control.- 2.3 Summary.- 3 Conclusions.- 3.1 Metazoan Phylogeny and the Mechanisms of Development.- 3.2 Toward a Predictive Theory of Evolution.- References.- Evolution of Animal Lectins.- 1 Introduction.- 2 Brief Overview of Lectins.- 3 Evolution of the C-Type Lectin Family.- 3.1 Overview of the Members of the C-Type Lectin Family.- 3.1.1 Receptor Proteins.- 3.1.2 Soluble Proteins.- 3.2 Biochemical Properties of C-Type Lectin.- 3.2.1 General Properties.- 3.2.2 Binding Specificity.- 3.2.3 Structure of the Sugar-Binding Site.- 3.3 Molecular Evolution of C-Type Lectins.- 4 Evolution of Galectins.- 4.1 Galectin: A New Family Name for a Group of Animal Lectins.- 4.1.1 The Early Period of Galectin Research.- 4.1.2 Expansion of the Galectin Family.- 4.2 Biochemical Properties of the Galectin Family.- 4.2.1 General Properties.- 4.2.2 Three Types of Galectins.- 4.3 Gene Structures of Galectins.- 4.4 Molecular Evolution of Galectins.- 4.4.1 Sequence Similarity Between Galectins.- 4.4.2 Divergence of Galectins.- 4.5 Galectins: Relatives of Legume Lectins?.- 5 Comparison of the Galectin Family and the C-Type Lectin Family.- 5.1 Family Size.- 5.2 Molecular Architecture.- 5.3 Binding Specificity.- 5.4 Localization.- 5.5 Different Missions Assigned to Galectins and C-Type Lectins.- 6 Evolution of Glycocodes.- 6.1 Galactose: A Special Position in Sugar Recognition.- 6.2 Selection of Elementary Sugars in the Life System.- 6.3 Monosaccharides: Biosynthesis from Glucose and Mannose.- 6.4 A Possible Scenario of the Origin of Carbohydrates.- References.- Molecular Phylogeny of Eumetazoa: Genes in Sponges (Porifera) Give Evidence for Monophyly of Animals.- 1 Introduction.- 2 Earlier Problems.- 3 Porifera (Sponges).- 3.1 Tissue.- 3.2 Cell Number.- 3.3 Genome Size.- 3.4 Phylogenetic Position.- 4 Rationale for a Classification of Sponges as Metazoa.- 4.1 Molecules Controlling Tissue Formation.- 4.2 Signal Transduction Molecules.- 4.2.1 Type I Receptors.- 4.2.2 Type II Receptors.- 4.2.3 Type III Receptors.- 4.3 Transcription Factors.- 4.4 Migration.- 4.5 Molecules of Sensory Organs?.- 4.6 Response to the Environment.- 4.7 Morphogens.- 4.8 Molecules Potentially Involved in Sponge Immunity.- 5 Genes in Sponges: Coding for Metazoan Proteins.- 5.1 Model Animal.- 5.2 Gene Structure.- 5.2.1 Lack of Introns.- 5.2.2 Intron Polymorphism.- 5.3 Genes/cDNAs Controlling Tissue Formation.- 5.3.1 Collagen.- 5.3.2 Integrin Receptor.- 5.3.3 “C-Type” Lectins — Galectins.- 5.3.4 Biological Role of Sponge Galectins.- 5.4 Signal Transduction Molecules.- 5.4.1 Receptor Tyrosine Kinase.- 5.4.2 Serine/Threonine Kinases.- 5.5 Transcription Factors.- 5.5.1 Homeodomain Proteins.- 5.5.2 Serum Response Factor.- 5.6 Migration.- 5.7 Molecules of Sensory Organs?.- 5.8 Response to the Environment.- 5.8.1 Heat-Shock Protein 70.- 5.8.2 Ubiquitin.- 5.8.3 DnaJ.- 5.8.4 GDP Dissociation Inhibitor.- 5.9 Molecules Potentially Involved in Sponge Immunity.- 5.9.1 Polymorphism in the Ig-Like Domains of the Receptor Tyrosine Kinase.- 5.9.2 Proteins and Genes in G. cydonium Related to the Human MHC.- 5.9.3 Proteins Featuring Scavenger Receptor Cysteine-Rich Domains.- 5.9.4 Molecules Comprising Short Consensus Repeats.- 6 Evolutionary Tempo.- 7 Conclusion.- References.- Homeobox Genes in the Freshwater Sponge Ephydatia fluviatilis.- 1 Introduction.- 2 Classification of Homeobox Genes.- 2.1 Characteristics of Homeodomains.- 2.2 Classification of Homeobox Genes in Drosophila.- 3 Homeobox Genes in Freshwater Sponges.- 3.1 Methods for the Identification of Hemeobox Genes in Low Metazoans.- 3.2 Homeobox Genes Isolated from Sponges.- 3.2.1 prox1, prox2, and prox3.- 3.2.2 spou-1 and spou-2.- 3.2.3 Other Homeobox Genes.- 4 Comparison of the Homeobox Genes of Sponges with Those of Other Animals.- 4.1 Comparison of the Amino Acid Sequences of the Homeodomains Encoded by prox1, prox2, and prox3 of Sponges with Those of Other Animals.- 4.2 Comparison of Amino Acid Sequences of POU-Specific Domains and POU-Type Homeodomains Encoded by spou-1 and spou-2 of Sponge with Those of Other Animals.- 5 Principles Associated with the Conservation and Diversification of Homeobox Genes During Animal Evolution.- 6 Conclusion.- References.- Homeobox-Containing Genes in Freshwater Sponges: Characterization, Expression and Phylogeny.- 1 Introduction.- 2 Materials and Methods.- 2.1 Purification and Labelling of DNA Fragments.- 2.2 Screening of a Sponge Genomic Library.- 2.3 Random Sequencing of the 12 kb-Cloned Sponge DNA.- 2.4 Sequence Analysis.- 2.5 Sponge Culture.- 2.6 RNA Extraction.- 2.7 RT-PCR Experiments.- 3 Results and Discussion.- 3.1 Cloning and Sequencing of the EmH-3 Homeobox-Containing Gene.- 3.2 EmH-3 Gene Organization.- 3.3 Analysis of the EmH-3 Homeobox Protein.- 3.4 Expression of the EmH-3 Gene in the Course of Development.- 3.5 Phylogeny of Sponge Homeobox-Containing Genes.- 4 Conclusions.- References.- Early Evolution of the Metazoa: An Inference from the Elongation Factor-1?.- 1 Introduction.- 2 Inference from EF-1? Sequences.- 3 Monophyly of the Metazoa.- 4 Phylogenetic Status of the Diploblasts.- 5 Conclusion.- References.