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8.1: Archaeplastida - Biology

8.1: Archaeplastida - Biology



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Red algae and green algae are included in the supergroup Archaeplastida. The red and green algae include unicellular, multicellular, and colonial forms.

Red Algae

Red algae, or rhodophytes lack flagella, and are primarily multicellular, although they range in size from microscopic, unicellular protists to large, multicellular forms grouped into the informal seaweed category. Red algae have a second cell wall outside an inner cellulose cell wall. Carbohydrates in this wall are the source of agarose used for electrophoresis gels and agar for solidifying bacterial media. The “red” in the red algae comes from phycoerythrins, accessory photopigments that are red in color and obscure the green tint of chlorophyll in some species. Other protists classified as red algae lack phycoerythrins and are parasites. Both the red algae and the glaucophytes store carbohydrates in the cytoplasm rather than in the plastid. Red algae are common in tropical waters where they have been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments. The red algae life cycle is an unusual alternation of generations that includes two sporophyte phases, with meiosis occurring only in the second sporophyte.

Green Algae: Chlorophytes and Charophytes

The most abundant group of algae is the green algae. The green algae exhibit features similar to those of the land plants, particularly in terms of chloroplast structure. In both green algae and plants, carbohydrates are stored in the plastid. That this group of protists shared a relatively recent common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes and the charophytes. The charophytes are the closest living relatives to land plants and resemble them in morphology and reproductive strategies. The familiar Spirogyra is a charophyte. Charophytes are common in wet habitats, and their presence often signals a healthy ecosystem.

The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist toward light sensed by its eyespot. More complex chlorophyte species exhibit haploid gametes and spores that resemble Chlamydomonas.

The chlorophyte Volvox is one of only a few examples of a colonial organism, which behaves in some ways like a collection of individual cells, but in other ways like the specialized cells of a multicellular organism (Figure 1). Volvox colonies contain 500 to 60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous glycoprotein secretion. Individual cells in a Volvox colony move in a coordinated fashion and are interconnected by cytoplasmic bridges. Only a few of the cells reproduce to create daughter colonies, an example of basic cell specialization in this organism. Daughter colonies are produced with their flagella on the inside and have to evert as they are released.

True multicellular organisms, such as the sea lettuce, Ulva, are also represented among the chlorophytes. In addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa exhibit flattened fern-like foliage and can reach lengths of 3 meters (Figure 2). Caulerpa species undergo nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate single cells.


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Paweł Mackiewicz
Department of Genomics, Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-383 Wrocław
Poland

Przemysław Gagat
Department of Genomics, Faculty of Biotechnology, University of Wrocław, Fryderyka Joliot-Curie 14a, 50-383 Wrocław
Poland

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Monophyly of Archaeplastida supergroup and relationships among its lineages in the light of phylogenetic and phylogenomic studies. Are we close to a consensus?

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Contents

The field of plant physiology includes the study of all the internal activities of plants—those chemical and physical processes associated with life as they occur in plants. This includes study at many levels of scale of size and time. At the smallest scale are molecular interactions of photosynthesis and internal diffusion of water, minerals, and nutrients. At the largest scale are the processes of plant development, seasonality, dormancy, and reproductive control. Major subdisciplines of plant physiology include phytochemistry (the study of the biochemistry of plants) and phytopathology (the study of disease in plants). The scope of plant physiology as a discipline may be divided into several major areas of research.

First, the study of phytochemistry (plant chemistry) is included within the domain of plant physiology. To function and survive, plants produce a wide array of chemical compounds not found in other organisms. Photosynthesis requires a large array of pigments, enzymes, and other compounds to function. Because they cannot move, plants must also defend themselves chemically from herbivores, pathogens and competition from other plants. They do this by producing toxins and foul-tasting or smelling chemicals. Other compounds defend plants against disease, permit survival during drought, and prepare plants for dormancy, while other compounds are used to attract pollinators or herbivores to spread ripe seeds.

Secondly, plant physiology includes the study of biological and chemical processes of individual plant cells. Plant cells have a number of features that distinguish them from cells of animals, and which lead to major differences in the way that plant life behaves and responds differently from animal life. For example, plant cells have a cell wall which restricts the shape of plant cells and thereby limits the flexibility and mobility of plants. Plant cells also contain chlorophyll, a chemical compound that interacts with light in a way that enables plants to manufacture their own nutrients rather than consuming other living things as animals do.

Thirdly, plant physiology deals with interactions between cells, tissues, and organs within a plant. Different cells and tissues are physically and chemically specialized to perform different functions. Roots and rhizoids function to anchor the plant and acquire minerals in the soil. Leaves catch light in order to manufacture nutrients. For both of these organs to remain living, minerals that the roots acquire must be transported to the leaves, and the nutrients manufactured in the leaves must be transported to the roots. Plants have developed a number of ways to achieve this transport, such as vascular tissue, and the functioning of the various modes of transport is studied by plant physiologists.

Fourthly, plant physiologists study the ways that plants control or regulate internal functions. Like animals, plants produce chemicals called hormones which are produced in one part of the plant to signal cells in another part of the plant to respond. Many flowering plants bloom at the appropriate time because of light-sensitive compounds that respond to the length of the night, a phenomenon known as photoperiodism. The ripening of fruit and loss of leaves in the winter are controlled in part by the production of the gas ethylene by the plant.

Finally, plant physiology includes the study of plant response to environmental conditions and their variation, a field known as environmental physiology. Stress from water loss, changes in air chemistry, or crowding by other plants can lead to changes in the way a plant functions. These changes may be affected by genetic, chemical, and physical factors.

The chemical elements of which plants are constructed—principally carbon, oxygen, hydrogen, nitrogen, phosphorus, sulfur, etc.—are the same as for all other life forms: animals, fungi, bacteria and even viruses. Only the details of their individual molecular structures vary.

Despite this underlying similarity, plants produce a vast array of chemical compounds with unique properties which they use to cope with their environment. Pigments are used by plants to absorb or detect light, and are extracted by humans for use in dyes. Other plant products may be used for the manufacture of commercially important rubber or biofuel. Perhaps the most celebrated compounds from plants are those with pharmacological activity, such as salicylic acid from which aspirin is made, morphine, and digoxin. Drug companies spend billions of dollars each year researching plant compounds for potential medicinal benefits.

Constituent elements Edit

Plants require some nutrients, such as carbon and nitrogen, in large quantities to survive. Some nutrients are termed macronutrients, where the prefix macro- (large) refers to the quantity needed, not the size of the nutrient particles themselves. Other nutrients, called micronutrients, are required only in trace amounts for plants to remain healthy. Such micronutrients are usually absorbed as ions dissolved in water taken from the soil, though carnivorous plants acquire some of their micronutrients from captured prey.

The following tables list element nutrients essential to plants. Uses within plants are generalized.


Primary acquisition of the plastid

The primary acquisition of the plastid in an ancestor of extant Archaeplastida was a pivotal event in the history of life. All possible relationships among Viridiplantae, Glaucophyta and Rhodophyta have been hypothesized, with alternative implications for the gain and loss of characters 35 in the early history of the three lineages. Strong support for the sister relationship of Viridiplantae and Glaucophyta 35 (Figs. 2, 3a) found here indicates that ancestral red algae lost flagella and peptidoglycan biosynthesis, perhaps associated with a reduction in genome size 36 . Peptidoglycan biosynthesis was independently lost early in the evolution of Chlorophyta 37 and within angiosperms 38 .


Part I Introduction 1

1.1 Receptors and Signaling 3

1.1.1 General Aspects of Signaling 3

1.1.2 Verbal and Physiological Signals 3

1.1.3 Criteria for Recognizing Transmitters and Receptors 4

1.1.6 Receptor&ndashEnzyme Similarities 4

1.2 Types of Receptors and Hormones 5

1.2.1 Receptor Superfamilies 5

1.3 Receptors Are the Chemical Expression of Reality 6

2 The Origins of Chemical Thinking 9

2.1 Overview of Early Pharmacological History 9

2.1.1 The Development of a Chemical Hypothesis 9

2.1.2 Chemical Structure and Drug Action 10

2.1.3 The Site of Drug Action 10

2.2 Modern Pharmacology 10

2.2.1 Langley and Ehrlich: the Origins of the Receptor Concept 10

2.2.2 Maturation of the Receptor Concept 13

2.3 Phylogenetics of Signaling 13

2.3.1 The First Communicators 13

Part II Fundamentals 15

3 Membranes and Proteins 17

3.1.1 The Cytoplasmic Membrane &ndash the Importance of Cell Membranes 17

3.1.2 History of Membrane Models 17

3.1.2.1 The Roles of Proteins in Membranes 18

3.1.2.2 Challenges to the Danielli&ndashDavson Model 19

3.1.2.3 A New View of Membrane Proteins 19

3.1.2.4 The Modern Concept of Membranes &ndash the Fluid Mosaic Model 19

3.1.3 Membrane Components 19

3.1.3.2 Asymmetry and Heterogeneity in Membrane Lipids 20

3.1.3.3 Membrane Construction and Insertion of Proteins 20

3.2 The Nature and Function of Proteins 21

3.2.1 Linear andThree-Dimensional Structures 22

3.2.3 Secondary Structure 23

3.2.4 Tertiary Structure 24

4 Hormones as First Messengers 27

4.1 Hormones and Cellular Communication 27

4.1.1 Discovery of Hormones 27

4.2.1 Pheromones for Signaling between Individuals 28

4.2.2 Archaea and Bacteria 28

4.2.3.2 Unikonts &ndash Amoebozoa, Fungi, Animals 29

4.2.3.3 Invertebrate Pheromones 31

4.2.3.4 Vertebrate Pheromones 31

4.3 Vertebrate Hormones and Transmitters 31

4.3.1 Peptide and Non-Peptide Agonists 31

4.3.2 Peptide Hormones of the G-Protein-Coupled Receptors 32

4.3.2.1 Hypothalamic-Pituitary Axis 32

4.3.2.2 The Anterior Pituitary Trophic Hormones 34

4.3.3 Other Neural Peptides 35

4.3.3.2 Non-Opioid Transmitter Peptides 36

4.3.4 Peptides from Non-Neural Sources 36

4.3.4.1 Digestive Tract Hormones 36

4.3.4.2 Hormones from Vascular Tissue 38

4.3.4.3 Hormones from the Blood 38

4.3.4.4 Peptide Hormones from Reproductive Tissues 39

4.3.4.5 Hormones from Other Tissues 39

4.3.5 Non-Peptides Acting on G-Protein-Coupled Receptors 39

4.3.5.1 Transmitters Derived from Amino Acids 39

4.3.5.2 Transmitters Derived from Nucleotides 40

4.3.5.3 Transmitters Derived from Membrane Lipids &ndash Prostaglandins and Cannabinoids 41

4.3.6 Transmitters of the Ion Channels 41

4.3.7 Hormones of the Receptor Kinases &ndash Growth Factor Receptors 43

4.3.7.2 Insulin-Like Growth Factors 43

4.3.7.3 Natriuretic Peptides 43

4.3.7.4 Peptide Signal Molecules Important in Embryogenesis 43

4.3.7.5 Pituitary Gland Hormones &ndash Somatotropin and Prolactin 43

4.3.8 Hormones of the Nuclear Receptors 44

4.3.8.2 Non-Steroid Nuclear Hormones 46

4.4 Analgesics and Venoms as Receptor Ligands 46

5.1 The Materialization of Receptors 47

5.2.1 Binding of Agonist to Receptor 48

5.3.1 Early Approaches to Understanding Receptor Action 49

5.3.1.1 The Occupancy Model 49

5.3.1.2 Processes That Follow Receptor Activation 52

5.3.1.3 Efficacy and Spare Receptors 52

5.3.2 Modern Approaches to Receptor Theory 52

5.3.2.1 The Two-State Model 52

5.3.2.2 The Ternary Complex Model 53

5.3.2.4 Cubic Ternary Complex (CTC) Model 55

5.3.3 Summary of Model States 55

5.4 Visualizing Receptor Structure and Function 55

5.4.1 Determination of Receptor Kd 55

5.4.2 Visualizing Ligand Binding 57

5.4.2.1 Receptor Preparation 58

5.4.2.2 Equilibrium Binding Studies 58

5.4.2.3 Competition Studies 58

5.4.3 X-ray Crystallography of Native and Agonist-Bound Receptors 59

5.4.4 Probe Tagging (Fluorescent and Photoaffinity) 60

5.5 Proteomics Approaches to Receptor Efficacy 60

5.6 Physical Factors Affecting Receptor Binding 61

5.6.2 Relation of Agonist Affinity and Efficacy to Distance Traveled Following Release 61

Part III Receptor Types and Function 63

6 Transduction I: Ion Channels and Transporters 65

6.1.1 Family Relationships 65

6.2 Small Molecule Channels 66

6.2.1 Osmotic and Stretch Detectors 66

6.2.2 Voltage-Gated Cation Channels 66

6.2.2.1 History of Studies on Voltage-Gated Channels 66

6.2.2.2 Structure and Physiology of Ion Channels 68

6.2.3 Potassium Channels 68

6.2.4.1 Bacterial Na+ Channels 70

6.2.4.2 Vertebrate Na+ Channels 70

6.2.6 Non-Voltage-Gated Cation Channels &ndash Transient Receptor Potential (TRP) Channels 72

6.3.1 Pumps and Facilitated Diffusion 73

6.3.2 The Chloride Channel 76

6.4 Major Intrinsic Proteins 76

6.4.2 Glycerol Transporters 77

6.5 Ligand-Gated Ion Channels 77

6.5.1 Four-TM Domains &ndash the Cys-Loop Receptors 77

6.5.1.1 The Four-TM Channels for Cations 78

6.5.1.2 The Four-TM Channels for Anions 80

6.5.2 Three-TM Domains &ndash Ionotropic Glutamate Receptors 82

6.5.2.1 Glutamate-Gated Channels 82

6.5.2.2 N-Methyl-D-aspartate (NMDA) Receptor 82

6.5.2.3 Non-NMDA Receptors 82

6.5.3 Two-TM Domains &ndash ATP-Gated Receptors (P2X) 82

7 Transduction II: G-Protein-Coupled Receptors 85

7.1.2 Sensory Transduction 87

7.1.2.1 Chemoreception in Non-Mammals 87

7.1.2.2 Chemoreception in Mammals 87

7.2 Families of G-Protein-Coupled Receptors 89

7.3 Transduction Mechanisms 89

7.3.1 Discovery of Receptor Control of Metabolism &ndash Cyclic AMP and G Proteins 89

7.3.1.1 Components of the Process of Metabolic Activation 89

7.3.1.2 Discovery of Cyclic AMP 90

7.3.1.3 Discovery of G Proteins 90

7.3.2 Actions of G Proteins 91

7.3.2.2 Roles of the Beta and Gamma Subunits 95

7.3.3 Proteins That Enhance (GEF) or Inhibit (GAP) GTP Binding 96

7.3.4 Signal Amplification 97

7.3.5 Signal Cessation &ndash Several Processes Decrease Receptor Activity 97

7.3.6 Interactions between Receptors and G Proteins 97

7.3.7 Summary of Actions of GPCRs: Agonists, Receptors, G Proteins, and Signaling Cascades 98

7.4 The Major Families of G Protein-Coupled Receptors 99

7.4.1 Family A &ndash Rhodopsin-Like 99

7.4.2 Family B &ndash Secretin-Like 104

7.4.3 Family C &ndash Metabotropic Glutamate and Sweet/Umami Taste Receptors 104

7.4.3.1 Taste 1 Receptors (T1Rs) 105

7.4.3.2 Calcium-Sensing Receptors 106

7.4.4 Family D &ndash Adhesion Receptors 106

7.4.5 Family F &ndash Frizzled-Smoothened Receptors 106

7.4.6 Family E &ndash Cyclic AMP Receptors 106

7.4.7 Other G-Protein-Coupled Receptor Types in Eukaryotes 106

7.4.7.1 Yeast Mating Pheromone Receptors 106

7.4.7.2 Insect Taste Receptors 106

7.4.7.3 Nematode Chemoreceptors 106

8 Transduction III: Receptor Kinases and Immunoglobulins 107

8.2 Receptors for Cell Division and Metabolism 108

8.2.1 Overview of Family Members 108

8.2.2 Overall Functions of RTK 108

8.2.2.1 Extracellular Domains 108

8.2.2.2 Intracellular Domains 109

8.2.3 Receptor Tyrosine Kinase Subfamilies 110

8.2.3.1 EGF Receptor Subfamily 111

8.2.3.2 Insulin Receptor Subfamily 111

8.2.3.3 FGF and PDGF Receptor Subfamilies 111

8.2.3.4 NGF Receptor Subfamily 111

8.3 Receptor Serine/Threonine Kinases 112

8.3.1 Transforming Growth Factor-Beta (TGF-&beta) Receptor 112

8.4 The Guanylyl Cyclase Receptor Subfamily &ndash Natriuretic Peptide Receptors 112

8.5 Non-Kinase Molecules &ndash LDL Receptors 113

8.5.1 Cholesterol Transport 113

8.5.2 The Low-Density Lipoprotein (LDL) Receptor 114

8.5.2.1 Clathrin-Coated Pits 114

8.6 Cell&ndashCell Contact Signaling 115

8.6.1 Notch&ndashDelta Signaling 115

8.7 Immune System Receptors, Antibodies, and Cytokines 115

8.7.1 The Innate Immune Responses 115

8.7.2 The Cells and Molecules of the Adaptive Immune System 116

8.7.3 T-Cell Receptors and Immunoglobulins 116

8.7.4 Cell-Surface Molecules 117

8.7.4.1 The MHC Proteins 117

8.7.4.2 Receptors of the B and T Cells 118

9 Transduction IV: Nuclear Receptors 121

9.2 Genomic Actions of Nuclear Receptors 122

9.2.1 Families of Nuclear Receptors 122

9.2.2 Transcription Control 122

9.2.3 Constitutively Active Nuclear Receptors 122

9.2.4 Liganded Receptors 122

9.2.5 History of Steroid Receptor Studies 123

9.2.6 Receptor Structure 123

9.2.7 The Ligand-Binding Module 124

9.2.8 The DNA-BindingModule 125

9.2.9 Specific Nuclear Actions 125

9.2.9.1 Family 1 &ndashThyroid Hormone and Vitamins A and D Receptors 125

9.2.9.2 Family 2 &ndash Fatty Acid (HNF4) and Retinoic X Receptors (RXR) 127

9.2.9.3 Family 3 &ndash Steroid Receptors for Estrogens, Androgens, Progestogens, Mineralocorticoids, and Glucocorticoids 128

9.3 Actions of Receptor Antagonists 129

9.4 Non-Traditional Actions of Steroid-Like Hormones andTheir Receptors 130

9.4.1 Cell-Membrane Progesterone Receptors 131

9.4.2 Cell-Membrane Mineralocorticoid and Glucocorticoid Receptors 131

9.4.3 Cell-MembraneThyroid Hormone and Vitamin A/D Receptors 131

9.4.4 Ligand-Independent Activation of Transcription 131

Part IV Applications 133

10 Signaling Complexity 135

10.2 Experimental Determination of Signaling Cascades 135

10.2.2 MAPK: a Phosphorylation Cascade 136

10.3 Transduction across theMembrane 138

10.3.2 G-Protein-Coupled Receptors 138

10.3.2.1 Other G-Protein-Like Transducers &ndash Ras 139

10.3.2.2 Other G-Protein-Like Transducers &ndash Ran 139

10.3.3 Cell Aggregation and Development 140

10.3.3.1 Coaggregation in Bacteria 140

10.3.3.2 Aggregation in Eukaryotes 140

10.3.3.3 The Molecules of Cell Adhesion 141

10.4 Complexity in Cross Talk &ndash Roles of PIP3, Akt, and PDK1 141

10.4.1 Signaling Cascades Using PIP3 142

10.4.3 Receptor Tyrosine Kinases 144

10.4.4 Cytokine Receptors and the JAK/STAT Proteins 144

10.4.5 Combined Cellular Signaling &ndash GPCR and RTK Actions 144

10.5.1 Constitutive versus Inducible Activation 144

10.6 Signaling Mediated by Gas Molecules 146

10.6.3 Hydrogen Sulfide 148

11 Cellular Interactions in Development 149

11.2 The Origins of Multicellularity 150

11.2.1 Multicellular Lineages in Prokaryotes 150

11.2.2 Multicellular Lineages in Eukaryotes 150

11.2.2.1 Chromalveolates &ndash Generally Unicellular but with One Multicellular Clade 151

11.2.2.2 Archaeplastida &ndash Algae and Plants 151

11.2.2.3 Amoebozoans, Fungi, Choanoflagellates, and Animals 151

11.3 The Origin of Symmetry and Axes 152

11.3.1 The Multicellular Body Plan 152

11.3.2 The Porifera &ndash Asymmetric with a Single Cell Layer 152

11.3.3 Cnidaria &ndash Radial Symmetry, Two Cell Layers, Tissues 153

11.4 Fertilization and Organization of the Multicellular Body Plan 154

11.4.1 Sperm&ndashEgg Recognition 154

11.4.1.1 Sea Urchin Fertilization 154

11.4.1.2 Mammalian Fertilization 157

11.5 Differentiation of Triploblastic Embryos &ndash Organogenesis 158

11.5.2 The Origin of Triploblastic Animals 158

11.5.3 Development in Protostomes 159

11.5.3.1 Segmentation and Organ Formation in Drosophila 159

11.5.3.2 Cellular Interactions in Later Drosophila Development 161

11.5.4 Development in Deuterostomes 162

11.5.4.1 Early Frog Development 162

11.6 Programmed Cell Death (Apoptosis) 165

11.6.1 Apoptosis During Development 166

11.6.2 Apoptosis During Adult Life 166

12 Receptor Mechanisms in Disease Processes 169

12.1 Genetic Basis for Receptor Function 169

12.1.1 Genotype and Phenotype 169

12.1.2 Classical Dominance Mechanisms 169

12.1.3 Other Levels of Gene Expression 170

12.1.4 Pre-receptor Mutations 170

12.1.5 Receptor Mutations 171

12.1.6 Post-receptor Mutations 171

12.2 Receptor Pathologies 171

12.2.1 Ion Channel Superfamily 171

12.2.1.1 Calcium Channels 172

12.2.1.2 Transient Receptor Protein (TRP) Channels 172

12.2.1.3 Voltage-Gated Na+ Channels 172

12.2.1.4 Ligand-Gated Na+ Channels 172

12.2.1.5 Chloride Transporter &ndash Cystic Fibrosis 172

12.2.2 G-Protein-Coupled Receptor Superfamily 172

12.2.2.2 Thyroid Diseases 173

12.2.2.3 Cardiovascular Disease 173

12.2.3 Immunoglobulin Superfamily 176

12.2.3.1 Diabetes Mellitus 176

12.2.3.2 Atherosclerosis 176

12.2.4 Nuclear Receptor Superfamily &ndash Steroid Receptors 176

12.2.4.1 Alterations in Transcription 176

12.2.4.2 Additional Effects 177

12.3 Signaling Mutations Leading to Cancer 177

12.3.1 Pathogenesis of Cancer 177

12.3.2 Cancer as a Disease of Signaling Molecules 178

12.3.2.1 Oncogenes that Encode Mutated Transmitters 178

12.3.2.2 Oncogenes that Encode Mutated RTKs 178

12.3.2.3 Oncogenes that Encode Mutated G Proteins 179

12.3.2.4 Oncogenes that Encode Mutated Transcription Factors &ndash Steroid Receptors 180

13 Receptors and the Mind 181

13.1 Origins of Behavior 181

13.1.1 Bacterial Short-Term Memory 181

13.1.2 AnimalsWithout True Neural Organization:The Porifera 182

13.1.3 Animals with Neural Networks: The Cnidaria 182

13.1.4 Bilaterally Symmetrical Animals: The Acoela 183

13.2.3.1 Synthesis and Release of Brain Transmitters 185

13.2.3.2 Converting Short-Term Memory to Long Term 186

13.3 Animal Memory: Invertebrates 186

13.3.1 Discovery of the Signaling Contribution to Memory 186

13.3.2 Receptor Mechanisms of Nerve Cell Interactions 186

13.3.2.1 The GillWithdrawal Reflex of Aplysia 186

13.3.2.2 Mechanisms Underlying Sensitization and Short-Term Memory 187

13.3.2.3 Ion Flows in Nerve Action Potentials 187

13.3.2.4 Consolidation into Long-Term Memory (LTP) 188

13.4 Animal Memory: Vertebrates 188

13.4.1 Intracellular Mechanisms of Potentiation 188

13.5 Receptors and Behavior: Addiction, Tolerance, and Dependence 190

13.5.1 Opioid Receptors 190

13.5.1.1 Opioid Neuron Pathways in the Brain 191

13.5.1.2 The Opioid Peptides and Receptors 192

13.5.1.3 Mechanisms of Transduction 192

13.5.1.4 Characteristics of Responses to Continued Drug Presence 192

13.5.2 Individual and Cultural Distributions of Depression 193

13.5.2.2 Polymorphisms in Neurotransmitter Transporters 194

13.5.2.3 Polymorphisms in Opioid Receptor Subtypes 194

13.5.2.4 Polymorphisms in Enzymes for Transmitter Disposition 194

13.5.2.5 Society-Level Actions 194

13.5.2.6 Possible Mechanisms 195

14 Evolution of Receptors, Transmitters, and Hormones 197

14.1.1 Phylogeny of Communication: General Ideas 197

14.2 Origins of Transmitters and Receptors 197

14.2.1 Evolution of Signaling Processes 197

14.2.2 Homologous Sequences 198

14.2.2.1 Orthologous and Paralogous Sequences 198

14.2.3 Phylogenetic Inference 199

14.2.4 Phylogenetic Illustration of Protein Relationships 199

14.2.5 Whole-Genome Duplication (WGD) 200

14.2.6 Origins of Novel Domains 201

14.2.7 Adaptation of Receptor Systems 201

14.2.8 Coevolution of Components of Signaling Pathways 202

14.2.9 Peptide Hormones and Their Receptors 202

14.2.10 Receptors and Their Non-Peptide Hormones 202

14.3 Evolution of Hormones 202

14.3.1 Peptide Hormones for G Protein-Coupled Receptors 202

14.3.1.1 The Yeast Mating Pheromones 203

14.3.1.2 The Anterior Pituitary Trophic Hormones 203

14.3.1.3 The Hypothalamic Releasing Hormones 203

14.3.1.4 The Posterior Pituitary Hormones 203

14.3.1.5 Miscellaneous Peptide Hormones 204

14.3.2 Hormones of the Receptor Tyrosine Kinases 204

14.3.2.1 The Insulin Family 204

14.3.2.2 The Neurotrophins 204

14.3.2.3 The Growth Hormone Family 204

14.4 Evolution of Receptor Superfamilies 205

14.4.1.1 Voltage-Gated Channels 205

14.4.1.2 Ligand-Gated Channels 205

14.4.2 G Protein-Coupled Receptors 206

14.4.2.1 G-Protein-Coupled Receptor Types 206

14.4.2.2 Family A Receptors &ndash Rhodopsin Family 206

14.4.2.3 Family B &ndash Secretin and Adhesion Receptors 207

14.4.2.4 Family F &ndash Frizzled and Smoothened Receptors 208

14.4.2.5 Elements of the GPCR Transduction Pathway 208

14.4.3 The Immunoglobulin Superfamily 210

14.4.3.1 The Receptor Tyrosine Kinases 210

14.4.3.2 Molecules of the Adaptive Immune System 211

14.4.4 Steroid, Vitamin A/D, andThyroid Hormone Receptors 211

14.4.4.1 Origin of Nuclear Receptors: The Role of Ligands 211

14.4.4.2 The Nuclear Receptor Families 211

14.4.4.3 Later Evolution of Nuclear Receptors &ndash Ligand Exploitation 212


Timing of morphological and ecological innovations in the cyanobacteria – a key to understanding the rise in atmospheric oxygen

When cyanobacteria originated and diversified, and what their ancient traits were, remain critical unresolved problems. Here, we used a phylogenomic approach to construct a well-resolved ‘core’ cyanobacterial tree. The branching positions of four lineages (Thermosynechococcus elongatus, Synechococcus elongatus, Synechococcus PCC 7335 and Acaryochloris marina) were problematic, probably due to long branch attraction artifacts. A consensus genomic tree was used to study trait evolution using ancestral state reconstruction (ASR). The early cyanobacteria were probably unicellular, freshwater, had small cell diameters, and lacked the traits to form thick microbial mats. Relaxed molecular clock analyses suggested that early cyanobacterial lineages were restricted to freshwater ecosystems until at least 2.4 Ga, before diversifying into coastal brackish and marine environments. The resultant increases in niche space and nutrient availability, and consequent sedimentation of organic carbon into the deep oceans, would have generated large pulses of oxygen into the biosphere, possibly explaining why oxygen rose so rapidly. Rapid atmospheric oxidation could have destroyed the methane-driven greenhouse with simultaneous drawdown in pCO2, precipitating ‘Snowball Earth’ conditions. The traits associated with the formation of thick, laminated microbial mats (large cell diameters, filamentous growth, sheaths, motility and nitrogen fixation) were not seen until after diversification of the LPP, SPM and PNT clades, after 2.32 Ga. The appearance of these traits overlaps with a global carbon isotopic excursion between 2.2 and 2.1 Ga. Thus, a massive re-ordering of biogeochemical cycles caused by the appearance of complex laminated microbial communities in marine environments may have caused this excursion. Finally, we show that ASR may provide an explanation for why cyanobacterial microfossils have not been observed until after 2.0 Ga, and make suggestions for how future paleobiological searches for early cyanobacteria might proceed. In summary, key evolutionary events in the microbial world may have triggered some of the key geologic upheavals on the Paleoproterozoic Earth.

Figure S1 Rooting the cyanobacterial tree.

Figure S2 Bayesian analyses using a covarion model.

Figure S3 Bootstrap support for SSU–LSU and SSU–RpoC trees.

Figure S4 ASR–RMC chronogram using the 139-gene MB tree.

Figure S5 ASR–RMC chronogram using SSU–RpoC tree with alternative topology A.

Figure S6 ASR–RMC chronogram using SSU–RpoC tree with alternative topology B.

Table S1 Sequence composition of genomic data sets.

Table S2 Accession Numbers for SSU, LSU and RpoC1 data and sequence composition of SSU–LSU and SSU–RpoC data sets.

Table S3 Inferred ancestral cell diameters (in μm) using multiple trees and methods.

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Endosimbioza

Glavni članak: Endosimbiotska teorija

Kako se pretpostavlja da su preci arheplastida hloroplaste stekli direktno gutajući cijanobakterije, dogaᄚj je poznat kao primarna endosimbioza (što se odra៪va na naziv izabran za skupinu &aposArchaeplastida&apos, tj. &aposdrevni plastid&apos). Jedna vrsta zelenih algi, Cymbomonas tetramitiformis iz reda Pyramimonadales, je miksotrof i sposobna je da se se hrani i kao phagotrof i fototrof. Još nije poznato je li to primitivna osobina i zato definira posljednjeg zajedničkog pretka Archaeplastide, koji bi mogao objasniti kako je dobijao hloroplaste ili je to osobina koju je vratio horizontalni prijenos gena. [12] Dokaz za primarnu endosimbozu uključuje prisustvo dvostruke membrane oko hloroplasta jedna je pripadala bakteriji, a druga eukariotu koji ju je zarobio. Vremenom, mnogi geni iz hloroplasta prebaპni su u ၾlijsko jedro domaćina. Prisustvo takvih gena u jedrima eukariota bez hloroplasta sugerira da se ovaj transfer desio poპtkom evolucije ove grupe. [13]

Izgleda da su drugi eukarioti hloroplaste stekli zahvaၺjući jednoၾlijskim arheplastidama s vlastitim hloroplastima koji potiču iz bakterija. Kako ovi dogaᄚji uključuju endosimbiozu ၾlija koje imaju svoje endosimbionte, proces se naziva "sekundarna endosimbioza". Hloroplasti takvih eukariota su obično okru៮ni s viᘞ od dvije membrane, što odra៪va shvatanje historije viᘞstrukog preuzimanja. Hloroplasti euglenida, chlorarachniophyte, hlorachniophyte i male grupa dinoflagellata izgleda da su preuzeti iz zelenih algi, [14] budući da izgleda da su oni kod preostalih fotosintetskih eukariota, poput algi heterokonta, kriptofita, haptofita i dinoflagelata, zarobljene crvene alge.


Contents

Charophyta are complex green algae that form a sister group to the Chlorophyta and within which the Embryophyta emerged. The chlorophyte and charophyte green algae and the embryophytes or land plants form a clade called the green plants or Viridiplantae, that is united among other things by the absence of phycobilins, the presence of chlorophyll a and chlorophyll b, cellulose in the cell wall and the use of starch, stored in the plastids, as a storage polysaccharide. The charophytes and embryophytes share several traits that distinguish them from the chlorophytes, such as the presence of certain enzymes (class I aldolase, Cu/Zn superoxide dismutase, glycolate oxidase, flagellar peroxidase), lateral flagella (when present), and, in many species, the use of phragmoplasts in mitosis. [13] Thus Charophyta and Embryophyta together form the clade Streptophyta, excluding the Chlorophyta.

Charophytes such as Palaeonitella cranii and possibly the yet unassigned Parka decipiens [14] are present in the fossil record of the Devonian. [12] Palaeonitella differed little from some present-day stoneworts.

Cladogram Edit

Below is a consensus reconstruction of green algal relationships, mainly based on molecular data. [13] [15] [16] [17] [8] [1] [5] [18] [19] [20] [21] [22] [23]

The phylogeny is not entirely uncontroversial. [23] The placement of the basal green algae (Mesostigmatophyceae, Spirotaenia, and Chlorokybophyceae) is more conventionally at the base of Streptophytes. [24]

Basal Streptophytes are filamentous, while Mesostigmatophyceae and Chlorokybophyceae are not. [25] [23] [20]

The Zygnematophyceae or, as they used to be called, Conjugatophyceae, generally possess two fairly elaborate chloroplasts in each cell, rather than many discoid ones. They reproduce asexually by the development of a septum between the two cell-halves or semi-cells (in unicellular forms, each daughter-cell develops the other semi-cell afresh) and sexually by conjugation, or the fusion of the entire cell-contents of the two conjugating cells. The saccoderm desmids and the placoderm or true desmids, unicellular or filamentous members of the Zygnematophyceae, are dominant in non-calcareous, acid waters of oligotrophic or primitive lakes (e.g. Wastwater), or in lochans, tarns and bogs, as in the West of Scotland, Eire, parts of Wales and of the Lake District. [26]

Klebsormidium, the type of the Klebsormidiophyceae, is a simple filamentous form with circular, plate-like chloroplasts, reproducing by fragmentation, by dorsiventral, biciliate swarmers and, according to Wille, a twentieth-century algologist, by aplanospores. [27] Sexual reproduction is simple and isogamous (the male and female gametes are outwardly indistinguishable). [27]

The various groups included in the Charophyta have diverse and idiosyncratic reproductive systems, sometimes with complex reproductive organs. The unique habit among the algae of protecting the overwintering zygote within the tissues of the parent gametophyte is one of several characteristics of Coleochaetales that suggest that they are a sister group to the embryophytes. [28]

The Charales or stoneworts are freshwater algae with slender green or grey stems the grey colour of many species results from the deposition of lime on the walls, masking the green colour of the chlorophyll. The main stems are slender and branch occasionally. Lateral branchlets occur in whorls at regular intervals up the stem, they are attached by rhizoids to the substrate. [29] The reproductive organs consist of antheridia and oogonia, though the structures of these organs differ considerably from the corresponding organs in other algae. As a result of fertilization a protonema is formed, from which the sexually reproducing algae develops.

Charophytes are frequently found in hard water with dissolved calcium or magnesium carbonates. They tolerate low concentrations of salt, and are found in the inner reaches of the Baltic Sea [30] and in tropical brackish lagoons [31] but not in marine environments. The water must be still, or only slow-flowing, oligotrophic or mesotrophic and little pollution due to sewage. [ citation needed ]

The Charophyceae are obligate aquatic algae, growing submerged in calcareous fresh water. They are distributed throughout the world from the tropics to cold temperate zones.

Six genera are recognized:

  • Chara
  • Lamprothamnium
  • Lychnothamnus
  • Nitella
  • Nitellopsis
  • Tolypella.[29]

Cell structure Edit

There are numerous small discoid chloroplasts, which are disposed around the periphery of the cells. No pyrenoids are present. The large internodal cells are sometimes multinucleate, and their nuclei often possess large nucleoli and little chromatin. In these cells the cytoplasm forms only a peripheral layer with a large central vacuole. The cell walls are composed of cellulose, though there may be also a superficial layer of a more gelatinous material of unknown composition.

The storage material is starch, except in the oospore, where oil also occurs. This starch also accumulates in special storage structures, termed bulbils, which consist of rounded cells of varying size which are developed in clusters on the lower stem-like and root-like nodes. They are mainly developed when the algae are growing in fine slimy mud.

Cytoplasmic streaming was first demonstrated in the giant cells of Chara internodes by Giovanni Battista Amici, in 1818.

Their body organization is three-dimensional, however there is no full division of labour thus are thaloids. [32]

Sexual reproduction Edit

The reproductive organs of the Charales show a high degree of specialization. The female organ, called an oogonium is a large oval structure with an envelope of spirally arranged, bright green filaments of cells. It is termed an oogonium. The male organ or is also large, bright yellow or red in colour, spherical in shape, and is usually termed an antheridium, though some workers regard it as a multiple structure rather than a single organ. The sex organs are developed in pairs from the adaxial nodal cell at the upper nodes of the primary lateral branches, the oogonium being formed above the antheridium. They are sufficiently large to be easily seen with the naked eye, especially the bright orange or red antheridium. Many species are dioecious. In others the monoecious condition is complicated by the development of the antheridium before the formation of the oogonium, thus preventing fertilization by antherozoids of the same alga. In this case the two types of sex organs usually arise from different points on the lateral branches.

All cells of the Charales are haploid except for the fertilized zygote, the large single cell in the interior of the oogonium, which becomes enclosed in a thickened hard wall to form an oospore that awaits favorable conditions for germination. Upon germination the diploid oospore undergoes meiosis, producing four haploid nuclei. A septum divides a small apical cell with one haploid nucleus from a large basal cell containing the other three nuclei, which will slowly degenerate. The oospore apical cell divides to produce the protonemal initial, from which the primary protonema arises, and the rhizoidal initial, from which the primary rhizoid descends. From these the alga continues its development. [33]

Vegetative propagation Edit

Vegetative propagation occurs readily in the Charales. Secondary protonemata may develop even more rapidly than primary ones. Fragments of nodes, dormant cells of algae after hibernation or the basal nodes of primary rhizoids may all produce these secondary protonemata, from which fresh sexual algae can arise. It is probably this power of vegetative propagation which explains the fact that species of Characeae are generally found forming dense clonal mats in the beds of ponds or streams, covering quite large areas.


Data availability

Raw transcriptome and genome reads from R. limneticus and R. marinus are deposited in GenBank (PRJNA544719), along with full SSU rRNA gene sequences for R. marinus (MK966712) and R. limneticus (MK966713). Assembled transcriptomes and genomes, along with raw light and electron-microscopy images, individual gene alignments, concatenated and trimmed alignments, single-gene trees, and maximum-likelihood and Bayesian tree files for the 151-taxon and 153-taxon datasets have been deposited in Dryad (https://doi.org/10.5061/dryad.tr6d8q2). The family Rhodelphidae (urn:lsid:zoobank.org:act:80B5C004-2954-4A57-A411-482BCD29E85D), genus Rhodelphis (urn:lsid:zoobank.org:act:6D09D4D9-D9FC-4D0C-8FB2-55FD9DDEAD53) and species Rhodelphis limneticus (urn:lsid:zoobank.org:act:695ACD0B-8151-4609-97FC-A044A312BE22) and Rhodelphis marinus (urn:lsid:zoobank.org:act:84233191-4710-43D1-A2DA-914B8E7B7E01) have been registered with the Zoobank database (http://zoobank.org/).


Conclusions

Returning to the question addressed (and partially answered) in the title, photorespiration can be regarded as wasteful, essential and an evolutionary stepping stone. Whilst at first glance the former two of these seem to be irreconcilable, this depends on the standpoint. In purely energetic terms, which is too much focussed on energy efficiency, photorespiration is inarguably wasteful in that it is costly in terms of CO2 and ATP losses. The mighty counter argument is that any reduction of photorespiratory capacity has dramatic consequences as it has evolved to be a central repair pathway embedded within the core of cyanobacterial and later plant photosynthetic metabolism (as well as having poorly defined roles in non-heterotrophic tissues Nunes-Nesi et al., 2010 ). This is not to imply that photorespiration merely hitch-hiked during the evolution of plant metabolism − far from it. Indeed, as discussed above, strong evidence suggests that the opposite is true and that photorespiration was a stepping stone towards the evolution of oxygenic photosynthesis as we know it and much later of C4 plants, which fix CO2 considerably more efficiently in warm climes (Sage et al., 2012 ). Thus, we are left with the conclusion that photorespiration does indeed have multiple personalities, yet it is clearly a highly important component of plant primary metabolism. The fact that attempts to improve photosynthesis by manipulating chloroplastidal glycolate metabolism have apparently proven successful remains somewhat of a conundrum. Similarly, with the exception of todays and still limited understanding of how altered 2PG levels affect the operation of the Calvin−Benson cycle, the mechanism by which the catalytic capacity of the photorespiratory pathway feeds back on photosynthetic carbon assimilation is not exactly known. However, a comprehensive analysis of the existing transgenic plants including broad range metabolite and flux profiling would allow the resolution of this issue and should be carried out with high priority. Whilst we have made great advances in our understanding as to how the photorespiratory pathway evolved and how it is currently fully embedded within the primary metabolism of plants and algae, new research avenues in understanding the native pathway still exist (Box 2). Prominent recent examples include the interaction of photorespiration with S metabolism maybe by providing serine for O-acetylserine and hence cysteine formation (Samuilov et al., 2018 ), and the intriguing suggestion that metal ion availability could regulate photorespiration (Bloom and Lancaster, 2018 ). Thus, considerable research is needed in order to complete our understanding of this fascinatingly complex pathway.


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