Progress in Botany Vol. 81 (Progress in Botany, 81)

Contents
Contributors
Curriculum Vitae
Nitrogen and Sulfur Metabolism in Microalgae and Plants: 50 Years of Research
	1 Nitrate Assimilation Pathway in Microalgae and Plant Leaves
		1.1 Nitrate Transport Systems
		1.2 NAD(P)H-Nitrate Reductase (NAD(P)H-NR)
		1.3 Ferredoxin-Nitrate Reductase (Fd-NR)
		1.4 Ferredoxin-Nitrite Reductase (Fd-NiR)
	2 Ammonium Assimilation and Re-assimilation in Microalgae and Plant Leaves
		2.1 Glutamine Synthetase (GS)
		2.2 Ferredoxin-Glutamate Synthase (Fd-GOGAT)
		2.3 NADH-Glutamate Synthase (NADH-GOGAT)
		2.4 NAD(P)H-Glutamate Dehydrogenase (NAD(P)H-GDH)
	3 Source of 2-Oxoglutarate for Ammonium Assimilation: Isocitrate Metabolism in Microalgae
		3.1 NAD-Isocitrate Dehydrogenase (NAD-IDH)
		3.2 NADP-Isocitrate Dehydrogenase (NADP-IDH)
		3.3 Isocitrate Lyase (ICL)
	4 Regulation of Nitrate Assimilation
		4.1 Eukaryotic Microalgae
		4.2 Cyanobacteria
	5 Metabolism of L-Asparagine in Lotus japonicus
		5.1 Asparagine Synthetase (ASN)
		5.2 L-Asparaginase (NSE)
		5.3 Serine-Glyoxylate Aminotransferase (SGAT)
	6 Sulfate Assimilation in Microalgae and Plant Leaves
		6.1 Sulfate Transport
		6.2 Activation of Sulfate
		6.3 The APS Reduction to Sulfite and Sulfide
		6.4 Sulfide Incorporation into Carbon Skeletons to Produce L-Cysteine
		6.5 Regulation of Sulfate Assimilation
		6.6 Effect of Abiotic Stress on Cysteine and Glutathione Biosynthesis
	7 Biotechnology of Microalgae
		7.1 Aquaculture and Food Technology
		7.2 Biofuel Production: Biodiesel, Bioethanol, and Biogas
		7.3 Production of High-Added Value Metabolites
		7.4 Biofertilizers in Agriculture
		7.5 Bioelimination of Contaminants
	References
Progress Toward Deep Sequencing-Based Discovery of Stress-Related MicroRNA in Plants and Available Bioinformatics Tools
	1 Introduction
	2 MicroRNAs and Abiotic Stress Response
		2.1 Cold Stress
		2.2 Heat Stress
		2.3 Oxidative Stress
		2.4 Heavy Metal Toxicity
		2.5 The Role of MicroRNA in Regulating Drought Stress
		2.6 MicroRNAs Regulate Salinity Stress in Plants in a Species-Dependent Manner
		2.7 miRNAs and Nutrient Acquisition in Plants
	3 Biotic Stress
		3.1 Fungal Defense
		3.2 The Role of MicroRNAs in Mediating Bacterial and Viral Infections in Plants
	4 Identifying Plant miRNA from Deep Sequencing Using Bioinformatics Approaches
		4.1 MicroRNA Databases
		4.2 Bioinformatics Tools Available for miRNAs Prediction
	5 Future Prospects
	References
Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics App...
	1 Introduction
	2 Technical Platforms and Methods
	3 From Proteomics to Biology Through Data Validation and Integration with Other Classic and -Omics Approaches
	4 Experimental Workflow in a Multi-omics Experiment
	5 Some Illustrative Investigations
	6 Concluding Remarks
	References
Membrane Trafficking and Plant Signaling
	1 Introduction
	2 Endocytosis
		2.1 Clathrin-Mediated Endocytosis
		2.2 Other Forms of Endocytosis
	3 Endosomal Trafficking
		3.1 Early Endosomal Sorting at the TGN
		3.2 Late Endosomal Sorting for Degradation
		3.3 Endosome Maturation and Fusion to Vacuoles
	References
Molecular Aspects of Iron Nutrition in Plants
	1 Introduction
	2 Iron Uptake Mechanisms
	3 Molecular Factors Involved in Fe Distribution Within the Plants
	4 Signalling Molecules and Fe Sensing Mechanisms
	5 The Role of Iron in Plant-Bacteria Symbiosis
	6 Legume and Nonlegume Root Nodules
	7 Legume Root Nodule Formation
	8 Impact of Soil Iron Deficiency in Nodulation
	9 Iron Requirements for Legume-Rhizobia Symbiosis
	10 Iron Uptake to the Nodule and Remobilization
	11 Iron Transport Within the Nodule
	12 Molecular Interactions of Fe with Other Nutrients
	13 Conclusion
	References
Urea in Plants: Metabolic Aspects and Ecological Implications
	1 Introduction
	2 General Features of Urea Absorption and Assimilation in Plants
		2.1 DUR3: High-Affinity Absorption Transporter of Urea
		2.2 Aquaporins as Low-Affinity Urea Transporters
		2.3 Urease as a Key Enzyme in Urea Assimilation
		2.4 N and Carbon Assimilation After Urea Hydrolysis by Urease
	3 Ecological Relevance of Urea
		3.1 Urea Utilization by Epiphytic Bromeliads
		3.2 Mycorrhization as Facilitator of N-Urea Absorption in Plants
	4 Biotechnological Aspects and Challenges to Improve Nitrogen Use Efficiency (NUE) in Plants
	References
Biosynthesis and Regulation of Secondary Cell Wall
	1 Introduction
	2 Cellulose
		2.1 Cellulose Synthase Complex (CSC)
		2.2 Proteins Associated with the CSC
		2.3 Regulation of Cellulose Synthesis
		2.4 Assembly of Rosettes and Translocation to Plasma Membrane
		2.5 Microfibril Organization
		2.6 Supply of UDP-Glucose
	3 Hemicelluloses
		3.1 Xylans
		3.2 Mannans
	4 Lignin
		4.1 Biosynthesis
		4.2 Transport of Monolignols
		4.3 Lignin Polymerization
		4.4 Laccases
		4.5 Peroxidases
	5 Transcriptional Regulation of Secondary Cell Wall Synthesis
		5.1 NAC Master Switches
		5.2 MYB Master Switches
		5.3 Additional Transcription Factors
	6 Conclusion
	References
Stress-Induced Microspore Embryogenesis in Crop Plants: Cell Totipotency Acquisition and Embryo Development
	1 Introduction
	2 Stress-Induced Autophagy and Programmed Cell Death
	3 Epigenetic Reprogramming and Chromatin Modifications
	4 The Role of Endogenous Auxin
	5 Cell Wall Remodeling: Pectin Methyl Esterases and AGPs Involvement
	6 Concluding Remarks
	References
Potential of Microalgae Biomass for the Sustainable Production of Bio-commodities
	1 Microalgae Biomass Applications
		1.1 Exploitation of Microalgae Biomass to Mitigate Environmental Consequences of Human Activities
		1.2 Microalgae as Natural Source of Nutrients and Bioactive Compounds
		1.3 Present Major Limitations of Algae Biotechnology
	2 Algae Metabolic Engineering to Increase Yield in Bio-commodities
		2.1 Challenges in Microalgae Metabolic Engineering
		2.2 Improving the Content of Bioactive Compounds
	3 Strategies to Improve Microalgae Biomass Productivity
		3.1 Challenges in Large-Scale Microalgae Cultivation
		3.2 Metabolic Engineering to Increase Microalgae Light-Use Efficiency
	4 Conclusions
	References
Crassulacean Acid Metabolism and Its Role in Plant Acclimatization to Abiotic Stresses and Defence Against Pathogens
	1 Introduction
	2 Crassulacean Acid Metabolism (CAM) as a Specific Mode of CO2 Assimilation
		2.1 CAM Phases
		2.2 CAM as an Adaptation to Abiotic Stresses
		2.3 Plasticity of CAM
		2.4 C3-CAM Intermediate Mesembryanthemum crystallinum as a Model System to Study Plant-Stress Factor Interactions
	3 Reactive Oxygen Species (ROS) and Antioxidant System in CAM Plants
	4 Plant-Pathogen Interactions: A General Overview
	5 The Role of Carbon and Nitrogen Metabolism in Plant´s Defence Against Pathogens
	6 Conclusions
	References
The Role of the Shikimate and the Phenylpropanoid Pathways in Root-Knot Nematode Infection
	1 Introduction
	2 The Shikimate Pathway
	3 The Phenylpropanoid Metabolism
	4 Lignin
	5 Flavonoids
	6 Flavonols
	7 Isoflavonoids
	8 Coumarins
	9 Tannins
	10 Conclusion
	References
Functional Diversity of Photosynthesis, Plant-Species Diversity, and Habitat Diversity
	1 Introduction
	2 Modes of Photosynthetic Carbon Gain
		2.1 C3 Photosynthesis
		2.2 C4 Photosynthesis
		2.3 C2 Photosynthesis
		2.4 Crassulacean Acid Metabolism (CAM)
		2.5 Dialectics of Feedback: Environment Shapes Species; Species Shape Environment
	3 Habitats
		3.1 Macrohabitats: Ecosystems up to Biomes
			3.1.1 Dominant C3 Photosynthesis
			3.1.2 Dominant C4 Photosynthesis
			3.1.3 Prominent Contribution of CAM
			3.1.4 Conclusion
		3.2 Selected Communities
			3.2.1 C4 Communities
			3.2.2 CAM Communities
			3.2.3 Selected Variety of Communities with C3 Species and CAM or C4 Species Immersed
				Coastal Sand Plains
				Atlantic Rainforest Complex
		3.3 Microhabitats
			3.3.1 Epiphytes
			3.3.2 Vegetation Mosaics
			3.3.3 Atlantic Rainforest Micro-Sites
	4 Competition and Facilitation: Interactions Between Plants with Different Modes of Photosynthesis in Their Habitat
	5 Conclusions: Understanding Biodiversity?
	References
When the Tree Let Us See the Forest: Systems Biology and Natural Variation Studies in Forest Species
	1 Introduction
	2 Combining Natural Variation and Systems Biology, Why?
		2.1 How?
			2.1.1 Using Omics Technology in Non-model Species
			2.1.2 Data Integration and Bioinformatic Tools
			2.1.3 Validation of Systems Biology-Based Discoveries
	3 What We Have Learned from Omics in Forest Species
		3.1 Metabolome Analysis of Natural Variation in P. pinaster Reveals Drought Resistance Is Related to Tree Origin
		3.2 Integrative Omics Approach Allowed to Unmask Possible Heat Resistance Biomarkers in P. radiata
		3.3 Last Step: Combining Omics Data and Molecular Biological Tools to Validate Candidates
	4 Concluding Remarks and Future Perspectives
	References
The Ecological Importance of Winter in Temperate, Boreal, and Arctic Ecosystems in Times of Climate Change
	1 Winter Climate Change
		1.1 Air Temperature
		1.2 Precipitation
		1.3 Snow
		1.4 Soil Temperature
	2 Ecosystem Responses to Winter Climate Change
		2.1 Primary Production
		2.2 Soil Biotic Activity, Litter Decomposition, and Mineralization
		2.3 Nutrient Leaching
	3 Feedbacks from Ecosystems to Climate
		3.1 Arctic
		3.2 Boreal
		3.3 Temperate
	4 Summary and Key Uncertainties
	References