ARCHAEA: STRUCTURE, HABITATS AND ECOLOGICAL SIGNIFICANCE -- ARCHAEA: STRUCTURE, HABITATS AND ECOLOGICAL SIGNIFICANCE -- Contents -- Preface -- The Archaeal Flagellum: A Novel Prokaryotic Motility Structure and the Role of Posttranslational Modifications in Its Assembly and Function -- Abstract -- Introduction -- Distribution of Flagella in the Domain Archaea -- General Features of Archaeal Flagella and their Relationship to Bacterial Flagella and Type IV Pili -- How Can One Differentiate among Flagellins, Pilins and Fibers? -- Archaeal Flagella Functions -- Structural Work on Archaeal Flagella -- Regulation -- Genetics of Archaeal Flagellation -- Posttranslational Modifications of Flagellins -- Signal Peptide Removal -- N-Linked Glycosylation of Flagellins -- Directed Studies on Archaeal Flagella -- Extreme Halophiles -- Halobacterium -- Haloferax -- Haloarcula -- Natrialba -- Sulfolobus -- Thermoplasma -- Methanococcus -- Methanospirillum -- Methanosarcina -- Methanoculleus and Methanothermus -- Thermococcus/Pyrococcus -- Phylogenomics of the Archaeal Flagella System -- Assembly Model for Archaeal Flagellum -- Concluding Comments -- Acknowledgments -- References -- Methanogenes and Ammonia-Oxidation Archaeal Communities in High Temperature Oil Reservoirs -- Abstract -- Introduction -- Materials and Methods -- Sample Collection -- Nucleic Acid Extraction -- Construction of 16S rRNA Gene Library -- Generation of Prokaryotic amoA Clone Library -- Sequencing and Phylogenetic Analysis -- In Situ Hybridization -- Statistical Analysis -- Real-Time PCR Assay -- Results -- Methanogens Community in Onshore Oil Reservoir -- Methanogens Community in Offshore Oil Reservoir -- Methanogens Distribution in Situ -- Presence and Diversity of Archaeal amoA Gene in Oilfield -- Phylogenetic Affiliation of Crenarchaeal amoA Gene in Oilfield.

Quantification of AOA in Oil Reservoirs -- Ammonia-Oxidizing Archaeal Communities Classification -- Geographic Distribution of Ammonia-Oxidizing Archaeal Communities -- Discussion -- Methanogens Community in Onshore Oil Reservoir -- Methanogens Community in Offshore Oil Reservoir -- Ammonia-Oxidization Archaeal Community in Oil Reservoirs -- Acknowledgments -- References -- Diversity, Function, and Processing of Archaeal Non-Coding RNAs -- Abstract -- 1. Introduction -- 2. Phylogeny of Archaea -- 3. Classical ncRNAs and Their Processing -- 3.1. Transfer RNA -- 3.2. Ribosomal RNA and BHB motif -- 3.3. RNA Processing Enzymes -- 4. Small RNAs -- 4.1. Small Nucleolar RNA -- 4.2. CRISPR RNA -- 4.3. Other Archaeal Small RNAs -- 5. Ribozymes -- 5.1. RNase P RNA -- 5.2. Group II Introns -- 6. RNA Elements -- Conclusion -- Acknowledgments -- References -- Archaea Diversity in Brazilian Aquatic Ecosystems -- Abstract -- 1. Introduction -- 1.1. Freshwater Ecosystems in Brazilian Amazon: Madeira River and Tucuruí Hydroelectric Power Station Reservoir -- 1.2. Brackish Ecosystems in São Paulo State: Santos and São Vicente Estuarine System and Cananeia And Bertioga Mangroves -- 2. Synthesis of the Study -- 3. Experimental Setup and Methods -- 3.1. Sampling and Environmental Parameters -- Freshwater Ecosystems -- Brackish Ecosystems -- 3.2. Assessment of Archaeal Diversity Using Culture-Independent Methods -- 4. Characterization of Archaea Communities in Brazilian Ecosystems -- 4.1. Madeira River -- 4.2. Tucuruí Reservoir -- 4.3. Estuary inthe Southeast Coast -- 4.4. Mangrove in the Southeast Coast -- Conclusion -- Acknowledgments -- References -- The Archaea Ribonuclease P: Molecular Mechanisms of Thermal Adaptation -- Abstract -- Introduction -- Methods -- Optimal Growth Temperature -- Sequence Data -- RNA Secondary Structure Analysis.

Proteins Composition Analysis -- Statistical Analyses -- Results -- Analysis of the Global GC Content in the Archaea RNase P RNA Component -- Compositional Analysis of the Secondary Structures of the Archaeal RNase P as a Function of OGT -- The Increase in the GC Content of the Stems Is More Prominent in the S-Domain of the RNase P RNA -- Analysis of Protein Composition Reveals Thermal Adaptation in the RNase P Protein Component -- Distribution of Amino Acids in the Structure of the RNase P Proteins -- Conclusion -- Acknowledgments -- References -- Mechanosensitive Channels in Archaea: Roles, Lipid-Protein Interactions and Future Questions -- Abstract -- Abbreviations -- Introduction -- The Physical Coupling between the Lipids and the Protein in MS Channels -- Future Prospects to Be Studied -- Conclusions -- References -- The Nanoarchaeota: Physiology, Genomics and Phylogeny -- Abstract -- Introduction -- "Nanoarchaeum Equitans" -- Ignicoccus Hospitalis, Host of "Nanoarchaeum Equitans" -- Environmental Distribution of Nanoarchaeotes -- N. Equitans: Ancestral or Highly Evolved? -- Nanoarchaea as a Novel Ancestral Phylum -- Nanoarchaea as a Highly Evolved Member of the Euryarchaea -- Conclusion -- References -- Chaperonin and Prefoldin - Two Molecular Chaperones that Work Cooperatively in Archaea and Eukaryotes -- Abstract -- 1. Group II Chaperonins -- Two Distinct Groups of Chaperonins -- Subunits and their Composition -- Structure and Lid of the Cavity -- Substrates and their Folding -- Conformational Change and ProteinFoldingMechanism -- 2. Prefoldin -- PFD Was Discovered as a Microtubule Biogenesis-Related Protein -- Subunit Composition -- Structure of PFD -- Eukaryotic PFDs Participate in MicrotubuleBiogenesis -- Archaeal PFD Recognizes a Wide Range of Non-Native Proteins -- Substrate InteractionMechanism of Archaeal PFD.

The Substrate-InteractionMechanism Differs between Archaeal PFD and Eukaryotic PFD -- Other Functions -- 3. Mechanism of Substrate Transfer from PFD to CPN -- PFD Transfers Substrate Protein to CPN -- PFD Binds to CPN Like the "Lid of a Pod" -- Binding Sites for Interaction between PFD and CPN -- Interaction between Archaeal PFD and CPN Is Important for Substrate Transfer -- Elucidated Mechanisms of Substrate Transfer from Archaeal PFD to CPN -- Comparison of the Mechanism of Substrate Transferfrom PFD to CPN between Eukaryotic and Archaeal Systems -- References -- Primary Production and Carbon Cycling in the Deep Sea: Archaeal Carbon Fixation and Methane Oxidation -- Occurrence and Diversity of Nonthermophilic Archaea in Water Column and Marine Sediments -- Abundance of Nonthermophilic Archaea in the Water Column and Marine Sediments -- Metabolic Pathways of Nonthermophilic Archaea in the Water Column and Marine Sediments -- Contribution of Nonthermophilic Archaea to Carbon and Nitrogen Cycles in the Deep Ocean -- References -- Index.