Planctomycetes-Verrucomicrobia-Chlamydiae Bacterial Superphylum: New Model Organisms for Evolutionary Cell Biology, 2nd Edition PDF Download
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Author: Laura van Niftrik
Publisher: Frontiers Media SA
ISBN: 2889459748
Category :
Languages : en
Pages : 170
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Book Description
The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) and related phyla have recently emerged as fascinating subjects for research in evolutionary cell biology, ecology, biotechnology, evolution and human health. This interest is prompted by particular characteristics observed in the PVC superphylum that are otherwise rarely observed in bacteria but are however still poorly described or understood, such as the presence of a complex endomembrane system, or compacted DNA throughout most of the cell cycle. Therefore, the members of the PVC superphylum represent an excellent example of the value of studying bacteria other than ‘classical’ models.
Author: Laura van Niftrik
Publisher: Frontiers Media SA
ISBN: 2889459748
Category :
Languages : en
Pages : 170
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Book Description
The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) and related phyla have recently emerged as fascinating subjects for research in evolutionary cell biology, ecology, biotechnology, evolution and human health. This interest is prompted by particular characteristics observed in the PVC superphylum that are otherwise rarely observed in bacteria but are however still poorly described or understood, such as the presence of a complex endomembrane system, or compacted DNA throughout most of the cell cycle. Therefore, the members of the PVC superphylum represent an excellent example of the value of studying bacteria other than ‘classical’ models.
Author:
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) and related phyla have recently emerged as fascinating subjects for research in evolutionary cell biology, ecology, biotechnology, evolution and human health. This interest is prompted by particular characteristics observed in the PVC superphylum that are otherwise rarely observed in bacteria but are however still poorly described or understood, such as the presence of a complex endomembrane system, or compacted DNA throughout most of the cell cycle. Therefore, the members of the PVC superphylum represent an excellent example of the value of studying bacteria other than 'classical' models.
Author: Olga K. Kamneva
Publisher:
ISBN: 9781303093975
Category : Bioinformatics
Languages : en
Pages : 276
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Book Description
The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) super-phylum is an emerging model bacterial group for studying the evolution of biological complexity because PVC bacteria possess extensive intracellular membranes of unknown function and evolutionary origin. The cell plan of Gemmata obscuriglobus, in particular, is argued to be analogous to the early evolutionary stages of cell compartmentalization in eukaryotes. The organisms of the super-phylum also have different life-styles ranging from free-living to obligate pathogens, providing an opportunity to study the evolutionary basis of life-style shifts. Our interest in multiple aspects of PVC super-phylum biology stimulated comprehensive comparative genomic analysis of these bacteria, as described below. We examined patterns of natural selection in different protein-coding genes within PVC bacteria, in order to identify genes potentially underlying the emergence of novel phenotypes. This work required development and application of a novel computational framework to quantify selective constraints on indel substitutions (use of dN/dS methods was not permitted due to saturation of synonymous sites). We found that indels in full-length proteins have accumulated faster than would be expected under neutrality on about 12% of evaluated gene tree branches, over all the examined gene trees. This is consistent with positive Darwinian selection acting on indels. Mapping genes with accelerated indel rates onto predicted biological functions, we revealed several trends. For instance, insertions in a-helices appeared to be affecting a large proportion of ribosomal proteins. This finding suggests interesting avenues for future experimental work, given the known partition of the PVC cell cytoplasm into ribosome-containing and ribosome-free regions, and the apparent segregation of G. obscuriglobus ribosomes from the nucleoid. The second major study explored how events of genome content evolution (HGT, gene duplication, and loss) have affected the PVC super-phylum, through analysis of gene families reconstructed for PVC genomes and a number of out-group species. We showed that evolutionary processes contributing to genome expansion have been accelerated and decelerated within Planctomycetes and Chlamydiae, respectively, and have balanced each other in Verrucomicrobia and Lentisphaerae. These processes were inferred through Bayesian modeling of event rates (in either a simple or mixture modeling framework). It also appeared that a large number of genes were acquired on various PVC lineages from phylum Acidobacteria, and from phylum Bacteroidetes on the lineage leading to Akkermansia muciniphila, an intestinal human commensal. In the last part of this study, we identified a highly conserved genetic module preferentially present in Planctomycetes, Verrucomicrobia , and Lentisphaerae species possessing additional intracellular membranes, and possibly associated with the complex PVC cell plan. These genes are excellent candidates for future functional studies. Within the set of proteins associated with PVC intracellular membranes, we detected over-representation of proteins bearing signal peptides. These sequences target proteins for translocation via the Sec pathway to the cytoplasmic membrane, periplasm, outer membrane, or cell exterior in Gram-negative bacteria, or to the endoplasmic reticulum in eukaryotic cells. This led us to hypothesize that in membrane-bearing PVC bacteria, Sec pathway proteins and/or signal peptides have undergone functional shifts to allow protein targeting to new destinations inside the cell. Systematic examination of compartmentalization-associated gene families showed that they bear canonical signal peptides, which indicates that they should be recognized and targeted by the canonical Sec translocase. Within the Sec pathway components, we found domain rearrangements and gene duplications affecting the SecA ATPase in a number of PVC genomes. Further analysis of the SecA2-related system revealed a potentially novel secretion system related to both the Sec pathway and the type I secretion system. In summary, the work described in this thesis has made contributions to multiple areas of PVC comparative genomic analysis, leading to an improvement in our understanding of the evolutionary structure and dynamics of the super-phylum, as well as identification of candidate genes underlying the cellular and molecular biology features of PVC organisms.
Author: John A. Fuerst
Publisher: Springer Science & Business Media
ISBN: 1627035028
Category : Science
Languages : en
Pages : 290
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Book Description
This book introduces Planctomycetes bacteria and deals in detail with their unusual structure, physiology, genomics and evolutionary significance. It is a definitive summary of recent knowledge of this important distinctive group of bacteria, microorganisms which challenge our very concept of the bacterium. Planctomycetes, and their relatives within the PVC superphylum of domain Bacteria, including verrucomicrobia and chlamydia, challenge our classical concept of the bacterium and its modes of life and provide new experimental models for exploring evolutionary cell biology and the full diversity of how living cells can be organized internally. Unique among bacteria, they include species possessing cells with intracellular membrane-bounded compartments and a peptidoglycan-less cell wall, and bacteria such as the anammox organisms performing unique anaerobic ammonium oxidation significant for global nitrogen cycle.
Author: Jan Löwe
Publisher: Springer
ISBN: 331953047X
Category : Science
Languages : en
Pages : 457
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Book Description
This book describes the structures and functions of active protein filaments, found in bacteria and archaea, and now known to perform crucial roles in cell division and intra-cellular motility, as well as being essential for controlling cell shape and growth. These roles are possible because the cytoskeletal and cytomotive filaments provide long range order from small subunits. Studies of these filaments are therefore of central importance to understanding prokaryotic cell biology. The wide variation in subunit and polymer structure and its relationship with the range of functions also provide important insights into cell evolution, including the emergence of eukaryotic cells. Individual chapters, written by leading researchers, review the great advances made in the past 20-25 years, and still ongoing, to discover the architectures, dynamics and roles of filaments found in relevant model organisms. Others describe one of the families of dynamic filaments found in many species. The most common types of filament are deeply related to eukaryotic cytoskeletal proteins, notably actin and tubulin that polymerise and depolymerise under the control of nucleotide hydrolysis. Related systems are found to perform a variety of roles, depending on the organisms. Surprisingly, prokaryotes all lack the molecular motors associated with eukaryotic F-actin and microtubules. Archaea, but not bacteria, also have active filaments related to the eukaryotic ESCRT system. Non-dynamic fibres, including intermediate filament-like structures, are known to occur in some bacteria.. Details of known filament structures are discussed and related to what has been established about their molecular mechanisms, including current controversies. The final chapter covers the use of some of these dynamic filaments in Systems Biology research. The level of information in all chapters is suitable both for active researchers and for advanced students in courses involving bacterial or archaeal physiology, molecular microbiology, structural cell biology, molecular motility or evolution. Chapter 3 of this book is open access under a CC BY 4.0 license.
Author: Vladimir P. Skulachev
Publisher: Springer Science & Business Media
ISBN: 3642729789
Category : Science
Languages : en
Pages : 453
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Book Description
Membrane bioenergetics is one of the most rapidly growing areas within physico-chemical biology. Main aspects treated in this book include energy conservation and utilization by membrane-linked molecular mechanisms such as intracellular respiration, photosynthesis, transport phenomena, rotation of bacterial flagella, and the regulation of heat production.
Author: Howard Ochman
Publisher:
ISBN: 9781621820376
Category : Science
Languages : en
Pages : 0
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Book Description
Bacteria have been the dominant forms of life on Earth for the past 3.5 billion years. They rapidly evolve, constantly changing their genetic architecture through horizontal DNA transfer and other mechanisms. Consequently, it can be difficult to define individual species and determine how they are related. Written and edited by experts in the field, this collection from Cold Spring Harbor Perspectives in Biology examines how bacteria and other microbes evolve, focusing on insights from genomics-based studies. Contributors discuss the origins of new microbial populations, the evolutionary and ecological mechanisms that keep species separate once they have diverged, and the challenges of constructing phylogenetic trees that accurately reflect their relationships. They describe the organization of microbial genomes, the various mutations that occur, including the birth of new genes de novo and by duplication, and how natural selection acts on those changes. The role of horizontal gene transfer as a strong driver of microbial evolution is emphasized throughout. The authors also explore the geologic evidence for early microbial evolution and describe the use of microbial evolution experiments to examine phenomena like natural selection. This volume will thus be essential reading for all microbial ecologists, population geneticists, and evolutionary biologists.
Author: Hermann Bothe
Publisher: Elsevier
ISBN: 0444531084
Category :
Languages : en
Pages : 451
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Book Description
Author: John Maynard Smith
Publisher: Oxford University Press
ISBN: 019850294X
Category : Nature
Languages : en
Pages : 361
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Book Description
During evolution there have been several major changes in the way genetic information is organized and transmitted from one generation to the next. These transitions include the origin of life itself, the first eukaryotic cells, reproduction by sexual means, the appearance of multicellular plants and animals, the emergence of cooperation and of animal societies. This is the first book to discuss all these major transitions and their implications for our understanding of evolution.Clearly written and illustrated with many original diagrams, this book will be welcomed by students and researchers in the fields of evolutionary biology, ecology, and genetics.
Author: Scott X. Chang
Publisher: MDPI
ISBN: 3039286668
Category : Science
Languages : en
Pages : 232
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Book Description
Forest ecosystems are often disturbed by agents such as harvesting, fire, wind, insects and diseases, and acid deposition, with differing intensities and frequencies. Such disturbances can markedly affect the amount, form, and stability of soil organic carbon in, and the emission of greenhouse gases, including CO2, CH4, and N2O from, forest ecosystems. It is vitally important that we improve our understanding of the impact of different disturbance regimes on forest soil carbon dynamics and greenhouse gas emissions to guide our future research, forest management practices, and policy development. This Special Issue provides an important update on the disturbance effects on soil carbon and greenhouse gas emissions in forest ecosystems in different climate regions.
