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Introduced by Crafoord Prize winner Carl Woese, this volumecombines reviews of the major developments in archaeal researchover the past 10–15 years with more specialized articlesdealing with important recent breakthroughs. Drawing on majorthemes presented at the June 2005 meeting held in Munich to honorthe archaea pioneers Wolfram Zillig and Karl O. Stetter, the bookprovides a thorough survey of the field from its controversialbeginnings to its ongoing expansion to include aspects ofeukaryotic biology. The editors have assembled articles from the premier researchersin this rapidly burgeoning field, including an account by CarlWoese of his original discovery of the Archaea (until 1990 termedarchaebacteria) and the initially mixed reactions of the scientificcommunity. The review chapters and specialized articles address theemerging significance of the Archaea within a broader scientificand technological context, and include accounts of cutting-edgeresearch developments. The book spans archaeal evolution,physiology, and molecular and cellular biology and will be anessential reference for both graduate students and researchers.
Biocommunication of Archaea by Guenther Witzany Pdf
Archaea represent a third domain of life with unique properties not found in the other domains. Archaea actively compete for environmental resources. They perceive themselves and can distinguish between ‘self’ and ‘non-self’. They process and evaluate available information and then modify their behaviour accordingly. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. These highly diverse competences show us that this is possible owing to sign(aling)- mediated communication processes within archaeal cells (intra-organismic), between the same, related and different archaeal species (interorganismic), and between archaea and nonarchaeal organisms (transorganismic). This is crucial in coordinating growth and development, shape and dynamics. Such communication must function both on the local level and between widely separated colony parts. This allows archaea to coordinate appropriate response behaviors in a differentiated manner to their current developmental status and physiological influences. This book will orientate further investigations on how archaeal ecosphere inhabitants communicate with each other to coordinate their behavioral patterns and whats the role of viruses in this highly dynamic interactional networks.
Respiration in Archaea and Bacteria by Davide Zannoni Pdf
The book summarizes the achievements of the past decade in the biochemistry, bioenergetics, structural and molecular biology of respiratory processes in selected genera of the domain Bacteria along with an extensive coverage of the redox chains of extremophiles belonging to the Archaean domain. The volume is a unique piece of work since it contains a series of chapters dealing with metabolic features having important microbiological and ecological relevance such as the use of ammonium, iron, methane, sulfur and hydrogen as respiratory substrates or nitrous compounds in denitrification processes. Particular attention is also dedicated to peculiar groups of prokaryotes such as Gram positives, acetic acid bacteria, pathogens of the genera Helicobacter and Campylobacter, nitrogen fixing symbionts and free-living species, oxygenic phototrophs (Cyanobacteria) and anoxygenic (purple non-sulfur) phototrophs. The book is intended to be a long-term source of information for Ph.D. students, researchers and undergraduates from disciplines such as microbiology, biochemistry and ecology, studying basic and applied sciences, medicine and agriculture.
This volume provides an overview of well-established methods optimized for diverse archaeal model organisms and is a source of protocols facilitating access to the molecular and cellular biology characterization of these fascinating organisms. Chapters are divided into five parts detailing available genetic tools, molecular and cellular biology methods, strategies to study the ecophysiology of archaea, and classroom protocol. Each main thematic part is also introduced by future-oriented and authoritative primers. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Archaea: Methods and Protocols aims to be a foundation for future studies and to be a source of inspiration for new investigations in the field.
Archaea by Haitham Sghaier,Afef Najjari,Kaïs Ghedira Pdf
Besides the Introductory Chapter that gives a brief overview of archaeal applications, the present book contains four chapters. The first chapter, by Castro-Fernandez et al., provides an interesting depiction of the phylum Euryarchaeota and its biotechnological applications. The second chapter, by Ben Hania and coauthors, focuses on the promotion of the idea that some specific Archaea are potential next-generation probiotics. The third chapter, by Torregrosa-Crespo et al., emphasizes the main characteristics of biocompounds from haloarchaea and their potential uses in biomedicine, pharmacy, and industry. The concluding chapter, by Mizuno et al., proposes a plasmid curing approach for improving the potential of thermophiles in various biotechnological applications and opens new perspectives on industrial valorization.
Molecular Biology of Archaea - 2022 by Marleen van Wolferen,Solenne Ithurbide,Michel Geovanni Santiago-Martínez,Arthur Charles-Orszag Pdf
Since their identification four decades ago, Archaea have proven to be a continuous source of exciting discoveries, contributing to the characterization of their unique molecular mechanisms, metabolisms, phylogeny, and cell biology. These discoveries have revealed the importance that Archaea play in ecology, biotechnology and the human microbiome. In addition, they highlighted the key position that Archaea occupy in the tree of life, bringing us closer to elucidating the origin and early forms of life. Despite these important findings and the larger audience that Archaea have consequently gained, much remains unexplored. Thanks to the recent and ongoing developments in the field, technical limitations at the often-extreme archaeal growth conditions are being resolved, allowing archaeal researchers to answer open and upcoming questions. This promises exciting new findings in the near future that will continue to build on our understanding of the various fields of archaeal biology.
Archaea in the Environment: Views on Archaeal Distribution, Activity, and Biogeography by Andreas Teske,Ricardo Amils,Gustavo Antonio Ramírez,Anna-Louise Reysenbach Pdf
Some Archaea thrive in extreme places such as in thermal pools, hot vents at the bottom of the sea, extremely salty water, and even in underground oil reserves. This book examines the diverse Archaea kingdom and the division of these organisms by their unusual biology into three main groups. It also explains why little in general is known about them, and why further classification of Archaea is so difficult.
RNA Metabolism and Gene Expression in Archaea by Béatrice Clouet-d'Orval Pdf
This book focuses on the regulation of transcription and translation in Archaea and arising insights into the evolution of RNA processing pathways. From synthesis to degradation and the implications of gene expression, it presents the current state of knowledge on archaeal RNA biology in 13 chapters. Topics covered include the modification and maturation of RNAs, the function of small non-coding RNAs and the CRISPR-Cas defense system. While Archaea have long been considered exotic microbial extremophiles, they are now increasingly being recognized as important model microorganisms for the study of molecular mechanisms conserved across the three domains of life, and with regard to the relevance of similarities and differences to eukaryotes and bacteria. This unique book offers a valuable resource for all readers interested in the regulation of gene expression in Archaea and RNA metabolism in general.
Recent advances in genomic and genetic studies in the Archaea by Frank T. Robb,Todd M. Lowe,Zvi Kelman Pdf
The accumulation of archaeal genomes has lagged significantly behind the Bacteria; however, in the last several years the coverage of the major phyla of Archaea has been significantly improved. There are now multiple genomes in several important genera such as Pyrobaculum, Sulfolobus, Thermococcus/Pyrococcus, Halobacterium, Methanosarcina, Methanopyrus and Methanocaldococcus. Comparative genomic studies are now under way, and in many cases there are several consortial multilaboratory groups, such as the SulfoSys community, which have started to break into new systems biology initiatives. At the same time, access to streamlined genetic approaches in the genera Sulfolobus, Thermococcus, Methanosarcina, and Halobacterium/Haloferax has improved significantly and is leveraging the genomic information in the Archaea. The result has been that genome-driven studies of metabolism, DNA replication and repair, transcription and translation, and posttranslational processing have become more detailed and that basic research findings are burgeoning. The areas of global gene regulation, the roles of small RNAs and mechanisms of transcription and DNA replication will be focus areas in the guidelines of this Research Topic. Recently, insights into the unique characteristics of archaeal transcription and the ability to study the effects of mutation in vivo following knock-in gene replacement have resulted in incisive findings.
Adaptation to Life at High Salt Concentrations in Archaea, Bacteria, and Eukarya by Nina Gunde-Cimerman,Aharon Oren,Ana Plemenitaš Pdf
Salt is an essential requirement of life. Already from ancient times (e. g. , see the books of the Bible) its importance in human life has been known. For example, salt symbolizes destruction (as in Sodom and Gomorra), but on the other hand it has been an ingredient of every sacrifice during the Holy Temple periods. Microbial life in concentrated salt solutions has fascinated scientists since its discovery. Recently there have been several international meetings and books devoted entirely to halophiles. This book includes the proceedings of the “Halophiles 2004” conference held in Ljubljana, Slovenia, in September 2004 (www. u- lj. si/~bfbhaloph/index. html). This meeting was attended by 120 participants from 25 countries. The editors have selected presentations given at the meeting for this volume, and have also invited a number of contributions from experts who had not been present in Ljubljana. This book complements “Halophilic Microorganisms”, edited by A. Ventosa and published by Springer-Verlag (2004), “Halophilic Microorganism and their Environments” by A. Oren (2002), published by Kluwer Academic Publishers as volume 5 of “Cellular Origins, Life in Extreme Habitats and Astrobiology” (COLE), and “Microbiology and Biogeochemistry of Hypersaline Environments” edited by A. Oren, and published by CRC Press, Boca Raton (1999). Salt-loving (halophilic) microorganisms grow in salt solutions above seawater salinity (~3. 5% salt) up to saturation ranges (i. e. , around 35% salt). High concentrations of salt occur in natural environments (e. g.
The Biochemistry of Archaea (Archaebacteria) by M. Kates,D.J. Kushner,A.T. Matheson Pdf
In the last 10 years, considerable information has accumulated on the biochemistry of archaea. In this volume, the subject as a whole is treated in a comprehensive manner. The book brings together recent knowledge concerning general metabolism, bioenergetics, molecular biology and genetics, membrane lipid and cell-wall structural chemistry and evolutionary relations, of the three major groups of archaea: the extreme halophiles, the extreme thermophiles, and the methanogens. Subjects included are: the evolutionary relationship of these microorganisms to all other living cells; special metabolic features of archeaea; protein structural chemistry; cell envelopes; molecular biology in archaea including DNA structure and replication, transcription apparatus, translation apparatus, and ribosomal structure; and a final chapter on the molecular genetics of archaea. This comprehensive scope ensures its usefulness to researchers, and stimulates further study in this rapidly developing field.
Archaeal Cell Envelope and Surface Structures by Sonja-Verena Albers,Mecky Pohlschroder Pdf
Archaea and Bacteria have complex cell envelopes that play important roles in several vital cellular processes, including serving as a barrier that protects the cytoplasm from the environment. Along with associated proteinaceous structures, cell envelopes also ensure cell stability, promote motility, mediate adherence to biotic and abiotic surfaces, and facilitate communication with the extracellular environment. While some aspects of the biosynthesis and structure of the cell are similar to the three domains of life, archaeal cell envelopes exhibit several unique characteristics. Moreover, recent analyzes have revealed that many features of cell envelopes can vary greatly between distantly related archaea. The collection of reviews and original research papers in this focused issue describes research that has been significantly expanded in our understanding of the mechanisms underlying the biogenesis and functions of archaeal cell envelopes and their constituent surface structures. Jain et al. (5) cytoplasmic membrane, isoprenoid lipid bilayer, as well as recently revealed the cytoplasmic membrane biosynthesis, which is conserved across the three domains of life. Complementing this review, Andreas Klingl summarizes the diverse structures and functions of archaeal cytoplasmic membranes (8). While most archaeal cells have a single membrane, the archaea have an outer membrane, which has been thought of in a different variety of archaeal lineages. One particular intriguing diderm is the hyperthermophilic archaeon. In the periplasmic space, ATP in the periplasmic space. Complementing this work, Kletzin provides an in-depth review of evolutionarily conserved and unique archaeal inner and outer membrane-associated cytochromes (7). The periplasmic space between the membranes of archaeal diderms does not contain a peptidoclycan layer. In fact, while the cytoplasmic membrane is superimposed by an S-layer in many monoderm archaea, it is unclear how diderms, and even some monoderm extremophiles that varnish to S-layer, withstand osmotic stress. As noted by Klingl (8), glycocalyx, lipoglycans, or other protective cell-associated glycoproteins, may take on the functions of a cell wall in some archaea. One such secreted protein, as described by Zenke et al., Is the halomucin of Haloquadratum walsbyi (15). While H. walsbyi does not have a cell wall, halomucine, an unusually large protein (9159aa), is thought to play an important role in protecting these extreme halophiles against desiccation. Interestingly, Candidatus Altiarchaeum hamiconexum, an uncultured diderm euryarchaeon, isolated from biofilms containing hammers, cell surface proteins with the appearance of grappling hooks that connect cells to each other and to abiotic surfaces. Perra's stunning imagery suggests that this is the case with the S-layer glycoproteins, possibly suggesting a case of divergent evolution (12). [0003] The present invention relates to a method and apparatus for the preparation of a medical device, Are conserved across the prokaryotic domains, being found in the majority of sequenced archaea, where, as in bacteria, they play key roles in processes necessary for biofilm formation (10, 13). Interestingly, as discussed by Albers and Jarrell (1), as well as Näther et al. (11), a type IV pilus-like structure is responsible for swimming motility in archaea. Many secreted proteins, including the S-layer glycoprotein and pilin-like proteins, are heavily post-translationally modified. [1]. [0002] The known proteolytic modifications of the proteins of the model haloarchaeon [1], vol. Using the results of proteomic studies, Leon et al. (9), providing an invaluable resource in silico prediction tools for the characterization of archaeal proteins, in general, but also specific phyla. Kandiba and Eichler review our current knowledge of N-glycosylation in archaea, including descriptions of the pathways the regulatory roles of this post-translational modification plays in cellular processes (6). Considering the unique aspects of the archaeal cell envelope, including not only the protein structures, but their post-translational modifications as well, it is not surprising that archaeal viruses have evolved specific mechanisms to infect and egress from archaeal cells, which are reviewed in this Issue by Quemin and Quax (14). Understanding the roles that can be seen in this book is a study of the development of biofuels in the field of bioinformatics, including mucosa-associated methanogenic archaea, can (2). (2) In this paper, Archaeal cell membranes and S-layer glycoproteins have been used to make liposomes and nanomaterials. Finally, a better understanding of the similarities and differences among the archaea as well as between the archaea and the other two domains will lead to the development of a more accurate phylogeny. In this issue, Forterre takes advantage of the latest profusion of genome studies, along with supporting in vivo work, to assemble an improved tree of life (3). Conflict of Interest Statement The authors declare that this is not the case. Acknowledgments The support of the National Science Foundation MCB-1413158 to MP and the ERC starting grant 311523 (archaellum) to SA are gratefully acknowledged. References: 1. Albers SV & Jarrell KF (2015) The archaellum: how Archaea swim. Frontiers in microbiology 6:23. 2. Bang C, et al. (2014) Biofilm formation of mucosa-associated methanoarchaeal strains. Frontiers in microbiology 5: 353. 3. Forterre P (2015) The Universal Tree: an update. Frontiers in Microbiology, in 4. Gimenez MI, Cerletti M, & De Castro RE (2015) Archaeal membrane-associated proteases: insights on Haloferax volcanii and other haloarchaea. Frontiers in microbiology 6:39. 5. Jain S, Caforio A, & Driessen AJ (2014) Biosynthesis of archaeal membrane ether lipids. Frontiers in microbiology 5: 641. 6. Kandiba L & Eichler J (2014) Archaeal S-layer glycoproteins: post-translational modification in the face of extremes. Frontiers in microbiology 5: 661. 7. Kletzin A, et al. (2015) Cytochromes c in Archaea: distribution, maturation, cell architecture, and the special case of Ignicoccus hospitalis. Frontiers in microbiology 6: 439. 8. Klingl A (2014) S-layer and cytoplasmic membrane - exceptions from the typical archaeal cell wall with a focus on double membranes. Frontiers in microbiology 5: 624. 9. Leon DR, et al. (2015) Mining proteomic data to expose protein modifications to methanosarcina mazei strain Go1. Frontiers in microbiology 6: 149. 10. Losensky G, Vidakovic L, Klingl A, Pfeifer F, & Frols S (2014) Novel pili-like surface structures of Halobacterium salinarum strain R1 are crucial for surface adhesion. Frontiers in microbiology 5: 755. 11. Nather-Schindler DJ, Schopf S, Bellack A, Rachel R, & Wirth R (2014) Pyrococcus furiosus flagella: biochemical and transcriptional analyzes identify the newly detected flaB0 gene to encode the major flagellin. Frontiers in microbiology 5: 695. 12. Perras AK, et al. (2015) S-layers at second glance? Altiarchaeal grappling hooks (hami) resemble archaeal S-layer proteins in structure and sequence. Frontiers in microbiology 6: 543. 13. Pohlschroder M & Esquivel RN (2015) Archaeal type IV pili and their involvement in biofilm formation. Frontiers in microbiology 6:19. 14. Quemin ER & Quax TE (2015) Archaeal viruses at the cell envelope: entry and egress. Frontiers in microbiology 6: 552. 15. Zenke R, et al. (2015) fluorescence microscopy visualization of halomucin, a secreted 927 kDa protein surrounding haloquadratum walsbyi cells. Frontiers in microbiology 6: 249.