A conventional view delineates cellular life into only two basic types called prokaryotes and eukaryotes. The prokaryotes are further subdivided into the Bacteria and the Archaea based on small subunit ribosomal RNA comparisons and conserved mechanisms for information processing. The study of archaeal prokaryotes has matured rapidly in part initiated by genomic science as well as a continuing interest in the biochemistry and metabolism of extremophiles. The authors present an expanding pattern of new information relevant to both the general and the technical reader. The book focuses on molecular biology and genomics and topics include the biology of metals, redox chemistry, respiration, sugar catabolism, nucleic acid modification, DNA replication, repair and recombination, transcriptomics, signal transduction and peptide antibiotics. Throughout the well referenced text the emphasis is on emerging topics in specific fields providing the reader with a vision of the future in the expanding world of Archaea. Essential reading for all archaea researchers and everyone with an interest in prokaryote molecular and cellular biology. A recommended book for all microbiology libraries.
Chapter 1 Respiratory Pathways in Archaea
Imke Schröder and Simon de Vries
Respiratory diversity allows archaea to adapt and thrive even in the most extreme places significantly impacting the geochemistry of this planet. This chapter will summarize the current advances in research on archaeal oxygen, nitrate and Fe(III) respiration. While much is known about the bioenergetics and biochemical properties of the enzymes involved in oxygen and nitrate respiration our understanding of the mechanisms of Fe(III) respiration in the archaea is in its infancy. Respiratory enzymes are greatly conserved amongst archaea and bacteria but archaeal enzymes and bioenergetics exhibit several features that may reflect early evolutionary variants or adaptations to extreme environments. Unique archaeal enzymes in oxygen respiration include the oxidase supercomplexes present in Sulfolobus species that allow for efficient electron transfer, and quinone linked N-oxide reductases with several cofactor modifications in Pyrobaculum species representing a simple electron transport chain. Thus, the archaeal respiratory repertoire diverges from bacterial energy-generating pathways and future discoveries of other archaea specific traits are likely.
Chapter 2 Archaea-metal Interactions: Metabolism and Strategies of Resistance
Elisabetta Bini
Transition metals are required by all living organisms. Because of their chemical properties, they are important cofactors of numerous enzymes and are essential to carry out the most diverse functions, from basic metabolic processes to highly specialized ones. Essential metals are required only in trace levels, becoming toxic when their intracellular concentration exceeds the physiological level. Other metals, not required by biological processes, can be harmful at very low concentrations. This chapter attempts to provide an overview of the ways developed by archaea for utilizing metals and their strategies to maintain metals within physiological ranges, and a review of the genetic determinants and regulators controlling the response to metals. There is a growing awareness that all microorganisms, including archaea, have an important impact on the biogeochemical cycling of elements. It is evident that in-depth investigations of the mechanisms underlying metal homeostasis and resistance in archaea are required. Fortunately, new and improved techniques of analysis, combined with an increasing number of genome sequences, are rapidly advancing the field of metal metabolism in archaea.
Chapter 3 Redox Enzymes in the Archaea
Edward J. Crane III, Charles S. Hummel and Evan T. Hal
One of the hallmarks of living systems is their ability to use favorable redox reactions in the conversion of energy to forms that are useful to the cell. Microbes in the kingdom archaea contain many unique redox enzymes, an observation which may result from the wide range of strategies they employ for energy conversion, the many extreme environments they inhabit, and the evolutionary separation of the archaea from bacteria that catalyze similar reactions. This chapter discusses archaeal redox enzymes, focusing mainly on enzymes that either 1) are unique to this kingdom, 2) appear to provide a selective advantage under extreme conditions, or 3) may be present outside the archaea but have been best characterized from archaeal sources. Subjects covered include enzymes involved in sulfur metabolism, including both sulfur oxidation and reduction and the hydrogenases frequently associated with sulfur reduction, as well as several enzymes involved in electron transport. The central metabolic pathways of many archaeons utilize unique enzymes, and these enzymes are also discussed, with a focus on tungsten and ferredoxin-dependent enzymes and small proteins that participate in electron transfer. Enzymes of archaeal anti-oxidant systems, including the superoxide reductase system of Pyrococcus are also covered, as are some enzymes from the uniquely archaeal methanogenesis pathway.
Chapter 4 Pentose Metabolism in Archaea
Harmen J.G. van de Werken, Stan J.J. Brouns and John van der Oost
Archaeal physiology has been studied extensively ever since the discovery that they constitute a distinct domain of life. The diversity of the archaeal metabolism is very high: they are able to grow fermentatively, but are also able to respire aerobically or anaerobically, and obtain their energy from light or (an)organic molecules. Initially, hexose conversions received most attention. Recently, however, significant insight has been gained in the archaeal pentose metabolism. Importantly, novel genomic, genetic and bioinformatical tools are applicable now to study the archaeal biology in more detail. We here compare the archaeal pentose pathways, the enzymes and their regulation to the bacterial and eukaryal counterparts, and also describe distinct archaeal metabolic features and their implications. The pentose metabolism in Archaea shows a mosaic of both bacterial and eukaryal anabolic and catabolic pathways, but has also unique archaeal conversions and novel enzymes and regulations. This reflects the archaeal evolution of a variable metabolic shell that adjusts to the availability of the substrates and the extreme conditions under which many Archaea live.
Chapter 5 DNA Replication in Archaea
Brian R. Berquist and Shiladitya DasSarma
Much initial study of archaeal DNA replication came as a direct result of complete genome sequencing, as the difficulty of culturing most archaea and their limited capability for genetic and biochemical manipulation in the laboratory had restricted the scope of studies. Here, we review bioinformatic, biochemical, and genetic work on identification of archaeal chromosomal DNA replication origins and the protein factors required for both DNA replication initiation and elongation. We highlight work done in both divisions of cultured archaea: the euryarchaea and the crenarchaea and attempt to provide unifying themes from analyses in diverse archaeal organisms.
Chapter 6 Recombination Processes and Proteins in the Archaea
Michael L. Rolfsmeier and Cynthia A. Haseltine
Since the identification of archaea as a distinct branch of the tree of life, general interest in these curious microbes has been steadily increasing. Archaea bear a strong physical resemblance to bacteria and generally approach central metabolic activities in a comparable manner. Their methods for DNA information processing, however, are strikingly similar to mechanisms found in eukaryotes. In recent years, significant advances have been made in understanding recombination processes in members of the archaeal domain. This review highlights both genetic and in vitro biochemical approaches that have helped to reveal mechanistic details of recombination and takes a look forward to the future of DNA recombination studies in archaea.
Chapter 7 DNA Repair and DNA Damage Tolerance in Archaeal Bacteria: Extreme Environments and Genome Integrity
Takehiko Nohmi, Masami Yamada and Petr Gruz
Maintenance of genome integrity is a mechanism central to cellular life. Many Archaeal species live in harsh habitats that are extreme challenges to genome stability. In the habitat at high ambient temperatures, deamination, oxidation and depurination are greatly accelerated and various lesions are supposed to accumulate in the genomic DNA. Thus, the organisms living in such extreme conditions seem to evolve novel strategies for repairing DNA damage and avoiding mutations caused by the lesions. In this chapter, we review mechanisms of DNA repair in archaeal bacteria and unique properties of archaeal DNA polymerases (Pols) to tolerate DNA damage. In general, archaeal DNA repair proteins are eukaryote-like although many counterparts are missing in the genome sequences. Archaeal B-family DNA Pols, such as Sso DNA Pol B1 or Pfu, halt DNA replication several base pairs before template uracil or hypoxanthine, deamination products of cytosine or adenine in template DNA, respectively, thereby apparently avoiding mutations (read-ahead mechanism). Fifteen out of 38 archaeal species whose genome sequences have been completely determined seem to possess Y-family DNA Pols, which are specialized to bypass lesions in DNA. Collectively, these molecular features warrant the future investigation on how Archaea accommodate DNA damage inevitably occurring in the extreme harsh environments.
Chapter 8 Modified Nucleotides in Archaeal RNAs
Henri Grosjean, Ramesh Gupta and E. Stuart Maxwell
Modified nucleotides increase the structural and functional diversity of RNA well beyond the four canonical bases. They are abundant in Archaea, Bacteria, and Eukarya and play important roles in regulating RNA function in all three domains of life. In Archaea, both transfer and ribosomal RNAs possess numerous modified nucleosides with some unique to Archaea and others shared with Bacteria and/or Eukarya. The diversity of archaeal nucleoside modifications is matched by the complexity of machineries and biosynthetic pathways that carry out these modifications. In this chapter, we discuss the diversity of nucleosides found in many different archaeal organisms and detail their occurrence in different RNA species. We also examine the enzymes used to accomplish these nucleoside modifications, reviewing both protein-only and RNA-guided ribonucleoprotein enzymes. Throughout this discussion, we provide the reader with additional reference sources that should be helpful for exploring further the modified nucleosides and modification enzymes of Archaea.
Chapter 9 Signal Transduction in the Archaea
Peter J. Kennelly
Adaptation to changing internal and environmental circumstances requires that living organisms develop mechanisms for monitoring relevant variables and triggering compensatory changes in the functional status of target proteins. The process by which sensory information is received and translated into cellular effects is called signal transduction. Mining of archaeal genomes for homologues of well-known bacterial and eucaryal signal transduction proteins has yielded surprisingly little. While some archaeons acquired copies of the sensor-response machinery that guide the chemotactic swimming of many Bacteria, the only recognizable signal transmission modules conserved throughout the Archaea are the eukaryotic protein kinases, the class II adenylate cyclases, the Pat-like protein acetylases, and several allosteric feedback loops. As the sensor response needs of the Archaea would appear to be, a priori, comparable to those of other microorganisms, it appears likely that members of the third domain of life have developed unique paradigms for transducing signals and/or novel ways for exploit known mechanisms.
Chapter 10 Functional Genomics of Stress Response in Extremophilic Archaea
Sabrina Tachdjian, Keith R. Shockley, Shannon B. Conners and Robert M. Kelly
Given that some members of the Archaea inhabit extreme environments while others occupy more hospitable biological niches, the mechanisms by which this group of microorganisms handles stress are well worth examining for clues to prokaryotic "disaster" management. The availability of genome sequence information for a number of archaea has provided a glimpse into the genetic basis for thriving at extremes of temperature, salinity, pH and metal concentrations. Such information has furthermore enabled the application of "omics" tools to examine the phenotype that results from perturbations that trigger both global and focused survival strategies.
Chapter 11 Archaeal Antimicrobials: An Undiscovered Country
Richard F. Shand and Kathryn J. Leyva
Peptide or protein antibiotics have been discovered in all three domains of life, and their production is nearly universal. Bacteriocin and eucaryocin research is well established, while research on archaeocins is still in its infancy. To date, only eight archaeocins (seven halocins and one sulfolobicin) have been partially or fully characterized, but hundreds of archaeocins are believed to exist, especially within the haloarchaea. The prevalence of archaeocins from other members of this domain is unknown simply because no one has looked for them. The discovery of new halocins hinges on recovery and cultivation of haloarchaeal organisms from the environment. For example, samples from a novel hypersaline field site, Wilson Hot Springs, recovered 350 halophilic organisms; preliminary analysis of 75 isolates showed that 48 were archaeal and 27 were bacterial. Significantly, 77% inhibited the growth of at least one other isolate. Inter-domain antagonisms were also present with 43 haloarchaeons inhibiting halophilic members of the domain Bacteria and 7 Bacteria antagonized haloarchaeons. Finally, archaeocin research provides excellent opportunities for discovery of novel antibiotics that may have clinical applications in addition to unique models for training students both in and outside the classroom.