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Category: Microbial Genetics and Molecular Biology; Environmental Microbiology
Since the discovery in 1977 that they constitute a distinct branch of the biological world, archaea have expanded and altered the field of microbiology. Archaea can thrive in some of the most extreme environments of the planet, from extremely alkaline or acid waters to high-temperature environments near thermal vents in the deep sea. This exceptional ability to survive and prosper has led scientists to speculate that archaea played a significant role in shaping all life on Earth and may provide valuable keys to the search for extra-terrestrial life.
This path-breaking book fully describes the molecular cell biology of the archaea in one accessible and readable volume. With twenty-three chapters by the world’s leading experts, this book emphasizes each author’s individual research expertise, while also being a general guide to the latest knowledge on archaea. The core of the book describes the key cellular processes such as DNA replication, transcription, translation, lipids and metabolism. It also explains their unique features including aminoacyl-tRNA synthesis, signal transduction, and post-translational modification. Above all, this volume details the latest discoveries of the twenty-first century and anticipates new progress expected in the future.
This volume is a timely and essential reference for researchers, instructors, practitioners in the field, and students of the unique qualities of Archaea. Archaea: Cellular and Molecular Biology will remain the authoritative reference source for the many disciplines interested in the archaea for years to come.
Hardcover, 523 pages, full-color insert, illustrations, index.
The discovery of the archaebacteria was serendipitous, but not unexpected. In the late 1960s, the author had begun assembling the program for inferring (organismal) genealogical relationships through rRNA sequence comparisons, as the structure of the universal phylogenetic tree was yet to be determined. Molecular evolution had been on the scene for the better part of a decade, and a universal framework within which to study evolution from the molecules on up was needed. The objective in establishing the phylogenetic program, however, was not to refine bacterial taxonomy per se, but to restore an evolutionary perspective/spirit to biology. This time the focus would be on the evolution of the cell itself, in particular, the evolution of its translation mechanism. The walls of the would-be archaeabacteria were not the most important clue, however, for they would turn out to be nonhomologous among themselves. Not only were the phenotypically diverged cousins of the methanogens beginning to show up, but so were the traits common to all archaebacteria. Though reluctant at first, microbiology did eventually come around to accepting the archaea. Molecular reductionism is now spent as a conceptual force and has settled into being a most useful body of technology. Microbial biology in the meanwhile has undergone a conceptual and methodological revolution of its own, freeing itself from its self-inflicted intellectual confinement. The future of biology lies in microbial ecology. Molecular biology is moving in an evolutionary direction-compelled by its own technology.
This chapter provides an overview of the Archaea and some of their morphological, physiological, biochemical, and molecular properties. It introduces model organisms and systems that have been used to study fundamental properties and principles of archaeal biology, in addition to those that have served as models for understanding the biology of more complex eucaryal cells. The chapter describes phylogeny of Archaea and the origin of life, and gives an overview of the characteristic properties of archaeal cells. Rather than one model organism, a broad range of archaea have proven useful for studying morphology, physiology, molecular mechanisms of adaptation, and so forth. These include Methanothermobacter thermautotrophicus, M. marburgensis, and Methanosarcina spp. for methanogenesis; Thermoplasma for proteolysis; Halobacterium for light-driven proton translocation, gene regulation, chemotaxis, and gas vesicles synthesis; Archaeoglobus for sulfate reduction; Pyrococcus and Acidianus ambivalens for inorganic sulfur metabolism; Sulfolobus, A. ambivalens, Pyrococcus, and the methanogens for electron transport chains; Sulfolobus and Pyrococcus for DNA replication and transcription; Halobacterium, Haloarcula, and Sulfolobus for translation. The chapter also describes the properties of major archaeal taxa according to their ecology and molecular similarity. Important characteristics of some of the key organisms are also included in this chapter. Methanosarcina barkeri, M. mazei, and M. acetivorans are the most well studied methanogens and are important model organisms for studies on acetoclastic methanogenesis, transcription, and chaperonins.
This chapter describes the recent advances that have been made in understanding the biochemical players that facilitate the complex macromolecular process that mediates faithful replication of archaeal chromosomes. The current state of knowledge of the machineries that drive the archaeal cell cycle is discussed. In bacteria, the functional single-stranded DNA-binding proteins (SSBs) is a homotetramer that wraps 65 nucleotides. Pol α, Pol δ, and Pol ε are the major replicative polymerases, with Pol δ acting on the lagging strand and both acting on the leading strand of DNA replication. Sliding clamps are well known for their role in DNA replication, but they also interact with factors involved in other cellular processes, such as DNA repair and recombination, and cell cycle regulators. While an ever-growing body of data has yielded considerable insight into the form and function of the archaeal DNA replication machinery, much less is known about the details of the archaeal cell cycle and its control. Indeed, what little is known appears to be suggesting that diverse mechanisms may be employed to regulate chromosome copy number, to coordinate DNA replication and cell division, and even to mediate the process of cell division itself. Researchers examined nucleoid distribution during the cell cycle, and the results suggested that chromosome segregation was concomitant with DNA replication, as was proposed for M. thermautotrophicus, in a mode akin to that employed by bacteria.
Procaryotic genomic DNA and associated proteins together form an irregularly shaped structure, designated as the nucleoid. In contrast to the range of different chromatin proteins identified in bacteria, almost all eucaryal genomes are compacted into nucleosomes, chromatin, and chromosomes by essentially the same four proteins, histones H2A, H2B, H3, and H4. This chapter describes several different families of archaeal chromatin proteins with unrelated structures, but with the common properties of abundance, small size, positive charge, and ability to bind to DNA with little or no sequence specificity. Alba does bind to both DNA and RNA in Sulfolobus species, but chromatin immunoprecipitation experiments argue convincingly that Alba is bound to genomic DNA and functions as a chromatin protein in S. solfataricus. Sul10a is the generic name of an abundant ~11 kDa DNA-binding protein investigated from S. acidocaldarius (Sac10a) and S. solfataricus (Sso10a). An NMR solution structure has been established for methanogen chromosomal protein 1 (MC1) from Methanosarcina sp. CHTI55. It is apparent that many different chromatin proteins have evolved, all of which must bind and compact DNA into complexes that are readily disassembled, or that are inherently compatible with DNA replication and transcription machineries. Gene expression requires transcription activators, for example, histone acetylases that help disassemble chromatin and so allow transcription factor access to the DNA. With the accumulation of genome sequences, it is now apparent that most archaea have the capacity to synthesize several different chromatin proteins.
This chapter examines the ‘’natural genetics’’ of methanogenic, halophilic, and thermophilic archaea, progressing from the molecular scale to cells and finally to populations. The simplest reconciliation of observations would seem to be that the thermophilic and hyperthermophilic archaea have alternative molecular strategies that assume the function of classical MMR and NER systems but do not involve homologous proteins. In its most general sense, genetic recombination means the creation of new DNA sequences from existing sequences by processes involving strand exchange rather than error-prone synthesis. ‘’Illegitimate’’ recombination breaks and joins DNA sequences with negligible influence of the sequences involved. Limited migration elevates the importance of mutation and recombination in the evolution of natural populations. Testing hypothesis that archaea, or major archaeal groups will involve measuring molecular processes central to the survival, reproduction, and evolution of archaea and to the development of experimental tools for establishing gene function at the molecular level. Compared with bacteria and unicellular eucarya, archaea that have been analyzed in genetic terms have rather low rates of neutral mutation and high rates of recombination. This combination of properties would seem ideal for evolutionary adaptation. Combining computational genetic analyses of natural populations with experimental analyses of cultured archaea will help clarify how molecular mechanisms of archaea determine genetic properties and how genetic properties of archaea affect genome stability and evolution.
The biochemical machinery involved in the processes of DNA replication, transcription, and translation shows a striking similarity and phylogenetic relationship to the equivalent machinery in eucarya. In particular, RNA polymerase (RNAP) and the basal transcriptional machinery of archaea share many properties with the eucaryal RNA polymerase II (RNAP II) transcription apparatus. Regulators of archaeal transcription repress initiation by preventing TFB/TBP access to the TATA-box region or RNAP recruitment to the transcription start site. The DNA-binding site of LrpA overlaps the RNAP-binding site, and DNA-bound LrpA inhibits transcription by blocking RNA polymerase recruitment. NrpR controls the transcription of the nif operon by binding cooperatively to two tandem operator sequences, OR1 and OR2, located downstream of the transcription start site. The stronger and promoter proximal NrpR-binding site (OR1) can mediate repression of nif transcription during growth on ammonia. Heat shock-induced upregulation of some TFB genes from haloarchaea and of TFB2 from Pyrococcus have been reported. In cell-free transcription reactions, the addition of the substrate (maltodextrins) of this transporter system causes TrmB to dissociate from the promoter and relieves inhibition of RNA synthesis. The lack of genetic systems in many archaea hampers analysis of transcriptional regulation in vivo. The striking similarity of the archaeal and eucaryal genetic machinery is described in this chapter.
Most organisms contain between 40 and 50 different transfer RNA (tRNA) molecules that read one or more of the 61 or 62 different sense codons through specific codon-anticodon interactions and position the appropriate amino acid for insertion into the growing polypeptide chain. Additional complexity in the tRNA processing and modification pathway occurs in cases where archaeal tRNA genes contain an intron. The chapter describes introns in archaeal transcripts. The genes for ribosomal RNA (rrn) are located in operons in the archaeal genome and are transcribed to produce multicistronic precursor RNAs. Two early studies used nuclease protection and primer extension assays to define the intermediates generated during processing of the primary rRNA transcript from two canonical rrn operons: the single-rrn operon in Halobacterium salinarum and the canonical rrnA operon in Haloarcula marismortui. The proportion of modified nucleotides in tRNA can approach 50% or more. The two most frequent modifications in RNA are ribose methylation and the pseudouridylation. In an attempt to distinguish between these two alternatives, actinomycin D was used to inhibit transcription and Northern hybridization was used to follow the decay of the various mRNA fragments. There was a strong correlation between fragment length and stability: the shorter the fragment, the longer the half-life. This correlation was used to argue that the transcript fragments are generated by endonucleotic cleavage rather than premature transcription termination, and that the distal sequences released following cleavage are selectively degraded.
The emergence of translation as a process was key to the evolution of modern cellular life. Primitive ‘’life’’ based on self-replicating nucleic acids without translation is conceivable. This chapter describes what is known about the translational apparatus and the protein-synthesis mechanism in archaea. Other essential components of the protein synthesis machinery that are found in all cells are specific sets of proteins known as translation factors. These are necessary to assist the different stages of translation, i.e., initiation, elongation, and termination. In addition, there are genes encoding tRNAs and the accessory proteins that function in translation initiation, elongation, and termination. The four genes encoding the universal initiation factors YciH/SUI1, IF1/IF1A, IF2/IF5B, and EFP/IF5A tend to be unlinked from other translational genes and are likely to be individually transcribed. The gene encoding the putative translation termination factor aRF1 is in general not clustered with other genes encoding components of the protein synthesis apparatus. eIF5A is required to trigger the formation of the first peptide bond. Eucaryal IF2 is an important translation initiation factor, as it specifically interacts with the initiator tRNA (met-tRNAi) and carries it to the 40S ribosomal subunit. The universal protein a(e)IF5A (EFP in bacteria) is usually classed as a translation initiation factors. This protein does little to help the selection of the translation start site and functions as a specialized elongation factor.
This chapter discusses four unique aspects of archaeal aa-tRNA formation that led to a much deeper understanding of this process not only in the Archaea, but in all domains of life. The topics are: (i) processing of half-tRNA genes to mature tRNA in Nanoarchaeum equitans, (ii) RNA-dependent cysteine synthesis in methanogens, (iii) pyrrolysyl-tRNA formation in the Methanosarcinaceae, and (iv) glutaminyl- tRNA synthesis in archaea. The bulge-helix-bulge (BHB) motifs postulated to form at the intron-exon junctions of archaeal tRNAs show divergence from the canonical structure. Once mature tRNA has been generated each tRNA species needs to be acylated (charged) with the correct amino acid. This is primarily achieved by the direct attachment of an amino acid to the corresponding tRNA by an aminoacyl-tRNA synthetase. However, since many organisms lack the complete set of 20 aminoacyl-tRNA synthetases (aaRSs), many biochemical, genetic, and genomic studies revealed the existence of an essential indirect two-step pathway that also provides correctly charged aa-tRNA. The aminoacyl-tRNA synthetases are an ancient family of enzymes that esterify an amino acid to the 3’ end of the cognate tRNA species. The current understanding of the Methanothermobacter thermautotrophicus Glu-tRNAGln amidotransferase GatDE is discussed. Discovery of the tRNA-dependent cysteine biosynthetic route in M. jannaschii may have implications that reach far beyond the only problem of the formation of Cys-tRNACys in three methanogenic archaea. The Methanosarcinaceae are an exception among the methanogens, as they are able to use compounds like methanol, methylated thiols, and methylamines as energy sources.
This chapter describes the known members of archaeal protein-folding pathways, including not only the heat-shock-regulated members, but also the non-heat-shock-regulated protein chaperones. The major chaperone classes, heat shock protein (Hsp) 100 and Hsp90/Hsp83, are absent from the genomes of the hyperthermophilic archaea, although they are present in several mesophilic and thermophilic archaea. In archaea, with one exception, prefoldins are hexamers consisting of two α-subunits and four β-subunits, which act as generalized holding chaperones. The holding-and-release mechanism of the archaeal prefoldins has recently been elucidated. The archaeal group II chaperonins form toroidal double rings with an eightor ninefold symmetry, consisting of homologous subunits. The subunit composition of the chaperonin complexes in several archaea changes with growth temperature. The known properties, arrest and ATPase activity, and structural characteristics of archaeal chaperonins are provided in this chapter. The helical protrusion is strictly conserved among group II chaperonins. The existing evidence indicates that asymmetric and symmetric molecules are present in the functional ATPase cycle of archaeal group II chaperonins. The coexistence of both groups of chaperonins in the same cytosol in the Methanosarcina species provides a useful model system for studying the differential substrate specificities of the group I and II chaperonins, and for elucidating how newly synthesized proteins are sorted from the ribosome to the appropriate chaperonin for folding.
This chapter focuses on other modalities of signal transduction, including intracellular second messengers, feedback regulation, and posttranslational modifications such as the phosphorylation-dephosphorylation of proteins. Empirical studies of archaeal-archaeal and archaeal-bacterial communication have been few in number and preliminary in nature. Inspection of archaeal genomes has revealed them to be devoid of homologs of the prototypic bacterial quorum-sensing proteins LuxS and LuxR. Two-component systems differ in several fundamental respects from protein-serine/threonine/tyrosine phosphorylation cascades. First, autophosohorylation is the predominant mechanism of phosphorylation in the two-component system, whereas protein-serine/threonine/tyrosine phosphorylation cascades rely primarily on phosphotransfer reactions catalyzed by protein kinases that are distinct from the phosphoacceptor protein. Second, the chemical nature of the phosphoryl moieties formed during two-component signaling differs significantly from that of protein-serine/threonine/tyrosine phosphorylation. Posttranslational modifications have discussed and demonstrated, at least in some instances, to modulate the function of one or more target proteins from the Archaea or other organisms. It is widely presumed that (poly)ADP-ribosylation regulates the functional properties of proteins, as is the case with other covalent modifications such as protein phosphorylation-dephosphorylation. Given that the members of the bacterial domain have been the subject of decades of intensive study, it appears highly likely that the Archaea will not only be found to contain new sensor-response mechanisms and molecules, but that they will provide new insights into this vital process in other organisms as well.
The pathways of central metabolism are at the heart of an organism’s total metabolic capacity, and their wide conservation suggests they were an early evolutionary invention. Consistent with this view are common themes that are found spanning the Archaea, Bacteria, and Eucarya, although variations are observed that reflect not only phylogeny but also particular lifestyles and requirements. The principal aim of this chapter is to describe the central metabolic pathways of the Archaea and to identify the unique or unusual features of archaeal metabolism. This chapter talks about the conversion of sugars to pyruvate, and the metabolic fate of pyruvate, either to organic end products or to CO2 by complete oxidation via the citric acid cycle. Growth on acetate is discussed as this may involve an additional cyclic pathway, the glyoxylate cycle. The catabolism of amino acids is included; while these do feed into the citric acid cycle, catabolism of branched-chain amino acids in particular deserves a special mention as it is in these reactions that the presence of a family of multienzyme complexes was discovered, which were until recently thought to be absent from all archaea. Sulfolobus species exhibit considerable metabolic diversity and versatility and are commonly considered to be opportunistic heterotrophs, capable of utilizing a wide range of carbohydrate energy sources. Central metabolism represents one of the most fundamental aspects of the biochemistry of the cell and is commonly perceived as invariant and sacrosanct.
Recent genomic sequencing, proteomic analyses, and development of genetic systems continue to expand one's understanding of methanogenesis and the Archaea. The conversion of the methyl group of acetate to methane (acetate fermentation pathway) produces about two-thirds of the annual production, whereas one-third derives from the reduction of carbon dioxide with electrons supplied from the oxidation of formate or hydrogen (carbon dioxide reduction pathway). Thus, the methanogens rely on the first two groups to supply substrates for growth and methanogenesis. Methanogens are the main constituency of the Euryarchaeota and are subdivided into five orders, including such as Methanobacteriales, Methanococcales and Methanomicrobiales; each with distinctive characteristics. Methanofuran (MF) and tetrahydromethanopterin (THMPT) function as one-carbon carriers, the latter coenzyme also functioning in methylotrophic microbes from the Bacteria domain. A proteomic and transcriptional analysis of cold adaptation has revealed the thermal regulation of several genes essential for methanogenesis by dismutation of the methyl group of trimethylamine. The extent of regulation of genes essential for methanogenesis and other fundamental processes in response to temperature is consistent with a role in providing the cell with an ecological advantage in cold environments. The genome sequences of M. acetivorans, M. mazei, and M. thermophila harbor two homologs of mtaA, three homologs of mtaB, and three homologs of mtaC encoding enzymes specific for methanogenesis from methanol.
The cell walls of the Archaea are composed of different polymers such as glutaminylglycan, heterosaccharide, methanochondroitin, pseudomurein, protein, glycoprotein, or glycocalyx. The S-layer glycoprotein of Halobacterium salinarum was the first glycoprotein discovered in bacteria and archaea. Initially, the novel cell wall structures were viewed as curiosities, and their taxonomic significance was not realized until the concept of the Archaea was published. At this time, the results of cell wall studies supported the new view of the phylogeny of the Bacteria and Archaea. Many archaea possess proteinaceous surface layers (S layers), which form two-dimensional regular arrays. The chemical structure of archaeal S-layer glycoproteins has been determined in detail for a few archaeal species, e.g., Methanothermus fervidus, H. salinarum and Haloferax volcanii, and Staphylothermus marinus. The filamentous chains of Methanospirillum hungatei and Methanosaeta concilii (formerly Methanothrix soehngenii) are held together by a proteinaceous fibrillary sheath. The majority of bacterial and archaeal exopolymers are polysaccharides, but exopolymers composed of L-or D-glutamate are also formed. The ultrastructure of N. equitans is similar to many archaea. Future investigations of the unusual symbiosis of these two hyperthermophilic archaea aim at elucidating which proteins of both cell envelopes are directly involved in the physical interaction and in the exchange of metabolites from one cell to the other. The cell envelopes of the Archaea are often directly exposed to extreme environmental conditions, and they cannot be stabilized by cellular factors. S layers represent the most common cell surface layer of Archaea.
This chapter summarizes the different biosynthetic steps of isoprenoid ether lipid biosynthesis in archaea, describing the underlying enzymatic reactions that have been characterized. The evolution of this lipid biosynthesis apparatus in a variety of archaea is discussed. The effect of the environment on the nature of the lipids present in archaeal cell membranes is scrutinized in an attempt to link structure and function. Similar to other isoprenoids, archaeal lipid side chains are assembled from two universal precursors: isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). In archaea, geranylgeranyl diphosphate (GGPP) synthase can elongate DMAPP to obtain both farnesyl diphosphate (FPP) and GGPP, the latter being the isoprenyl forming the side chains of C20-C20 diether lipids. However, similar to the studies on partially saturated side chains, there is little experimental evidence on when these structures are formed during the process of archaeal lipid biosynthesis. The detection of CDP-archaeol synthase and archaetidylserine synthase activities in Methanothermobacter thermautotrophicus suggests that the biochemical steps for the addition of polar head groups on archaeal lipid precursors, might proceed in a manner analogous to fatty acid biosynthesis in bacteria. High-performance liquid chromotography (HPLC), in combination with electrospray mass spectrometry (ES-MS) was used to characterize the membrane phospholipids and glycolipids of halophilic archaea and the cold-adapted methanogen M. burtonii.
This chapter discusses solute transport in Archaea. The fluidity and permeability properties of the lipid membranes are mainly determined by their lipid composition. The archaeal lipid chain contains isoprenoid units where every fourth carbon atom is linked to a methyl group. Most of the archaeal phytanyl chains are fully saturated isoprenoids. ATP-binding cassettes (ABC) transporters have a typical modular domain structure which usually comprises two integral membrane proteins that form the permease domain, and two cytoplasm-located ATPases which drive the transport of the substrate by the hydrolysis of ATP. In a report on secondary transporters in archaea, a lactose transporter was identified in Sulfolobus solfataricus by functionally complementing a mutant strain that was unable to grow on lactose. The distinction between the carbohydrate uptake transporters (CUT) and di/oligopeptide classes of ATP-binding cassettes (ABC) transporters is also evident for the protein-domain organization of the binding proteins. Members of the CUT class of binding proteins from S. solfataricus contain type IV pilinlike signal peptides and do not contain secretory signal peptides. A general feature of bacteria and archaea is that they are equipped with defense systems against toxic compounds from the environment. This protection mechanism involves multiple drug transport systems that extrude toxic compounds from the cell. In general, the drug transport systems belong to the class of secondary transporters or ABC transporters.
Recent analyses of the archaeal Sec and Tat pathways have revealed novel and crucial information about archaeal protein translocation, as well as protein translocation in general. This chapter provides an overview on protein translocation into and across archaeal cytoplasmic membranes. The Sec pathway is the only known universally conserved protein translocation pathway. Protein translocation may be driven by one or several extracytoplasmic activities that provide directionality by preventing movement of the polypeptide chain back into the cytoplasm. In vitro studies suggest that the proton motive force (PMF), in concert with the action of SecA, facilitates bacterial secretion via the Sec pore. Furthermore, the PMF is apparently sufficient to drive translocation of proteins via the twin-arginine translocation (Tat) pore. Thus, it is possible that an ion gradient across the archaeal membrane is the sole source of energy for protein translocation. Many bacteria and archaea possess an additional general secretion pathway, described as the Tat pathway. The presence of the twin-arginine motif in the Tat signal sequence provided a means of identifying novel Tat substrates by computational pattern-matching techniques. Recent in vivo, in vitro, and in silico studies have led to a better understanding of archaeal protein translocation. Moreover, the elucidation of an archaeal Sec-pore X-ray crystal structure strikingly demonstrates how analysis of this pathway in archaea can significantly advance the field of protein translocation as a whole. In addition to standard molecular and biochemical approaches, it is now crucial to develop in vitro Sec and Tat protein translocation systems that will more clearly define the mechanisms of these pathways and reveal the energetics of these cellular processes in archaea.
One of the better-studied aspects of archaea physiology is the understanding of various types of taxis (phototaxis, chemotaxis), especially in halobacteria. Bacterial flagella and archaeal flagella are responsible for swimming, while type IV pili are involved in surface translocation or twitching. The study of phototaxis and chemotaxis in Halobacterium salinarum is a rare instance where significant biochemical and genetic studies on taxis in an archaeon have been reported. Transducer proteins are responsible for the detection of the external signal that is transmitted to the internal components of the chemotaxis system. An htrXI deletional mutant is defective in chemotaxis toward glutamic acid and aspartic acid and devoid of methyltransferase activity. Continued study of archaeal flagellation and chemotaxis is expected to yield the same far-ranging information about the much less well-studied archaea. Significant progress in understanding motility, flagellation, and chemotaxis will occur as the genetic tools continue to improve in the various model organisms. Study of the flagella-associated genes which are often cotranscribed with flagellins will, it is hoped, yield important information about their, so far completely unknown, role in archaeal flagellation. It is expected that the continued study of archaeal flagellation and chemotaxis will lead to novel discoveries about these structures and processes in archaea, and these may in turn lead to insights into the understanding of bacterial chemotaxis and type IV pili assembly, structure, and function.
The existence of many informational proteins that are common to Archaea and Eucarya and absent from Bacteria is not only true for DNA replication, but also for translation, transcription, and RNA and protein processing. Many reviews have summarized insight from newly sequenced archaeal genomes and have usually focused on aspects of comparative genomics. This chapter focuses on the description of archaeal genomes and what can be learned from archaeal genomics about the mechanisms of genome evolution, and the history of the Archaea domain itself. Compared with Bacteria, the number of completely sequenced archaeal genomes is much smaller. The larger genomes are from mesophilic archaea and contain a high proportion of genes recruited from bacteria by horizontal gene transfer (HGT). The chromosome terminus appears to be a hot spot of recombination in archaea, as it is in bacteria. This was clearly shown from a genome comparison of the two closely related species, Pyrococcus abyssi and Pyrococcus horikoshii. Comparative genomics has shown that gene loss, gene duplication, and integration of foreign DNA are major forces shaping genome evolution. The continuous evolution of archaeal genomes by gene loss and acquisition is obvious from the comparative analyses of the proteomes of closely related species. In a recent study using unfolding simulation experiments to determine amino acid composition, the number of charged residues in hyperthermophiles was reported to be much greater than it would need to be for the stabilization. Ongoing metagenomics projects will continue to broaden the understanding of archaeal diversity and evolution.
As genetic systems for archaea become further developed and implemented, functional genomics tools can be expanded to enable a full systems biology approach to studying archaea. This chapter provides a review of the current status of functional genomics efforts to investigate archaea. In this discussion, functional genomics refers to transcriptional response (transcriptomics), protein inventory and differential abundance (proteomics), and protein structural attributes (structural genomics) examined in the context of entire genomes. Currently, certain archaea are emerging as model systems for functional genomics studies. This realization was sobering given the need for highly sophisticated, analytical, and statistical skills, as well as the significant expense, that are typically part and parcel of functional genomics approaches. As is the case with many facets of archaeal biology, the field of proteomics can be divided into accomplishments achieved with three different groups of archaea: methanogens, halophiles, and organisms that fit into neither category. A proteomics approach to investigate protein levels in cells grown at low (4°C) and optimal temperatures was recently reported. This study represented the first global analysis of proteins involved in cold adaptation. Coupled with useful genetic systems, strategic use of functional genomics approaches will form the basis for complete and accurate genome annotation. Information gained from ongoing and emerging functional genomics efforts focusing on archaea will provide clues and insights that will accelerate the genetic system’s development.
This chapter discusses molecular genetics of Archaea. Gene transfer systems currently exist for species within all three physiological groups of archaea, halophiles, methanogens, and nonmethanogenic hyperthermophiles. The chapter reviews the development of these systems. Colonization of methanogenic and nonmethanogenic hyperthermophiles on solidified medium is equally problematic, as agar is rapidly dehydrated at high temperatures, especially at the concentrations required for it to remain solidified. Therefore, gellan gum (Gelrite) is used as the solidifying agent for growth of thermophiles and hyperthermophiles, which are incubated in a plastic bag or anaerobe jar to minimize dehydration. Haloarchaea are transformed via polyethylene glycol (PEG) mediated transformation, which was first described in Haloferax volcanii. Gene disruption is required to identify and confirm the function of genes within the archaea. Random mutagenesis using chemical and UV radiation has been successfully used for H. volcanii, Methanococcus voltae, Methanococcus maripaludis, and Pyrococcus abyssi. Progress in the development of methodologies for archaeal genetics has rapidly accelerated in the past decade. Additional methods are currently under development for all three archaeal phyla, including additional systems for markerless exchange, gene expression, topological mapping, protein tagging and expression, as well as others. The choice of archaeal genomes for sequencing is now largely driven by the availability of genetic systems, which at present include complete genomes of the halophiles Haloarcula marismortui and Halobacterium sp.
The biotechnology of the Archaea has been reviewed in recent articles. This chapter covers topics that include enzymes and molecules from archaea and the use of archaeal whole cells. It updates the current state of biotechnology of the Archaea, paying special attention to distinguish between extant and potential applications, to provide a realistic overview of the impact of these organisms on biotechnology. Among hydrolases, proteases, esterases/lipases, and glycoside hydrolases are important in industry. Glycosidases synthesize oligosaccharides in reactions of reverse hydrolysis or transglycosylation in which an alcohol or another sugar acts as acceptor instead of water. Microbial exopolysaccharides (EPS) are used as stabilizers, thickeners, and emulsifiers in several industries, and the major commercial exopolysaccharides derives from the bacterium Xanthomonas campestris. Compatible solutes from archaea have biotechnological roles as cryoprotectants and preservatives. Hydrogen gas is an attractive alternative to fossil fuel as it is a clean, nonpolluting source of energy. However, conventional production is based, at present, on the steam reforming of natural gas and petroleum, and microbial production of H2 is gaining increasing interest. Many studies on the microbial production of H2 have focused on the bacterial genera, Clostridium and Enterobacter. Extremophilic archaea have been considered an interesting source of molecules for novel biotechnological applications. Their stability and activity to extreme conditions make them useful alternatives to labile mesophilic counterparts.
Archaeosomes have been developed from various archaea for use as drug delivery systems and vaccine applications that utilize their adjuvant properties. This chapter describes the mechanism of archaeosome adjuvants as self-adjuvanting antigen carrier systems that are taken up by specific receptor-mediated endocytosis to promote both CD4+ and CD8+ T-cell responses. Effects of lipid structure on the immune response are also reviewed in this chapter. Archaeal lipids possess several features that make them ideal for the preparation of archaeosomes. The first is the inherent stability of the polar lipids. Second, archaeal lipids form archaeosomes over physiological temperature ranges, allowing preparation of vaccines at ambient temperatures. Third, once formed, archaeosomes of 50 to 250-nm diameters remain suspended indefinitely and resist fusion or aggregation over long storage periods. Two signals are required to activate T cells. The first is antigen presentation in the context of MHC, and the second is costimulation of the specific T cell recognizing the presented antigen. Several lines of evidence support a phosphatidylserine (PS) receptormediated endocytic mechanism. Data using test antigens indicate the strong potential for archaeosome vaccines to achieve immunity against intracellular bacteria. Because Listeria monocytogenes is an intracellular pathogen that is typically cleared by the host CD8+ T-cell immunity, this model has been used as a test for potency of archaeosome vaccines.
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At A Glance
Since the discovery in 1977 that they constitute a distinct branch of the biological world, archaea have expanded and altered the field of microbiology. Archaea can thrive in some of the most extreme environments of the planet, from extremely alkaline or acid waters to high-temperature environments near thermal vents in the deep sea. This exceptional ability to survive and prosper has led scientists to speculate that archaea played a significant role in shaping all life on Earth and may provide valuable keys to the search for extra-terrestrial life. This path-breaking book fully describes the molecular cell biology of the archaea in one accessible and readable volume. With twenty-three chapters by the world's leading experts, this book emphasizes each author's individual research expertise, while also being a general guide to the latest knowledge on archaea. The core of the book describes the key cellular processes such as DNA replication, transcription, translation, lipids and metabolism. It also explains their unique features including aminoacyl-tRNA synthesis, signal transduction, and post-translational modification. Above all, this volume details the latest discoveries of the twenty-first century and anticipates new progress expected in the future. This volume is a timely and essential reference for researchers, instructors, practitioners in the field, and students of the unique qualities of Archaea. Archaea: Molecular and Cellular Biology will remain the authoritative reference source for the many disciplines interested in the archaea for years to come.
Description
This impressive book describes the unique features of the Archaea organisms. It reviews the extent of information currently known about the newly discovered organisms that are "clearly distinguished from the Bacteria and Eucarya."
Purpose
The purpose of this book, according to the editor, is "to be the authoritative reference source for the many disciplines interested in the Archaea." The authors and editors of this challenging and remarkable book have accomplished their purpose. It will serve as the primary reference for researchers and students within this broad and growing field of microbiology for many years.
Audience
This book clearly will be a primary reference source for researchers in the field of Archaea. The authors are the experts and cover each topic with great detail and explanation. It will serve as a major teaching text for students at many levels.
Features
The first of the book's 23 chapters explains in detail the history of the discovery and subsequent study of the Archaea. At times, this chapter reads more like an editorial, but it is very informative and descriptive of the human nature of the scientific process. The second chapter, which is the longest, describes the unique features of the Archaea and includes detailed examples of the different organisms as well as the variety of sizes and shapes that these organisms take. Included in this chapter is a descriptive table that lists various characteristics of the organisms within the Archaea. These descriptions include habitat, optimal temperature, optimal pH, metabolism, substrates used, and electron acceptors. The chapters that follow provide details about the cellular operations of these organisms from nucleic acid replication to transcription and cell wall synthesis as well as many additional topics relating to organism survival. The last two chapters are focused on the use of these organisms in biotechnology and vaccine development. Each chapter closes with a section entitled "Perspective: the next five years." I expect this will set the stage for the second edition in which many of these projections will have produced fruit.
Assessment
This will become the primary reference for Archaea. The quality with which each topic is presented is the highest. The authors' efforts have resulted in a great gift to microbiology and science. I look forward to watching the development and research that this inspires.
Doody Enterprises
Reviewer: Rebecca Horvat, PhD, D(ABMM) (University of Kansas Medical Center)
Review Date: Unknown
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