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Sonja-verena Albers - One of the best experts on this subject based on the ideXlab platform.
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taxis in Archaea
Emerging Topics in Life Sciences, 2018Co-Authors: Tessa E F Quax, Sonja-verena Albers, Friedhelm PfeifferAbstract:Microorganisms can move towards favorable growth conditions as a response to environmental stimuli. This process requires a motility structure and a system to direct the movement. For swimming motility, Archaea employ a rotating filament, the archaellum. This Archaea-specific structure is functionally equivalent, but structurally different, from the bacterial flagellum. To control the directionality of movement, some Archaea make use of the chemotaxis system, which is used for the same purpose by bacteria. Over the past decades, chemotaxis has been studied in detail in several model bacteria. In contrast, Archaeal chemotaxis is much less explored and largely restricted to analyses in halophilic Archaea. In this review, we summarize the available information on Archaeal taxis. We conclude that Archaeal chemotaxis proteins function similarly as their bacterial counterparts. However, because the motility structures are fundamentally different, an Archaea-specific docking mechanism is required, for which initial experimental data have only recently been obtained.
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Archaeal biofilm formation
Nature Reviews Microbiology, 2018Co-Authors: Marleen Wolferen, Alvaro Orell, Sonja-verena AlbersAbstract:Archaea have been found in biofilms in a variety of habitats. In this Review, Albers and colleagues explore the different stages of Archaeal biofilm development and highlight the similarities and differences between Archaea and bacteria. They also consider their role in different industrial processes. Biofilms are structured and organized communities of microorganisms that represent one of the most successful forms of life on Earth. Bacterial biofilms have been studied in great detail, and many molecular details are known about the processes that govern bacterial biofilm formation, however, Archaea are ubiquitous in almost all habitats on Earth and can also form biofilms. In recent years, insights have been gained into the development of Archaeal biofilms, how Archaea communicate to form biofilms and how the switch from a free-living lifestyle to a sessile lifestyle is regulated. In this Review, we explore the different stages of Archaeal biofilm development and highlight similarities and differences between Archaea and bacteria on a molecular level. We also consider the role of Archaeal biofilms in industry and their use in different industrial processes.
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Versatile cell surface structures of Archaea.
Molecular Microbiology, 2017Co-Authors: Paushali Chaudhury, Tessa E F Quax, Sonja-verena AlbersAbstract:Archaea are ubiquitously present in nature and colonize environments with broadly varying growth conditions. Several surface appendages support their colonization of new habitats. A hallmark of Archaea seems to be the high abundance of type IV pili (T4P). However, some unique non T4 filaments are present in a number of Archaeal species. Archaeal surface structures can mediate different processes such as cellular surface adhesion, DNA exchange, motility and biofilm formation and represent an initial attachment site for infecting viruses. In addition to the functionally characterized Archaeal T4P, Archaeal genomes encode a large number of T4P components that might form yet undiscovered surface structures with novel functions. In this review, we summarize recent advancement in structural and functional characterizations of known Archaeal surface structures and highlight the diverse processes in which they play a role.
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eLS - Archaeal Cell Walls
eLS, 2014Co-Authors: Benjamin H. Meyer, Sonja-verena AlbersAbstract:Next to the bacterial and eukaryal domains, Archaea form the third domain of life. One major difference to bacteria is the composition of the cell wall. The cell wall of most Archaea is formed by a proteinaceous surface (S-) layer. S-layer proteins have the intrinsic ability to form two-dimensional crystals, which can have an oblique (p2), square (p4) or hexagonal (p3 or p6) symmetry. All currently studied Archaeal S-layer proteins were found to be modified by the attachment of N-linked and, in some cases, additionally by O-linked glycans. Next to the S-layer (glyco-)proteins, sugar polymers like pseudomurein, methanochondroitin or heteropolysaccharides are also found in Archaeal cell walls. These polymeric cell wall structures can either form the sole cell wall structure or be supported by an additional S-layer cover. A few Archaeal species even completely lack a cell wall. Key Concepts: Archaeal cell envelopes lack murein or a lipopolysaccharide (LPS)-containing outer membrane. Most Archaea posses a glycosylated proteinaceous surface layer (S-layer) as their sole cell wall structure. In some Archaea, the cell wall is composed of glycan polymers, like glutaminylglycan, heterosaccharide, methanochondroitin or pseudomurein. Keywords: Archaea; cell envelope; glutaminylglycan; glycosylation; heteropolysaccharide; methanochondroitin; pseudomurein; S-layer (glyco-)protein
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Archaeal type iv pilus like structures evolutionarily conserved prokaryotic surface organelles
Current Opinion in Microbiology, 2011Co-Authors: Mecky Pohlschrode, Abhrajyoti Ghosh, Manuela Tripepi, Sonja-verena AlbersAbstract:In both bacteria and Archaea, the biosynthesis of type IV pilus-related structures involves a set of core components, including a prepilin peptidase that specifically processes precursors of pilin-like proteins. Although in silico analyses showed that most sequenced Archaeal genomes encode predicted pilins and conserved pilus biosynthesis components, recent in vivo analyses of Archaeal pili in genetically tractable crenArchaea and euryArchaea revealed Archaea-specific type IV pilus functions and biosynthesis components. Studies in a variety of Archaeal species will reveal which type IV pilus-like structures are common in Archaea and which are limited to certain species within this domain. The insights gleaned from these studies may also elucidate the roles played by these types of structures in adapting to specific environments.
Wf Doolittle - One of the best experts on this subject based on the ideXlab platform.
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Phylogenetic analyses of two ``Archaeal'' genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria
Molecular Biology and Evolution, 2001Co-Authors: Cl Nesbo, Stéphane L'haridon, Ko Stetter, Wf DoolittleAbstract:The genome sequence of Thermotoga maritima revealed that 24% of its open reading frames (ORFs) showed the highest similarity scores to Archaeal genes in BLAST analyses. Here we screened 16 strains from the genus Thermotoga and other related Thermotogales for the occurrence of two of these ``Archaeal'' genes: the gene encoding the large subunit of glutamate synthase (gltB) and the mpo-inositol 1P synthase gene (ino1). Both genes were restricted to the Thermotoga species within the Thermotogales. The distribution of the two genes, along with results from phylogenetic analyses, showed that they were acquired from Archaea during the divergence of the Thermotogales. Database searches revealed that three other bacteria-Dehalococcoides ethenogenes, Sinorhizobium meliloti, and Clostridium difficile-possess Archaeal-type gltBs, and the phylogenetic analyses confirmed at least two lateral gene transfer (LGT) events between Bacteria and Archaea. These LGT events were also strongly supported by gene structure data, as the three domains in bacterial-type gltB are homologous to three independent ORFs in Archaea and Bacteria with Archaeal-type gltBs. The ino1 gene has a scattered distribution among Bacteria, and apart from the Thermotoga strains it is found only in Aquifex aeolicus, D. ethenogenes, and some high-G + C Gram-positive bacteria. Phylogenetic analysis of the ino1 sequences revealed three highly supported prokaryotic clades, all containing a mixture of Archaeal and bacterial sequences, and suggested that all bacterial ino1 genes had been recruited from Archaeal donors. The Thermotoga strains and A. aeolicus acquired this gene independently from different Archaeal species. Although transfer of genes from hyperthermophilic Archaea may have facilitated the evolution of bacterial hyperthermophily, between-domain transfers also affect mesophilic species. For hyperthermophiles, we hypothesize that LGT may be as much a consequence as the cause of adaptation to hyperthermophily.
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Bacterial origin for the isoprenoid biosynthesis enzyme HMG-CoA reductase of the Archaeal orders thermoplasmatales and archaeoglobales
Molecular Biology and Evolution, 2001Co-Authors: Y Boucher, Stéphane L'haridon, Ko Stetter, H Huber, Wf DoolittleAbstract:The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMG-CoA reductase or HMGR) fulfills an essential role in Archaea, as it is required for the synthesis of isoprenoid ethers, the main component of Archaeal cell membranes. There are two clearly homologous but structurally different classes of the enzyme, one found mainly in eukaryotes and Archaea (class 1), and the other found in bacteria (class 2). This feature facilitated the identification of several cases of interdomain lateral gene transfer (LGT), in particular, the bacterial origin for the HMGR gene from the archaeon Archaeoglobus fulgidus. In order to investigate if this LGT event was recent and limited in its scope of had a broad and long-term impact on the recipient and its related lineages, the HMGR gene was amplified and sequenced From a variety of Archaea. The survey covered close relatives of A. fulgidus, the only archaeon known prior to this study to possess a bacterial-like HMGR; representatives of each main euryArchaeal group were also inspected. All culturable members of the Archaeal group Archaeoglobales were found to display an HMGR very similar to the enzyme of the bacterium Pseudomonas mevalonii. Surprisingly, two species of the genus Thermoplasma also harbor an HMGR of bacterial origin highly similar to the enzymes found in the Archaeoglobales. Phylogenetic analyses of the HMGR gene and comparisons to reference phylogenies from other genes confirm a common bacterial origin for the HMGRs of Thermoplasmatales and Archaeoglobales. The most likely explanation of these results includes an initial bacteria-to-Archaea transfer, followed by a another event between Archaea. Their presence in two divergent Archaeal lineages suggests an important adaptive role for these laterally transferred genes.
Christa Schleper - One of the best experts on this subject based on the ideXlab platform.
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Meet the relatives of our cellular ancestor
Nature, 2020Co-Authors: Christa Schleper, Filipa L. SousaAbstract:Microorganisms called Asgard Archaea have been grown in the laboratory. Microorganisms related to lineages of the Asgard Archaea group are thought to have evolved into complex eukaryotic cells. Now the first Asgard Archaeal species to be grown in the laboratory reveals its metabolism and cell biology.
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metagenomics of kamchatkan hot spring filaments reveal two new major hyper thermophilic lineages related to thaumarchaeota
Research in Microbiology, 2013Co-Authors: Laila J Reigstad, Anja Spang, Christa Schleper, Anders Lanzen, Thomas Weinmaier, Thomas Rattei, Celine BrochierarmanetAbstract:Based on phylogenetic analyses and gene distribution patterns of a few complete genomes, a new distinct phylum within the Archaea, the Thaumarchaeota, has recently been proposed. Here we present analyses of six Archaeal fosmid sequences derived from a microbial hot spring community in Kamchatka. The phylogenetic analysis of informational components (ribosomal RNAs and proteins) reveals two major (hyper-)thermophilic clades (“Hot Thaumarchaeota-related Clade” 1 and 2, HTC1 and HTC2) related to Thaumarchaeota, representing either deep branches of this phylum or a new Archaeal phylum and provides information regarding the ancient evolution of Archaea and their evolutionary links with Eukaryotes.
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genomic studies of uncultivated Archaea
Nature Reviews Microbiology, 2005Co-Authors: Christa Schleper, German Jurgens, Melanie JonuscheitAbstract:Archaea represent a considerable fraction of the prokaryotic world in marine and terrestrial ecosystems, indicating that organisms from this domain might have a large impact on global energy cycles. However, many novel Archaeal lineages that have been detected by molecular phylogenetic approaches have remained elusive because no laboratory-cultivated strains are available. Environmental genomic analyses have recently provided clues about the potential metabolic strategies of several of the uncultivated and abundant Archaeal species, including non-thermophilic terrestrial and marine crenarchaeota and methanotrophic euryarchaeota. These initial studies of natural Archaeal populations also revealed an unexpected degree of genomic variation that indicates considerable heterogeneity among Archaeal strains. Here, we review genomic studies of uncultivated Archaea within a framework of the phylogenetic diversity and ecological distribution of this domain.
Mecky Pohlschröder - One of the best experts on this subject based on the ideXlab platform.
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Diversity of Archaeal type IV pilin-like structures
Extremophiles, 2009Co-Authors: Sonja-verena Albers, Mecky PohlschröderAbstract:Bacterial type IV pili perform important functions in such disparate biological processes as surface adhesion, cell–cell interactions, autoaggregation, conjugation, and twitching motility. Unlike bacteria, Archaea use a type IV pilus related structure to drive swimming motility. While this unique flagellum is the best-studied example of an Archaeal IV pilus-like structure, recent in silico, in vivo and structural analyses have revealed a highly diverse set of Archaeal non-flagellar type IV pilus-like structures. Accumulating evidence suggests that these structures play important diverse roles in Archaea.
Eugene V. Koonin - One of the best experts on this subject based on the ideXlab platform.
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Virus-borne mini-CRISPR arrays are involved in interviral conflicts
Nature Communications, 2019Co-Authors: Sofia Medvedeva, Konstantin Severinov, David Prangishvili, Ying Liu, Eugene V. Koonin, Mart KrupovicAbstract:CRISPR-Cas immunity is at the forefront of antivirus defense in bacteria and Archaea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRISPR arrays. Here, we perform deep sequencing of the CRISPRome—all spacers contained in a microbiome—associated with hyperthermophilic Archaea of the order Sulfolobales recovered directly from an environmental sample and from enrichment cultures established in the laboratory. The 25 million CRISPR spacers sequenced from a single sampling site dwarf the diversity of spacers from all available Sulfolobales isolates and display complex temporal dynamics. Comparison of closely related virus strains shows that CRISPR targeting drives virus genome evolution. Furthermore, we show that some Archaeal viruses carry mini-CRISPR arrays with 1–2 spacers and preceded by leader sequences but devoid of cas genes. Closely related viruses present in the same population carry spacers against each other. Targeting by these virus-borne spacers represents a distinct mechanism of heterotypic superinfection exclusion and appears to promote Archaeal virus speciation.Here, the authors investigate the diversity and dynamics of the CRISPRome in the hyperthermophilic Archaea of the order Sulfolobales , and find the most abundant spacers to come from mini-CRISPR arrays of Archaeal viruses, which might represent a strategy for superinfection exclusion and promotion of Archaeal virus speciation.
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phyletic distribution and lineage specific domain architectures of Archaeal two component signal transduction systems
Journal of Bacteriology, 2017Co-Authors: Michael Y Galperin, Kira S Makarova, Yuri I Wolf, Eugene V. KooninAbstract:ABSTRACT The two-component signal transduction (TCS) machinery is a key mechanism of sensing environmental changes in the prokaryotic world. TCS systems have been characterized thoroughly in bacteria but to a much lesser extent in Archaea. Here, we provide an updated census of more than 2,000 histidine kinases and response regulators encoded in 218 complete Archaeal genomes, as well as unfinished genomes available from metagenomic data. We describe the domain architectures of the Archaeal TCS components, including several novel output domains, and discuss the evolution of the Archaeal TCS machinery. The distribution of TCS systems in Archaea is strongly biased, with high levels of abundance in haloArchaea and thaumArchaea but none detected in the sequenced genomes from the phyla Crenarchaeota, Nanoarchaeota, and Korarchaeota. The Archaeal sensor histidine kinases are generally similar to their well-studied bacterial counterparts but are often located in the cytoplasm and carry multiple PAS and/or GAF domains. In contrast, Archaeal response regulators differ dramatically from the bacterial ones. Most Archaeal genomes do not encode any of the major classes of bacterial response regulators, such as the DNA-binding transcriptional regulators of the OmpR/PhoB, NarL/FixJ, NtrC, AgrA/LytR, and ActR/PrrA families and the response regulators with GGDEF and/or EAL output domains. Instead, Archaea encode multiple copies of response regulators containing either the stand-alone receiver (REC) domain or combinations of REC with PAS and/or GAF domains. Therefore, the prevailing mechanism of Archaeal TCS signaling appears to be via a variety of protein-protein interactions, rather than direct transcriptional regulation. IMPORTANCE Although the Archaea represent a separate domain of life, their signaling systems have been assumed to be closely similar to the bacterial ones. A study of the domain architectures of the Archaeal two-component signal transduction (TCS) machinery revealed an overall similarity of Archaeal and bacterial sensory modules but substantial differences in the signal output modules. The prevailing mechanism of Archaeal TCS signaling appears to involve various protein-protein interactions rather than direct transcription regulation. The complete list of histidine kinases and response regulators encoded in the analyzed Archaeal genomes is available online at http://www.ncbi.nlm.nih.gov/Complete_Genomes/TCSArchaea.html.
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Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer
Biology Direct, 2012Co-Authors: Yuri I Wolf, Kira S Makarova, Natalya Yutin, Eugene V. KooninAbstract:Background Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. Results The updated version of the arCOG database incorporates 91% of the pangenome of 120 Archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of Archaeal ancestral forms and gene gain and loss events in Archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant Archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all Archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria , acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major ‘highways’ of horizontal gene transfer. Conclusions The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new Archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of Archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time. Reviewers This article was reviewed by (for complete reviews see the Reviewers’ Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).
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The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all Archaea and eukaryotes
Biology Direct, 2012Co-Authors: Kira S Makarova, Eugene V. Koonin, Zvi KelmanAbstract:Background In eukaryotes, the CMG (CDC45, MCM, GINS) complex containing the replicative helicase MCM is a key player in DNA replication. Archaeal homologs of the eukaryotic MCM and GINS proteins have been identified but until recently no homolog of the CDC45 protein was known. Two recent developments, namely the discovery of Archaeal G INS- a ssociated n uclease (GAN) that belongs to the RecJ family of the DHH hydrolase superfamily and the demonstration of homology between the DHH domains of CDC45 and RecJ, show that at least some Archaea possess a full complement of homologs of the CMG complex subunits. Here we present the results of in-depth phylogenomic analysis of RecJ homologs in Archaea. Results We confirm and extend the recent hypothesis that CDC45 is the eukaryotic ortholog of the bacterial and Archaeal RecJ family nucleases. At least one RecJ homolog was identified in all sequenced Archaeal genomes, with the single exception of Caldivirga maquilingensis . These proteins include previously unnoticed remote RecJ homologs with inactivated DHH domain in Thermoproteales . Combined with phylogenetic tree reconstruction of diverse eukaryotic, Archaeal and bacterial DHH subfamilies, this analysis yields a complex scenario of RecJ family evolution in Archaea which includes independent inactivation of the nuclease domain in Crenarchaeota and Halobacteria, and loss of this domain in Methanococcales. Conclusions The Archaeal complex of a CDC45/RecJ homolog, MCM and GINS is homologous and most likely functionally analogous to the eukaryotic CMG complex, and appears to be a key component of the DNA replication machinery in all Archaea. It is inferred that the last common archaeo-eukaryotic ancestor encoded a CMG complex that contained an active nuclease of the RecJ family. The inactivated RecJ homologs in several Archaeal lineages most likely are dedicated structural components of replication complexes. Reviewers This article was reviewed by Prof. Patrick Forterre, Dr. Stephen John Aves (nominated by Dr. Purificacion Lopez-Garcia) and Prof. Martijn Huynen. For the full reviews, see the Reviewers' Comments section.
