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1
Kellner, Siri, Anja Spang, Pierre Offre, Gergely J. Szöllősi, Celine Petitjean, and Tom A. Williams. "Genome size evolution in the Archaea." Emerging Topics in Life Sciences 2, no. 4 (November 14, 2018): 595–605. http://dx.doi.org/10.1042/etls20180021.
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What determines variation in genome size, gene content and genetic diversity at the broadest scales across the tree of life? Much of the existing work contrasts eukaryotes with prokaryotes, the latter represented mainly by Bacteria. But any general theory of genome evolution must also account for the Archaea, a diverse and ecologically important group of prokaryotes that represent one of the primary domains of cellular life. Here, we survey the extant diversity of Bacteria and Archaea, and ask whether the general principles of genome evolution deduced from the study of Bacteria and eukaryotes also apply to the archaeal domain. Although Bacteria and Archaea share a common prokaryotic genome architecture, the extant diversity of Bacteria appears to be much higher than that of Archaea. Compared with Archaea, Bacteria also show much greater genome-level specialisation to specific ecological niches, including parasitism and endosymbiosis. The reasons for these differences in long-term diversification rates are unclear, but might be related to fundamental differences in informational processing machineries and cell biological features that may favour archaeal diversification in harsher or more energy-limited environments. Finally, phylogenomic analyses suggest that the first Archaea were anaerobic autotrophs that evolved on the early Earth.
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Ngcobo, Phelelani Erick, Bridget Valeria Zinhle Nkosi, Wanping Chen, David R. Nelson, and Khajamohiddin Syed. "Evolution of Cytochrome P450 Enzymes and Their Redox Partners in Archaea." International Journal of Molecular Sciences 24, no. 4 (February 19, 2023): 4161. http://dx.doi.org/10.3390/ijms24044161.
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Cytochrome P450 monooxygenases (CYPs/P450s) and their redox partners, ferredoxins, are ubiquitous in organisms. P450s have been studied in biology for over six decades owing to their distinct catalytic activities, including their role in drug metabolism. Ferredoxins are ancient proteins involved in oxidation-reduction reactions, such as transferring electrons to P450s. The evolution and diversification of P450s in various organisms have received little attention and no information is available for archaea. This study is aimed at addressing this research gap. Genome-wide analysis revealed 1204 P450s belonging to 34 P450 families and 112 P450 subfamilies, where some families and subfamilies are expanded in archaea. We also identified 353 ferredoxins belonging to the four types 2Fe-2S, 3Fe-4S, 7Fe-4S and 2[4Fe-4S] in 40 archaeal species. We found that bacteria and archaea shared the CYP109, CYP147 and CYP197 families, as well as several ferredoxin subtypes, and that these genes are co-present on archaeal plasmids and chromosomes, implying the plasmid-mediated lateral transfer of these genes from bacteria to archaea. The absence of ferredoxins and ferredoxin reductases in the P450 operons suggests that the lateral transfer of these genes is independent. We present different scenarios for the evolution and diversification of P450s and ferredoxins in archaea. Based on the phylogenetic analysis and high affinity to diverged P450s, we propose that archaeal P450s could have diverged from CYP109, CYP147 and CYP197. Based on this study’s results, we propose that all archaeal P450s are bacterial in origin and that the original archaea had no P450s.
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Rafiq, Muhammad, Noor Hassan, Maliha Rehman, Muhammad Hayat, Gullasht Nadeem, Farwa Hassan, Naveed Iqbal, et al. "Challenges and Approaches of Culturing the Unculturable Archaea." Biology 12, no. 12 (December 7, 2023): 1499. http://dx.doi.org/10.3390/biology12121499.
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Since Carl Woese’s discovery of archaea as a third domain of life, numerous archaeal species have been discovered, yet archaeal diversity is poorly characterized. Culturing archaea is complicated, but several queries about archaeal cell biology, evolution, physiology, and diversity need to be solved by culturing and culture-dependent techniques. Increasing interest in demand for innovative culturing methods has led to various technological and methodological advances. The current review explains frequent hurdles hindering uncultured archaea isolation and discusses features for more archaeal cultivation. This review also discusses successful strategies and available media for archaeal culturing, which might be helpful for future culturing practices.
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Gribaldo, Simonetta, and Celine Brochier-Armanet. "The origin and evolution of Archaea: a state of the art." Philosophical Transactions of the Royal Society B: Biological Sciences 361, no. 1470 (May 9, 2006): 1007–22. http://dx.doi.org/10.1098/rstb.2006.1841.
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Environmental surveys indicate that the Archaea are diverse and abundant not only in extreme environments, but also in soil, oceans and freshwater, where they may fulfil a key role in the biogeochemical cycles of the planet. Archaea display unique capacities, such as methanogenesis and survival at temperatures higher than 90 °C, that make them crucial for understanding the nature of the biota of early Earth. Molecular, genomics and phylogenetics data strengthen Woese's definition of Archaea as a third domain of life in addition to Bacteria and Eukarya. Phylogenomics analyses of the components of different molecular systems are highlighting a core of mainly vertically inherited genes in Archaea. This allows recovering a globally well-resolved picture of archaeal evolution, as opposed to what is observed for Bacteria and Eukarya. This may be due to the fact that no rapid divergence occurred at the emergence of present-day archaeal lineages. This phylogeny supports a hyperthermophilic and non-methanogenic ancestor to present-day archaeal lineages, and a profound divergence between two major phyla, the Crenarchaeota and the Euryarchaeota, that may not have an equivalent in the other two domains of life. Nanoarchaea may not represent a third and ancestral archaeal phylum, but a fast-evolving euryarchaeal lineage. Methanogenesis seems to have appeared only once and early in the evolution of Euryarchaeota. Filling up this picture of archaeal evolution by adding presently uncultivated species, and placing it back in geological time remain two essential goals for the future.
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Williams, Tom A., Gergely J. Szöllősi, Anja Spang, Peter G. Foster, Sarah E. Heaps, Bastien Boussau, Thijs J. G. Ettema, and T. Martin Embley. "Integrative modeling of gene and genome evolution roots the archaeal tree of life." Proceedings of the National Academy of Sciences 114, no. 23 (May 22, 2017): E4602—E4611. http://dx.doi.org/10.1073/pnas.1618463114.
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A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood–Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.
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Forterre, Patrick. "The Common Ancestor of Archaea and Eukarya Was Not an Archaeon." Archaea 2013 (2013): 1–18. http://dx.doi.org/10.1155/2013/372396.
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It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.
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VERHEES, Corné H., Servé W. M. KENGEN, Judith E. TUININGA, Gerrit J. SCHUT, Michael W. W. ADAMS, Willem M. de VOS, and John van der OOST. "The unique features of glycolytic pathways in Archaea." Biochemical Journal 375, no. 2 (October 15, 2003): 231–46. http://dx.doi.org/10.1042/bj20021472.
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An early divergence in evolution has resulted in two prokaryotic domains, the Bacteria and the Archaea. Whereas the central metabolic routes of bacteria and eukaryotes are generally well-conserved, variant pathways have developed in Archaea involving several novel enzymes with a distinct control. A spectacular example of convergent evolution concerns the glucose-degrading pathways of saccharolytic archaea. The identification, characterization and comparison of the glycolytic enzymes of a variety of phylogenetic lineages have revealed a mosaic of canonical and novel enzymes in the archaeal variants of the Embden–Meyerhof and the Entner–Doudoroff pathways. By means of integrating results from biochemical and genetic studies with recently obtained comparative and functional genomics data, the structure and function of the archaeal glycolytic routes, the participating enzymes and their regulation are re-evaluated.
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Zhu, Pengfei, Jialin Hou, Yixuan Xiong, Ruize Xie, Yinzhao Wang, and Fengping Wang. "Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis." Microorganisms 12, no. 4 (March 30, 2024): 707. http://dx.doi.org/10.3390/microorganisms12040707.
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Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA’s enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.
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Tamarit, Daniel, Eva F. Caceres, Mart Krupovic, Reindert Nijland, Laura Eme, Nicholas P. Robinson, and Thijs J. G. Ettema. "A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses." Nature Microbiology 7, no. 7 (June 27, 2022): 948–52. http://dx.doi.org/10.1038/s41564-022-01122-y.
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AbstractAsgard archaea have recently been identified as the closest archaeal relatives of eukaryotes. Their ecology, and particularly their virome, remain enigmatic. We reassembled and closed the chromosome of Candidatus Odinarchaeum yellowstonii LCB_4, through long-range PCR, revealing CRISPR spacers targeting viral contigs. We found related viruses in the genomes of diverse prokaryotes from geothermal environments, including other Asgard archaea. These viruses open research avenues into the ecology and evolution of Asgard archaea.
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Fouqueau, Thomas, Fabian Blombach, Gwenny Cackett, Alice E. Carty, Dorota M. Matelska, Sapir Ofer, Simona Pilotto, Duy Khanh Phung, and Finn Werner. "The cutting edge of archaeal transcription." Emerging Topics in Life Sciences 2, no. 4 (November 14, 2018): 517–33. http://dx.doi.org/10.1042/etls20180014.
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The archaeal RNA polymerase (RNAP) is a double-psi β-barrel enzyme closely related to eukaryotic RNAPII in terms of subunit composition and architecture, promoter elements and basal transcription factors required for the initiation and elongation phase of transcription. Understanding archaeal transcription is, therefore, key to delineate the universally conserved fundamental mechanisms of transcription as well as the evolution of the archaeo-eukaryotic transcription machineries. The dynamic interplay between RNAP subunits, transcription factors and nucleic acids dictates the activity of RNAP and ultimately gene expression. This review focusses on recent progress in our understanding of (i) the structure, function and molecular mechanisms of known and less characterized factors including Elf1 (Elongation factor 1), NusA (N-utilization substance A), TFS4, RIP and Eta, and (ii) their evolution and phylogenetic distribution across the expanding tree of Archaea.
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van Passel, M. W. J., C. S. Smillie, and H. Ochman. "Gene decay in archaea." Archaea 2, no. 2 (2007): 137–43. http://dx.doi.org/10.1155/2007/165723.
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The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.
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Lee, Dong-Hun, Jung-Hyun Kim, Yung Mi Lee, Alina Stadnitskaia, Young Keun Jin, Helge Niemann, Young-Gyun Kim, and Kyung-Hoon Shin. "Biogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort Sea." Biogeosciences 15, no. 24 (December 20, 2018): 7419–33. http://dx.doi.org/10.5194/bg-15-7419-2018.
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Abstract. In this study, we report lipid biomarker patterns and phylogenetic identities of key microbial communities mediating anaerobic oxidation of methane (AOM) in active mud volcanoes (MVs) on the continental slope of the Canadian Beaufort Sea. The carbon isotopic compositions (δ13C) of sn-2- and sn-3-hydroxyarchaeol showed the highly 13C-depleted values (−114 ‰ to −82 ‰) associated with a steep depletion in sulfate concentrations within 0.7 m of sediment depths. This suggested the presence of methanotrophic archaea involved in sulfate-dependent AOM, albeit in a small amount. The ratio of sn-2-hydroxyarchaeol to archaeol (> 1) and operational taxonomic units (OTUs) indicated that the anaerobic methanotrophic archaea (ANME) clades ANME-2c and ANME-3 were involved in AOM. Higher δ13C values of archaeol and biphytanes (BPs; -55.2±10.0 ‰ and -39.3±13.0 ‰, respectively) suggested that archaeal communities were also assimilating AOM-derived inorganic carbon. Furthermore, the distinct distribution patterns of methanotrophs in the three MVs appears to be associated with varying intensities of ascending gas fluids. Consequently, our results suggest that the niche diversification of active mud volcanoes has shaped distinct archaeal communities that play important roles in AOM in the Beaufort Sea.
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Nishida, Hiromi. "Comparative Analyses of Base Compositions, DNA Sizes, and Dinucleotide Frequency Profiles in Archaeal and Bacterial Chromosomes and Plasmids." International Journal of Evolutionary Biology 2012 (March 26, 2012): 1–5. http://dx.doi.org/10.1155/2012/342482.
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In the present paper, I compared guanine-cytosine (GC) contents, DNA sizes, and dinucleotide frequency profiles in 109 archaeal chromosomes, 59 archaeal plasmids, 1379 bacterial chromosomes, and 854 bacterial plasmids. In more than 80% of archaeal and bacterial plasmids, the GC content was lower than that of the host chromosome. Furthermore, most of the differences in GC content found between a plasmid and its host chromosome were less than 10%, and the GC content in plasmids and host chromosomes was highly correlated (Pearson’s correlation coefficient in bacteria and 0.917 in archaea). These results support the hypothesis that horizontal gene transfers have occurred frequently via plasmid distribution during evolution. GC content and chromosome size were more highly correlated in bacteria () than in archaea (). Interestingly, there was a tendency for archaea with plasmids to have higher GC content in the chromosome and plasmid than those without plasmids. Thus, the dinucleotide frequency profile of the archaeal plasmids has a bias toward high GC content.
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Long, Xi, Hong Xue, and J. Tze-Fei Wong. "Descent of Bacteria and Eukarya From an Archaeal Root of Life." Evolutionary Bioinformatics 16 (January 2020): 117693432090826. http://dx.doi.org/10.1177/1176934320908267.
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The 3 biological domains delineated based on small subunit ribosomal RNAs (SSU rRNAs) are confronted by uncertainties regarding the relationship between Archaea and Bacteria, and the origin of Eukarya. The similarities between the paralogous valyl-tRNA and isoleucyl-tRNA synthetases in 5398 species estimated by BLASTP, which decreased from Archaea to Bacteria and further to Eukarya, were consistent with vertical gene transmission from an archaeal root of life close to Methanopyrus kandleri through a Primitive Archaea Cluster to an Ancestral Bacteria Cluster, and to Eukarya. The predominant similarities of the ribosomal proteins (rProts) of eukaryotes toward archaeal rProts relative to bacterial rProts established that an archaeal parent rather than a bacterial parent underwent genome merger with bacteria to generate eukaryotes with mitochondria. Eukaryogenesis benefited from the predominantly archaeal accelerated gene adoption (AGA) phenotype pertaining to horizontally transferred genes from other prokaryotes and expedited genome evolution via both gene-content mutations and nucleotidyl mutations. Archaeons endowed with substantial AGA activity were accordingly favored as candidate archaeal parents. Based on the top similarity bitscores displayed by their proteomes toward the eukaryotic proteomes of Giardia and Trichomonas, and high AGA activity, the Aciduliprofundum archaea were identified as leading candidates of the archaeal parent. The Asgard archaeons and a number of bacterial species were among the foremost potential contributors of eukaryotic-like proteins to Eukarya.
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Forterre, Patrick, Celine Brochier, and Hervé Philippe. "Evolution of the Archaea." Theoretical Population Biology 61, no. 4 (June 2002): 409–22. http://dx.doi.org/10.1006/tpbi.2002.1592.
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Wang, Yinzhao, Gunter Wegener, Tom A. Williams, Ruize Xie, Jialin Hou, Chen Tian, Yu Zhang, Fengping Wang, and Xiang Xiao. "A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism." Science Advances 7, no. 27 (July 2021): eabj1453. http://dx.doi.org/10.1126/sciadv.abj1453.
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Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. However, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we present evidence that methylotrophic methanogenesis was the ancestral form of this metabolism. Carbon dioxide–reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Anaerobic multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short-chain or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca.) Bathyarchaeia, Ca. Lokiarchaeia, Ca. Hadarchaeia, and the methanogenic Ca. Methanoliparia.
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De Lise, Federica, Roberta Iacono, Marco Moracci, Andrea Strazzulli, and Beatrice Cobucci-Ponzano. "Archaea as a Model System for Molecular Biology and Biotechnology." Biomolecules 13, no. 1 (January 6, 2023): 114. http://dx.doi.org/10.3390/biom13010114.
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Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes’ functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.
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Rother, Michael, and Joseph A. Krzycki. "Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea." Archaea 2010 (2010): 1–14. http://dx.doi.org/10.1155/2010/453642.
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Methanogenic archaea are a group of strictly anaerobic microorganisms characterized by their strict dependence on the process of methanogenesis for energy conservation. Among the archaea, they are also the only known group synthesizing proteins containing selenocysteine or pyrrolysine. All but one of the known archaeal pyrrolysine-containing and all but two of the confirmed archaeal selenocysteine-containing protein are involved in methanogenesis. Synthesis of these proteins proceeds through suppression of translational stop codons but otherwise the two systems are fundamentally different. This paper highlights these differences and summarizes the recent developments in selenocysteine- and pyrrolysine-related research on archaea and aims to put this knowledge into the context of their unique energy metabolism.
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Brueckner, Julia, and William F. Martin. "Bacterial Genes Outnumber Archaeal Genes in Eukaryotic Genomes." Genome Biology and Evolution 12, no. 4 (March 6, 2020): 282–92. http://dx.doi.org/10.1093/gbe/evaa047.
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Abstract Eukaryotes are typically depicted as descendants of archaea, but their genomes are evolutionary chimeras with genes stemming from archaea and bacteria. Which prokaryotic heritage predominates? Here, we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups. By downsampling, we obtain estimates for the bacterial and archaeal proportions. Eukaryotic genomes possess a bacterial majority of genes. On average, the majority of bacterial genes is 56% overall, 53% in eukaryotes that never possessed plastids, and 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic lineage. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. Such adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.
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Béjà, Oded, Eugene V. Koonin, L. Aravind, Lance T. Taylor, Heidi Seitz, Jefferey L. Stein, Daniel C. Bensen, Robert A. Feldman, Ronald V. Swanson, and Edward F. DeLong. "Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces." Applied and Environmental Microbiology 68, no. 1 (January 2002): 335–45. http://dx.doi.org/10.1128/aem.68.1.335-345.2002.
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ABSTRACT Planktonic crenarchaeotes are present in high abundance in Antarctic winter surface waters, and they also make up a large proportion of total cell numbers throughout deep ocean waters. To better characterize these uncultivated marine crenarchaeotes, we analyzed large genome fragments from individuals recovered from a single Antarctic picoplankton population and compared them to those from a representative obtained from deeper waters of the temperate North Pacific. Sequencing and analysis of the entire DNA insert from one Antarctic marine archaeon (fosmid 74A4) revealed differences in genome structure and content between Antarctic surface water and temperate deepwater archaea. Analysis of the predicted gene products encoded by the 74A4 sequence and those derived from a temperate, deepwater planktonic crenarchaeote (fosmid 4B7) revealed many typical archaeal proteins but also several proteins that so far have not been detected in archaea. The unique fraction of marine archaeal genes included, among others, those for a predicted RNA-binding protein of the bacterial cold shock family and a eukaryote-type Zn finger protein. Comparison of closely related archaea originating from a single population revealed significant genomic divergence that was not evident from 16S rRNA sequence variation. The data suggest that considerable functional diversity may exist within single populations of coexisting microbial strains, even those with identical 16S rRNA sequences. Our results also demonstrate that genomic approaches can provide high-resolution information relevant to microbial population genetics, ecology, and evolution, even for microbes that have not yet been cultivated.
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Frohn, Béla P., Tobias Härtel, Jürgen Cox, and Petra Schwille. "Tracing back variations in archaeal ESCRT-based cell division to protein domain architectures." PLOS ONE 17, no. 3 (March 31, 2022): e0266395. http://dx.doi.org/10.1371/journal.pone.0266395.
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The Endosomal Sorting Complex Required for Transport (ESCRT) system is a multi-protein machinery that is involved in cell division of both Eukaryotes and Archaea. This spread across domains of life suggests that a precursor ESCRT machinery existed already at an evolutionary early stage of life, making it a promising candidate for the (re)construction of a minimal cell division machinery. There are, however, only few experimental data about ESCRT machineries in Archaea, due to high technical challenges in cultivation and microscopy. Here, we analyse the proteins of ESCRT machineries in archaea bioinformatically on a protein domain level, to enable mechanistical comparison without such challenging experiments. First, we infer that there are at least three different cell division mechanisms utilizing ESCRT proteins in archaea, probably similar in their constriction mechanisms but different in membrane tethering. Second, we show that ESCRT proteins in the archaeal super-phylum Asgard are highly similar to eukaryotic ESCRT proteins, strengthening the recently developed idea that all Eukaryotes descended from archaea. Third, we reconstruct a plausible evolutionary development of ESCRT machineries and suggest that a simple ESCRT-based constriction machinery existed in the last archaeal common ancestor. These findings not only give very interesting insights into the likely evolution of cell division in Archaea and Eukaryotes, but also offer new research avenues by suggesting hypothesis-driven experiments for both, cell biology and bottom-up synthetic biology.
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Schiraldi, Chiara, Mariateresa Giuliano, and Mario De Rosa. "Perspectives on biotechnological applications of archaea." Archaea 1, no. 2 (2002): 75–86. http://dx.doi.org/10.1155/2002/436561.
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Many archaea colonize extreme environments. They include hyperthermophiles, sulfur-metabolizing thermophiles, extreme halophiles and methanogens. Because extremophilic microorganisms have unusual properties, they are a potentially valuable resource in the development of novel biotechnological processes. Despite extensive research, however, there are few existing industrial applications of either archaeal biomass or archaeal enzymes. This review summarizes current knowledge about the biotechnological uses of archaea and archaeal enzymes with special attention to potential applications that are the subject of current experimental evaluation. Topics covered include cultivation methods, recent achievements in genomics, which are of key importance for the development of new biotechnological tools, and the application of wild-type biomasses, engineered microorganisms, enzymes and specific metabolites in particular bioprocesses of industrial interest.
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Lemmens, Liesbeth, Rani Baes, and Eveline Peeters. "Heat shock response in archaea." Emerging Topics in Life Sciences 2, no. 4 (November 22, 2018): 581–93. http://dx.doi.org/10.1042/etls20180024.
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An adequate response to a sudden temperature rise is crucial for cellular fitness and survival. While heat shock response (HSR) is well described in bacteria and eukaryotes, much less information is available for archaea, of which many characterized species are extremophiles thriving in habitats typified by large temperature gradients. Here, we describe known molecular aspects of archaeal heat shock proteins (HSPs) as key components of the protein homeostasis machinery and place this in a phylogenetic perspective with respect to bacterial and eukaryotic HSPs. Particular emphasis is placed on structure–function details of the archaeal thermosome, which is a major element of the HSR and of which subunit composition is altered in response to temperature changes. In contrast with the structural response, it is largely unclear how archaeal cells sense temperature fluctuations and which molecular mechanisms underlie the corresponding regulation. We frame this gap in knowledge by discussing emerging questions related to archaeal HSR and by proposing methodologies to address them. Additionally, as has been shown in bacteria and eukaryotes, HSR is expected to be relevant for the control of physiology and growth in various stress conditions beyond temperature stress. A better understanding of this essential cellular process in archaea will not only provide insights into the evolution of HSR and of its sensing and regulation, but also inspire the development of biotechnological applications, by enabling transfer of archaeal heat shock components to other biological systems and for the engineering of archaea as robust cell factories.
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Lang, Xiu-lu, Xiang Chen, Ai-ling Xu, Zhi-wen Song, Xin Wang, and He-bing Wang. "Variation of Bacterial and Archaeal Community Structures in a Full-Scale Constructed Wetlands for Wastewater Treatment." Archaea 2018 (October 16, 2018): 1–12. http://dx.doi.org/10.1155/2018/9319345.
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Microorganisms play important roles in the reduction of organic and inorganic pollutants in constructed wetlands used for the treatment of wastewater. However, the diversity and structure of microbial community in constructed wetland system remain poorly known. In this study, the Illumina MiSeq Sequencing of 16S rDNA was used to analyze the bacterial and archaeal microbial community structures of soil and water in a free surface flow constructed wetland, and the differences of bacterial communities and archaeal compositions between soil and water were compared. The results showed that the Proteobacteria were the dominant bacteria, making up 35.38%~48.66% relative abundance. Euryarchaeotic were the absolute dominant archaea in the influent sample with the relative abundance of 93.29%, while Thaumarchaeota showed dominance in the other three samples, making up 50.58%~75.70%. The relative abundances of different species showed great changes in bacteria and archaea, and the number of dominant species in bacteria was much higher than that in archaea. Compared to archaea, the community compositions of bacteria were more abundant and the changes were more significant. Meanwhile, bacteria and archaea had large differences in compositions between water and soil. The microbial richness in water was significantly higher than that in soil. Simultaneously, soil had a significant enrichment effect on some microbial flora.
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Ohene-Adjei, Samuel, Ronald M. Teather, Michael Ivan, and Robert J. Forster. "Postinoculation Protozoan Establishment and Association Patterns of Methanogenic Archaea in the Ovine Rumen." Applied and Environmental Microbiology 73, no. 14 (May 18, 2007): 4609–18. http://dx.doi.org/10.1128/aem.02687-06.
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ABSTRACT Association patterns between archaea and rumen protozoa were evaluated by analyzing archaeal 16S rRNA gene clone libraries from ovine rumen inoculated with different protozoa. Five protozoan inoculation treatments, fauna free (negative control), holotrich and cellulolytic protozoa, Isotricha and Dasytricha spp., Entodinium spp., and total fauna (type A) were tested. We used denaturing gradient gel electrophoresis, quantitative PCR, and phylogenetic analysis to evaluate the impact of the protozoan inoculants on the respective archaeal communities. Protozoan 18S ribosomal DNA clone libraries were also evaluated to monitor the protozoal population that was established by the inoculation. Phylogenetic analysis suggested that archaeal clones associated with the fauna-free, the Entodinium, and the type A inoculations clustered primarily with uncultured phylotypes. Polyplastron multivesiculatum was the predominant protozoan strain established by the holotrich and cellulolytic protozoan treatment, and this resulted predominantly in archaeal clones affiliated with uncultured and cultured methanogenic phylotypes (Methanosphaera stadtmanae, Methanobrevibacter ruminantium, and Methanobacterium bryantii). Furthermore, the Isotricha and Dasytricha inoculation treatment resulted primarily in archaeal clones affiliated with Methanobrevibacter smithii. This report provides the first assessment of the influence of protozoa on archaea within the rumen microbial community and provides evidence to suggest that different archaeal phylotypes associate with specific groups of protozoa. The observed patterns may be linked to the evolution of commensal and symbiotic relationships between archaea and protozoa in the ovine rumen environment. This report further underscores the prevalence and potential importance of a rather large group of uncultivated archaea in the ovine rumen, probably unrelated to known methanogens and undocumented in the bovine rumen.
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Oost, John van der. "How the Archaea live: Unique features of archaeal metabolism." Biochemist 26, no. 3 (June 1, 2004): 7–10. http://dx.doi.org/10.1042/bio02603007.
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A major scientific milestone was Carl Woese's discovery that the evolution of life on Earth has resulted in three distinct types of living systems:Archaea, Bacteria and Eukarya1. Organisms that belong to the eukaryal domain are clearly different from the former two because of their more complex structural organization: without exception, they possess intracellular compartments (at least a nucleus, often with additional organelles), and in addition they often have a multicellular composition. The Archaea and the Bacteria are prokaryotes: they have neither a nucleus nor any other cytoplasmic compartments, and are generally unicellular.
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Hartman, Hyman, Paola Favaretto, and Temple F. Smith. "The archaeal origins of the eukaryotic translational system." Archaea 2, no. 1 (2006): 1–9. http://dx.doi.org/10.1155/2006/431618.
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Among the 78 eukaryotic ribosomal proteins, eleven are specific to Eukarya, 33 are common only to Archaea and Eukarya and 34 are homologous (at least in part) to those of both Bacteria and Archaea. Several other translational proteins are common only to Eukarya and Archaea (e.g., IF2a, SRP19, etc.), whereas others are shared by the three phyla (e.g., EFTu/EF1A and SRP54).Although this and other analyses strongly support an archaeal origin for a substantial fraction of the eukaryotic translational machinery, especially the ribosomal proteins, there have been numerous unique and ubiquitous additions to the eukaryotic translational system besides the 11 unique eukaryotic ribosomal proteins. These include peptide additions to most of the 67 archaeal homolog proteins, rRNA insertions, the 5.8S RNA and the Alu extension to the SRP RNA. Our comparative analysis of these and other eukaryotic features among the three different cellular phylodomains supports the idea that an archaeal translational system was most likely incorporated by means of endosymbiosis into a host cell that was neither bacterial nor archaeal in any modern sense. Phylogenetic analyses provide support for the timing of this acquisition coinciding with an ancient bottleneck in prokaryotic diversity.
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Liao, Yan, Solenne Ithurbide, Roshali T. de Silva, Susanne Erdmann, and Iain G. Duggin. "Archaeal cell biology: diverse functions of tubulin-like cytoskeletal proteins at the cell envelope." Emerging Topics in Life Sciences 2, no. 4 (December 14, 2018): 547–59. http://dx.doi.org/10.1042/etls20180026.
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The tubulin superfamily of cytoskeletal proteins is widespread in all three domains of life — Archaea, Bacteria and Eukarya. Tubulins build the microtubules of the eukaryotic cytoskeleton, whereas members of the homologous FtsZ family construct the division ring in prokaryotes and some eukaryotic organelles. Their functions are relatively poorly understood in archaea, yet these microbes contain a remarkable diversity of tubulin superfamily proteins, including FtsZ for division, a newly described major family called CetZ that is involved in archaeal cell shape control, and several other divergent families of unclear function that are implicated in a variety of cell envelope-remodelling contexts. Archaeal model organisms, particularly halophilic archaea such as Haloferax volcanii, have sufficiently developed genetic tools and we show why their large, flattened cells that are capable of controlled differentiation are also well suited to cell biological investigations by live-cell high-resolution light and electron microscopy. As most archaea only have a glycoprotein lattice S-layer, rather than a peptidoglycan cell wall like bacteria, the activity of the tubulin-like cytoskeletal proteins at the cell envelope is expected to vary significantly, and may involve direct membrane remodelling or directed synthesis or insertion of the S-layer protein subunits. Further studies of archaeal cell biology will provide fresh insight into the evolution of cells and the principles in common to their fundamental activities across the full spectrum of cellular life.
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Hamerly, Timothy, Brian Tripet, Louie Wurch, Robert L. Hettich, Mircea Podar, Brian Bothner, and Valérie Copié. "Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR." Archaea 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/472726.
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Lipids composed of condensed isoprenyl units connected to glycerol backbones by ether linkages are a distinguishing feature of Archaea. Data suggesting that fatty acids with linear hydrocarbon chains are present in some Archaea have been available for decades. However, lack of genomic and biochemical evidence for the metabolic machinery required to synthesize and degrade fatty acids has left the field unclear on this potentially significant biochemical aspect. Because lipids are energy currency and cell signaling molecules, their presence in Archaea is significant for understanding archaeal biology. A recent large-scale bioinformatics analysis reignited the debate as to the importance of fatty acids in Archaea by presenting genetic evidence for the presence of enzymes required for anabolic and catabolic fatty acid metabolism across the archaeal domain. Here, we present direct biochemical evidence from gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy for the presence of fatty acids in two members of the Crenarchaeota,Sulfolobus solfataricusandIgnicoccus hospitalis. This is the first report providing biochemical data for the existence of fatty acids in these Crenarchaeota, opening new discussions on energy balance and the potential for the discovery of new thermostable enzymes for industry.
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Rusch, Antje. "Molecular Tools for the Detection of Nitrogen Cycling Archaea." Archaea 2013 (2013): 1–10. http://dx.doi.org/10.1155/2013/676450.
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Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic capacities, which sets them up for potentially major roles in the biogeochemistry of their ecosystems. The detection, characterization, and quantification of archaeal functions in mixed communities require Archaea-specific primers or probes for the corresponding metabolic genes. Five pairs of degenerate primers were designed to target archaeal genes encoding key enzymes of nitrogen cycling: nitrite reductases NirA and NirB, nitrous oxide reductase (NosZ), nitrogenase reductase (NifH), and nitrate reductases NapA/NarG. Sensitivity towards their archaeal target gene, phylogenetic specificity, and gene specificity were evaluated in silico and in vitro. Owing to their moderate sensitivity/coverage, the novelnirB-targeted primers are suitable for pure culture studies only. ThenirA-targeted primers showed sufficient sensitivity and phylogenetic specificity, but poor gene specificity. The primers designed for amplification of archaealnosZperformed well in all 3 criteria; their discrimination against bacterial homologs appears to be weakened when Archaea are strongly outnumbered by bacteria in a mixed community. The novelnifH-targeted primers showed high sensitivity and gene specificity, but failed to discriminate against bacterial homologs. Despite limitations, 4 of the new primer pairs are suitable tools in several molecular methods applied in archaeal ecology.
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Yoshinaga, Marcos Y., Lars Wörmer, Marcus Elvert, and Kai-Uwe Hinrichs. "Novel Cardiolipins from Uncultured Methane-Metabolizing Archaea." Archaea 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/832097.
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Novel cardiolipins from Archaea were detected by screening the intact polar lipid (IPL) composition of microbial communities associated with methane seepage in deep-sea sediments from the Pakistan margin by high-performance liquid chromatography electrospray ionization mass spectrometry. A series of tentatively identified cardiolipin analogues (dimeric phospholipids or bisphosphatidylglycerol, BPG) represented 0.5% to 5% of total archaeal IPLs. These molecules are similar to the recently described cardiolipin analogues with four phytanyl chains from extreme halophilic archaea. It is worth noting that cardiolipin analogues from the seep archaeal communities are composed of four isoprenoidal chains, which may contain differences in chain length (20 and 25 carbon atoms) and degrees of unsaturation and the presence of a hydroxyl group. Two novel diether lipids, structurally related to the BPGs, are described and interpreted as degradation products of archaeal cardiolipin analogues. Since archaeal communities in seep sediments are dominated by anaerobic methanotrophs, our observations have implications for characterizing structural components of archaeal membranes, in which BPGs are presumed to contribute to modulation of cell permeability properties. Whether BPGs facilitate interspecies interaction in syntrophic methanotrophic consortia remains to be tested.
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Raymann, Kasie, Céline Brochier-Armanet, and Simonetta Gribaldo. "The two-domain tree of life is linked to a new root for the Archaea." Proceedings of the National Academy of Sciences 112, no. 21 (May 11, 2015): 6670–75. http://dx.doi.org/10.1073/pnas.1420858112.
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One of the most fundamental questions in evolutionary biology is the origin of the lineage leading to eukaryotes. Recent phylogenomic analyses have indicated an emergence of eukaryotes from within the radiation of modern Archaea and specifically from a group comprising Thaumarchaeota/“Aigarchaeota” (candidate phylum)/Crenarchaeota/Korarchaeota (TACK). Despite their major implications, these studies were all based on the reconstruction of universal trees and left the exact placement of eukaryotes with respect to the TACK lineage unclear. Here we have applied an original two-step approach that involves the separate analysis of markers shared between Archaea and eukaryotes and between Archaea and Bacteria. This strategy allowed us to use a larger number of markers and greater taxonomic coverage, obtain high-quality alignments, and alleviate tree reconstruction artifacts potentially introduced when analyzing the three domains simultaneously. Our results robustly indicate a sister relationship of eukaryotes with the TACK superphylum that is strongly associated with a distinct root of the Archaea that lies within the Euryarchaeota, challenging the traditional topology of the archaeal tree. Therefore, if we are to embrace an archaeal origin for eukaryotes, our view of the evolution of the third domain of life will have to be profoundly reconsidered, as will many areas of investigation aimed at inferring ancestral characteristics of early life and Earth.
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Navarro-Noya, Yendi E., César Valenzuela-Encinas, Alonso Sandoval-Yuriar, Norma G. Jiménez-Bueno, Rodolfo Marsch, and Luc Dendooven. "Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil." Archaea 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/646820.
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In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic CandidatusNitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils.Halobiforma,Halostagnicola,Haloterrigena, andNatronomonaswere found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH.
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Gunbin, K. V., V. V. Suslov, and D. A. Afonnikov. "Phylogenetic analysis of housekeeping Archaeal proteins and early stages of Archaea evolution." Paleontological Journal 47, no. 9 (November 28, 2013): 1041–47. http://dx.doi.org/10.1134/s0031030113090098.
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Cowie, Rebecca O. M., Elizabeth W. Maas, and Ken G. Ryan. "Archaeal diversity revealed in Antarctic sea ice." Antarctic Science 23, no. 6 (May 25, 2011): 531–36. http://dx.doi.org/10.1017/s0954102011000368.
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AbstractArchaea, once thought to be only extremophiles, are now known to be abundant in most environments. They can predominate in microbial communities and be significantly involved in many global biogeochemical cycles. However, Archaea have not been reported in Antarctic sea ice. Our understanding of the ecology of Antarctic sea ice prokaryotes is still in its infancy but this information is important if we are to understand their diversity, adaptations and biogeochemical roles in Antarctic systems. We detected Archaea in sea ice at two sampling sites taken from three subsequent years using conserved 16S rRNA gene archaeal primers and PCR. Archaeal abundance was measured using quantitative PCR and community diversity was investigated by sequencing cloned 16S rRNA gene PCR products. Archaea in Antarctic sea ice were found to be in low abundance consisting of ≤ 6.6% of the prokaryotic community. The majority, 90.8% of the sequences, clustered with the recently described phylumThaumarchaeota, one group closely clustered with the ammonia-oxidizing CandidatusNitrosopumilus maritimus. The remainder of the clones grouped with theEuryarchaeota.
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Lazar, Cassandre Sara, Wenke Stoll, Robert Lehmann, Martina Herrmann, Valérie F. Schwab, Denise M. Akob, Ali Nawaz, et al. "Archaeal Diversity and CO2Fixers in Carbonate-/Siliciclastic-Rock Groundwater Ecosystems." Archaea 2017 (2017): 1–13. http://dx.doi.org/10.1155/2017/2136287.
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Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few surface soil-inhabiting Archaea were present in the groundwater suggesting a restricted input from the surface. Dominant groups in the groundwater belonged to the marine group I (MG-I) Thaumarchaeota and the Woesearchaeota. Most of the groups detected in the aquitard and aquifer rock samples belonged to either cultured or predicted lithoautotrophs (e.g., Thaumarchaeota or Hadesarchaea). Furthermore, to target autotrophs, a series of13CO2stable isotope-probing experiments were conducted using filter pieces obtained after filtration of 10,000 L of groundwater to concentrate cells. These incubations identified the SAGMCG Thaumarchaeota and Bathyarchaeota as groundwater autotrophs. Overall, the results suggest that the majority of Archaea on rocks are fixing CO2, while archaeal autotrophy seems to be limited in the groundwater.
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Giaquinto, Laura, Paul M. G. Curmi, Khawar S. Siddiqui, Anne Poljak, Ed DeLong, Shiladitya DasSarma, and Ricardo Cavicchioli. "Structure and Function of Cold Shock Proteins in Archaea." Journal of Bacteriology 189, no. 15 (June 1, 2007): 5738–48. http://dx.doi.org/10.1128/jb.00395-07.
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ABSTRACT Archaea are abundant and drive critical microbial processes in the Earth's cold biosphere. Despite this, not enough is known about the molecular mechanisms of cold adaptation and no biochemical studies have been performed on stenopsychrophilic archaea (e.g., Methanogenium frigidum). This study examined the structural and functional properties of cold shock proteins (Csps) from archaea, including biochemical analysis of the Csp from M. frigidum. csp genes are present in most bacteria and some eucarya but absent from most archaeal genome sequences, most notably, those of all archaeal thermophiles and hyperthermophiles. In bacteria, Csps are small, nucleic acid binding proteins involved in a variety of cellular processes, such as transcription. In this study, archaeal Csp function was assessed by examining the ability of csp genes from psychrophilic and mesophilic Euryarchaeota and Crenarchaeota to complement a cold-sensitive growth defect in Escherichia coli. In addition, an archaeal gene with a cold shock domain (CSD) fold but little sequence identity to Csps was also examined. Genes encoding Csps or a CSD structural analog from three psychrophilic archaea rescued the E. coli growth defect. The three proteins were predicted to have a higher content of solvent-exposed basic residues than the noncomplementing proteins, and the basic residues were located on the nucleic acid binding surface, similar to their arrangement in E. coli CspA. The M. frigidum Csp was purified and found to be a single-domain protein that folds by a reversible two-state mechanism and to exhibit a low conformational stability typical of cold-adapted proteins. Moreover, M. frigidum Csp was characterized as binding E. coli single-stranded RNA, consistent with its ability to complement function in E. coli. The studies show that some Csp and CSD fold proteins have retained sufficient similarity throughout evolution in the Archaea to be able to function effectively in the Bacteria and that the function of the archaeal proteins relates to cold adaptation. The initial biochemical analysis of M. frigidum Csp has developed a platform for further characterization and demonstrates the potential for expanding molecular studies of proteins from this important archaeal stenopsychrophile.
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Baquero, Diana P., Anastasia D. Gazi, Martin Sachse, Junfeng Liu, Christine Schmitt, Maryse Moya-Nilges, Stefan Schouten, David Prangishvili, and Mart Krupovic. "A filamentous archaeal virus is enveloped inside the cell and released through pyramidal portals." Proceedings of the National Academy of Sciences 118, no. 32 (August 2, 2021): e2105540118. http://dx.doi.org/10.1073/pnas.2105540118.
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The majority of viruses infecting hyperthermophilic archaea display unique virion architectures and are evolutionarily unrelated to viruses of bacteria and eukaryotes. The lack of relationships to other known viruses suggests that the mechanisms of virus–host interaction in Archaea are also likely to be distinct. To gain insights into archaeal virus–host interactions, we studied the life cycle of the enveloped, ∼2-μm-long Sulfolobus islandicus filamentous virus (SIFV), a member of the family Lipothrixviridae infecting a hyperthermophilic and acidophilic archaeon Saccharolobus islandicus LAL14/1. Using dual-axis electron tomography and convolutional neural network analysis, we characterize the life cycle of SIFV and show that the virions, which are nearly two times longer than the host cell diameter, are assembled in the cell cytoplasm, forming twisted virion bundles organized on a nonperfect hexagonal lattice. Remarkably, our results indicate that envelopment of the helical nucleocapsids takes place inside the cell rather than by budding as in the case of most other known enveloped viruses. The mature virions are released from the cell through large (up to 220 nm in diameter), six-sided pyramidal portals, which are built from multiple copies of a single 89-amino-acid-long viral protein gp43. The overexpression of this protein in Escherichia coli leads to pyramid formation in the bacterial membrane. Collectively, our results provide insights into the assembly and release of enveloped filamentous viruses and illuminate the evolution of virus–host interactions in Archaea.
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Tirumalai, Madhan R., Raghavan V. Sivaraman, Layla A. Kutty, Eric L. Song, and George E. Fox. "Ribosomal Protein Cluster Organization in Asgard Archaea." Archaea 2023 (September 29, 2023): 1–16. http://dx.doi.org/10.1155/2023/5512414.
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It has been proposed that the superphylum of Asgard Archaea may represent a historical link between the Archaea and Eukarya. Following the discovery of the Archaea, it was soon appreciated that archaeal ribosomes were more similar to those of Eukarya rather than Bacteria. Coupled with other eukaryotic-like features, it has been suggested that the Asgard Archaea may be directly linked to eukaryotes. However, the genomes of Bacteria and non-Asgard Archaea generally organize ribosome-related genes into clusters that likely function as operons. In contrast, eukaryotes typically do not employ an operon strategy. To gain further insight into conservation of the r-protein genes, the genome order of conserved ribosomal protein (r-protein) coding genes was identified in 17 Asgard genomes (thirteen complete genomes and four genomes with less than 20 contigs) and compared with those found previously in non-Asgard archaeal and bacterial genomes. A universal core of two clusters of 14 and 4 cooccurring r-proteins, respectively, was identified in both the Asgard and non-Asgard Archaea. The equivalent genes in the E. coli version of the cluster are found in the S10 and spc operons. The large cluster of 14 r-protein genes (uS19-uL22-uS3-uL29-uS17 from the S10 operon and uL14-uL24-uL5-uS14-uS8-uL6-uL18-uS5-uL30-uL15 from the spc operon) occurs as a complete set in the genomes of thirteen Asgard genomes (five Lokiarchaeotes, three Heimdallarchaeotes, one Odinarchaeote, and four Thorarchaeotes). Four less conserved clusters with partial bacterial equivalents were found in the Asgard. These were the L30e (str operon in Bacteria) cluster, the L18e (alpha operon in Bacteria) cluster, the S24e-S27ae-rpoE1 cluster, and the L31e, L12..L1 cluster. Finally, a new cluster referred to as L7ae was identified. In many cases, r-protein gene clusters/operons are less conserved in their organization in the Asgard group than in other Archaea. If this is generally true for nonribosomal gene clusters, the results may have implications for the history of genome organization. In particular, there may have been an early transition to or from the operon approach to genome organization. Other nonribosomal cellular features may support different relationships. For this reason, it may be important to consider ribosome features separately.
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Lorentzen, E., B. Siebers, R. Hensel, and E. Pohl. "Structure, function and evolution of the Archaeal class I fructose-1,6-bisphosphate aldolase." Biochemical Society Transactions 32, no. 2 (April 1, 2004): 259–63. http://dx.doi.org/10.1042/bst0320259.
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FBPA (fructose-1,6-bisphosphate aldolase) catalyses the reversible aldol condensation of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate to form fructose 1,6-bisphosphate. Two classes of FBPA, which rely on different reaction mechanisms, have so far been discovered, class I mainly found in Eucarya and class II mainly in Bacteria. Only recently were genes encoding proteins with FBPA activity identified in Archaea. Archaeal FBPAs do not share any significant overall sequence identity with members of the traditional classes of FBPAs, raising the interesting question of whether they have evolved independently by convergent evolution or diverged from a common ancestor. Biochemical characterization of FBPAs of the two hyperthermophilic Archaea Thermoproteus tenax and Pyrococcus furiosus showed that the enzymes use a Schiff-base mechanism and thus belong to the class I aldolases. The crystal structure of the archaeal FBPA from T. tenax revealed that the protein fold, as for the classical FBPA I and II, is that of a parallel (βα)8 barrel. A substrate-bound crystal structure allowed detailed active-site comparisons which showed the conservation of six important catalytic and substrate-binding residues between the archaeal and the classical FBPA I. This observation provides further evidence that the two sequence families of proteins share a common evolutionary origin. Furthermore, structure and sequence analysis indicate that the class I FBPA shares a common evolutionary origin with several other enzyme superfamilies of the (βα)8 barrel fold.
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Soares, Laís Américo, André Cordeiro Alves Dos Santos, Iolanda Cristina Silveira Duarte, Emiliana Manesco Romagnoli, and Maria do Carmo Calijuri. "Distribution of Archaeal and Bacterial communities in a subtropical reservoir." Acta Limnologica Brasiliensia 27, no. 4 (December 2015): 411–20. http://dx.doi.org/10.1590/s2179-975x3615.
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Abstract Aim: Microbial communities play a central role in environmental process such as organic matter mineralization and the nutrient cycling process in aquatic ecosystems. Despite their ecological importance, variability of the structure of archaeal and bacterial communities in freshwater remains understudied. Methods In the present study we investigated the richness and density of archaea and bacteria in the water column and sediments of the Itupararanga Reservoir. We also evaluated the relationship between the communities and the biotic and abiotic characteristics. Samples were taken at five depths in the water column next to the dam and three depths next to the reservoir entrance. Results PCR-DGGE evaluation of the archaeal and bacterial communities showed that both were present in the water column, even in oxygenated conditions. Conclusions The density of the bacteria (qPCR) was greater than that of the archaea, a result of the higher metabolic plasticity of bacteria compared with archaea.
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Spang, Anja, Joran Martijn, Jimmy H. Saw, Anders E. Lind, Lionel Guy, and Thijs J. G. Ettema. "Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution." Archaea 2013 (2013): 1–12. http://dx.doi.org/10.1155/2013/202358.
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The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life.
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Peeters, Eveline, and Daniel Charlier. "The Lrp Family of Transcription Regulators in Archaea." Archaea 2010 (2010): 1–10. http://dx.doi.org/10.1155/2010/750457.
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Archaea possess a eukaryotic-type basal transcription apparatus that is regulated by bacteria-like transcription regulators. A universal and abundant family of transcription regulators are the bacterial/archaeal Lrp-like regulators. The Lrp family is one of the best studied regulator families in archaea, illustrated by investigations of proteins from the archaeal model organisms:Sulfolobus,Pyrococcus,Methanocaldococcus, andHalobacterium. These regulators are extremely versatile in their DNA-binding properties, response to effector molecules, and molecular regulatory mechanisms. Besides being involved in the regulation of the amino acid metabolism, they also regulate central metabolic processes. It appears that these regulatory proteins are also involved in large regulatory networks, because of hierarchical regulations and the possible combinatorial use of different Lrp-like proteins. Here, we discuss the recent developments in our understanding of this important class of regulators.
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Yip, W. S. Vincent, Nicholas G. Vincent, and Susan J. Baserga. "Ribonucleoproteins in Archaeal Pre-rRNA Processing and Modification." Archaea 2013 (2013): 1–14. http://dx.doi.org/10.1155/2013/614735.
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Given that ribosomes are one of the most important cellular macromolecular machines, it is not surprising that there is intensive research in ribosome biogenesis. Ribosome biogenesis is a complex process. The maturation of ribosomal RNAs (rRNAs) requires not only the precise cleaving and folding of the pre-rRNA but also extensive nucleotide modifications. At the heart of the processing and modifications of pre-rRNAs in Archaea and Eukarya are ribonucleoprotein (RNP) machines. They are called small RNPs (sRNPs), in Archaea, and small nucleolar RNPs (snoRNPs), in Eukarya. Studies on ribosome biogenesis originally focused on eukaryotic systems. However, recent studies on archaeal sRNPs have provided important insights into the functions of these RNPs. This paper will introduce archaeal rRNA gene organization and pre-rRNA processing, with a particular focus on the discovery of the archaeal sRNP components, their functions in nucleotide modification, and their structures.
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Shin, David S., Ashley J. Pratt, and John A. Tainer. "Archaeal Genome Guardians Give Insights into Eukaryotic DNA Replication and Damage Response Proteins." Archaea 2014 (2014): 1–24. http://dx.doi.org/10.1155/2014/206735.
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As the third domain of life, archaea, like the eukarya and bacteria, must have robust DNA replication and repair complexes to ensure genome fidelity. Archaea moreover display a breadth of unique habitats and characteristics, and structural biologists increasingly appreciate these features. As archaea include extremophiles that can withstand diverse environmental stresses, they provide fundamental systems for understanding enzymes and pathways critical to genome integrity and stress responses. Such archaeal extremophiles provide critical data on the periodic table for life as well as on the biochemical, geochemical, and physical limitations to adaptive strategies allowing organisms to thrive under environmental stress relevant to determining the boundaries for life as we know it. Specifically, archaeal enzyme structures have informed the architecture and mechanisms of key DNA repair proteins and complexes. With added abilities to temperature-trap flexible complexes and reveal core domains of transient and dynamic complexes, these structures provide insights into mechanisms of maintaining genome integrity despite extreme environmental stress. The DNA damage response protein structures noted in this review therefore inform the basis for genome integrity in the face of environmental stress, with implications for all domains of life as well as for biomanufacturing, astrobiology, and medicine.
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Baker, Brett J., Valerie De Anda, Kiley W. Seitz, Nina Dombrowski, Alyson E. Santoro, and Karen G. Lloyd. "Diversity, ecology and evolution of Archaea." Nature Microbiology 5, no. 7 (May 4, 2020): 887–900. http://dx.doi.org/10.1038/s41564-020-0715-z.
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Klenk, Hans-Peter, and W. Ford Doolittle. "Evolution: Archaea and eukaryotes versus bacteria?" Current Biology 4, no. 10 (October 1994): 920–22. http://dx.doi.org/10.1016/s0960-9822(00)00206-2.
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Besseling, Marc A., Ellen C. Hopmans, R. Christine Boschman, Jaap S. Sinninghe Damsté, and Laura Villanueva. "Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone." Biogeosciences 15, no. 13 (July 4, 2018): 4047–64. http://dx.doi.org/10.5194/bg-15-4047-2018.
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Abstract. Benthic archaea comprise a significant part of the total prokaryotic biomass in marine sediments. Recent genomic surveys suggest they are largely involved in anaerobic processing of organic matter, but the distribution and abundance of these archaeal groups are still largely unknown. Archaeal membrane lipids composed of isoprenoid diethers or tetraethers (glycerol dibiphytanyl glycerol tetraether, GDGT) are often used as archaeal biomarkers. Here, we compare the archaeal diversity and intact polar lipid (IPL) composition in both surface (0–0.5 cm) and subsurface (10–12 cm) sediments recovered within, just below, and well below the oxygen minimum zone (OMZ) of the Arabian Sea. Archaeal 16S rRNA gene amplicon sequencing revealed a predominance of Thaumarchaeota (Marine Group I, MG-I) in oxygenated sediments. Quantification of archaeal 16S rRNA and ammonia monoxygenase (amoA) of Thaumarchaeota genes and their transcripts indicated the presence of an active in situ benthic population, which coincided with a high relative abundance of hexose phosphohexose crenarchaeol, a specific biomarker for living Thaumarchaeota. On the other hand, anoxic surface sediments within the OMZ and all subsurface sediments were dominated by archaea belonging to the Miscellaneous Crenarchaeota Group (MCG), the Thermoplasmatales and archaea of the DPANN (superphylum grouping Micrarchaeota, Diapherotrites, Aenigmarchaeota, Nanohaloarchaeota, Parvarchaeota, Nanoarchaeota, Pacearchaeota and Woesearchaeota). Members of the MCG were diverse, with a dominance of subgroup MCG-12 in anoxic surface sediments. This coincided with a high relative abundance of IPL GDGT-0 with an unknown polar head group. Subsurface anoxic sediments were characterized by higher relative abundance of GDGT-0, -2 and -3 with dihexose IPL types, GDGT-0 with a cyclopentanetetraol molecule and hexose, as well as the presence of specific MCG subgroups, suggesting that these groups could be the biological sources of these archaeal lipids.
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Harish, Ajith. "What is an archaeon and are the Archaea really unique?" PeerJ 6 (October 18, 2018): e5770. http://dx.doi.org/10.7717/peerj.5770.
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The recognition of the group Archaea as a major branch of the tree of life (ToL) prompted a new view of the evolution of biodiversity. The genomic representation of archaeal biodiversity has since significantly increased. In addition, advances in phylogenetic modeling of multi-locus datasets have resolved many recalcitrant branches of the ToL. Despite the technical advances and an expanded taxonomic representation, two important aspects of the origins and evolution of the Archaea remain controversial, even as we celebrate the 40th anniversary of the monumental discovery. These issues concern (i) the uniqueness (monophyly) of the Archaea, and (ii) the evolutionary relationships of the Archaea to the Bacteria and the Eukarya; both of these are relevant to the deep structure of the ToL. To explore the causes for this persistent ambiguity, I examine multiple datasets and different phylogenetic approaches that support contradicting conclusions. I find that the uncertainty is primarily due to a scarcity of information in standard datasets—universal core-genes datasets—to reliably resolve the conflicts. These conflicts can be resolved efficiently by comparing patterns of variation in the distribution of functional genomic signatures, which are less diffused unlike patterns of primary sequence variation. Relatively lower heterogeneity in distribution patterns minimizes uncertainties and supports statistically robust phylogenetic inferences, especially of the earliest divergences of life. This case study further highlights the limitations of primary sequence data in resolving difficult phylogenetic problems, and raises questions about evolutionary inferences drawn from the analyses of sequence alignments of a small set of core genes. In particular, the findings of this study corroborate the growing consensus that reversible substitution mutations may not be optimal phylogenetic markers for resolving early divergences in the ToL, nor for determining the polarity of evolutionary transitions across the ToL.
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Cabello, Purificación, M. Dolores Roldán, and Conrado Moreno-Vivián. "Nitrate reduction and the nitrogen cycle in archaea." Microbiology 150, no. 11 (November 1, 2004): 3527–46. http://dx.doi.org/10.1099/mic.0.27303-0.
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The nitrogen cycle (N-cycle) in the biosphere, mainly driven by prokaryotes, involves different reductive or oxidative reactions used either for assimilatory purposes or in respiratory processes for energy conservation. As the N-cycle has important agricultural and environmental implications, bacterial nitrogen metabolism has become a major research topic in recent years. Archaea are able to perform different reductive pathways of the N-cycle, including both assimilatory processes, such as nitrate assimilation and N2 fixation, and dissimilatory reactions, such as nitrate respiration and denitrification. However, nitrogen metabolism is much less known in archaea than in bacteria. The availability of the complete genome sequences of several members of the eury- and crenarchaeota has enabled new approaches to the understanding of archaeal physiology and biochemistry, including metabolic reactions involving nitrogen compounds. Comparative studies reveal that significant differences exist in the structure and regulation of some enzymes involved in nitrogen metabolism in archaea, giving rise to important conclusions and new perspectives regarding the evolution, function and physiological relevance of the different N-cycle processes. This review discusses the advances that have been made in understanding nitrate reduction and other aspects of the inorganic nitrogen metabolism in archaea.