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Artykuły w czasopismach na temat „Archaebacteria”

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Data publikacji: 4 czerwca 2021

Data aktualizacji: 25 lutego 2023

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1

Cammarano, P., O. Tiboni i A. M. Sanangelantoni. "Phylogenetic conservation of antigenic determinants in archaebacterial elongation factors (Tu proteins)". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 2–10. http://dx.doi.org/10.1139/m89-002.

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By using affinity chromatography methods, we have purified elongation factor Tu (EF-Tu) proteins from a host of archaebacteria covering all known divisions in the archaebacterial tree except halophiles, and from such distantly related eubacteria as Thermotoga maritima and Escherichia coli. Polyclonal antibodies were raised against the Tu proteins of Sulfolobus solfataricus, Thermoproteus tenax, Thermococcus celer, Pyrococcus wosei, Archaeoglobus fulgidus, Methanococcus thermolitotrophicus, Thermoplasma acidophilum, and Thermotoga and used to probe the immunochemical relatedness of elongation factors both within and across kingdom boundaries. A selection of the results, presented here, indicates that (i) every archaebacterial EF-Tu is closer (immunochemically) to every other archaebacterial EF-Tu than to the functionally analogous proteins of eubacteria and eukaryotes, with only one possible exception concerning die recognition of eukaryotic (EF-1α) factors by Thermococcus EF-Tu antibodies, and (ii) within the archaebacteria there appears to be a correlation between EF-Tu immunochemical similarities and the phylogenetic relatedness of the organisms inferred from other (sequence) criteria. On the whole, immunochemical similarity data argue against the proposal that the archaebacterial taxon should be split and redistributed between two superkingdoms.Key words: phylogeny, archaebacteria, elongation factor Tu antibodies, eubacteria, eukaryotes.

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2

Fedorov, Oleg V., Michael G. Pyatibratov, Alla S. Kostyukova, Natalja K. Osina i Valery Yu Tarasov. "Protofilament as a structural element of flagella of haloalkalophilic archaebacteria". Canadian Journal of Microbiology 40, nr 1 (1.01.1994): 45–53. http://dx.doi.org/10.1139/m94-007.

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Flagella of the haloalkalophilic archaebacterium Natronobacterium magadii were purified and characterized. The diameter of the flagella was 10 nm. It was shown that the flagella consist of four major proteins with molecular weights of 105 000, 60 000, 59 000, and 45 000. With decreasing NaCl concentration, the flagella dissociated into protofilaments. The structure of dissociated flagella and individual flagellins was studied by limited proteolysis. It was found that proteolytic cleavage of flagellins in dissociated flagella into high molecular weight fragments (about 40 000) did not lead to protofilament degradation. It was shown that the most stable fragment is formed from the 60 000 molecular weight flagellin. Cleavage of this fragment led to complete disappearance of protofilaments. On the basis of the data obtained, possible principles of archaebacterial flagellar construction are discussed.Key words: flagellin, archaebacteria, protofilaments, Natronobacterium magadii.

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3

Amils, R., L. Ramírez, J. L. Sanz, I. Marín, A. G. Pisabarro i D. Ureña. "The use of functional analysis of the ribosome as a tool to determine archaebacterial phylogeny". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 141–47. http://dx.doi.org/10.1139/m89-021.

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Forty different antibiotics with diverse kingdom and functional specificities were used to measure the functional characteristics of the archaebacterial translation apparatus. The resulting inhibitory curves, which are characteristic of the cell-free system analyzed, were transformed into quantitative values that were used to cluster the different archaebacteria analyzed. This cluster resembles the phylogenetic tree generated by 16S rRNA sequence comparisons. These results strongly suggest that functional analysis of an appropriate evolutionary clock, such as the ribosome, is of intrinsic phylogenetic value. More importantly, they indicate that the study of the nexus between genotypic and phenotypic (functional) information may shed considerable light on the evolution of the protein synthetic machinery.Key words: antibiotics, ribosomes, archaebacteria, phylogeny, functional analysis.

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4

Olsen, Gary J., i Carl R. Woese. "A brief note concerning archaebacterial phylogeny". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 119–23. http://dx.doi.org/10.1139/m89-018.

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Critical analysis of the recently proposed alternative to the normal archaebacterial tree, the new eocyte tree, shows that the latter's central topology, in which the eubacteria branch from an entirely different section of the unrooted archaebacterial tree than the eukaryotes, is consistent with an artifact. The effects of the alignment used and the particular composition of the sequence quartets analyzed to infer this tree are discussed in detail.Key words: archaebacteria, molecular phylogeny, 16S ribosomal RNA, evolution, eocyte tree.

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5

Wolters, Jörn, i Volker A. Erdmann. "The structure and evolution of archaebacterial ribosomal RNAs". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 43–51. http://dx.doi.org/10.1139/m89-007.

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A cladistic analysis of 553 5S rRNA sequences has revealed a Ur-5S rRNA, the ancestor of all present-day 5S rRNA molecules. Previously stated characteristic differences between the eubacterial and eukaryotic molecules, namely, the length base-pairing schemes of helices D, can be used as a marker for the various archaebacterial branches. One model comprises Thermococcus, Thermoplasma, methanobacteria, and halobacteria; a second comprises the Sulfolobales; and a third is represented only by the single organism Octopus Spring species 1. A relaxed selection pressure on helix E with subsequent deletions is observed in Methanobacteriales, Methanococcales, and eubacteria. The secondary structures are supported by enzymatic digestion and chemical modification studies of the 5S rRNAs. Reconstitution of eubacterial 50S ribosomal subunits with 5S rRNA from Halobacterium and Thermoplasma has revealed 100% incorporation, while eukaryotic 5S rRNAs yielded a 50% incorporation. Relevant positions of the small-subunit rRNA are selected to answer the question of the monophyly of archaebacteria. Eight positions account for monophyly, eight for an ancestry of eubacteria with halophile methanogens and eukaryotes with eocytes (paraphyly of archaebacteria), and two for an ancestry of eubacteria with eocytes. A refinement of the neighborliness method of S. Sattath and A. Tversky resulted in a monophyly of archaebacteria when all positions are treated equally and in a paraphyly when tranversions are weighted twice over transitions.Key words: archaebacteria, ribosomal RNA, evolution, cladistic analysis.

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6

Ramirez, Celia, Lawrence C. Shimmin, C. Hunter Newton, Alastair T. Matheson i Patrick P. Dennis. "Structure and evolution of the L11, L1, L10, and L12 equivalent ribosomal proteins in eubacteria, archaebacteria, and eucaryotes". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 234–44. http://dx.doi.org/10.1139/m89-036.

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The genes corresponding to the L11, L1, L10, and L12 equivalent ribosomal proteins (L11e, L1e, L10e, and L12e) of Escherichia coli have been cloned and sequenced from two widely divergent species of archaebacteria, Halobacterium cutirubrum and Sulfolobus solfataricus, and the L10 and four different L12 genes have been cloned and sequenced from the eucaryote Saccharomyces cerevisiae. Alignments between the deduced amino acid sequences of these proteins and to other available homologous proteins of eubacteria and eucaryotes have been made. The data suggest that the archaebacteria are a distinct coherent phylogenetic group. Alignment of the proline-rich L11e proteins reveals that the N-terminal region, believed to be responsible for interaction with release factor 1, is the most highly conserved region and that there is specific conservation of most of the proline residues, which may be important in maintaining the highly elongated structure of the molecule. Although L11 is the most highly methylated protein in the E. coli ribosome, the sites of methylation are not conserved in the archaebacterial L11e proteins. The L1e proteins of eubacteria and archaebacteria show two regions of very high similarity near the center and the carboxy termini of the proteins. The L10e proteins of all kingdoms are colinear and contain approximately three fourths of an L12e protein fused to their carboxy terminus, although much of this fusion has been lost in the truncated eubacterial protein. The archaebacterial and eucaryotic L12e proteins are colinear, whereas the eubacterial protein has suffered a rearrangement through what appear to be gene fusion events. Within the L12e derived region of the L10e proteins there exists a repeated module of 26 amino acids, present in two copies in eucaryotes, three in archaebacteria, and one in eubacteria. This modular sequence is apparently also present in the L12e proteins of all kingdoms and may play a role in L12e dimerization, L10e–L12e complex formation, and the function of the L10e–L12e complex in translation.Key words: translation, ribosome.

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7

Hensel, Reinhard, Peter Zwickl, Stefan Fabry, Jutta Lang i Peter Palm. "Sequence comparison of glyceraldehyde-3-phosphate dehydrogenases from the three urkingdoms: evolutionary implication". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 81–85. http://dx.doi.org/10.1139/m89-012.

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The primary structure of the glyceraldehyde-3-phosphate dehydrogenase from the archaebacteria shows striking deviation from the known sequences of eubacterial and eukaryotic sequences, despite unequivocal homologies in functionally important regions. Thus, the structural similarity between the eubacterial and eukaryotic enzymes is significantly higher than that between the archaebacterial enzymes and the eubacterial and eukarytic enzymes. This preferred similarity of eubacterial and eukaryotic glyceraldehyde-3-phosphate dehydrogenase structures does not correspond to the phylogenetic distances among the three urkingdoms as deduced from comparisons of ribosomal ribonucleic acid sequences. Indications will be presented that the closer relationship of the eubacterial and eukaryotic glyceraldehyde-3-phosphate dehydrogenase resulted from a gene transfer from eubacteria to eukaryotes after the segregation of the three urkingdoms.Key words: glyceraldehyde-3-phosphate dehydrogenase, archaebacteria, protein evolution.

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8

Akanni, Wasiu A., Karen Siu-Ting, Christopher J. Creevey, James O. McInerney, Mark Wilkinson, Peter G. Foster i Davide Pisani. "Horizontal gene flow from Eubacteria to Archaebacteria and what it means for our understanding of eukaryogenesis". Philosophical Transactions of the Royal Society B: Biological Sciences 370, nr 1678 (26.09.2015): 20140337. http://dx.doi.org/10.1098/rstb.2014.0337.

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The origin of the eukaryotic cell is considered one of the major evolutionary transitions in the history of life. Current evidence strongly supports a scenario of eukaryotic origin in which two prokaryotes, an archaebacterial host and an α -proteobacterium (the free-living ancestor of the mitochondrion), entered a stable symbiotic relationship. The establishment of this relationship was associated with a process of chimerization, whereby a large number of genes from the α-proteobacterial symbiont were transferred to the host nucleus. A general framework allowing the conceptualization of eukaryogenesis from a genomic perspective has long been lacking. Recent studies suggest that the origins of several archaebacterial phyla were coincident with massive imports of eubacterial genes. Although this does not indicate that these phyla originated through the same process that led to the origin of Eukaryota, it suggests that Archaebacteria might have had a general propensity to integrate into their genomes large amounts of eubacterial DNA. We suggest that this propensity provides a framework in which eukaryogenesis can be understood and studied in the light of archaebacterial ecology. We applied a recently developed supertree method to a genomic dataset composed of 392 eubacterial and 51 archaebacterial genera to test whether large numbers of genes flowing from Eubacteria are indeed coincident with the origin of major archaebacterial clades. In addition, we identified two potential large-scale transfers of uncertain directionality at the base of the archaebacterial tree. Our results are consistent with previous findings and seem to indicate that eubacterial gene imports (particularly from δ - Proteobacteria, Clostridia and Actinobacteria) were an important factor in archaebacterial history. Archaebacteria seem to have long relied on Eubacteria as a source of genetic diversity, and while the precise mechanism that allowed these imports is unknown, we suggest that our results support the view that processes comparable to those through which eukaryotes emerged might have been common in archaebacterial history.

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9

Zillig, Wolfram, Hans-Peter Klenk, Peter Palm, Gabriela Pühler, Felix Gropp, Roger A. Garrett i Henrik Leffers. "The phylogenetic relations of DNA-dependent RNA polymerases of archaebacteria, eukaryotes, and eubacteria". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 73–80. http://dx.doi.org/10.1139/m89-011.

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Unrooted phylogenetic dendrograms were calculated by two independent methods, parsimony and distance matrix analysis, from an alignment of the derived amino acid sequences of the A and C subunits of the DNA-dependent RNA polymerases of the archaebacteria Sulfolobus acidocaldarius and Halobacterium halobium with 12 corresponding sequences including a further set of archaebacterial A + C subunits, eukaryotic nuclear RNA polymerases, pol I, pol II, and pol III, eubacterial β′ and chloroplast β′ and β″ subunits. They show the archaebacteria as a coherent group in close neighborhood of and sharing a bifurcation with eukaryotic pol II and (or) pol IIIA components. The most probable trees show pol IA branching off from the tree separately at a bifurcation with the eubacterial β′ lineage. The implications of these results, especially for understanding the possibly chimeric origin of the eukaryotic nuclear genome, are discussed.Key words: transcription, evolution, taxonomy, subunits, gene organization.

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10

Fewson, Charles A. "Archaebacteria". Biochemical Education 14, nr 3 (lipiec 1986): 103–15. http://dx.doi.org/10.1016/0307-4412(86)90167-6.

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11

Shimmin, Lawrence C., C. Hunter Newton, Celia Ramirez, Janet Yee, Willa Lee Downing, Andrea Louie, Alastair T. Matheson i Patrick P. Dennis. "Organization of genes encoding the L11, L1, L10, and L12 equivalent ribosomal proteins in eubacteria, archaebacteria, and eucaryotes". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 164–70. http://dx.doi.org/10.1139/m89-025.

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Archaebacterial and eucaryotic cytoplasmic ribosomes contain proteins equivalent to the L11, L1, L10, and L12 proteins of the eubacterium Escherichia coli. In E. coli the genes encoding these ribosomal proteins are clustered, cotranscribed, and autogenously regulated at the level of mRNA translation. Genomic restriction fragments encoding the L11e, L1e, L10e, and L12e (equivalent) proteins from two divergent archaebacteria, Halobacterium cutirubrum and Sulfolobus solfataricus, and the L10e and L12e proteins from the eucaryote Saccharomyces cerevisiae have been cloned, sequenced, and analyzed. In the archaebacteria, as in eubacteria, the four genes are clustered and the L11e, L1e, L 10e, and L12e order is maintained. The transcription pattern of the H. cutirubrum cluster is different from the E. coli pattern and the flanking genes on either side of the tetragenic clusters in E. coli, H. cutirubrum, and Sulfolobus solfataricus are all unrelated to each other. In the eucaryote Saccharomyces cerevisiae there is a single L10e gene and four separate L12e genes that are designated L12eIA, L12eIB, L12eIIA, and L12eIIB. These five genes are not closely linked and each is transcribed as a monocistronic mRNA; the L10e, L12eIA, L12eIB, and the L12eIIA genes are contiguous and uninterrupted, whereas the L12eIIB gene is interrupted by a 301 nucleotide long intron located between codons 38 and 39.Key words: archaebacteria, ribosome, Halobacterium, Sulfolobus.

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12

Forterre, Patrick, Christiane Eue, Mouldy Sioud i Abdellah Hamal. "Studies on DNA polymerases and topoisomerases in archaebacteria". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 228–33. http://dx.doi.org/10.1139/m89-035.

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We have isolated DNA polymerases and topoisomerases from two thermoacidophilic archaebacteria: Sulfolobus acidocaldarius and Thermoplasma acidophilum. The DNA polymerases are composed of a single polypeptide with molecular masses of 100 and 85 kDa, respectively. Antibodies against Sulfolobus DNA polymerase did not cross react with Thermoplasma DNA polymerase. Whereas the major DNA topoisomerase activity in S. acidocaldarius is an ATP-dependent type I DNA topoisomerase with a reverse gyrase activity, the major DNA topoisomerase activity in T. acidophilum is a ATP-independent relaxing activity. Both enzymes resemble more the eubacterial than the eukaryotic type I DNA topoisomerase. We have found that small plasmids from halobacteria are negatively supercoiled and that DNA topoisomerase II inhibitors modify their topology. This suggests the existence of an archaebacterial type II DNA topoisomerase related to its eubacterial and eukaryotic counterparts. As in eubacteria, novobiocin induces positive supercoiling of halobacterial plasmids, indicating the absence of a eukaryotic-like type I DNA topoisomerase that relaxes positive superturns.Key words: archaebacteria, DNA topoisomerases, DNA polymerases, DNA topology, gyrase.

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13

Schopf, J. William. "Precambrian Prokaryotes and Stromatolites". Notes for a Short Course: Studies in Geology 18 (1987): 20–33. http://dx.doi.org/10.1017/s0271164800001482.

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In terms of biochemical and intracellular organization, living systems can be divided into two major “Superkingdoms,” eukaryotes and prokaryotes.Eukaryotes, comprising the more advanced and later evolving Superkingdom, include unicellular or multicellular organisms (viz., members of the Kingdoms Protista, Fungi, Plantae and Animalia) characterized by nucleus-, mitochondrion-, and (in plants and some protists) chloroplast-containing cells that are capable typically of mitotic cell division. Paleontologic evidence indicates that the eukaryotic cell originated during the Middle Proterozoic, probably about 1.4 to 1.5 Ga ago (Schopf and Oehler, 1976).Prokaryotes, comprising the more primitive and earlier evolving Superkingdom, include microbial microorganisms (viz., members of the Kingdom Monera: bacteria, cyanobacteria, archaebacteria, and prochlorophytes) characterized by cells that lack membrane-bound nuclei, mitochondria, chloroplasts, and similar organelles and that reproduce by non-mitotic and non-meiotic division. Some authors (e.g., Woese and Fox, 1977) subdivide prokaryotes (monerans) into two kingdoms, the Kingdom Archaebacteriae (including methanogenic, extremely halophilic and some thermoacidophilic bacteria) and the Kingdom Eubacteriae (including all non-archaebacterial prokaryotes), based on the chemistry of their cell walls, membranes, transfer RNA's and RNA polymerase subunits. Paleontologic evidence indicates that prokaryotes originated early in Earth history - the group was extant, morphologically varied and evidently physiologically advanced at least as early as 3.3 to 3.5 Ga ago (Schopf and Packer, 1987).

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14

Cavalier-Smith, Thomas, i Ema E.-Yung Chao. "Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)". Protoplasma 257, nr 3 (3.01.2020): 621–753. http://dx.doi.org/10.1007/s00709-019-01442-7.

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AbstractPalaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many ‘rDNA-phyla’ belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including ‘Asgardia’) and Euryarchaeota sensu-lato (including ultrasimplified ‘DPANN’ whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

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15

Fewson, Charles A. "Archaebacteria '85". Biochemical Education 16, nr 2 (kwiecień 1988): 117. http://dx.doi.org/10.1016/0307-4412(88)90104-5.

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16

Lake, James A., Ryan G. Skophammer, Craig W. Herbold i Jacqueline A. Servin. "Genome beginnings: rooting the tree of life". Philosophical Transactions of the Royal Society B: Biological Sciences 364, nr 1527 (12.08.2009): 2177–85. http://dx.doi.org/10.1098/rstb.2009.0035.

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A rooted tree of life provides a framework to answer central questions about the evolution of life. Here we review progress on rooting the tree of life and introduce a new root of life obtained through the analysis of indels, insertions and deletions, found within paralogous gene sets. Through the analysis of indels in eight paralogous gene sets, the root is localized to the branch between the clade consisting of the Actinobacteria and the double-membrane (Gram-negative) prokaryotes and one consisting of the archaebacteria and the firmicutes. This root provides a new perspective on the habitats of early life, including the evolution of methanogenesis, membranes and hyperthermophily, and the speciation of major prokaryotic taxa. Our analyses exclude methanogenesis as a primitive metabolism, in contrast to previous findings. They parsimoniously imply that the ether archaebacterial lipids are not primitive and that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer. These results explain the similarities previously noted by others between the lipid synthesis pathways in eubacteria and archaebacteria. The new root also implies that the last common ancestor was not hyperthermophilic, although moderate thermophily cannot be excluded.

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17

Spiridonova, V. A., A. S. Akhmanova, V. K. Kagramanova, A. K. E. Köpke i A. S. Mankin. "Ribosomal protein gene cluster of Halobacterium halobium: nucleotide sequence of the genes coding for S3 and L29 equivalent ribosomal proteins". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 153–59. http://dx.doi.org/10.1139/m89-023.

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A 1643 base pair fragment encoding the S3 and L29 equivalent ribosomal proteins has been sequenced from the archaebacterium Halobacterium halobium. The incomplete open reading frame present upstream from the S3 gene encodes a protein homologous to the eubacterial ribosomal protein L22. The initiation codons of the S3 and L29 genes overlap with the termination codons of the upstream genes. A tight physical organization suggests that these genes are transcribed as a polycistronic operon. Peculiarities of the protein structure and gene organization are discussed.Key words: archaebacteria, ribosomal protein, halobacteria, gene structure, evolution.

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18

Thompson, Leo D., Larean D. Brandon, Daniel T. Nieuwlandt i Charles J. Daniels. "Transfer RNA intron processing in the halophilic archaebacteria". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 36–42. http://dx.doi.org/10.1139/m89-006.

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An in vitro assay system has been developed for the Halobacterium volcanii tRNA intron endonuclease using in vitro generated precursor RNAs. A partially purified enzyme preparation is capable of precise and accurate excision of the intron from the halobacterial tRNATrp precursor. The cleavage reaction produces products having 5′ hydroxyl and 2′,3′ cyclic phosphate termini. Processing of precursor molecules containing deletions within the exon regions indicates that the halobacterial endonuclease does not require intact mature tRNA structure in the substrate; this is in contrast to the eukaryotic endonuclease enzyme that has an absolute requirement for these structures. The large halobacterial tRNATrp intron does not appear to be a primary site for recognition by the endonuclease, however, its removal affects cleavage efficiency. Through a comparison of the structural and sequence features of the halobacterial substrates and the precursors of other archaebacterial intron-containing precursors, a common element is proposed for the recognition of substrates by intron endonuclease.Key words: archaebacteria, intron, tRNA, evolution, manipulation.

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19

Hackett, Neil R., i Shiladitya DasSarma. "Characterization of the small endogenous plasmid of Halobacterium strain SB3 and its use in transformation of H. halobium". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 86–91. http://dx.doi.org/10.1139/m89-013.

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To study the molecular biology of the halophilic archaebacterium Halobacterium halobium, the introduction of DNA engineered in vitro is desirable. As a first step in developing a cloning vector, the complete 1736 base pair nucleotide sequence of the natural, high copy number, Halobacterium plasmid pHSB1 has been determined. The plasmid was found to show homology to the small plasmids of Halobacterium strains GRB and GN101. Plasmid pHSB1 encodes a 317 amino acid protein of unknown function. The related halophile, H. halobium, could be transformed by pHSB1, demonstrating its utility as the basis of a cloning vector.Key words: archaebacteria, Halobacterium, plasmid.

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20

Zhou, D., i R. H. White. "Transsulfuration in archaebacteria." Journal of Bacteriology 173, nr 10 (1991): 3250–51. http://dx.doi.org/10.1128/jb.173.10.3250-3251.1991.

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21

Cavalier-Smith, T. "Archaebacteria and Archezoa". Nature 339, nr 6220 (maj 1989): 100–101. http://dx.doi.org/10.1038/339100a0.

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22

Nicolaus, Barbara, Agata Gambacorta, Anna Lisa Basso, Raffaele Riccio, Mario De Rosa i William D. Grant. "Trehalose in Archaebacteria". Systematic and Applied Microbiology 10, nr 3 (sierpień 1988): 215–17. http://dx.doi.org/10.1016/s0723-2020(88)80003-1.

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23

Martin, William, i Michael J. Russell. "On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells". Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 358, nr 1429 (29.01.2003): 59–85. http://dx.doi.org/10.1098/rstb.2002.1183.

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All life is organized as cells. Physical compartmentation from the environment and self–organization of self–contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life's most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide–rich hydrothermal fluid and iron(II)–containing waters of the Hadean ocean floor. The naturally arising, three–dimensional compartmentation observed within fossilized seepage–site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free–living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl–methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre–biotic syntheses occurred at the inner surfaces of these metal–sulphide–walled compartments, which furthermore restrained reacted products from diffusion into the ocean, providing sufficient concentrations of reactants to forge the transition from geochemistry to biochemistry. The chemistry of what is known as the RNA–world could have taken place within these naturally forming, catalyticwalled compartments to give rise to replicating systems. Sufficient concentrations of precursors to support replication would have been synthesized in situ geochemically and biogeochemically, with FeS (and NiS) centres playing the central catalytic role. The universal ancestor we infer was not a free–living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred. The first free–living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from their inorganic confines. We propose that the emergence of these prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane–lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca . 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non–free–living universal ancestor and before the origin of the free–living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The attributes unique to eukaryotes are viewed as inventions specific to their lineage. The origin of the eukaryotic endomembrane system and nuclear membrane are suggested to be the fortuitous result of the expression of genes for eubacterial membrane lipid synthesis by an archaebacterial genetic apparatus in a compartment that was not fully prepared to accommodate such compounds, resulting in vesicles of eubacterial lipids that accumulated in the cytosol around their site of synthesis. Under these premises, the most ancient divide in the living world is that between eubacteria and archaebacteria, yet the steepest evolutionary grade is that between prokaryotes and eukaryotes.

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24

May, Bruce P., Patrick Tam i Patrick P. Dennis. "The expression of the superoxide dismutase gene in Halobacterium cutirubrum and Halobacterium volcanii". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 171–75. http://dx.doi.org/10.1139/m89-026.

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The gene encoding the Mn-containing superoxide dismutase (SOD) from Halobacterium cutirubrum has been cloned and sequenced. The deduced amino acid sequence is homologous to the sequences of Fe and Mn SODs from eubacteria. The high degree of amino acid identity between the archaebacterial and eubacterial proteins suggests that a SOD gene may have been laterally transferred between eubacteria and archaebacteria sometime after the accumulation of atmospheric oxygen. Consensus elements of halobacterial promoters are found upstream of the coding region, however, the spacing between them and the transcription start site is greater than in other genes. Termination of transcription occurs in five consecutive T residues that are preceded by a GC-rich sequence that has short inverted repeats. In addition to the authentic SOD gene, H. cutirubrum also contains a putative pseudogene. The SOD levels and growth rates of H. cutirubrum and Halobacterium volcanii were tested in response to treatment by paraquat, an intracellular generator of superoxide. In H. volcanii the growth rate slowed, and SOD was strongly induced throughout prolonged treatment with paraquat. In H. cutirubrum the same effects were noticed initially, but after 48 h exposure to the drug, the growth rate increased and the SOD level decreased. Production of paraquat resistant mutants of H. cutirubrum may play a part in this process, however, some type of physiological adaptation is also probably required.Key words: archaebacteria, oxygen radicals, paraquat.

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25

Hidayah, Maulida Ulfa, Sonja V. T. Lumowa i Didimus Tanah Boleng. "The needs analysis of archaebacteria and eubacteria web-based biology learning media". JPBIO (Jurnal Pendidikan Biologi) 5, nr 2 (29.11.2020): 193–201. http://dx.doi.org/10.31932/jpbio.v5i2.727.

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The media used in learning archaebacteria and eubacteria are very varied, but there are still obstacles in the delivery of subject matter, so it is necessary that the formulation of media developed. The purpose of this research was to analyze the needs of developing web-based biology learning media on archaebacteria and eubacteria material for students of X-grade high school. The research sample was determined by a purposive sampling technique considering school status, conditions, school facilities, and students' characteristics. There are 3 samples of schools, namely 2 public schools and 1 private school in Balikpapan city. The research data were collected using observation and interview guidelines, the research data were also analyzed descriptively and quantitatively. The conclusions of this study: 1) the use of learning media as a teaching resource in the biology learning process that occurs in the field has not been carried out optimally; 2) archaebacteria and eubacteria material is difficult material; 3) Learning media that need to be developed on archaebacteria and eubacteria material is web-based media, namely multimedia that combines learning resources in the form of text, images, animation, practice questions, glossaries, sounds, and videos equipped with back sounds and captions.Keywords: Needs analysis, media learning, web-based, archaebacteria, eubacteria

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26

Martin, William. "Pathogenic archaebacteria: do they not exist because archaebacteria use different vitamins?" BioEssays 26, nr 5 (2004): 592–93. http://dx.doi.org/10.1002/bies.20044.

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Köpke, Andreas K. E., i Brigitte Wittmann-Liebold. "Comparative studies of ribosomal proteins and their genes from Methanococcus vannielii and other organisms". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 11–20. http://dx.doi.org/10.1139/m89-003.

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Using data from a partial protein sequence analysis of ribosomal proteins derived from the archaebacterium Methanococcus vannielii, oligonucleotide probes were synthesized. The probes enabled us to localize several ribosomal protein genes and to determine their nucleotide sequences. The amino acid sequences that were deduced from the genes correspond to proteins L12 and L10 from the rif operon, according to the genome organization in Escherichia coli, and to proteins L23 and L2, which have comparable locations, as in the Escherichia coli S10 operon. Various degrees of similarity were found when the four proteins were compared with the corresponding ribosomal proteins of prokaryotic or eukaryotic organisms. The highest sequence homology was found in counterparts from other archaebacteria, such as Halobacterium marismortui, Halobacterium halobium, or Sulfolobus. In general, the M. vannielii protein sequences were more related to the eukaryotic kingdom than to the Gram-positive or Gram-negative eubacteria. On the other hand, the organization of the ribosomal protein genes clearly follows the operon structure of the Escherichia coli genome and is different from the monocistronic eukaryotic gene arrangements. The protein coding regions were not interrupted by introns. Furthermore, the Shine–Dalgarno type sequences of methanogenic bacteria are homologous with those of eubacteria, and also their terminator regions are similar.Key words: archaebacteria, ribosomal proteins, evolution, gene organization, Methanococcus vannielii.

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28

ZILLIG, WOLFRAM. "Eukaryotic Traits in Archaebacteria." Annals of the New York Academy of Sciences 503, nr 1 Endocytobiolo (lipiec 1987): 78–82. http://dx.doi.org/10.1111/j.1749-6632.1987.tb40599.x.

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29

Walker, Richard T. "Archaebacteria—the third kingdom". Journal of Biological Education 24, nr 4 (grudzień 1990): 229–32. http://dx.doi.org/10.1080/00219266.1990.9655150.

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30

Kelly, D. P. "Microbiology: Crossroads for archaebacteria". Nature 313, nr 6005 (luty 1985): 734. http://dx.doi.org/10.1038/313734a0.

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31

Dennis, P. P. "Molecular biology of archaebacteria." Journal of Bacteriology 168, nr 2 (1986): 471–78. http://dx.doi.org/10.1128/jb.168.2.471-478.1986.

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32

Noll, K. M., i T. S. Barber. "Vitamin contents of archaebacteria." Journal of Bacteriology 170, nr 9 (1988): 4315–21. http://dx.doi.org/10.1128/jb.170.9.4315-4321.1988.

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33

Yang, Decheng, Brain P. Kaine i Carl R. Woese. "The Phylogeny of Archaebacteria". Systematic and Applied Microbiology 6, nr 3 (grudzień 1985): 251–56. http://dx.doi.org/10.1016/s0723-2020(85)80027-8.

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34

Rosa, Mario De, i Agata Gambacorta. "Lipid biogenesis in archaebacteria". Systematic and Applied Microbiology 7, nr 2-3 (maj 1986): 278–85. http://dx.doi.org/10.1016/s0723-2020(86)80020-0.

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35

Ford Doolittle, W. "Archaebacteria coming of age". Trends in Genetics 1 (styczeń 1985): 268–69. http://dx.doi.org/10.1016/0168-9525(85)90101-5.

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36

Eisenberg, Henryk. "Archaebacteria coming of age". Trends in Biochemical Sciences 13, nr 11 (listopad 1988): 416–17. http://dx.doi.org/10.1016/0968-0004(88)90207-1.

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37

Leffers, Henrik, Jørgen Kjems, Laust Østergaard, Niels Larsen i Roger A. Garrett. "Evolutionary relationships amongst archaebacteria". Journal of Molecular Biology 195, nr 1 (maj 1987): 43–61. http://dx.doi.org/10.1016/0022-2836(87)90326-3.

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38

Carteni-Farina, M., M. Porcelli, G. Cacciapuoti, M. Rosa, A. Gambacorta, W. D. Grant i H. N. M. Ross. "Polyamines in halophilic archaebacteria". FEMS Microbiology Letters 28, nr 3 (lipiec 1985): 323–27. http://dx.doi.org/10.1111/j.1574-6968.1985.tb00814.x.

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39

Dennis, Patrick P. "Molecular biology of archaebacteria". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 1. http://dx.doi.org/10.1139/m89-001.

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De Rosa, Mario, i Agata Gambacorta. "The lipids of archaebacteria". Progress in Lipid Research 27, nr 3 (styczeń 1988): 153–75. http://dx.doi.org/10.1016/0163-7827(88)90011-2.

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THURL, Stephan, Walter WITKE, Ingrid BUHROW i Wolfram SCHÄFER. "Quinones from Archaebacteria, II. Different Types of Quinones from Sulphur-Dependent Archaebacteria". Biological Chemistry Hoppe-Seyler 367, nr 1 (styczeń 1986): 191–98. http://dx.doi.org/10.1515/bchm3.1986.367.1.191.

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42

Sakane, T., I. Fukuda, T. Itoh i A. Yokota. "Long-term preservation of halophilic archaebacteria and thermoacidophilic archaebacteria by liquid drying". Journal of Microbiological Methods 16, nr 4 (grudzień 1992): 281–87. http://dx.doi.org/10.1016/0167-7012(92)90080-n.

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43

Gupta, Radhey S. "Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes". Microbiology and Molecular Biology Reviews 62, nr 4 (1.12.1998): 1435–91. http://dx.doi.org/10.1128/mmbr.62.4.1435-1491.1998.

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SUMMARY The presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. An alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. In this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryotes. They are believed to be descended from the most primitive organisms. Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria, and I suggest that this evolution occurred in response to antibiotic selection pressures. Evidence is presented that diderm prokaryotes (i.e., gram-negative bacteria), which have a bilayered cell wall, are derived from monoderm prokaryotes. Signature sequences in different proteins provide a means to define a number of different taxa within prokaryotes (namely, low G+C and high G+C gram-positive, Deinococcus-Thermus, cyanobacteria, chlamydia-cytophaga related, and two different groups of Proteobacteria) and to indicate how they evolved from a common ancestor. Based on phylogenetic information from indels in different protein sequences, it is hypothesized that all eukaryotes, including amitochondriate and aplastidic organisms, received major gene contributions from both an archaebacterium and a gram-negative eubacterium. In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes.

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44

Allmansberger, Rudolf, Martin Bokranz, Lothar Kröckel, Jürgen Schallenberg i Albrecht Klein. "Conserved gene structures and expression signals in methanogenic archaebacteria". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 52–57. http://dx.doi.org/10.1139/m89-008.

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A comparative analysis of cotranscribed gene clusters comprising the structural genes mcrA, mcrB, mcrC, mcrD, and mcrG was carried out in three species of methanogens. mcrA, mcrB, and mcrG are the structural genes for the three subunits of methyl coenzyme M reductase, while the two other genes encode polypeptides of unknown functions. The degree of conservation of the mcr gene products among different species of methanogens varies. No correlation was found between the conservation of the G + C contents of the homologous genes and of the amino acid sequences of their products among the different bacteria. The comparison of RNA polymerase core subunit genes of Methanobacterium thermoautotrophicum as evolutionary markers with their equivalents in Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster showed that homologous polypeptide domains are encoded by different numbers of genes suggesting gene fusion of adjacent genes in the course of evolution. The archaebacterial subunits exhibit much stronger homology with their eukaryotic than with their eubacterial equivalents on the polypeptide sequence level. All the analyzed genes are preceded by ribosome binding sites of eubacterial type. In addition to known putative promoter sequences, conserved structural elements of the DNA were detected surrounding the transcription initiation sites of the mcr genes.Key words: archaebacteria, methanogens, gene structure, RNA polymerase, promoter.

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45

Datta, Prasun K., Lynda K. Hawkins i Ramesh Gupta. "Presence of an intron in elongator methionine-tRNA of Halobacterium volcanii". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 189–94. http://dx.doi.org/10.1139/m89-029.

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The gene for the elongator (internal) methionine transfer RNA [Formula: see text] in the archaebacterium Halobacterium volcanii contains a 75 base pair intron (intervening sequence) and lacks the 3′-terminal CCA sequence of the mature tRNA. There is a single copy of this gene in the genome and it is expressed. Northern hybridization experiments indicate that the precursor is processed to produce mature tRNA and a free intron species. A secondary structure of the transcript can be formed in which the anticodon stem of the tRNA is extended. Two symmetrically placed three-base bulge loops separated by a 4 base pair stem are present in this extension. The cleavage sites for the removal of the intron are placed between the middle and 3′ residues of these loops.Key words: archaebacteria, methionine-tRNA, intron, splicing.

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46

Khotimah, Fina Nurul. "MISKONSEPSI KONSEP ARCHAEBACTERIA DAN EUBACTERIA". EDUSAINS 6, nr 2 (3.03.2015): 117–28. http://dx.doi.org/10.15408/es.v6i2.1112.

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Penelitian ini bertujuan untuk mengidentifikasi miskonsepsi siswa pada konsep Archaebacteria dan Eubacteria. Penelitian ini menggunakan metode survei dengan instrumen berupa pilihan ganda beralasan terbuka sebagai alat ukur. Unit analisis dalam penelitian adalah siswa MAN kelas X berjumlah 72 orang. Hasil analisis ditemukan ketidakpahaman pada konsep Archaebacteria dan Eubacteria (61%) yang mendominasi kategori lainnya. Sedangkan kategori Paham konsep dan Miskonsepsi hanya sebesar 19% dan 20%. Miskonsepsi yang dialami siswa dari hasil diagnosa alasan terbuka menunjukkan lebih banyak miskonsepsi utuh dibandingkan dengan miskonsepsi sebagian. Miskonsepsi utuh teridentifikasi dengan siswa beranggapan bahwa bakteri lebih banyak menimbulkan kerugian daripada keuntungan bagi manusia dan lingkungan.

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47

Stupar, Milanko. "Genetic recombination and the origin of mitochondrion". Archive of Oncology 11, nr 1 (2003): 35–38. http://dx.doi.org/10.2298/aoo0301035s.

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Division of ancestral prokaryotic genome into two circular double-stranded DNA molecules is a basis for future separate evolution of nuclear and mitochondrion compartments. Universal double sheet of lipid molecules by invagination, at the level of membrane-hairpin attachment, formed two-layered envelope completely surrounding those two DNAs. Presumed ancestral prokaryote in this case is an Archaebacteria, which would lead to formation of six main groups of organisms: Archaebacteria (Archaea) eubacteria, Protista, Fungi, Plantae and Animalia.

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48

Thomm, Michael, Günter Wich, James W. Brown, Gerhard Frey, Bruce A. Sherf i Gregory S. Beckler. "An archaebacterial promoter sequence assigned by RNA polymerase binding experiments". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 30–35. http://dx.doi.org/10.1139/m89-005.

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To identify an archaebacterial promoter sequence, nuclease protection studies with the purified RNA polymerase of Methanococcus vannielii were performed. The enzyme binds specifically both at protein-encoding (hisA and methyl CoM reductase, component C) and tRNA–rRNA genes. The binding region of the RNA polymerase extends from 30 base pairs (bp) upstream (−30) to 20 bp downstream (+20) from the in vivo transcription start site. This finding indicates that the archaebacterial enzyme recognizes promoters without transacting traascription factors. The DNA segment protected from nuclease digestion by bound RNA polymerase contains an octanucleotide sequence centered at −25, which is conserved between the protein-encoding and the stable RNA genes. According to the specific binding of the enzyme to only DNA-fragments harbouring this motif, we propose the sequence TTTATATA as the major recognition signal of the Methanococcus RNA polymerase. Comparison of this motif with published archaebacterial DNA sequences revealed the presence of homologous sequences at the same location upstream of 36 genes. We therefore consider the overall consensus [Formula: see text] as a general element of promoters in archaebacteria. In spite of the specific binding of the enzyme, most preparations of the Methanococcus vannielii RNA polymerase are unable to initiate transcription at the correct sites in vitro. Here we present first evidence for the possible existence of a transcription factor conferring the ability to the enzyme to initiate and terminate transcription specifically in vitro.Key words: promoter, footprint, TATA box, RNA polymerase, transcription.

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Ree, Heesoo K., Kaiming Cao, David L. Thurlow i Robert A. Zimmermann. "The structure and organization of the 16S ribosomal RNA gene from the archaebacterium Thermoplasma acidophilum". Canadian Journal of Microbiology 35, nr 1 (1.01.1989): 124–33. http://dx.doi.org/10.1139/m89-019.

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The complete nucleotide sequence of the 16S rRNA gene from Thermoplasma acidophilum, as well as its 5′ and 3′ flanking regions, were determined by the dideoxynucleotide chain termination method. The 16S rRNA gene encodes 1471 nucleotides. The primary and secondary structures of T. acidophilum 16S rRNA both exhibit typical archaebacterial features. The sequence appears to be more closely related to 16S rRNAs of the methanogen–halophile group than to those of the thermoacidophile group. Secondary-structure comparisons generally support this relationship, although there are several examples in which the single-stranded loops in particular helices of T. acidophilum 16S rRNA more strongly resemble their counterparts in the 16S rRNA of Sulfolobus solfataricus, a member of the thermoacidophile group. In contrast to the polycistronic rRNA operons found in most organisms, the three rRNA genes from T. acidophilum occur in only a single copy per genome and appear to be physically unlinked. Consistent with this, the 16S rRNA gene is flanked by putative promoter and terminator sequences that are comparable to the transcription control signals from other archaebacterial genes. The sequence TATATATA, which is very similar to the archaebacterial promoter consensus TTTAT/AATA, is located 18 bases before the probable site of transcription initiation, TGCACAT. There is a potential transcription termination site immediately downstream from the gene that consists of a relatively stable stem and loop structure followed by stretches of Tresidues.Key words: archaebacteria, thermoacidophile, rRNA sequence, rRNA secondary structure, promoter.

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50

SUCKOW, Jörg Michael, i Masashi SUZUKI. "Genomic DNA shuffling in archaebacteria". Proceedings of the Japan Academy. Ser. B: Physical and Biological Sciences 75, nr 1 (1999): 10–15. http://dx.doi.org/10.2183/pjab.75.10.

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