Biomedical subjects
W Zillig
Publications and source records attributed to W Zillig.
Rooting the archaebacterial tree: the pivotal role of Thermococcus celer in archaebacterial evolution.
The sequence of the 16S ribosomal RNA gene from the archaebacterium Thermococcus celer shows the organism to be related to the methanogenic archaebacteria rather than to its phenotypic counterparts, the extremely thermophilic archaebacteria. This conclusion turns on the position of the root of the archaebacterial phylogenetic tree, however. The problems encountered in rooting this tree are analyzed in detail. Under conditions that suppress evolutionary noise both the parsimony and evolutionary distance methods yield a root location (using a number of eubacterial or eukaryotic outgroup sequences) that is consistent with that determined by an "internal rooting" method, based upon an (approximate) determination of relative evolutionary rates.
Putative promoter elements for the ribosomal RNA genes of the thermoacidophilic archaebacterium Sulfolobus sp. strain B12.
In Sulfolobus sp. strain B12, single-copy genes encode the three ribosomal RNAs. The genes for the 16S rRNA and for the 23S rRNA are closely linked but separated from the 5S rRNA gene. Transcription of the 16S/23S rRNA gene cluster starts 139 nucleotides upstream of the 5'-end of mature 16S rRNA. For the 5S rRNA gene the point of transcription initiation coincides with the 5'-end of mature 5S rRNA. The comparison of the upstream regions for these transcriptional start sites shows the presence of a completely conserved trinucleotide sequence around the point of transcription initiation and a completely conserved octanucleotide sequence about 22 nucleotides upstream of it. These sequences are only moderately homologous to putative promoter elements for stable RNA genes in the closely related archaebacterium Thermoproteus tenax (1), but they are very similar to corresponding sequences in the distantly related archaebacterium Methanococcus vannielii (2). The consensus sequence found for Sulfolobus and Methanococcus could therefore constitute the archetype of an archaebacterial promoter for stable RNA genes.
Gene expression in archaebacteria: physical mapping of constitutive and UV-inducible transcripts from the Sulfolobus virus-like particle SSV1.
The transcription of the genome of the UV-inducible Sulfolobus virus-like particle SSV1 was studied. Eight different transcripts could be distinguished by Northern analysis that were present in uninduced cells and the coordinately increased in amount after UV induction of SSV1. Using single-stranded DNA probes from different parts of the genome, the approximate map positions of these RNAs and the directions of transcription were determined. In two cases, terminator read-through resulted in the formation of more than one RNA species from a single 5' end and therefore the eight different RNAs corresponded to only five different transcriptional starts. Two RNAs sharing a common 5' end encode SSV1 structural proteins. The 5' end of these transcripts was determined by S1 nuclease analysis. About 20 nucleotides upstream of the transcriptional start of these RNAs, there is an AT-rich region resembling putative promoter sequences which have been found at a similar distance 5' to the genes encoding stable RNAs in Thermoproteus. In addition to the eight constitutive transcripts, a UV-inducible RNA of 0.3 kb was mapped on the SSV1 genome. In contrast to all other RNAs, it was not detectable in uninduced cells and it is expressed shortly before the amplification and packaging of the SSV1 genome commences.
Eukaryotic traits in Archaebacteria. Could the eukaryotic cytoplasm have arisen from archaebacterial origin?
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Archaebacteria and the origin of the eukaryotic cytoplasm.
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A new ribosome structure.
Ribosomes derived from the sulfur-dependent archaebacteria are structurally distinct from those types found in ribosomes from eubacteria, eukaryotes, and other archaebacteria. All four ribosome types share a common structural core, but each type also has additional independent structural features. In the smaller subunit derived from sulfur-dependent archaebacteria ("eocytes"), lobes, similar to those found at the base of the eukaryotic small subunits, and an archaebacterial bill, similar to those found on the smaller subunit of archaebacteria and eukaryotes, are present. On the larger subunit from sulfur-dependent archaebacteria, an eocytic lobe, eocytic gap, and eocytic bulge are present. These features, with the exception of the eocytic gap, are found in a slightly modified form on eukaryotic large subunits. These novel ribosomal properties are in general consistent with other molecular biological properties peculiar to these organisms.
SAV 1, a temperate u.v.-inducible DNA virus-like particle from the archaebacterium Sulfolobus acidocaldarius isolate B12.
Sulfolobus acidocaldarius, strain B12, which harbours a double-stranded DNA species both as a plasmid and in a linear form, which is integrated at a specific site of the chromosome, produces virus-like particles upon u.v. irradiation. These particles contain the same circular DNA and a number of coat proteins and are probably surrounded by a lipid membrane. They are lemon shaped, 100 x 60 nm in size and carry tail structures at one pole. The host cell recovers and remains lysogenic after virus production. Though a large fraction of liberated particles is found attached to structures derived from the cells, neither adsorption nor infection of a number of Sulfolobus isolates has so far been observed.
The phylogenetic relationships of three sulfur dependent archaebacteria.
Oligonucleotide catalogs have been determined for the 16S ribosomal RNAs of three sulfur dependent (i.e. "thermoacidophilic") archaebacteria--Sulfolobus acidocaldarius, S. solfataricus, and Thermoproteus tenax. The three form a group specifically related to one another, but are only distantly related to the other archaebacteria--i.e. the group comprising the methanogens, extreme halophiles, and (peripherially) the genus Thermoplasma. The three catalogs exhibit two features unique among bacteria: (1) an unusually high number of long pyrimidine runs, and (2) a remarkably high number of (post-transcriptionally) modified nucleotides.
Genome organization and transcription in archaebacteria.
The genome organization of the archaebacteria is investigated in three model systems: a) rRNA genes of various archaebacteria, b) a plasmid of 15.6 kb from Sulfolobus acidocaldarius which exists in free or integrated form, c) the 59 kb genome of phage phi H of Halobacterium halobium as a model for the unusual structural variability of DNA in this organism. Several variants of this phage have been isolated, their genomes differ by several insertions, a deletion, and an inversion. The frequent inversion and circularization of a 12 kb segment of DNA appears to be linked to the presence of two copies of an IS element at its flanks. DNA-dependent RNA polymerases have been isolated from a large number of archaebacteria including representatives of 4 families of the novel order Thermoproteales . As shown by immunological methods, they are closely related to those of eukaryotes. Two different types of RNA polymerase exist in the two main branches of the archaebacteria. The role of one component of the enzyme of Thermoplasma acidophilum was elucidated using an in vitro transcription system.
DNA-dependent RNA polymerase from the extremely halophilic archaebacterium Halococcus morrhuae.
Pure and absolutely DNA-dependent RNA polymerase has been isolated from the extremely halophilic archaebacterium, Halococcus morrhuae. It is composed of five heavy (142 000; 88 000; 73 000; 52 500; and 49 500 Da) and five small components (13 300; 11 200; 10 800; 10 500; 9 900 Da). The peptides of 49 500 Da and 52 500 Da probably represent one component in different modification states. Single-stranded DNA shows the highest template efficiency, although archaebacterial chromosomal DNAs are efficiently transcribed. Rifampicin, streptolydigin and alpha-amanitin do not inhibit transcription by this enzyme. Heparin permits elongation but not initiation of transcription. The activity of H. morrhuae RNA polymerase is strongly stimulated by glycerol and dimethylsulfoxide.
A form of the DNA-dependent RNA polymerase of Halobacterium halobium, containing an additional component, is able to transcribe native DNA.
A revised procedure for the purification of DNA-dependent RNA polymerase from Halobacterium halobium, including two-phase partition, yields pure, highly active and absolutely DNA-dependent enzyme. Two forms of the enzyme, one containing, the other not containing a previously not observed component, epsilon, show striking differences in activity. RNA polymerase without component epsilon has a significant activity on poly[d(A-T)] but only insignificant activity on all other templates. The enzyme containing a stoichiometric amount of component epsilon transcribes poly[d(A-T)] and native templates efficiently.
Chemolithoautotrophic metabolism of anaerobic extremely thermophilic archaebacteria.
Several types of extremely thermophilic archaebacteria have recently been isolated from solfataric water holes, hot springs and hot sea floors. It has been shown that some of them can live using sulphur respiration of reduced carbon substrates as a source of energy, a type of metabolism previously described for the eubacterium Desulfuromonas. We report here that several extremely thermophilic archaebacteria can live with carbon dioxide as their sole carbon source, obtaining energy from the oxidation of hydrogen by sulphur, producing hydrogen sulphide. They are thus capable of a new type of anaerobic, purely chemolithoautotrophic metabolism, a possible primaeval mode of life.
Structural homology between different archaebacterial DNA-dependent RNA polymerases analyzed by immunological comparison of their components.
The archaebacterial DNA-dependent RNA polymerases have a complex structure containing eight or more components. Immunochemical analysis shows an extensive homology between the components of the enzymes of nine different species. Two enzyme subtypes can be distinguished: that of the thermoacidophilic and/or sulfur-metabolizing archaebacteria with the composition BACDEFGHIJ and that of the methanogenic plus halophilic archaebacteria with the composition ABB'C(D).... Components B and B' of the latter subtype probably evolved by the division of the large component B of the BACD... type enzyme. The existence of the two subtypes corroborates the division of the archaebacteria into two phylogenetic main branches.
Archaebacteria and eukaryotes possess DNA-dependent RNA polymerases of a common type.
DNA-dependent RNA polymerases of archaebacteria not only resemble the nuclear RNA polymerases of eukaryotes rather than the eubacterial enzymes in their complex component patterns but also show striking immunochemical, i.e., structural, homology with the eukaryotic polymerases at the level of single components. Thus, eukaryotic and archaebacterial RNA polymerases are indeed of the same type, distinct from the eubacterial enzymes, which, however, are also derived from a common ancestral structure.
Component E of the DNA-dependent RNA polymerase of the archaebacterium Thermoplasma acidophilum is required for the transcription of native DNA.
The role of component E of the DNA-dependent RNA polymerase of the archaebacterium Thermoplasma acidophilum in the transcription of Thermoplasma DNA has been analyzed. Component E (Mr 22000) is released upon formation of the binary complex of the polymerase with the DNA. Enzyme not containing component E is inactive on DNA but active on poly[d(A-T) X d(A-T)]. The activity on DNA can be restored by addition of component E. Two states of the binding complex between RNA polymerase and DNA, differing in their ionic strength stabilities, have been distinguished both in the presence and absence of component E. The transition temperature between the two states is 43 degrees C. Component E appears to open productive binding sites in native DNA in addition to the non-productive strong binding sites available for component-E-deficient enzyme.
Organization of rRNA structural genes in the archaebacterium Thermoplasma acidophilum.
In the archaebacterium Thermoplasma acidophilum, each of the structural genes for 5S, 16S and 23S rRNA occur once per genome. In contrast to those of eubacteria and eukaryotes, they appear unlinked. The distance between the 16S and the 23S rDNA is at least 7.5 Kb, that between 23S and 5S rDNA at least 6 Kb and that between 16S and 5S rDNA at least 1.5 Kb. No linkage between those genes has been found by the analysis of recombinant plasmids carrying Bam HI and Hind III rDNA fragments as by hybridizing those plasmids to fragments of Thermoplasma DNA generated by 6 individual restriction endonucleases, recognizing hexanucleotide sequences.
The role of the components sigma and y of the DNA-dependent RNA polymerase of Lactobacillus curvatus in promotor selection.
An average of 0.44 molecule each of the initiation factor sigma and the RNA polymerase binding protein y and 0.54 molecule of the subunit gamma per molecule of Lactobacillus curvatus DNA-dependent RNA polymerase have been found in the cell. Free factor y displaces sigma from free holo enzyme, E sigma. The formation of a binary complex from Ey, free sigma, and poly[d(A-T)], leads to immediate release of factor y. The release of the sigma factor occurs upon the transition of the binary to a ternary complex. A mixture of E and sigma forms binary complexes with all T7 DNA HpaII restriction fragments. In contrast a mixture of Ey and sigma binds selectively to promoter-containing DNA fragments, indicating that the stimulatory effect of y on transcription is due to an increase in the rate of promoter selection. The same RNA products are synthesised by E sigma and by Ey plus sigma with T7 DNA as template. Thus the nonspecific complexes formed by E sigma and T7 DNA are nonproductive. On the basis of these findings we propose a model for the transcription cycle in Lactobacillus curvatus.