Search PubMed⌕ Search

Biomedical subjects

P Palm

Publications and source records attributed to P Palm.

At least 37 records · Page 2Linked to original sources
PubMed1990

Identification and characterization of a defective SSV1 genome integrated into a tRNA gene in the archaebacterium Sulfolobus sp. B12.

Within the chromosome of the archaebacterium Sulfolobus sp. B12, a 7.4 kb region was identified which displayed extensive sequence similarities to the 15.5 kb genetic element SSV1 carried by the same strain both as a circular form and as a site-specifically integrated copy. DNA sequence analysis indicated that this 7.4 kb region (designated SSV1intB) represented an SSV1-like element distinguishable from the full-length integrated copy (designated SSV1intA) by extensive deletions and point mutations. The physical organization of DNA sequences of SSV1intB indicated that this element was integrated at the same attP site as previously identified for SSV1intA. A comparison of the DNA sequences at the left attachment sites of SSV1intA and SSV1intB revealed that they both represented very similar putative arginine tRNA genes followed by a 10 bp inverted repeat sequence. S1 nuclease mapping experiments indicated that these tRNA genes are transcribed.

Archaea↗
PubMed1990

Phylogenetic analysis of the RNA polymerases of Trypanosoma brucei, with special reference to class-specific transcription.

We have sequenced the genes encoding to largest subunits of the three classes of DNA-dependent RNA polymerases of Trypanosoma brucei. The nucleotide and deduced amino acid sequences were compared and aligned with the corresponding sequences of other eukaryotes. Phylogenetic relationships were subsequently calculated with a distant matrix, a bootstrapped parsimony and a maximum-likelihood method. These independent calculations resulted in trees with very similar topologies. The analyses show that all the largest subunits of T. brucei are evolutionarily distant members within each of the three RNA polymerase classes. An early separation of the trypanosomal subunits from the eukaryotic lineage might form the fundamental basis for the unusual transcription process of this species. Finally, all dendrograms show a separate ramification for the largest subunit of RNA polymerase I, II and III. RNA polymerase II and/or III form a bifurcation with the archaebacterial lineage, RNA polymerase I, however, arises separately from the eubacterial beta' lineage. This suggests that the three eukaryotic RNA polymerase classes are not simply derived by two gene duplications of an ancestral gene with subsequent differentiation.

Amino Acid Sequence↗
PubMed1989

Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements.

The DNA sequences were determined at the boundaries of the integrated copy of the archaebacterial genetic element SSV1. A 44 bp sequence present as a single copy on the 15.5 kb circular SSV1 DNA flanked the integrated copy as a direct DNA sequence repeat, suggesting that SSV1 integration occurred by recombination between this 44 bp SSV1 sequence and an identical sequence on the bacterial chromosome. At the left attachment site, a region encompassing the 44 bp attachment core sequence and the 31 nucleotides upstream of it displayed all characteristics expected for an arginine tRNA gene. An analysis of published attachment site sequences of other systems revealed that tRNA genes also constitute the bacterial attachment site in the case of three temperate phages and two transmissible plasmids in eubacteria, indicating a widespread occurrence of tRNA genes as integration target sites. This finding may be important for the understanding of mechanisms and evolution of site-specific recombination.

Archaea↗
PubMed1989

Archaebacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome.

Genes for DNA-dependent RNA polymerase components B, A, and C from the archaebacterium Sulfolobus acidocaldarius and for components B", B', A, and C from the archaebacterium Halobacterium halobium were cloned and sequenced. They are organized in gene clusters in the order above, which corresponds to the order of the homologous rpoB and rpoC genes in the corresponding operon of the Escherichia coli genome. Derived amino acid sequences of archaebacterial components A and C were aligned with each other and with the sequences of corresponding (largest) subunits from the archaebacterium Methanobacterium thermoautotrophicum, with sequences of various eukaryotic nuclear RNA polymerases I, II, and III, and with the sequence of the beta' component from E. coli polymerase. The archaebacterial genes for component A are homologous to about the first two-thirds of genes for the eukaryotic component A and the eubacterial component beta', and the archaebacterial genes for component C are homologous to the last third of the genes for the eukaryotic component A and the eubacterial component beta'. Unrooted phylogenetic dendrograms derived from both distance matrix and parsimony analyses show the archaebacteria are a coherent group closely related to the eukaryotic nuclear RNA polymerase II and/or III lineages. The eukaryotic polymerase I lineage appears to arise separately from a bifurcation with the eubacterial beta' component lineage.

Amino Acid Sequence↗
PubMed1989

The phylogenetic relations of DNA-dependent RNA polymerases of archaebacteria, eukaryotes, and eubacteria.

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 beta' and chloroplast beta' and beta" 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 beta' lineage. The implications of these results, especially for understanding the possibly chimeric origin of the eukaryotic nuclear genome, are discussed.

Amino Acid Sequence↗
PubMed1989

Sequence comparison of glyceraldehyde-3-phosphate dehydrogenases from the three urkingdoms: evolutionary implication.

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 eukaryotic 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.

Amino Acid Sequence↗
PubMed1989

Expression and regulation of Halobacterium halobium phage phi H genes.

In this paper we describe five distinct modes of phi H gene expression: (i) transcription of phage phi H during lytic growth on the sensitive host bacterium (Halobacterium halobium strain R1); (ii) transcription of the circularized prophage phi H1 in strain R(1)24; (iii) transcription of the L region of phi H present as 12-kilobase-plasmid in the immune strain R1L; (iv) transcription during the lytic growth of phage mutants containing an ISH23/50 in the immune strain R1L; (v) transcription during lytic growth of ISH23/50-insertion mutants in the sensitive host bacterium R1 showing enhancement of early transcripts. The sequential expression of the phage genome is described together with a detailed analysis of the transcription of early lytic, constitutive, and immune genes that map in the L region. The putative promoter sequences determined for several phage genes were compared with the upstream sequences of the H. halobium DNA-dependent RNA polymerase large subunit genes and with the gene for the ribosomal protein S12 homolog of H. halobium. The similarity of these putative promoter elements revealed conserved motifs that are discussed in relation to the TATA-box motif recognized by the eukaryotic DNA-dependent RNA polymerase II.

Bacteriophages↗
PubMed1988

Comparative evaluation of gene expression in archaebacteria.

Gene organization, gene structure, especially regarding transcription and translation signals, and the structure of essential components of the gene expression machinery of archaebacteria are compared with those of eubacteria and eukaryotes. Many features of the genetic machinery of archaebacteria are shared either with eubacteria or with eukaryotes. For example, the translation signals including ribosome-binding sites are the same as in eubacteria, but the consensus sequence of archaebacterial promoters closely resembles that of the eukaryotic polymerase II promoters. Archaebacterial genes can be organized in transcription units resembling those of eubacteria. But the sequences of several protein components of the genetic machinery have strikingly more homology with those of their eukaryotic than with those of their eubacterial correspondents. The sequences of the large components of DNA-dependent RNA polymerases of archaebacteria closely resemble those of the eukaryotic RNA polymerases II and, somewhat less, III. In a dendrogram calculated from percentage homology data, the eukaryotic RNA polymerase I component A shares a branching point with the eubacterial component. The implications of these findings for the origin and the evolution of the eukaryotic ancestry are discussed.

Archaea↗
PubMed1988

Transcription termination in the archaebacterium Sulfolobus: signal structures and linkage to transcription initiation.

The precise map positions were determined for the 3'-termini of five transcripts of the Sulfolobus virus-like particle SSV1. In all cases analyzed, these 3'-termini mapped immediately downstream of a sequence TTTTTYT which was part of a pyrimidine-rich region of 16-19 nucleotides length. No correlation was evident between the position of the 3'-termini and possible secondary structures within the RNA. In two cases, the 3'-termini of SSV1 transcripts mapped in the immediate vicinity of transcriptional initiation sites suggesting that transcription termination can be linked to the re-initiation of RNA synthesis.

Archaea↗
PubMed1988

Analysis of transcription in the archaebacterium Sulfolobus indicates that archaebacterial promoters are homologous to eukaryotic pol II promoters.

The 5'-termini were precisely mapped for five constitutive and one UV-inducible transcript from the Sulfolobus virus-like particle SSV1. The comparison of the DNA sequences around these transcriptional initiation sites revealed the presence of two conserved sequence elements: a trinucleotide sequence close to the initiation site itself and an AT-rich hexanucleotide sequence centered about 26 nucleotides upstream of it. Similar DNA sequences were found upstream of the transcriptional start sites for the ribosomal RNA genes in Sulfolobus and upstream of transcriptional start sites in other archaebacteria, allowing the derivation of a general consensus sequence for archaebacterial promoters. This consensus sequence is unlike that found in eubacteria but it resembles promoters recognized by eukaryotic RNA polymerase II.

Archaea↗
PubMed1987

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.

Archaea↗
PubMed1987

Large-scale preparation of a DNA fragment containing the strong promoter A1 of the phage T7.

A procedure has been developed to isolate DNA fragments on a large scale. A DNA fragment of 130 base-pairs containing the strong promoter A1 of the phage T7 was purified to homogeneity in amounts of 10 mg. The procedure includes the rapid purification of gram amounts of plasmid DNA, a new, simple method to separate small DNA fragments from the vector by a phenol/water partitioning system, and a liquid-liquid PEG-dextran partition chromatography for the final purification of the fragment. The fragment was cloned in two vector systems: The vector pDS1, to1+ (1), containing an efficient terminator downstream from the promoter integration site, gives high yields, 3-4 mg plasmid DNA per liter medium. In the plasmid pWH802 (2), which is not specially designed for the amplification of a strong promoter, the integration of the promoter was possible but the yield decreased by a factor of about 50. The stability of the inserts was tested in both systems. Monomeric inserts were stable in both plasmids, multimeric inserts up to a tetramer were only stable in pWH802. Only one orientation of the fragment was found.

Biotechnology↗
PubMed1987

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.

Base Sequence↗
PubMed1984

Sequence analysis of the insertion element ISH1.8 and of associated structural changes in the genome of phage PhiH of the archaebacterium Halobacterium halobium.

We have sequenced the insertion element ISH1.8 which can be present in one or two copies in the genome of phage PhiH of Halobacterium halobium. ISH1.8 is 1895 bp long, has no inverted repeat at its ends, and one only of the two copies is flanked by two 5-bp duplications. An 8-bp sequence composed of 4 bp from each end of ISH1.8 is present in both sites lacking the element. This 8-bp sequence could either be a specific insertion sequence or a part of the element that is left behind upon deletion. The plasmid pPhiHL, consisting of the invertible L segment of the phage genome which is, in PhiH2 and PhiH5, flanked by two copies of ISH1.8, contains 112 bp of ISH1.8 and is released from the phage genome by recombination within a direct repeat of 9 bp. This 9-bp sequence (TCCCGCCCT) exists as an inverted repeat in ISH1.8 and therefore as two distinct repeats in phage genomes containing two copies of ISH1.8 in inverted orientation.

Journal Article↗
PubMed1981

Control of promoter utilization by bacteriophage T4-induced modification of RNA polymerase alpha subunit.

After infection of Escherichia coli cells, bacteriophage T4 induces several changes in the host DNA-dependent RNA polymerase. A well-characterized chemical change is a two-step ADP-ribosylation of the enzyme's alpha subunit (1). In order to investigate the effect of this change on RNA polymerase transcriptional properties in an in vitro system, we have reconstituted the enzyme from separated individual subunits which were obtained from normal or T4-modified RNA polymerases. It is demonstrated that the enzymes containing T4-modified alpha differ from the enzymes with normal alpha in two respects: (i) their overall activity on T4 DNA is reduced and (ii) they fail to utilize certain T4 promotors while efficiently utilizing other promoters. Among the promoters which are switched off by alpha modification are the two promoters of the D region and one of the two promoters of the T4 tRNA gene cluster. The differential effect of alpha modification on the expression of the tRNA and the D regions in vitro correlates with the previously established pattern of their transcription in vivo. It is suggested that the T4-induced ADP-ribosylation of RNA polymerase alpha subunit is involved in the shutoff of the early bacteriophage genes at the late stage of phage development.

DNA-Directed RNA Polymerases↗