Evolutionary relationships amongst archaebacteria

Leffers, Henrik; Kjems, Jørgen; Østergaard, Louise; Larsen, Niels; Garrett, Roger A.

doi:10.1016/0022-2836(87)90326-3

Cited by 179 publications

(63 citation statements)

References 56 publications

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“…Initially, we were sceptical about formation ofthe bulge-helix-bulge structure in pre-23S RNA of D. mobilis because it would require a substantial RNA rearrangement, after cleavage, to generate the mature 23S RNA (8,19). However, subsequently, we found an intron-containing pre-tRNA (9), in addition to two described earlier for Thermoproteus tenax (6), and now the pre-rRNA from S. marinus, all of which form a bulge-helixbulge feature at the expense ofthe mature RNA structure (35,36).…”

Section: Discussionmentioning

confidence: 99%

“…Cloning was performed by replacing the internal BamHI fragment of A-EMBL3 (18) with genomic DNA cut with BamHI. The rRNA genes were selected by using a mixture of randomly labeled RNA fragments from the 3' half of 23S RNA from other extreme thermophiles (17,19,20). An -8-kbp BamHI fragment was isolated from S. marinus and a 2.2-kbp BamHI-Pvu II fragment, containing 1.8 kbp of the 23S RNA gene, was subcloned in M13mpl9.…”

Section: Methodsmentioning

confidence: 99%

“…1). They occur after nucleotides A-2098 and C-2769 and both precede the mobilis 23S RNA are used (19 The primers were extended by using reverse transcriptase. Ligation sites are marked with arrows and the RNA sequences across these sites are shown.…”

Section: Splicing Inmentioning

confidence: 99%

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Ribosomal RNA introns in archaea and evidence for RNA conformational changes associated with splicing.

Kjems¹,

Garrett²

1991

Proc. Natl. Acad. Sci. U.S.A.

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The single 23S rRNA gene of the archaeon Staphylothermus marinus exhibits two introns which, at the RNA level, are located in highly conserved regions of domains IV and V. The RNA introns, which are 56 and 54 nucleotides long, respectively, can form single hairpin structures. In vivo, RNA splicing occurs efficiently, whereas in vitro pre-rRNA transcripts containing each intron were cleaved efficiently when incubated with archaeal cell extracts but were poorly ligated. The introns are cleaved by a mechanism which differs from the mechanisms of eukaryotic rRNA introns but resembles those of the rRNA intron of Desulfurococcus mobilis and the archaeal tRNA introns. The cleavage enzyme recognizes and cuts a putative bulge-helix-bulge structure that can form at the archaeal exon-intron junctions. Using a phylogenetic sequence comparison approach, we defime the parts of this structural feature that are essential for cleavage. We also provide evidence for conformational changes occurring in the S. maninus 23S RNA, after cleavage, at both exon-exon junctions, which may account for the low yields of ligation observed in vitro.Introns occur widely among eukaryotic nuclei and organelles in genes for proteins, ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs) (1, 2). Among archaea they have been detected in one rRNA gene (3) and in some tRNA genes (4-9). So far, they have not been detected in bacterial genomes, although they occur in protein genes of some bacteriophages (10, 11).The only archaeal rRNA intron detected to date lies within the 23S RNA gene of Desulfurococcus mobilis (3). On excision, it yields a circular RNA which is large [622 base pairs (bp)] and stable and probably encodes a single protein (12). Although its splicing mechanism is special and differs in many respects from the mechanisms of eukaryotic group I introns, it shows similarities to the splicing of the intron in pre-tRNA Trp of extreme halophiles (13) and other archaeal tRNA introns (4, 6-9); thus all can generate a bulge-helixbulge structure at the exon-intron junction that may constitute a substrate for the cleavage enzyme (8,9,13,14).A possible basis for this similar mechanism of rRNA and tRNA cleavage is that the D. mobilis intron lies in a region of 23S RNA that appears isostructural with the D and anticodon arms of tRNA (12,15). Therefore, to establish whether this intron and its location were an exception among archaeal pre-rRNAs, we searched for new rRNA introns among extreme thermophiles. The 23S rRNA genes from four recently discovered organisms were examined and one ofthem, from Staphylothermus marinus (16), exhibited two introns. ¶ Their mechanisms of cleavage are shown to be similar to those of the D. mobilis intron, and both require a rearrangement of base pairing, after cleavage, to generate the mature 23S RNA structure. MATERIALS AND METHODSPreparation of Cells, Cellular DNA, and RNA; Cloning and DNA Sequencing. Cells from S. marinus, Pyrobaculum islandicum, Pyrococcus furiosus, and Pyrodictium occultum were kindly provided by ...

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Ribosomal RNA introns in archaea and evidence for RNA conformational changes associated with splicing.

Kjems¹,

Garrett²

1991

Proc. Natl. Acad. Sci. U.S.A.

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“…In the halophilic branch of archaebacteria, the primary structures of a number of stable RNA genes from different species are now available [2][3][4][5]. However, only a few protein genes from halobacteria have been sequenced [6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

The nucleotide sequence of the genes coding for the S19 and L22 equivalent ribosomal proteins from Halobacterium halobium

Mankin¹

1989

FEBS Letters

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“…This sequence information indicated that the evolutionary relationships between eubacteria, archaebacteria and eukaryotes are equidistant [ 11. Similar studies on the evolutionary relationships between these three groups were based on the sequences of the 23 S-like rRNAs [2] and the 5 S rRNAs [3]. The results of the 23 S-like rRNAs are essentially the same as those from the 16 S-like rRNAs, while the data from 5 S rRNAs are somewhat different in that the archaebacteria may have diverged directly from eukaryotes.…”

Section: Introductionmentioning

confidence: 48%

Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui Comparison of the ribosomal protein S11 family

Kimura

Hatakeyama

1988

FEBS Letters

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The complete amino acid sequences of ribosomal proteins Sl 1 from the Gram-positive eubacterium Bacillus sfearorhermophilus and of S19 from the archaebacterium Hulobocterium marismortui have been determined. A search for homologous sequences of these proteins revealed that they belong to the ribosomal protein Sl 1 family. Homologous proteins have previously been sequenced from Escherichia cofi as well as from chloroplast, yeast and mammalian ribosomes. A pairwise comparison of the amino acid sequences showed that Bacillus protein Sl 1 shares 68% identical residues with Sl 1 from Escherichiu coli and a slightly lower homology (52%) with the homologous chloroplast protein. The halophilic protein S19 is more related to the eukaryotic (45549%) than to the eubacterial counterparts (35%).

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Evolutionary relationships amongst archaebacteria

Cited by 179 publications

References 56 publications

Ribosomal RNA introns in archaea and evidence for RNA conformational changes associated with splicing.

Ribosomal RNA introns in archaea and evidence for RNA conformational changes associated with splicing.

The nucleotide sequence of the genes coding for the S19 and L22 equivalent ribosomal proteins from Halobacterium halobium

Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui Comparison of the ribosomal protein S11 family

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