Genes for the 16S and 5S Ribosomal RNAs and the 7S RNA of Pyrodictium occultum

Kaine, Brian P.; Schurke, Christine M.; Stetter, Karl O.

doi:10.1016/s0723-2020(89)80035-9

Cited by 22 publications

(5 citation statements)

References 41 publications

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“…The measured molecular weight of one of the oligonucleotides, 2914.45, was consistent with the composition C5A3G > p (2,3-cyclic phosphate terminus) plus one acetyl group and one methyl group (calculated molecular weight 2914.87). Inspection of the P. occultum 5 rRNA gene sequence [49], revealed that C5A3G was the expected composition of the 9-mer, 28-CAACACCCG-36.…”

Section: Discussionmentioning

confidence: 99%

A novel method for the determination of posttranscriptional modification in RNA by mass spectrometry

et al. 1993

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A method is described for the detection, chemical characterization and sequence placement of post-transcriptionally modified nucleotides in RNA. Molecular masses of oligonucleotides produced by RNase T1 hydrolysis can be measured by electrospray mass spectrometry with errors of less than 1 Da, which provides exact base composition, and recognition of modifications resulting from incremental increases in mass. Used in conjunction with combined liquid chromatography-mass spectrometry and gene sequence data, modified residues can be completely characterized at the nucleoside level, and assigned to sequence sites within oligonucleotides defined by selective RNase cleavage. The procedures are demonstrated using E.coli 5S rRNA, in which all RNase T1 fragments predicted from the rDNA sequence are identified solely on the basis of their molecular masses, and using E.coli 16S rRNA for analysis of post-transcriptional modification, including placement of 3-methyluridine at position 1498. The principles described are generally applicable to other covalent structural modifications of RNA which produce a change in mass, such as those resulting from editing, photochemical cross-linking, or xenobiotic modification.

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Section: Discussionmentioning

confidence: 99%

A novel method for the determination of posttranscriptional modification in RNA by mass spectrometry

et al. 1993

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“…1998); D26490 (Kurosawa et al . 1995); M21087 (Kaine et al . 1989); U39635, U40238 and U40240 (Stein et al .…”

Section: Methodsmentioning

confidence: 99%

Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I

2000

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The SAR11 cluster and the Group I of marine Archaea represent probably the best two examples of uncultured marine prokaryotes of widespread occurrence. To study their microdiversity and distribution, a total of 81 and 48 clones, respectively, were sequenced from Mediterranean and Antarctic waters at different locations and depths. The DNA regions chosen for the analysis were the last third, approximately, of the 16S rRNA gene and the 16S-23S intergenic spacer (also known as internal transcribed spacer [ITS]). There was a high concordance in both, even with the extremely variable ITS, where potential probes have been proposed for the identification and isolation of these micro-organisms. In terms of community structure, our results show that although depth-related factors seem to be predominant in the final associations of the clones, geography also plays a significant role. A major group of surface-associated sequences was found in both SAR11 and marine Archaea. In both cases this group was relatively homogeneous containing little diversity in terms of sequence, while sequences retrieved from deep samples and some surface clones contained much more heterogeneity. As a whole, both groups of prokaryotes seem to fall within the limits of well-defined taxonomic units.

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“…The compilation of the available SRP-RNA sequences, includes those from 6 bacteria (eubacteria), 9 archaea (archaebacteria), and 24 eucaryotes. Since the last review of the structure and function of SRP-RNA (7), several archaeal sequences have appeared (10,11,12,13,14), and the similarity between bacterial 4.5S RNAs and the conserved portion of the other SRP-RNAs has been recognized (15,16,17).…”

Section: Introductionmentioning

confidence: 99%