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Nucleic Acids Research, 1983, Vol. 11, No. 5 1245-1252
© 1983

MOLECULAR BIOLOGY

Sequences of the 5S rRNAs of Azotobacter vinelandii, Pseudomonas aeruginosa and Pseudomonas fluorescens with some notes on 5S RNA secondary structure

Erna Dams, Antoon Vandenberghe and Rupert De Wachter*

Departement Celbiologie, Universiteit Antwerpen Universiteitsplein 1, B-2610 Wilrijk, Belgium

*To whom correspondence should be addressed

Received January 17, 1983. Revised February 15, 1983. Accepted February 15, 1983.

Recently published alignments of available 5 S rRNA sequences have shown that a rigid base pairing pattern, pointing to the existence of a universal five-helix secondary structure for all 5 S RNAs, can be superimposed on such alignments. For a few species, the alignment and the base pairing pattern show distortions with respect to the large majority of sequences. Their 5 S RNAs may form exceptional secondary structures, or there may just be errors in the published sequences. We have examined such a case, Pseudomonas fluorescens, and found the sequence to be in error. The corrected sequence, as well as those of the related species Azotobaoter vinelandii and Pseudomonas aeruginosa, fit perfectly in the 5 S RNA sequence alignment and in the five-helix secondary structure model. There exists comparative evidence for the frequent presence of non-standard base pairs at several points of the 5 S RNA secondary structure.


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