.=) 1991 Oxford University Press
Compilation of 5S rRNA
Nucleic Acids Research, Vol. 19, Supplement 2189
and
5S rRNA
gene sequences
Thomas Specht, Jorn Wolters' and Volker A.Erdmann*
Institut fOr Biochemie, Fachbereich Chemie, Freie Universitat Berlin, Otto-Hahn-Bau, Thielallee 63,
D-1000 Berlin 33, Dahlem and 1lnstitut fOr Aligemeine Mikrobiologie, Christian-Albrechts-Universitat
Kiel, Olshausenstrasse 40, D-1000 Kiel 1, FRG
ABSTRACT
This is an update for the 5S rRNA sequences of the
BERLIN RNA DATABANK last published in 1990 (1).
The new entry consists of 25 eubacterial and 2
eukaryotic 5S rRNA sequences and 10 plant 5S rRNA
pseudogenes (Table 1). Thus the BERLIN RNA
DATABANK contains as of Febuary 1, 1991 the 5S rRNA
sequences of 44 archaebacteria, 292 eubacteria, 20
plastids, 6 mitochondria, 321 eukaryotes and 21
eukaryotic pseudogenes. The BERLIN RNA DATABANK
uses the format of the EMBL Nucleotide Sequence Data
Library complemented by a Sequence Alignment (SA)
field including secondary structure information.
QUALITY OF THE SEQUENCE DATA
Although the methods of RNA sequencing have been improved,
the RNA sequence data still lies below that of DNA. Mainly at
5'and 3'end deviations are found. Detailed phylogenetic analyses
still lead to sequencing errors. For detailed information see (2).
THE ALIGNMENT
The SA fields of the database present a universal alignment of
all organisms. The alignment has been obtained by using the
program ALIGNSTAT (technoma GmBH, Heidelberg) designed
for the IBM XT/AT/PS2 and compatibles which performes
multisequence alignment of up to 180 5S rRNA sequences in one
step by the method of Kruger and Osterburg (3). It was manually
adjusted to account for common secondary structure elements.
An example is shown in Figure 1.
Alignment positions occuring only in a single species should
always be treated with caution especially if they are not present
*
To whom correspondence should be addressed
in close relatives and not confirmed by
further information see (1,2).
a
DNA
sequence.
For
THE SECONDARY STRUCTURE
The secondary structures of all types of 5S rRNAs consist of
five helices, named A to E, which are connected by loops
designated as a to e (1). The 5S rRNA sequences listed in this
update support the secondary structures shown in reference 1.
AVAILABILITY
The 5S rRNA primary and secondary structure and alignment
information are available upon request from the authors on
1.2 MB 5 1/4" or 1.44 MB 3 1/2" diskettes.
ACKNOWLEDGEMENTS
We thank all those colleagues who have sent us their preprints
saving us enormous time. The BERLIN RNA DATABANK is
supported by the Deutsche Forschungsgemeinschaft (Sfb-9/B5,
Forderpreis im Gottfried-Wilhelm-Leibniz-Programm) and the
Fonds der Chemischen Industrie e.V..
REFERENCES
1. Specht T., Wolters J., Erdmann V.A. (1990) Nucl. Acids Res. 18 (Supplem.),
2215-2230.
2. Wolters J., Erdmann V.A. (1988) Nucl. Acids Res. 16, rl-r70.
3. Kruiger M., Osterburg G. (1983) Comp. Progr. Biomed. 16, 68-70.
4. Comish-Bowden A. (1985) Nucl. Acids Res. 13, 3021-3030.
5. Delihas N., Andersen J. (1982) Nucl. Acids Res. 10, 7323-7344.
2190 Nucleic Acids Research, Vol. 19, Supplement
TABLE 1. Listing of 5S rRNA sequences in the 1991 update
EUBACTERIA:
VIBRIO ADAPTATUS #STRAIN ATCC 19263
VIBRIO CYCLOSITES #STRAIN ATCC 14635
VIBRIO HOLLISAE #STRAIN ATCC 33564
V1BRIO NEOCISTES #STRAIN ATCC 14636
CHLOROBIUM LIMICOLA # STRAIN DSM 249
CHLOROBIUM PHAEOBACTEROIDES # STRAIN DSM 266
PROSTHECOCHLORIS AESTUARII # STRAIN SK 413
THERMOMICROBIUM ROSEUM # STRAIN ATCC 27502
CYTOPHAGA AQUATILIS #STRAIN ATCC 29551
CYTOPHAGA HEPARINA #STRAIN ATCC 13125
CYTOPHAGA JOHNSONAE # STRAIN DSM 425
FLAVOBACTERIUM BREVE # STRAIN ATCC 14234
FLEXIBACTER SPEC. # STRAIN DSM 527
SAPROSPIRA GRANDIS #STRAIN ATCC 23119
METHYLOCOCCUS CAPSULATUS #STRAIN ATCC 19069
'METHYLOMONAS AGILE' #STRAIN A20
'METHYLOMONAS RUBRA' # STRAIN 15S
METHYLOMONAS METHANICA # STRAIN 12
'METHYLOBACTER CAPSULATUS' #STRAIN Y
'METHYLOSINUS TRICHOSPORIUM' #STRAIN 4E
'METHYLOCYSTIS PARVUS' # STRAIN 492
METHYLOPHILUS METHYLOTROPHUS #STRAIN NCIB 10515
ACETOBACTER SPEC. # STRAIN 914
METHYLOBACTERIUM EXTORQUENS # STRAIN AMI
LEPTOSPIRA INTERROGANS # STRAIN MOULTON
EUKARYOTA:
MAGNOLIA COBUS
MAGNOLIA STELLATA
PSEUDOGENES (PLANTS ONLY):
TRITICUM MONOCOCCUM L. # STRAIN K8555 # CLONE PTM5S7
TRITICUM DURUM # STRAIN K32063
AEGILOPS LONGISSIMA # STRAIN K202
AEGILOPS TAUSCHII A # STRAIN K773
TRITICUM AESTIVUM # VAR KOMETA
TRITICUM TIMOPHEEVII #STRAIN K29566
TRITICUM URARTU # STRAIN K363364
TRMTICUM MONOCOCCUM # STRAIN K45297
AEGILOPS TAUSCHII B # STRAIN K773
AEGILOPS SPELTOIDES # STRAIN K48
CORRECTIONS AND ADDITIONS:
EUBACTERIA:
ACETOBACTER SPEC. #STRAIN MB 58
HYPHOMICROBIUM VULGARE #STRAIN NP-160
HYPHOMICROBIUM SPEC. #STRAIN GIO
METHYLOBACTERIUM ORGANOPHILUM #STRAIN NP-220
METHYLOBACTERIUM EXTORQUENS #STRAIN AMI
EUKARYOTA:
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