k. 1992 Oxford University Press
Nucleic Acids Research, Vol. 20, Supplement 2075-2089
Compilation of small ribosomal subunit RNA sequences Peter De Rijk, Jean-Marc Neefs, Yves Van de Peer and Rupert De Wachter* Departement Biochemie, Universiteit Antwerpen, UIA, Universiteitsplein 1, B-2610 Antwerp, Belgium
INTRODUCTION The database on small ribosomal subunit RNA (further abbreviated as SSU rRNA) structure has more than doubled in size in one year's time and currently contains 927 aligned sequences. Table 1 only lists the 475 sequences (references 1-475) that were added to the database since publication of the last compilation (476). The latter should be consulted for data and references concerning the sequences entered previously. The total set of 927 entries now consists of 197 eukaryotic cytoplasmic, 21 archaeal, 625 bacterial, 21 plastidial, and 63 mitochondrial SSU rRNAs. This set includes partial sequences, but only if they satisfy the criterion defined in detail in the previous compilation (476) and in footnote (f) of Table 1, in short if the combined lengths of the sequenced segments corresponds to at least 70% of the Escherichia coli 16S rRNA sequence. Sequence alignment is based largely on the adopted secondary structure model, which in turn is corroborated by the observation of compensating substitutions in the alignment. Therefore, the secondary structure model can be gradually refined as more sequences become available. Some improvements to the secondary structure model for eukaryotic SSU rRNAs are described below.
SECONDARY STRUCTURE MODEL Prokaryotic and eukaryotic models Fig. 1 shows the prokaryotic secondary structure model, applicable to SSU rRNAs from archaea, bacteria, plastids and mitochondria. The model of Fig. 2 applies to eukaryotic cytoplasmic SSU rRNAs. Areas of conserved primary and secondary structure are drawn in bold lines. Areas of variable primary and secondary structure, drawn in thin lines, are labelled VI to V9. Variability in secondary structure often consists in extension or reduction in size of helices in some species with respect to others. Long insertions present in a limited number of species result in the presence of extra helices, drawn in broken lines. The prokaryotic model is identical to the one shown in the previous compilation (476), but the eukaryotic model has been adapted, the changes being enumerated below. The two models are distinguished, even though they have many helices in common, because helix P21, which usually forms variable area V4 of prokaryotic SSU rRNAs, apparently is not homologous to any of the helices E21-1 to E21-10 forming area V4 in eukaryotic SSU rRNAs. *
To whom correspondence should be addressed
Helix numbering system Helices are given a different number if separated by a multibranched loop, (e.g. helices 9 and 10), by a pseudoknot loop (e.g. helices 1 and 2), or by a single stranded area that does not form a loop (e.g. helices 2 and 30). A single number is attributed to 48 'universal' helices, which are present in all hitherto known SSU rRNAs from archaea, bacteria, and plastids. They are also present in all known eukaryotic SSU rRNAs except that of the microsporidian Vairimorpha necatrix, which lacks helices 10, 11, and 44. Additional helices specific to the prokaryotic model (Fig. 1) are given composite numbers of the form Pa-b, where a is the number of the preceding universal helix and b sequentially numbers all helices inserted between universal helices a and a+ 1. Helices specific to the eukaryotic model (Fig. 2) are similarly numbered Ea-b. Mitochondrial SSU rRNAs, though they can be described by the prokaryotic model, show extreme variability in length, ranging from about 600 nucleotides in flagellates to about 2000 nucleotides in plants. This coincides with the absence of several universal helices in the smaller molecules and with the presence of extra helices of the P-series in the larger ones. A tentative helix occupancy table for mitochondrial SSU rRNAs and examples of secondary structure models can be found in the previous compilation (476). The alignment of, and transposition of secondary structure models to mitochondrial SSU rRNAs is less dependable than for other SSU rRNAs, not only because of the variability in length, but also because some of the sequences are very monotonous due to a high A+U content. Changes made to the eukaryotic secondary structure model (Fig. 2) Alignment of additional sequences has brought to light new compensating substitutions, leading to changes in the base pairing scheme adopted for helices 8 and 18. In addition, helices E2 1-1 to E21-4 of the previous model (476) have been rejected in favour of a different structure, and the numbering of the helices in area V4 was changed in consequence. Table 2 gives the helix occupancy for area V4 of eukaryotic SSU rRNAs according to the new structure and numbering system. Fig. 3 shows the secondary structure presently adopted for Saccharomyces cerevisiae SSU rRNA, which is typical for the majority of eukaryotic structures. Fig. 4 shows the new secondary structure for Drosophila melanogaster SSU rRNA, which is one of the species containing extra helices E21-3 and E21-4. The structure in the area of helix E21-10 (Fig. 2) remains uncertain. The insert present in this area in a number of species (see Table 2) may
2076 Nucleic Acids Research, Vol. 20, Supplement
Fig. 1. Secondary structure model for prokaryotic SSU rRNAs. The 5'-terminus is symbolized by a dot, the 3-terminus by an arrowhead. Helices are numbered in the order of occurrence from 5'- to 3'-terrninus. Helices bearing a single number are common to the prokaryotic and eukaryotic (Fig. 2) models. Helices bearing a composite number preceded by P are prokaryote-specific. Areas of relatively conserved structure are drawn in bold lines. Nine variable areas labeled VI to V9 are drawn in thin lines. Helices drawn in broken lines are present exceptionally.
actually form more than one extra helix, but it is not possible as yet to derive a reliable model on the basis of the available sequences.
COMPLETENESS, ACCURACY, AND AVAILABILITY OF THE DATA SSU rRNA sequences deposited into the GenBank and EMBL nucleotide sequence libraries are obtained weekly from the EMBL file server by electronic mail. An appropriate set of programs is used for alignment of a new sequence, indication of secondary structure elements by comparison with a closely related sequence, checking the consistency of the postulated secondary structure, and checking for errors by comparison with the original record. Files containing all the SSU rRNA sequences present in our database are available in the following three formats. 1. The sequences, listed one by one, written continuously without the gaps needed for alignment and without indication of secondary structure elements. 2. The sequences, listed one by one, but with nucleotide symbols interspersed with the gaps necessary for alignment. In these files, each sequence covers 4284 positions, which is the present length of the complete alignment of all eukaryotic, archaeal, bacterial, and organellar sequences.
Fig. 2. Secondary structure model for eukaryotic SSU rRNAs. Symbols are as in Fig. 1. Helices bearing a composite number preceded by E are eukaryotespecific. The area corresponding to V6 in Fig. 1 is more conserved among eukaryotic SSU rRNAs. See Table 2 for a complete survey of helix occupancy in known structures.
3. The sequences, listed in the form of an alignment with indication of the secondary structure elements. The alignment is divided into 43 pages each comprising 100 positions containing a nucleotide or a gap. These positions alternate with extra positions that are either blank or contain a symbol indicating the beginning or end of a secondary structure element. The secondary structure model adopted for each SSU rRNA sequence is completely defined in these files. In addition, there are files containing a taxonomic list of species and general documentation on the database. The database will be made available through 'anonymous ftp' on host uiam3.uia.ac.be (143.169.8.1). A previous, less complete version of the database was written on the CD-ROM disk distributed in December 1991 by the EMBL nucleotide sequence library at Heidelberg. Updates of the database will be similarly put at the disposal of the EMBL nucleotide sequence library for distribution on future releases of the CD-ROM, and in order to be made available on the EMBL file server as well. Due to the increasing volume of the database, copying it onto diskettes is getting cumbersome. However, researchers who do not have access to the aforementioned distribution channels can inquire about the availability of the database on magnetic media by writing to the authors or by sending an electronic mail message to
[email protected] or to
[email protected] .BE.
Nucleic Acids Research, Vol. 20, Supplement 2077 Saccharomyces cerevisiae
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2078 Nucleic Acids Research, Vol. 20, Supplement Drosophila melanogaster
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Nucleic Acids Research, Vol. 20, Supplement 2079
ACKNOWLEDGEMENTS Our research is supported by the Incentive Programme on Fundamental Research in the Life Sciences (contract BIO/03) and the Programme on Interuniversity Poles of Attraction (contract 23) of the Office for Science Policy Programming of the Belgian State, and by the Fund for Medical Scientific Research. P. De Rijk is research assistant of the National Fund for Scientific Research.
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Nucleic Acids Research, Vol. 20, Supplement 2089 Table 2. Helix occupancy in eukaryotic SSU rRNAs.
Helices (a) Taxon
Taxonomic level
1
I
1
E21 2
1
E43
2 3
4
5
6
7
8
9 10
I -
1
Insecta
Class
-
*
*
*
*
*
*
*
*
*
*
Platyhelminthes
Phylum
-
*
*
*
*
*
*
*
*
*
*
-
Schizosaccharomyces pombe
Species
-
*
*
*
*
*
*
*
*
*
Yarrowia lipolytica
Species
-
*
*
*
*
*
*
*
*
Blastocladiella emersonii
Species
**
*
Euplotes aediculatus
Species
Plasmodium
Genus
Physarum polycephalum
Species
*
*
Kinetoplastidea
Phylum
*
*
Euglena gracilis
Species
*
*
Babesia bigemina
Species
-
*
Vairimorpha necatrix
Species
-
Giardia
Genus
-
_
_-*
*
*
*
Naegleria gruberi
Species
-
*
*
*
*
_
*
*
*
*
*
*
Acanthamoeba castellanii
Species
-
*
_
*
*
_
*
*
*
*
*
*
*
_
*
*
*
*
*
*
*
All other eukaryotes
a)
E10
E8
*
| * |
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
*
_
*
*
*
*
*
*
*
*
*
*
-
-
-
*
*
*
*
*
*
_
*
-
|
-_
_ |
* *
_
|
The presence of a helix is indicated by an asterisk. Only eukaryote-specific helices are listed since universal helices are present in all eukaryotic SSU rRNAs, except for Vairimorpha necatrix SSU rRNA, which misses helices 10, 11 and 44.
