1. Nucleic Acids Research, 1993, Vol. 21, No. 13 3051-3054
Collection of small subunit (16S- and 16S-like) ribosomal
RNA structures
Robin Ray Gutell
MCB Biology, Campus Box 347, University of Colorado, Boulder, CO 80309-0347, USA
INTRODUCTION
Inferring higher-order structure for complex RNA molecules,
such as the ribosomal RNAs has relied primarily on comparative
methods. Underlying these methods is the premise that molecules
with different primary structure and similar functional
characteristics have similar secondary and tertiary structure
[Reviewed in: 1]. For these methods to be effective, the RNA
molecules under study need to be sufficiently similar at the
primary structure level to obtain good sequence alignments,
however these same sequences also need to be proportionately
different for positional covariance to occur, the indicator
suggesting the existence of a basepair.
The higher-order structure models for 16S rRNA have evolved
in stages. Initially, with a small number of 16S rRNA sequences
in hand, a minimal secondary structure was proposed. Increases
in the number and diversity of available 16S rRNA sequences
and paralleled with improvements in correlation analysis
algorithms has lead to the continual refinement of this structure
model. In the earlier stages only secondary structure pairings were
identified. In contrast during the latter stages only minor
refinements in these pairings occurred while several novel tertary
and non-canonical pairing constraints were proposed [reviewed
in: 2-3]. And now with over 2,200 16S and 16S-like rRNA
available sequences spanning the three phylogenetic domains and
the two organelles (Mitochondria and Chloroplast), detailed
phylogenetic, structural, and structural evolution information is
now being deciphered in great detail, although the resulting
analysis from different groups is not always congruent.
Over the years several groups have developed 16S rRNA
secondary structure models. The current versions for each are
fairly analogous with one another[2, 4-7], although this has not
always been the case. And while the current differences are small,
some are significant for the Escherichia coli and other Bacterial,
Archaea, Eucarya, and mitochondrial structure models. These
versions should also not be considered final as these models are
expected to undergo minor revisions as the number and diversity
of 16S and 16S-like sequences increases and is paralleled with
continued improvements and alternative correlation analysis
interpretations [8, unpublished work].
Over the next few years this collection, and the accompanying
23S rRNA (see Gutell, Gray, Schnare, this issue) will grow in
size and detail. The complexity of structure and the evolutionary
dimension of these structures presents us with a wonderful
opportunity to investigate RNA structural motifs and map with
some precision, the evolution ofthese RNAs and underlying RNA
structural characteristics associated with different phylogenetic
assemblages. This collection of structures should also be ofvalue
to the experimentalist studying rRNA structure and function. And
equally valuable to those studying rRNA based phylogeny.
OBJECTIVES
The objectives for this annual collection are:
1. Present our most current comparative interpretation of the
Escherichia coli 16S rRNA secondary structure [with
general agreement between C.R.Woese, H.F.Noller, and
myselfl. While this secondary structure model is stable,
minor adjustments are expected in some of the helical
pairings.
2. Present other significant correlations that suggest tertiary
and other complex structure in the Escherichia coli model.
The numbers for such structural interactions should increase
over the next few years.
3. Present a sampling of different 16S and 16S-like rRNA
higher-order structure models. Starting with a broad
sampling of phylogenetically and structurally distinct
models, additional examples will be developed to fill in this
broad phylogenetic and structure matrix. A parallel effort
will refine all previously proposed models as new
comparative structure information is obtained. To be
discussed elsewhere and in more detail, this collection of
structures will serve as the database for detailed analysis
of RNA evolution and RNA structural motifs.
The first 16S and 16Slike structure release is set for
summer/fall- 1993, and will include major representatives
from the three phylogenetic domains and organelles. The
approximate numbers will be: 25 (eu)bacteria, 10 archaea,
15 eucarya, 2 chloroplast, and 10 mitochondria. Readers
are encouraged to contact the author with suggestions for
additional higherorder structure models not currently
available.
4. Illustrated in this article are three divergent 16S and 16S-
like rRNAs structure models for: Escherichia coli, a
member of the (eu)bacteria phylogenetic domain; nuclear
encoded Saccharomyces cerevisiae, a member of the
eucarya domain; and Caenorhabditis elegans mitochondria,
one of the smallest known 16S-like rRNAs.
This work is an adjunct to the monumental effort of the RDP
(Ribosomal Database Project, see this issue); Their mandate being
to generate and make various tpes of ribosomal RNA data and
interpretation generally available. On-line access to these 16S
rRNA secondary structure files is available from the RDP
k.l 1993 Oxford University Press

2. 3052 Nucleic Acids Research, 1993, Vol. 21, No. 13
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Figure 1. Higher-order structure diagram for Escherichia coil 16S rRNA [2-3]. For secondary structure basepairings, short lines connect canonical pairs (C:G,
U:A), G:U pairs are denoted with dots, A:G pairings with larger open circles, and other non-canonical pairings with closed circles. Terdary interactions are connected
with thicker and longer solid lines. Every 10th nucleotide position is marked with a tic mark, while every 50th posiion is numbered [Sequence Accession number is J01695].
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3. Nucleic Acids Research, 1993, Vol. 21, No. 13 3053
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Figure 2. Higher-order structure diagram for Saccharomyces cerevisiae nucleocytoplasmic 16S-like rRNA. Higher-order structure interactions illustrated and noted
as in Fig. 1. [Sequence is slighdy modified from acccession number J01353].
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4. 3054 Nucleic Acids Research, 1993, Vol. 21, No. 13
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FIgr 3. Higher-order structure diagram for Caenorhabditis elegans mitochondrial 16S-like rRNA. Higher-order structre interactions illustrated and noted as in
Fig. 1. [Sequence Accession number is X54252].
anonymous ftp site (info.mcs.anl.gov). Currently, these
PostScript files are maintained in the
'/pub/RDP/SSU rRNA/sec_struct' directory. Additional
information about this server and access to the Ribosomal
Database Project is described in their article in this issue. Readers
unable to access this on-line information, can obtain a set of 16S
rRNA hardcopy diagrams from the author.
The interactive graphics program XRNA (developed by Bryn
Weiser, UC Santa Cruz) facilitated the generation ofthe higher-
order structure models displayed here and the PostScript files
available at the RDP anonymous ftp site. Manual alignment of
these 16S and 16S-like rRNA sequences was facilitated with the
interactive sequence alignment editor AE2 (developed by Tom
Macke, Scripps Clinic).
ACKNOWLEDGMENTS
Refining and interpreting these rRNA structure models is an on-
going and long term collaboration with Drs Carl Woese and
Harry Noller. Bryn Weiser and Tom Macke are greatfully
acknowleged for developing the wonderful programs that make
much of this analysis and presentation possible. I also wish to
tank the W.M.Keck Foundation for their generous support of
RNA science on the Boulder campus, and SUN Microsystems
for their timely donation of computer equipment. The author is
an Associate in the Program in Evolutionary Biology of the
Canadian Institute of Advanced Research. This work was
supported by the NIH (GM 48207).
REFERENCES
1. Gutell R.R. (1993a) Curr. Opin. Struct. Biol. 3, in press.
2. Gutell R.R., Larsen N., and Woese C.R. (1993). In Zimmernmann R.A, and
Dahlberg A.E.(eds). Ribosomal RNA: Stucue, Evolution, Gene Expression
and Function in Protein Synthesis. CRC Press, Boca Raton, FL. in press.
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Franceschi F., and Wittman-Liebold B. (eds). The Translational Apparatus.
Plenum Publishing Corporation, NY, NY in press.
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