© 1992 Oxford University Press
Nucleic Acids Research, Vol. 20, Supplement
2095-2109
A compilation of large subunit (23S- and 23S-like)
ribosomal RNA structures
Robin R.Gutell*, Murray N.Schnare1 and Michael W.Gray1*
Molecular, Cellular, and Developmental Biology, Campus Box 347, University of Colorado, Boulder,
CO 80309 and department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7,
Canada
INTRODUCTION
The present edition of large subunit (LSU; 23S and 23S-like)
rRNA secondary structures updates and refines the collections
of 1988 [1] and 1990 [2]. As in [1] and [2], each LSU rRNA
sequence is presented as a secondary structure, a two-dimensional
format that represents, in part, the biologically relevant
conformation of the rRNA molecule. When LSU rRNA
sequences are configured in this manner, valuable phylogenetic
information is readily extracted, facilitating the identification of
conserved and variable regions. At the same time, the secondary
structure serves as an effective template for relating form to
function.
GROWTH OF THE DATABASE
The collection of LSU rRNA sequences has continued its steady
increase in the twelve years following publication of the first
complete and correct 23S rRNA sequence [3]. The growth of
this collection is tracked in Table 1, with numbers reflecting those
sequences that are in the public domain. Within the past few
years, a small but growing number of sequences have been
released through the GenBank/EMBL databases prior to formal
publication; some of these entries still lack a journal citation.
Those sequences new to our collection are appropriately noted
in Table 2.
MODELS OF HIGHER-ORDER STRUCTURE
In deducing higher-order structure, comparative analysis is used
to reveal features common to all homologous rRNAs. This
approach has resulted in detailed and progressively refined higherorder structures for the 23S and 16S rRNAs of Escherichia coli,
the standards to which all other homologous rRNA structures
are referred. Initially, with a minimal number of LSU rRNA
sequences available for comparison, several alternative secondary
structures were proposed [4—6]. As both the number and
phylogenetic diversity of LSU rRNA sequences increased, it
became possible to test and correct existing models, taking out
or adding helices and/or base pairs as appropriate. More recently,
expansion of the sequence dataset has made it possible to identify
* To whom correspondence should be addressed
a number of tertiary pairings. The current version of the E. coli
23S rRNA secondary structure is the culmination of over ten
years of analysis [7,8]; all of the secondary structure pairings
and proposed tertiary interactions are now strongly supported
by comparative data. We anticipate, however, that additional
tertiary interactions will continue to be discovered as new LSU
rRNA sequences appear.
The evolutionary process has affected the size as well as the
primary structure of LSU rRNAs. The smallest such RNAs are
those found in the kinetoplast (mitochondrion) of the
trypanosomatid flagellates, such as Crithidia fasciculata (1141
nt), while the largest are those in the cytoplasmic ribosomes of
vertebrates, e.g., humans (5182 nt; 5.8S + 28S). While
comparative analysis has defined a core of higher-order structure
common to all LSU rRNAs, certain other structures are found
only within particular phylogenetic subsets. Elucidation of these
phylogenetically restricted structures requires comparison of at
least several related LSU rRNA sequences (the number depending
on the rate at which such structures are diverging).
In the case of those LSU rRNAs comparable in size to E. coli
23S rRNA, secondary structures have been modeled in their
entirety. Larger LSU rRNAs (eucaryotic cytoplasmic and some
mitochondrial) contain apparent insertions relative to the E. coli
structure. Within the past year, a number of these previously
unstructured regions have been configured by comparative
methods. As additional LSU rRNA sequences are determined,
especially within localized phylogenetic divisions, we anticipate
that each remaining unstructured region will be resolved. It is
of interest that within the eucaryotic nucleocytoplasmic lineage,
several of these recently structured regions are common only to
a relatively narrow phylogenetic grouping.
All secondary structures follow the convention and layout
established for the E. coli 23S rRNA model, the de facto
reference structure. The majority of homologous primary and
secondary structure features are displayed in an analogous
graphical manner to emphasize this structural homology. In a
small number of cases, due to insertion/deletion events, this
graphical representation varies somewhat for structural elements
deemed to be homologous. In future editions of this secondary
structure compendium, we will begin to incorporate tertiary
interactions that satisfy comparative criteria.
2096 Nucleic Acids Research, Vol. 20, Supplement
AVAILABILITY AND STATUS OF STRUCTURE
FIGURES
As in [2], the actual 23S rRNA secondary structures are not
published here. Instead, readers will find (i) a table of complete
LSU rRNA sequences, grouped according to phylogenetic
division and including GenBank/EMBL Accession Numbers
(Table 2), and (ii) a publication reference list for these sequences.
The comprehensive set of LSU rRNA secondary structures may
be obtained in one of two ways. Hardcopy printouts of this
set are available directly from us (inquiries should be referred
to M.W.G. at the address listed below). Release 1.0, which
comprises 88 structures (see Table 2), is immediately available.
This release contains virtually finalized archaebacterial,
eubacterial and plastid structures. Mitochondrial structures have
been extensively revised from those first presented in [1], but
a further round of (relatively minor) revision is necessary before
these models will be in final form. Eukaryotic cytoplasmic
structures in Release 1.0 are largely unchanged from those given
in [1]; an exception is the newly modeled Euglena gracilis
cytoplasmic secondary structure [9], which does contain revisions
that are being incorporated into the secondary structures of other
nucleus-encoded LSU rRNAs. Newly modeled and refined LSU
rRNA secondary structures will be included in Release 2.0,
hardcopies of which should be ready for distribution before the
end of 1992. Inquiries about hardcopy printouts should state
explicitly which Release (1.0 or 2.0) is being requested.
Alternatively, individuals with access to the Internet
telecommunications network and a laser printer capable of
processing PostScript™ files may elect to obtain files of LSU
rRNA secondary structures by anonymous file transfer protocol
(ftp). These files are deposited with the Ribosomal RNA
Database Project [10] on the RDP computer at the Argonne
National Laboratory, and may be accessed as indicated below.
Inquiries concerning this on-line service may be directed to
R.R.G. (e-mail and postal addresses as noted below).
As time and facilities permit, the rRNA information available
on-line will be increased. Initially, it will include the complete
set of LSU rRNA secondary structures (in PostScript™ format),
the table of LSU rRNA sequences and their accession numbers,
and the associated publication reference list. Refinements to
existing secondary structures as well as newly modeled secondary
structures will be released on-line as soon as we have completed
our own analysis. From time to time, we will also update the
associated table and reference list. Currently we include only
those LSU rRNA sequences that are complete (or nearly so).
ACCURACY OF THE DATA
Ambiguous positions in a published sequence are specified
according to the nomenclature recommended by IUPAC (e.g.,
Y = pyrimidine ; R = purine; etc.). As noted in Table 2 and
the List of References, there are independently determined
versions of the same primary sequence for several LSU rRNAs.
Usually, these alternative versions differ from one another at a
number of positions, and at least some of these differences are
likely to be sequencing errors. Often, the secondary structure
predicts which version of the sequence is likely to be correct at
a particular position. On the other hand, it is probable that some
of the variation actually reflects genuine inter- or intra-strain
sequence heterogeneity, particularly if the differences occur
within variable regions [11]. We have also noted that a few
published primary sequences differ at one or more positions from
their GenBank/EMBL listings, without an indication that the
database entry represents a subsequently revised version of the
original published sequence. Again, secondary structure modeling
may or may not indicate which version is likely to be correct.
It is our intent to provide brief annotation in the hardcopy and
electronic versions of the secondary structure figures to indicate
which version of the primary sequence has been used at discrepant
positions.
In compiling the reference list, we have checked each of these
citations against the original published paper. We note that citation
information in the GenBank/EMBL database is occasionally
inaccurate, and for that reason we have provided complete
references, including titles.
Finally, we invite further comments from readers, and welcome
suggested revisions/alternative interpretations to the proposed
secondary structures, as well as suggestions for improvement in
the content and/or form of the database. We also solicit newly
determined LSU rRNA sequences in advance of publication, in
order to accelerate their inclusion in the compendium.
ACKNOWLEDGMENTS
We gratefully acknowledge the computer programming expertise
of Bryn Weiser and Tom Macke in this endeavor. Work on this
compendium by M.N.S. and M.W.G. is supported by an
operating grant (MT-11212) from the Medical Research Council
of Canada to M.W.G. We thank the Canadian Institute for
Advanced Research (CIAR) for providing funds in support of
the production and distribution of secondary structure figures.
M.W.G. is a Fellow and R.R.G. is an Associate in the Program
in Evolutionary Biology of the CIAR. We also thank the
W.M.Keck Foundation for their generous support of RNA
science on the Boulder campus.
REQUESTS
For hard copies of LSU rRNA secondary structures, either
the complete compilation or selected portions thereof (please
specify Release 1.0 or 2.0):
M.W. Gray,
Department of Biochemistry,
Sir Charles Tupper Medical Building,
Dalhousie University,
Halifax, Nova Scotia B3H 4H7, Canada.
FAX:
(902)494-1355
e-mail:
[email protected] (via Bitnet)
For information about on-line availability of LSU rRNA
secondary structure files and other information contained in
this compendium:
R.R. Gutell,
Molecular, Cellular, and Developmental Biology,
Campus Box 347,
University of Colorado,
Boulder, Colorado 80309, U.S.A.
FAX:
(303)492-7744
e-mail:
[email protected]
Nucleic Acids Research, Vol. 20, Supplement 2097
To obtain PostScript™ files of LSU rRNA secondary
structures via anonymous ftp on the Internet
telecommunications network:
ftp site: info.mcs.anl.gov
directory: /pub/RDP/Contrib/RobinGutell
REFERENCES
1. Gutell,R.R. and Fox,G.E. (1988) Nucleic Acids Res. 16, Supplement,
rl75-r269.
2. Gutell.R.R., Schnare.M.N. and Gray,M.W. (1990) Nucleic Acids Res. 18,
Supplement, 2319-2330.
3. Brosius,J., Dull.T.J. and Noller.H.F. (1980) Proc. Nail. Acad. Sci. U.S.A.
77, 201 -204.
4. Glotz.C, Zwieb.C, Brimacombe.R., Edwards, K. and Kossel.H. (1981)
Nucleic Acids Res. 9, 3287-3306.
5. Branlant.C, Krol.A., Machatt.M.A., Pouyet,J., Ebel,J.-P., Edwards.K. and
K6ssel,H. (1981) Nucleic Acids Res. 9, 4303-4324.
6. Noller.H.F., Kop,J., Wheaton,V., BrosiusJ., Gutell,R.R., Kopylov.A.M.,
Dohme,F., Herr.W., Stahl.D.A., Gupta.R. and Woese.C.R. (1981) Nucleic
Acids Res. 9, 6167-6189.
7. Larsen,N. (1992) Proc. Natl. Acad. Sci. U.S.A., in press.
8. Gutell.R.R., Larsen,N. and Woese.C.R. (1992) In Ribosomal RNA: Structure,
Evolution, Gene Expression and Function in Protein Synthesis
(Zimmermann,R.A. and Dahlberg,A.E., eds), The Telford Press, Caldwell,
N.J., in press.
9. Schnare,M.N. and Gray.M.W. (1990)7. Mol. Biol. 215, 73-83.
10. Olsen.G.J., Larsen,N. and Woese.C.R. (1991) Nucleic Acids Res. 19,
Supplement, 2017-2021.
11. Gonzalez,].L., Gorski.J.L., Campen,T.J., Dorney.D.J., Erickson.J.M.,
Sylvester.J.E. and Schmickel.R.D. (1985) Proc. Natl. Acad. Sci. U.S.A.
82, 7666-7670.
The present publication should be quoted as reference for secondary structure
data obtained either as hard copies from the authors or from the electronically
accessible compilation.
2098 Nucleic Acids Research, Vol. 20, Supplement
Table 1. Growth of the LSU rRNA database
Archaebactenal
Eubacterial
Plastid
Mitochondria]
Eukaryotic (nuclear)
All
1988
1990
1992
6
5
4
17
10
42
7
13
12
21
13
54
28
128
8
27
16
71
Table 2. List of complete LSU rRNA sequences
Organism name 1
Status2 Accession Number
ARCHAEBACTERIA (ARCHAEA 3 )
Euryarchaeota 3
Archaeoglobus fulgidus
Halobacterium halobium
Halobacterium marismortui
Halococcus morrhuae
Methanobacterium thermoautotrophicum
Methanococcus vannielii
Methanospirillum hungatei
Thermoplasma acidophilum
*#
+
+
+
+
+
*#
+#
M64487
X00872,X03407
X13738
X05481
X15364
X02729
M61738,M81323
M20822,M32298
Desulfurococcus mobilis
Sulfolobus solfataricus
Thermofilum pendens
Thermoproteus tenax
+
*#
+#
+
X05480
M67495
X14835
+#
M55343
X06484
X56657
M27245
X55435.X61478
Crenarchaeota3
EUBACTERIA (BACTERIA 3 )
Gram positive bacteria 4
High G+C subdivision
Frankia sp.
Micrococcus luteus
Mycobacterium leprae
Streptomyces ambofaciens
Streptomyces griseus
Low G+C subdivision
Bacillus sp.
Bacillus stearothermophilus
Bacillus subtilis
Purple photosynthetic bacteria and their relatives 4
Alpha subdivision
Rhodobacter capsulatus
Rhodobacter sphaeroides
Beta subdivision
Pseudomonas cepacia
Gamma subdivision
Escherichia coli
Pseudomonas aeruginosa
Ruminobacter amylophilus
*#
*#
X60981
K02663
K00637,M10606,X00007
+#
X06485
X53853,X53854,X53855
X16368
J01695
Y00432
X06765
Nucleic Acids Research, Vol. 20, Supplement 2099
Organism name1
Spirochetes and their relatives 4
Leptospira interrogans
Bacteroides, flavobacteria and cytophagas and relatives 4
Flavobacterium odoratum
Flexibacter flexilis
Cyanobacteria 4
Anacystis nidulans
Green sulfur bacteria 4
Chlorobium limicola
Planctomyces and their relatives 4
Pirellula marina
Radio-resistant micrococci4
Thermus thermophilus
Status2 Accession Number
+
X14249
+#
+#
M32365.M62807
M31904.M62806
+
X00343,X00512
+#
M31904,M62805
+
X07408
+
X12612
PLASTIDS
Protoctista 5
Apicomplexa6
Plasmodium falciparum6
Euglenophyta (euglenoid flageUates)
Astasia longa
Euglena gracilis
Chlorophyta (unicellular green algae)
Chlamydomonas eugametos
Chlamydomonas reinhardtii
Chlorella ellipsoidea
X61660
+
+
X14386
X13310
*#
+
+
X15727,X16686,X16687
M36158
+
X01647.X04465
*#
*#
+
+
+#
+
M76448,M75722,M75719
X59768
J01446.Z00044
X15901
M37430
X01365
+
+#
+
+
+
X02548
X51736
X02354
J03814
X02547
+
M22649,M25123-25130,X54860
+
+
+#
K00634
K01749,X15917
M58010.M58011
Plantae
Bryophyta
Marchantia polymorpha (liverwort)
Angiospermophyta (flowering plants)
Alnus incana (alder)
Conopholis americana
Nicotiana tabacum (tobacco)
Oryza sativa (rice)
Pisum sativum (pea)
Zea mays (maize)
MITOCHONDRIA
Protoctista 5
Zoomastigina (zooflagellates)
Crithidia fasciculata
Crithidia oncopelti
Leishmania tarentolae
Leptomonas sp.
Trypanosoma brucei
Chlorophyta (unicellular green algae)
Chlamydomonas reinhardtii
Ciliophora (ciliates)
Parameciiim primaurelia
Paramecium tetraurelia
Tetrahymena pyriformis
2100 Nucleic Acids Research, Vol. 20, Supplement
Organism name1
Status2 Accession Number
Aspergillus nidulans
Neurospora crassa
Podospora anserina
Saccharomyces cerevisiae
Schizosaccharomyces pombe
+
+#
+
+
+
Fungi
Ascomycota
X06961
X55443
M30937.X14735
J01527
X06597
Plantae
Bryophyta
Marchantia polymorpha (liverwort)
Angiospermophyta (flowering plants)
Oenothera berteriana (primrose)
Triticum aestivum (wheat)
Zea mays (maize)
M68929
+
+
+
X02559
M37274
K01868
*#
*#
X54253
X54252
+
+
+
+#
+
+
*#
X01078
X05011
M21833.X12965
X53506
X03240
X05287
M76713
+
+
J04815
X12631
• #
M86496
M55540
X61145
J01394
M86494
M55541
M86498
M35875
X61010
M86499
X52392
M86501
J01415,M12548,V00710
M35876
M86497
M86495
M35877
J01420
M35874
M86500
X12841
Animalia
Nematoda
Ascaris suum
Caenorhabditis elegans
Arthropoda
Aedes albopictus (mosquito)
Apis mellifera (honeybee)
Anemia salina (brine shrimp)
Drosophila melanogaster (fruit fly)
Drosophila yakuba (fruit fly)
Locusta migratoria (locust)
Spodoptera frugiperda
Echinodermata (sea urchins)
Paracentrotus Hvidus
Strongylocentrotus purpuratus
Chordata
Aepyceros melampus
Antilocapra americana
Balaenoptera physalus (fin whale)
Bos taurus (ox)
Boselaphus tragocamelus
Capra hircus (goat)
Cephalophus maxwelli
Cervus unicolor (sambar deer)
Cyprinus carpio (carp)
Damaliscus dorcas
Gallus gallus domesticus (chicken)
Gazella thomsoni
Homo sapiens (human)
Hydropotes inermis (Chinese water deer)
Kobus ellipsiprymnus
Madoqua Idrki
Muntiacus reevesi (Reeves' muntjac)
Mus musculus (mouse)
Odocoileus virginianus (white-tailed deer)
Oryx gazella
Rana catesbeiana (frog)
+#
*#
+
*#
+#
*#
+#
*#
*#
+#
•#
+
+#
*#
*#
+#
+
+#
*#
+
Nucleic Acids Research, Vol. 20, Supplement 2101
Organism name1
Rattus norvegicus (rat)
Tragelaphus imberbis
Tragulus napu
Xenopus laevis (toad)
Status2 Accession Number
*#
+#
J01438
M86493
M55539
M10217
EUCARYOTES (EUCARYA3) (NUCLEOCYTOPLASMIC)
Archezoa7
Giardia ardeae
Giardia intestinalis
Protoctista5
Dinoflagellata (dinoflagellates)
Prorocentrum micans
Euglenophyta (euglenoid flagellates)
Euglena gracilis
Zoomastigina (zooflagellates)
Crithidia fasciculata
Trypanosoma brucei
Ciliophora (ciliates)
Tetrahymena pyriformis
Tetrahymena thermophila
Acrasiomycota (cellular slime molds)
Dictyostelium discoideum
Myxomycota (plasmodial slime molds)
Didymium iridis
Physarum polycephalum
*#
*#
X58290
X52949
*
X15973,X16108
+#
X53361
+
*#
Y00055
X14553
*#
+#
M10752,X54004
X54512
X00601
*#
+
X60210
V01159
Fungi
Zygomycota
Mucor racemosus
M26190
Ascomycota
Saccharomyces carlsbergensis
Saccharomyces cerevisiae
Plantae
Angiospermophyta (flowering plants)
Arabidopsis thaliana
Citrus limon (lemon)
Fragaria ananassa (strawberry)
Lycopersicon esculentum (tomato)
Oryza sativa (rice)
Sinapsis alba (mustard)
+
*
V01285
J01355,K01048
*#
*
*#
*
+
*#
X52320
X05910
X15589.X58118
X07889.X13557
Ml 1585
X15915.X57137
Animalia
Nematoda
Caenorhabditis elegans
X03680
Arthropoda
Drosophila melanogaster
M21017
Chordata
Herdmania momus
Homo sapiens (human)
Mus musculus (mouse)
X53538
J01866.M11167
J01871.X00525
2102 Nucleic Acids Research, Vol. 20, Supplement
Organism name 1
Status2 Accession Number
Rattus norvegicus (rat)
+
Xenopus borealis (toad)
Xenopus laevis (toad)
*#
+
J01881,K01591,X00521,
X01069
X59733
K01376,X00136,X59734
'Eucaryotic organisms are classified according to the scheme of Margulis.L. and Schwartz.K.V. (1988) [Five Kingdoms. An Illustrated Guide to the
Phyla of Life on Earth (2nd edition). W.H. Freeman and Co., New York].
2
New listings that did not appear in the previous edition [Gutell.R.R., Schnare.M.N. and Gray.M.W. (1990) Nucleic Acids Res. 18, Supplement,
2319—2330] are denoted by ' #'. Secondary structures now available inhardcopy form in Release 1.0 are denoted by ' + ', while newly modeled structures
that will be included in future releases are indicated by '*'.
3
See Woese.C.R., Kandler.O. and Wheelis,M.L. (1990) Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and
Eucarya. Proc. Nail. Acad. Sci. U.S.A. 87, 4576-4579.
4
See Woese,C.R., Stackebrandt,E., Macke.T.J. and Fox, G.E. (1985) A phylogenetic definition of the major eubacterial taxa. System. Appl. Microbiol.
6, 143-151.
5
The term 'Protoctista', as defined and used by Margulis and Schwartz (1988), includes but is not limited to the 'Protista' (unicellular eucaryotes, or
protists).
6
See note in List of References, below.
7
See Cavalier-Smith.T. (1987) Eukaryotes with no mitochondria. Nature 326, 332-333.
List of references to LSU rRNA sequences (# = new this edition)
ARCHAEBACTERIA
Archaeoglobus fulgidus
#Woese,C.R., Achenbach.L., Rouviere.P. and Mandelco.L. (1991) System. Appl. Microbiol. 14, 364-371.
Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts.
Desulfumcoccus mobUis
Leffers.H., Kjems.J., Ostergaard.L., Larsen.N. and Garrett.R.A. (1987) J. Mol. Biol. 195, 4 3 - 6 1 .
Evolutionary relationships amongst archaebacteria. A comparative study of 23 S ribosomal RNAs of a sulpur-dependent extreme thermophile, an extreme
halophile and a thermophilic methanogen.
Halobacterium halobium
Mankin.A.S. and Kagramanova.V.K. (1986) Mol. Gen. Genet. 202, 152-161.
Complete nucleotide sequence of the single ribosomal RNA operon of Halobacterium halobium: secondary structure of the archaebacterial 23S rRNA.
Halobacterium marismortui
Brombach.M., Specht.T., Erdmann.V.A. and Ulbrich.N. (1989) Nucleic Acids Res. 17, 3293.
Complete nucleotide sequence of a 23S ribosomal RNA gene from Halobacterium marismortui.
Halococcus morrhuae (see Desulfumcoccus mobilis)
Methanobacterium thermoautotrophicum (see Desulfumcoccus mobilis)
Methanococcus vannielii
Jarsch.M. and Bock.A. (1985) Mol. Gen. Genet. 200, 305-312.
Sequence of the 23S rRNA gene from the archaebacterium Methanococcus vannielii: evolutionary and functional implications.
Methanospirillum hungatei
#Burggraf,S., Ching.A., Stetter,K.O. and Woese.C.R. (1991) System. Appl. Microbiol. 14, 358-363.
The sequence of Methanospirillum hungatei 23S rRNA confirms the specific relationship between the extreme halophiles and the Methanomicrobiales.
Sulfolobus solfalaricus
# Woese.C.R. Unpublished.
ThermofUum pendens
#Kjems,J., Leffers.H., Olesen.T., Holz,I. and Garrett.R.A. (1990) System. Appl. Microbiol. 13, 117-127.
Sequence, organization and transcription of the ribosomal RNA operon and the downstream tRNA and protein genes in the archaebacterium Thermofilum
pendens.
Thermoplasma acidophilum
tfRee.H.K. and Zimmermann,R.A. (1990) Nucleic Acids Res. 18, 4471-4478.
Organization and expression of the 16S, 23S and 5S ribosomal RNA genes from the archaebacterium Thermoplasma acidophilum.
Thermopmteus tenax
Kjems,J., Leffers.H., Garrett.R.A., Wich.G., Leinfelder.W. and Bock A. (1987) Nucleic Acids Res. 15, 4821-4835.
Gene organization, transcription signals and processing of the single ribosomal RNA operon of the archaebacterium Thermoproteus tenax.
EUBACTERIA
Anacystis nidulans
Kumano.M., Tomioka,N. and Sugiura.M. (1983) Gene 24, 219-225.
The complete nucleotide sequence of a 23S rRNA gene from a blue-green alga, Anacystis nidulans.
Douglas.S.E. and Doolittle.W.F. (1984) Nucleic Acids Res. 12, 3373-3386.
Complete nucleotide sequence of the 23S rRNA gene of the Cyanobacterium, Anacystis nidulans.
Nucleic Acids Research, Vol. 20, Supplement 2103
Bacillus sp.
#Fink,P.S., Zhao.Y., Prochaska.L.J. and Leffak.M. (1991) Nucleic Acids Res. 19, 5437.
Nucleotide sequence of a 23S and a 5S-like rRNA gene from the thermophilic Bacillus sp.strain PS3.
Bacillus stearothermophiius
Kop,J., Wheaton,V., Gupta.R., Woese.C.R. and Noller.H.F. (1984) DNA 3, 347-357.
Complete nucleotide sequence of a 23S ribosomal RNA gene from Bacillus stearolhermophilus.
Bacillus subtilis
Green.C.J., Stewart.G.C, Hollis.M.A., Vold.B.S. and Bott,K.F. (1985) Gene 37, 261-266.
Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rmB.
Chlorobium limicola
#Woese,C.R., Mandelco.L., Yang,D., Gherna,R. and Madigan,M.T. (1990) System. Appl. Microbiol. 13, 258-262.
The case for relationship of the Flavobacteria and their relatives to the green sulfur bacteria.
Escherichia coli
Brosius,J., Dull.T.J. and Noller.H.F. (1980) Proc. Natl. Acad. Sci. U.S.A. 77, 201-204.
Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli.
Branlant,C, Krol,A., Machatt.M.A., Pouyet.J., Ebel,J.-P., Edwards.K. and Kossel.H. (1981) Nucleic Acids Res. 9, 4303-4324.
Primary and secondary structures of Escherichia coli MRE 600 23S ribosomal RNA. Comparison with models of secondary structure for maize chloroplast
23S rRNA and for large portions of mouse and human 16S mitochondrial rRNAs.
Flavobacterium odoratum (see Chlorobium limicola)
Flexibacter flexilis (see Chlorobium limicola)
Frankia sp.
# Normand.P. Unpublished.
Leptospira interrogans
Fukunaga,M., Horie,!. and Mifuchi.I. (1989) Nucleic Acids Res. 17, 2123.
Nucleotide sequence of a 23S ribosomal RNA gene from Leptospira interrogans serovar canicola strain Moulton.
Micrococcus luteus
Regensburger.A., Ludwig,W., Frank.R., Blocker.H. and Schleifer.K.H. (1988) Nucleic Acids Res. 16, 2344.
Complete nucleotide sequence of a 23S ribosomal RNA gene from Micrococcus luteus.
Mycobacterium leprae
#Liesack,W., Sela,S., Bercovier.H., Pitulle.C. and Stackebrandt,E. (1991) FEBS Lett. 281, 114-118.
Complete nucleotide sequence of the Mycobacterium leprae 23 S and 5 S rRNA genes plus flanking regions and their potential in designing diagnostic
oligonucleotide probes.
Pirellula marina
Liesack.W., Hopfl.P. and Stackebrandt.E. (1988) Nucleic Acids Res. 16, 5194.
Complete nucleotide sequence of a 23S ribosomal RNA gene from Pirellula marina.
Pseudomonas aeruginosa
Toschka.H.Y., Hopfl.P., Ludwig.W., Schleifer.K.H., Ulbrich.N. and Erdmann.V.A. (1987) Nucleic Acids Res. 15, 7182.
Complete nucleotide sequence of a 23S ribosomal RNA gene from Pseudomonas aeruginosa.
Pseudomonas cepacia
Hopfl.P., Ludwig.W., Schleifer.K.H. and Larsen.N. (1989) Eur. J. Biochem. 185, 355-364.
The 23S ribosomal RNA higher-order structure of Pseudomonas cepacia and other prokaryotes.
Rhodobacter capsulatus
Hopfl.P., Ludwig.W. and Schleifer.K.H. (1988) Nucleic Acids Res. 16, 2343.
Complete nucleotide sequence of a 23S ribosomal RNA gene from Rhodobacter capsulatus.
Rhodobacter sphaeroides
#Dryden,S.C. and Kaplan.S. (1990) Nucleic Acids Res. 18, 7267-7277.
Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides.
Ruminobacter amylophilus
Spiegl.H., Ludwig.W., Schleifer.K.H. and Stackebrandt.E. (1988) Nucleic Acids Res. 16, 2345.
Complete nucleotide sequence of a 23S ribosomal RNA gene from Ruminobacter amylophilus.
Streptomyces ambofaciens
Pernodet,J.-L., Boccard.F., Alegre,M.-T., Gagnat.J. and Guerineau.M. (1989) Gene 79, 33-46.
Organization and nucleotide sequence analysis of a ribosomal RNA gene cluster from Streptomyces ambofaciens.
Streptomyces griseus
#Kim,E. Unpublished.
Thermus thermophUus
H6pfl,P., Ulrich.N., Hartmann,R.K., Ludwig.W. and Schleifer.K.H. (1988) Nucleic Acids Res. 16, 9043.
Complete nucleotide sequence of a 23S ribosomal RNA gene from Thermus thermophUus HB8.
PLASTIDS
Alnus incana
#Levesque,M. and Johnson,D.A. Unpublished.
Sequence of the chloroplast 23S rRNA gene from the alder Alnus incana.
Astasia longa
#Siemeister,G. and Hachtel.W. (1990) Curr. Genet. 17, 433-438.
Organization and nucleotide sequence of ribosomal RNA genes on a circular 73 kbp DNA from the colourless flagellate, Astasia longa.
2104 Nucleic Acids Research, Vol. 20, Supplement
Chlamydomonas eugametos
#Turmel,M., Boulanger.J., Schnare.M.N., Gray.M.W. and Lemieux.C. (1991) J. Mol. Biol. 218, 293-311.
Six group I introns and three internal transcribed spacers in the chloroplast large subunit ribosomal RNA gene of the green alga Chlamydomonas eugametos.
Chlamydomonas reinhardtii
Lemieux,C, Boulanger.J., Otis.C, and Turmel.M. (1989) Nucleic Acids Res. 17, 7997.
Nucleotide sequence of the chloroplast large subunit rRNA gene from Chlamydomonas reinhardtii.
Chlorella ellipsoidea
YamadaX and Shimaji.M. (1987) Curr. Genet. 11, 347-352.
An intron in the 23S rRNA gene of the Chlorella chloroplasts: Complete nucleotide sequence of the 23S rRNA gene.
Conopholis americana.
#Wimpee,C.F., Morgan,R. and Wrobel.R. (1992) Plant Mol. Biol. 18, 275-285.
An aberrant plastid ribosomal RNA gene cluster in the root parasite Conopholis americana.
Euglena gracilis
Yepiz-Plascencia.G.M., Jenkins.M.E. and Hallick.R.B. (1988) Nucleic Acids Res. 16, 9340.
Nucleotide sequence of the Euglena gracilis chloroplast 23S rRNA gene of the rmC operon.
#Schnare,M.N., Yepiz-Plascencia,G.M., Copertino,D.W., Hallick.R.B. and Gray,M.W. (1992) Nucleic Acids Res. 20, in press.
5'- and 3'-terminal sequences of the chloroplast 16S and 23S ribosomal RNAs of Euglena gracilis.
Marchantia polymorpha
Ohyama.K., Fukuzawa.H., Kohchi.T., Shirai.H., Sano,T., Sano.S., Umesono.K., Shiki.Y., Takeuchi.M., Chang,Z., Aota.S., inokuchi.H. and Ozeki.H.
(1986) Plant Mol. Biol. Reporter A, 148-175.
Complete nucleotide sequence of liverwort Marchantia polymorpha chloroplast DNA.
[See also: Nature ill, 572-574 (1986). Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast
DNA.]
KohchiX, Shirai.H., Fukuzawa.H., Sano.T., Komano.T., Umesono,K., Inokuchi.H., Ozeki.H. and Ohyama.K. (1988) J. Mol. Biol. 203, 353-372.
Structure and organization of Marchantia polymorpha chloroplast genome. IV. Inverted repeat and small single copy regions.
Nicotiana tabacum
Takaiwa.F. and Sugiura.M. (1982) Eur. J. Biochem. Y2A, 13-19.
The complete nucleotide sequence of a 23-S rRNA gene from tobacco chloroplasts.
Shinozaki.K., Ohme,M., Tanaka.M., Wakasugi.T., Hayashida.N., Matsubayashi.T., Zaita.N., Chunwongse.J., Obokata.J., Yamaguchi-Shinozaki.K.,
Ohto.C, Torazawa.K., Meng.B.Y., Sugita,M., Deno.H., Kamogashira.T., Yamada.K., Kusuda.J., Takaiwa.F., Kato.A., Tohdoh.N., Shimada.H.
and Sugiura.M. (1986) Plant Mol. Biol. Reporter 4, 111-147.
The complete nucleotide sequence of the tobacco chloroplast genome.
[See also: EMBOJ. 5, 2043-2049 (1986). The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression.)
Oryza saliva
Hiratsuka.J., Shimada.H., Whittier.R., Ishibashi.T., Sakamoto.M., Mori.M., Kondo,C, Honji.Y., Sun,C.-R., Meng,B.-Y., Li,Y.-Q., Kanno.A.,
Nishizawa,Y., Hirai.A., Shinozaki.K.and Sugiura.M. (1989) Mol. Gen. Genet. 217, 185-194.
The complete sequence of the rice (Oryza saliva) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major
plastid DNA inversion during the evolution of the cereals.
Pisum sativum
#Stummann,B.M., Lehmbeck.J., Bookjans.G. and Henningsen.K.W. (1988) Physiologia Plantarum 72, 139-146.
Nucleotide sequence of the single ribosomal RNA operon of pea chloroplast DNA.
Plasmodium falciparum
# Wilson,R.J.M., Gardner.M.J., Feagin.J.E., Moore,D., Rangachari.K. and Williamson,D.H. Unpublished.
A large subunit ribosomal RNA gene from the inverted repeat within the 35-kb circular DNA of the malaria parasite Plasmodium falciparum.
[Note that preliminary phylogenetic analysis suggests that the P. falciparum 35-kbp DNA may be a plastid DNA remnant; see #Gardner,M.J., FeaginJ.E.,
Moore.D.J., Spencer.D.F., Gray.M.W., Wilhamson.D.H. and Wilson,R.J.M. (1991) Mol. Biochem. Parasitol. 48, 77-88.]
Zea mays
Edwards.K. and K6ssel,H. (1981) Nucleic Acids Res. 9, 2853-2869.
The rRNA operon from Zea mays chloroplasts: nucleotide sequence of 23S rDNA and its homology with E. coli 23S rDNA.
MITOCHONDRIA
Aedes albopictus
HsuChen,C.-C, Kotin.R.M. and Dubin.D.T. (1984) Nucleic Acids Res. 12, 7771-7785.
Sequences of the coding and flanking regions of the large ribosomal subunit RNA gene of mosquito mitochondria.
Aepyceros melampus
#Allard,M.W., Miyamoto.M.M., Jarecki.L., Kraus,F. and Tennant.M.R. (1992) Proc. Natl. Acad. Sci. U.S.A., in press.
DNA Systematics and evolution of the artiodactyl family Bovidae.
Antilocapra americana
#Kraus,F. and Miyamoto,M.M.(1991) Syst. Zool. 40, 117-130.
Rapid cladogenesis among the pecoran ruminants: Evidence from mitochondrial DNA sequences.
Apis mellifera
Vlasak.I., Burgschwaiger.S. and Kreil,G. (1987) Nucleic Acids Res. 15, 2388.
Nucleotide sequence of the large ribosomal RNA of honeybee mitochondria.
Artemia satina
Palmero.I., Renart,J. and Sastre.L. (1988) Gene 68, 239-248.
Isolation of cDNA clones coding for mitochondrial 16S ribosomal RNA from the crustacean Artemia.
Nucleic Acids Research, Vol. 20, Supplement
Ascaris suum
#Okimoto,R., Macfarlane.J.L., Clary.D.O. and Wolsteholme.D.R. (1992) Genetics, in press.
The mitochondria! genomes of two nematodes, Caenorhabditis elegans and Ascaris suum.
Aspergillus nidulans
Netzker.R.. Kochel.H.G., Basak.N. and Kuntzel.H. (1982) Nucleic Acids Res. 10, 4783-4794.
Nucleotide sequence of Aspergillus nidulans mitochondrial genes coding for ATPase subunit 6, cytochrome oxidase subunit 3, seven unidentified proteins,
four tRNAs and L-rRNA.
Dyson.N.J., Brown,T.A., Waring,R.B. and Davies R.W. (1989) Gene 75,109-118.
The mitochondrial ribosomal RNA molecules of Aspergillus nidulans.
Balaenoptera physalus
#Arnason,U., Gullberg.A. and Widegren.B. (1991) J. Mol. Evol. 33, 556-568.
The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus.
Bos taunts
Anderson.S., de Bruijn.M.H.L., Coulson.A.R., Eperon.I.C, Sanger.F. and Young,I.G. (1982) J. Mol. Biol. 156, 683-717.
Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome.
Boselaphus tragocamelus (see Aepyceros melampus)
Caenorhabditis elegans (see Ascaris suum)
Capra hircus (see Antilocapra americana)
Cephalophus maxwelli (see Aepyceros melampus)
Cervus unicolor
H Miyamoto,M.M., Kraus.F. and Ryder.O.A. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 6127-6131.
Phylogeny and evolution of antlered deer determined from mitochondrial DNA sequences.
Chlamydomonas reinhardtii
Boer,P.H. and Gray.M.W. (1988) Cell 55, 399-411.
Scrambled ribosomal RNA gene pieces in Chlamydomonas reinhardtii mitochondrial DNA.
#Boer,P.H. and Gray,M.W. (1988) EMBO J. 7, 3501-3508.
Genes encoding a subunit of respiratory NADH dehydrogenase (ND1) and a reverse transcriptase-like protein (RTL) are linked to ribosomal RNA
gene pieces in Chlamydomonas reinhardtii mitochondrial DNA.
#Boer,P.H. and Gray.M.W. (1991) Curr. Genet. 19, 309-312.
Short dispersed repeats localized in spacer regions of Chlamydomonas reinhardtii mitochondrial DNA.
Crithidia fasciculata
Sloof,P., Van den Burg,J., Voogd.A., Benne,R., Agostinelli.M., Borst.P., Gutell.R. and Noller.H. (1985) Nucleic Acids Res. 13, 4171-4190.
Further characterization of the extremely small mitochondrial ribosomal RNAs from trypanosomes: a detailed comparison of the 9S and 12S RNAs
from Crithidia fasciculata and Trypanosoma brucei with rRNAs from other organisms.
Crithidia oncopelti
#Horvith,A., Maslov.D.A. and Kolesnikov,A.A. (1990) Nucleic Acids Res. 18, 2811.
The nucleotide sequence of the 12S ribosomal RNA gene from kinetoplast DNA of the protozoan Crithidia oncopelti.
Cyprinus carpio
#Chang,Y.S. and Huang.F.I. Unpublished.
C. carpio complete mitochondrial genome DNA.
Damaliscus dorcas (see Aepyceros melampus)
Drosophila melanogaster
#Kobayashi,S. and Okada.M. (1990) Nucleic Acids Res. 18, 4592.
Complete cDNA sequence encoding mitochondrial large ribosomal RNA of Drosophila melanogaster.
Drosophila yakuba
Clary,D.O. and Wolstenholme.D.R. (1985) Nucleic Acids Res. 13, 4029-4045.
The ribosomal RNA genes of Drosophila mitochondrial DNA.
Gallus gallus domesticus
# Desjardins.P. and Morais.R. (1990) J. Mol. Biol. 212, 599-634.
Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates.
Gazella (homsoni (see Aepyceros melampus)
Homo sapiens
Eperon.I.C., Anderson.S. and Nierlich,D.P. (1980) Nature 286, 460-467.
Distinctive sequence of human mitochondrial ribosomal RNA genes.
Anderson.S., Bankier.A.T., Barrell.B.G., de Bruijn.M.H.L., Coulson,A.R., DrouinJ., Eperon.I.C., Nierlich.D.P., Roe.B.A., Sanger.F., Schreier.P.H.,
Smith.A.J.H., Staden.R. and Young.I.G. (1981) Nature 290, 457-465.
Sequence and organization of the human mitochondrial genome.
Hydropotes inermis (Chinese water deer) (see Cervus unicolor)
Kobus ellipsiprymnus (see Aepyceros melampus)
Leishmania larentolae
de la Cruz,V.F., Simpson.A.M., Lake.J.A. and Simpson,L. (1985) Nucleic Acids Res. 13, 2337-2356.
Primary sequence and partial secondary structure of the 12S kinetoplast (mitochondrial) ribosomal RNA from Leishmania tarentolae: conservation of
peptidyl-transferase structural elements.
2105
2106 Nucleic Acids Research, Vol. 20, Supplement
Leptomonas sp.
Lake,J.A., de la Cruz.V.F., Ferreira.P.C.G., Morel.C. and Simpson.L. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 4779-4783.
Evolution of parasitism: Kinetoplastid protozoan history reconstructed from mitochondrial rRNA gene sequences.
Locusta migratoria
Uhlenbusch.I., McCracken.A. and Gellissen.G. (1987) Curr. Genet. 11, 631-638.
The gene for the large (16S) ribosomal RNA from the Locusta migratoria mitochondrial genome.
Madoqua kirki (see Aepycems melampus)
Marchantia polymorpha
#Oda,K., Yamato.K., Ohta,E., Nakamura.Y., Takemura.M., Nozato.N., Akashi.K., Kanegae.T., Ogura.Y., Kohchi,T. and Ohyama.K. (1992)/
Mol. Biol. 223, 1-7.
Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA: a primitive form of plant mitochondrial
genome.
Muntiacus reevesi (see Cervus unicolor)
Mus musculus
Van Etten.R.A., Walberg.M.W. and Clayton.D.A. (1980) Cell 22, 157-170.
Precise localization and nucleotide sequence of the two mouse mitochondrial rRNA genes and three immediately adjacent novel tRNA genes.
Bibb.M.J., Van Etten.R.A., Wright.C.T., Walberg.M.W. and Clayton, D.A. (1981) Cell 26, 167-180.
Sequence and gene organization of mouse mitochondrial DNA.
Neurospora crassa
#Abdel-Malik,M.S., Court.D.A., Cheng,C.-K. and Bertrand.H. (1990) Nucleic Acids Res. 18, 7440.
Nucleotide sequence of the exons of the large subunit rRNA of Neurospora crassa mitochondria.
Odocoileus virginianus (see Cervus unicolor)
Oenothera berteriana
Manna.E. and Brennicke.A. (1985) Curr. Genet. 9, 505-515.
Primary and secondary structure of 26S ribosomal RNA of Oenothera mitochondria.
Oryx gazella (see Aepyceros melampus)
Paracentrotus lividus
Cantatore,P., Roberti.M., Rainaldi.G., Gadaleta.M.N. and Saccone,C. (1989)7. Biol. Chem. 264, 10965-10975.
The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus.
Paramecium primaurelia
Seilhamer,J.J. and Cummings.D.J. (1981) Nucleic Acids Res. 9, 6391 -6406.
Structure and sequence of the mitochondrial 20S rRNA and tRNA tyr gene of Paramecium primaurelia.
Seilhamer,J.J., Gutell.R.R. and Cummings.D.J. (1984)7. Biol. Chem. 259, 5173-5181.
Paramecium mitochondrial genes. II. Large subunit rRNA gene sequence and microevolution.
Paramecium tetraurelia (see also Paramecium primaurelia)
#Pritchard,A.E., Seilhamer.J.J., Mahalingam.R., Sable.C.L., Venuti.S.E. and Cummings.D.J. (1990) Nucleic Acids Res. J8, 173-180.
Nucleotide sequence of the mitochondrial genome of Paramecium.
Podospora anserina
Cummings.D.J., Domenico.J.M. and Nelson,J. (1989)7. Mol. Evol. 28, 242-255.
DNA sequence and secondary structures of the large subunit rRNA coding regions and its two class I introns of mitochondrial DNA from Podospora anserina.
#Cummings.D.J., McNally.K.L., Domenico.J.M. and Matsuura.E.T. (1990) Curr. Genet. 17, 375-402.
The complete DNA sequence of the mitochondrial genome of Podospora anserina.
Rana catesbeiana
Nagae.Y., Fujii.H., Yoneyama.Y., Goto.Y. and Okazaki.T. (1988) Nucleic Acids Res. 16, 10363.
Nucleotide sequences of the Rana catesbeiana mitochondrial small (I2S) and large (16S) ribosomal RNA genes.
Rattus norvegicus
Saccone,C, Cantatore.P., Gadaleta.G., Gallerani.R., Lanave.C, Pepe.G. and Kroon.A.M. (1981) Nucleic Acids Res. 9, 4139-4148.
The nucleotide sequence of the large ribosomal RNA gene and the adjacent tRNA genes from rat mitochondria.
Gadaleta.G., Pepe.G., De Candia, G., Quagliariello.C, Sbisa.E. and Saccone.C. (1989) J. Mol. Evol. 28, 497-516.
The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates.
Saccharomyces cerevisiae
Sor,F. and Fukuhara.H. (1983) Nucleic Adds Res. 11, 339-348.
Complete DNA sequence coding for the large ribosomal RNA of yeast mitochondria.
Schizosaccharomyces pombe
Lang.B.F., Cedergren.R. and Gray.M.W. (1987) Eur. J. Biochem. 169, 527-537.
The mitochondrial genome of the fission yeast, Schizosaccharomyces pombe. Sequence of the large-subunit ribosomal RNA gene, comparison of potential
secondary structure in fungal mitochondrial large-subunit rRNAs and evolutionary considerations.
Spodoptera frugiperda
flPashley.D.P. and Ke.L.D. Unpublished.
Sequence evolution in the large ribosomal and ND-1 genes in a lepidopteran mitochondrial genome: Implications for phylogenetic analyses.
Strongylocentrotus purpuratus
Jacobs.H.T., Elliott.D.J., Math.V.B. and Farquharson.A. (1988) J. Mol. Biol. 202, 185-217.
Nucleotide sequence and gene organization of sea urchin mitochondrial DNA.
Nucleic Acids Research, Vol. 20, Supplement 2107
Tetrahymena pyriformis
#Heinonen,T.Y.K., Schnare.M.N. and Gray.M.W. (1990)7. Biol Chem. 265, 22336-22341.
Sequence heterogeneity in the duplicate large subunit ribosomal RNA genes of Tetrahymena pyriformis mitochondrial DNA.
Tragelaphus imberbis (see Aepyceros melampus)
Tragulus napu (see AntUocapra americana)
Triticum aestivum
Falconet,D., Sevignac.M. and Quetier.F. (1988) Curr. Genet. 13, 75-82.
Nucleotide sequence and determination of the extremities of the 26S ribosomal RNA gene in wheat mitochondria: evidence for sequence rearrangements
in the ribosomal genes of higher plants.
Trypanosoma brucei (see Crithidia fasciculate)
Also:
Eperon.I.C, Janssen.J.W.G., Hoeijmakers.J.H.J. and Borst.P. (1983) Nucleic Acids Res. 11, 105-125.
The major transcripts of the kinetoplast DNA of Trypanosoma brucei are very small ribosomal RNAs.
Xenopus laevis
Roe.B.A., Ma,D.-P., Wilson.R.K. and Wong,J.F.-H. (1985) J. Biol. Chem. 260, 9759-9774.
The complete nucleotide sequence of the Xenopus laevis mitochondrial genome.
Zea mays
Dale.R.M.K., Mendu.N., Ginsburg,H. and Kridl,J.C. (1984) Plasmid 11, 141-150.
Sequence analysis of the maize mitochondrial 26 S rRNA gene and flanking regions.
EUCARYOTES (NUCLEOCYTOPLASMIC)
Arabidopsis lhaliana
#Unfried,I. and Gruendler,P. (1990) Nucleic Acids Res. 18, 4011.
Nucleotide sequence of the 5.8S and 25S rRNA genes and of the internal transcribed spacers from Arabidopsis thaliana.
Caenorhabditis elegans
Ellis.R.E., Sulston.J.E. and Coulson.A.R. (1986) Nucleic Acids Res. 14, 2345-2364.
The rDNA of C. elegans: sequence and structure.
Citrus limon
Kolosha.V.O. and Fodor.I.I. (1986) Dokl. Akad. Nauk S.S.S.R. 290, 1006-1011.
High homology of the nucleotide sequences of the cistron of 26 S rRNA of Citrus limon and Saccharomyces cerevisiae.
Kolosha.V.O. and Fodor.I. (1990) Plant Mol. Biol. 14, 147-161.
Nucleotide sequence of Citrus limon 26S rRNA gene and secondary structure model of its RNA.
Crithidia fasciculata
Spencer.D.F., Collings.J.C, Schnare.M.N. and Gray.M.W. (1987) EMBO J. 6, 1063-1071.
Multiple spacer sequences in the nuclear large subunit ribosomal RNA gene of Crithidia fasciculata.
Dictyostelium discoideum
Oraki.T., Hoshikawa.Y., Iida.Y. and Iwabuchi.M. (1984) Nucleic Acids Res. 12, 4171-4184.
Sequence analysis of the transcribed and 5' non-transcribed regions of the ribosomal RNA gene in Dictyostelium discoideum.
Didymium iridis
Johansen.S., Johansen.T. and Haugli.F. Unpublished.
Extrachromosomal ribosomal DNA of Didymium iridis: sequence analysis of large subunit ribosomal RNA gene and sub-telomeric region.
Drosophila melanogaster
Tautz.D., Hancock.J.M., Webb.D.A., Tautz.C. and Dover,G.A. (1988) Mol. Biol. Evol. 5, 366-376.
Complete sequences of the rRNA genes of Drosophila melanogaster.
[Minor correction: # Linares,A.R., Hancock.J.M. and Dover,G.A. (1991) J. Mol. Biol. 219, 381-390. Secondary structure constraints on the evolution
of Drosophila 28 S ribosomal RNA expansion segments.]
Euglena gracilis
ttSchnare.M.N. and Gray.M.W. (1990) J. Mol. Biol. 215, 7 3 - 8 3 .
Sixteen discrete RNA components m the cytoplasmic ribosome of Euglena gracilis.
#Schnare,M.N., CookJ.R. and Gray.M.W. (1990)7. Mol. Biol. 215, 8 5 - 9 1 .
Fourteen internal transcribed spacers in the circular ribosomal DNA of Euglena gracilis.
Fragaria ananassa
#Simovic,N., Wolyn.D. and Jelenkovic.G. Unpublished.
Strawberry (octoploid) DNA for 5.8S ribosomal RNA.
#Simovic,N. and Jelenkovic.G. Unpublished.
The nucleotide sequence of 26S rDNA gene isolated from Fragariaxananassa Duch.-cultivated octoploid strawberry.
Giardia ardeae
#van Keulen.H., Horvat.S., Erlandsen.S.L. and Jarroll.E.L. (1991) Nucleic Acids Res. 19, 6050.
Nucleotide sequence of the 5.8S and large subunit rRNA genes and the internal transcribed spacer and part of the external spacer from Giardia ardeae.
Giardia intestinalis
#Healey,A., Mitchell.R., Upcroft,J.A., Boreham.P.F.L. and Upcroft.P. (1990) Nucleic Acids Res. 18, 4006.
Complete nucleotide sequence of the ribosomal RNA tandem repeat unit from Giardia inlestinalis.
Herdmania momus
#Degnan,B.M., Yan,J., Hawkins.C.J. and Lavin.M.F. (1990) Nucleic Acids Res. 18, 7063-7070.
rRNA genes from the lower chordate Herdmania momus: structural similarity with higher eukaryotes.
2108 Nucleic Acids Research, Vol. 20, Supplement
Homo sapiens
#Maden,B.E.H., Dent.C.L., Farrell,T.E., Garde.J., McCallum.F.S. and Wakeman.J.A. (1987) Biochem J. 246, 519-527.
Clones of human ribosomal DNA containing the complete 18 S-rRNA and 28 S-rRNA genes. Characterization, a detailed map of the human ribosomal
transcription unit and diversity among clones.
[Correction to eliminate extra GC (following position 50) in the original 5.8S rRNA sequence of Khan,M.S. N and Maden,B.E.H. (1977) Nucleic Acids
Res. 4, 2495-2505. Nucleotide sequence relationships between vertebrate 5.8 S ribosomal RNAs.]
Gonzalez.I.L., Gorski.J.L., Campen.T.J., Dorney.D.J., Erickson.J.M., Sylvester,.).E. and Schmickel,R.D. (1985)/Voc. Natl. Acad. Sci. U.S.A. 82,
7666-7670.
Variation among human 28S ribosomal RNA genes.
Lycopersicon esculentum
Kiss,T., Kis,M., Abel.S. and Solymosy,F. (1988) Nucleic Acids Res. 16, 7179.
Nucleotide sequence of the 17S-25S spacer region from tomato rDNA.
Kiss,T., Kis,M. and Solymosy,F. (1989) Nucleic Acids Res. 17, 796.
Nucleotide sequence of a 25S rRNA gene from tomato.
Mucor racemosus
#Ji,G.E. and Orlowski.M. (1990) Curr. Genet. 17, 499-506.
Primary and secondary structure of the 25S rRNA from the dimorphic fungus Mucor racemosus.
Mus musculus
Michot.B., Bachellerie,J.-P. and Raynal.F. (1982) Nucleic Acids Res. 10, 5273-5283.
Sequence and secondary structure of mouse 28S rRNA 5'terminal domain. Organisation of the 5.8S-28S rRNA complex.
Hassouna,N., Michot.B. and Bachellerie,J.-P. (1984) Nucleic Acids Res. 12, 3563-3583.
The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes.
Oryza saliva
Takaiwa.F., Oono,K. and Sugiura.M. (1985) Plant Mol Biol. 4, 355-364
Nucleotide sequence of the 17S-25S spacer region from rice rDNA.
Takaiwa.F., Oono.K., Iida.Y. and Sugiura.M. (1985) Gene 37, 255-259.
The complete nucleotide sequence of a rice 25SrRNA gene.
Physarum polycephalum
Otsuka.T., Nomiyama,H., Yoshida.H., Kukita.T., Kuhara.S. and Sakaki.Y. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 3163-3167.
Complete nucleotide sequence of the 26S rRNA gene of Physarum polycephalum: Its significance in gene evolution.
Prorocentrum micans
Maroteaux.L., Herzog.M. and Soyer-Gobillard.M.-O. (1985) BioSystems 18, 307-319.
Molecular organization of dinoflagellate ribosomal DNA: evolutionary implications of the deduced 5.8S rRNA secondary structure.
Lenaers,G., Maroteaux.L., Michot.B. and Herzog.M. (1989) J. Mol. Evol. 29, 4 0 - 5 1 .
Dinoflagellates in evolution. A molecular phylogenetic analysis of large subunit ribosomal RNA.
Rattus norvegicus
Subrahmanyam.C.S., Cassidy.B., Busch.H. and Rothblum.L.I. (1982) Nucleic Acids Res. 10, 3667-3680.
Nucleotide sequence of the region between the 18S rRNA sequence and the 28S rRNA sequence of rat ribosomal DNA.
Chan,Y.-L., Olvera.J. and Wool.I.G. (1983) Nucleic Acids Res. 11, 7819-7831.
The structure of rat 28S ribosomal ribonucleic acid inferred from the sequence of nucleotides in a gene.
HadjioIov.A.A., Georgiev.O.I., Nosikov.V.V. and Yavachev.L.P. (1984) Nucleic Acids Res. 12, 3677-3693.
Primary and secondary structure of rat 28 S ribosomal RNA.
Wool,I.G. (1986) In Hardesty.B. and Kramer.G. (eds.). Structure, Function, and Genetics of Ribosomes. Springer-Verlag, New York, pp. 391 - 4 1 1 .
Studies on the structure of eukaryotic (mammalian) ribosomes.
Saccharomyces carlsbergensis
Veldman.G.M., Klootwijk.J., de Regt.V.C.H.F., Planta,R.J., Branlant.C, Krol.A. and Ebel,J.-P. (1981) Nucleic Acids Res. 9, 6935-6952.
The primary and secondary structure of yeast 26S rRNA.
Saccharomyces cerevisiae
Rubin.G.M. (1973)7. Biol. Chem. 248, 3860-3875.
The nucleotide sequence of Saccharomyces cerevisiae 5.8 S ribosomal ribonucleic acid.
Georgiev.O.I., Nikolaev.N., HadjioIov.A.A., Skryabin.K.G.. Zakharyev.V.M. and Bayev.A.A. (1981) Nucleic Acids Res. 9. 6953-6958.
The structure of the yeast ribosomal RNA genes. 4. Complete sequence of the 25 S rRNA gene from Saccharomyces cerevisiae.
Sinapsis alba
SCapesius.I. (1991) Plant Mol. Biol. 16, 1093-1094.
Nucleotide sequence of a 25S rRNA gene from mustard (Sinapsis alba).
# Rathgeber,J. and Capesius.I. (1989) Nucleic Acids Res. 17, 7522.
Nucleotide sequence of the 18S-25S spacer region from mustard DNA.
Tetrahymena pyriformis
#Engberg,J., Nielsen,H., Lenaers.G., Murayama.O., Fujitani.H. and Higashinakagawa,T. (1990) /. Mol. Evol. 30, 514-521.
Comparison of primary and secondary 26S rRNA structures in two Tetrahymena species: Evidence for a strong evolutionary and structural contraint
in expansion segments.
Tetrahymena thermophila (see also Tetrahymena pyriformis)
#Engberg,J. and Nielsen,H. (1990) Nucleic Acids Res. 18, 6915-6919.
Complete sequence of the extrachromosomal rDNA molecule from the ciliate Tetrahymena thermophila strain B1868VII.
Nucleic Acids Research, Vol. 20, Supplement 2109
Trypanosoma brucei
#Campbell,D. Unpublished.
Trypanosoma brucei gene for ribosomal RNA large subunit.
#Campbell,D.A., Kubo, K., Clark,C.G. and Boothroyd,J.C. (1987) J. Mot. Biol. 196, 113-124.
Precise identification of cleavage sites involved in the unusual processing of trypanosome ribosomal RNA.
#White,T.C, Rudenko.G. and Borst.P. (1986) Nucleic Acids Res. 14, 9471-9489.
Three small RNAs within the 10 kb trypanosome rRNA transcription unit are analogous to Domain VII of other eukaryotic 28S rRNAs.
Xenopus borealis
#Ajuh,P.M., Heeney,P.A. and Maden,B.E.H. (1991) Proc. R. Soc. bond., B, Biol. Sci. 245, 6 5 - 7 1 .
Xenopus borealis and Xenopus laevis 28S ribosomal DNA and the complete 40S ribosomal precursor RNA coding units of both species.
Xenopus laevis (see also Xenopus borealis)
Hall.L.M.C. and Maden,B.E.H. (1980) Nucleic Acids Res. 8, 5993-6005.
Nucleotide sequence through the 18S-28S intergene region of a vertebrate ribosomal transcription unit.
Ware.V.C, Tague,B.W., Clark.C.G., Gourse.R.L., Brand,R.C.and Gerbi.S.A. (1983) Nucleic Acids Res. 11, 7795-7817.
Sequence analysis of 28S ribosomal DNA from the amphibian Xenopus laevis.
[Corrections to sequence of Domain V: # Stebbins-Boaz,B. and Gerbi.S.A. (1991)7 Mol. Biol. 217,93-112. Structural analysis of the peptidyl transferase
region in ribosomal RNA of the eukaryote Xenopus laevis.]
#Schnare,M.N. and Gray.M.W. (1992) Nucleic Acids Res. 20, in press.
A new 3'-terminus for Xenopus laevis 28S ribosomal RNA.