Department of Biology, Franklin and Marshall College, PO Box 3003, Lancaster , PA 17604, USA

Received September 17, 1996; Accepted September 19, 1996

ABSTRACT

The Ribosomal RNA Mutation Databases (16SMDB and 23SMDB) provide lists of mutated positions in 16S and 23S ribosomal RNA from Escherichia coli and the identity of each alteration. Information provided for each mutation includes: (i) a brief description of the phenotype(s) associated with each mutation; (ii) whether a mutant phenotype has been detected by in vivo or in vitro methods; and (iii) relevant literature citations. The databases are available via ftp and on the World Wide Web. Expansion of the databases to include information about mutations isolated in organisms other than E.coli is currently in progress.

DESCRIPTION

The 16S Ribosomal RNA Mutation Database (16SMDB), currently at Franklin and Marshall College, consists of an annotated list of 233 alterations distributed over 134 positions in 16S ribosomal RNA from Escherichia coli. Table 1 illustrates the format for presentation of the data and provides a list of 13 new alterations added to the database since the previous announcement ( 27 , 29 ). Mutated positions are arranged in order beginning with the 5' end of 16S rRNA and ending with the 3' end. Phenotypes associated with each alteration are briefly described and designated as to whether the phenotypes were detected in vivo or in vitro . Appropriate references are provided for each alteration. A review of the data and genetic methods employed in the detection of 16S rRNA mutant phenotypes has been published elsewhere ( 28 ).

The 23S Ribosomal RNA Mutation Database (23SMDB), currently at Franklin and Marshall College, consists of an annotated list of 235 alterations distributed over 129 positions in 23S ribosomal RNA from E.coli. Table 2 provides a list of 56 new alterations added to the database since the previous announcement ( 30 ).

Table 1 New single and double mutations in 16S ribosomal RNA

Position	Alteration	Phenotype	Reference
920 a	[Delta]U	Severe reduction in tRNA binding c	5
921 a	U921G/G922U	Severe reduction in tRNA binding c	5
922 a	G to U	Severe reduction in tRNA binding c	5
	G922U/U921G	Severe reduction in tRNA binding c	5
926 a	[Delta]G	Moderate reduction in tRNA binding c	5
1394 a	[Delta]A	Negligible tRNA binding c	5
	A to C, G or U	Wild-type tRNA binding c	5
1491	G to A	Suppressor of UGA nonsense mutation in trpA b	10
1530 a	G1530A/A1531G	Lethal under high copy number expression b
		Deficient initiation complex formation,
		subunit association, and IF3 binding c	7
1531 a	A1531G/G1530A	Lethal under high copy number expression b
		Deficient initiation complex formation,
		subunit association, and IF3 binding c	7
1533	C to A	Slight reduction in tRNA binding c	5

^a Highly conserved among the 16S-like rRNAs in all three primary kingdoms. ^b In vivo. ^c In vitro .

Table 2 New single and double mutations in 23S ribosomal RNA

Position	Alteration	Phenotype	Reference
33	C to U	Suppressor of temperature-sensitive protein L24 mutation a	16
1056	G to A	Binding of both L11 and thiostrepton is weakened in RNA fragments b	22
	G to C	Binding of thiostrepton is weakened in RNA fragments b	22
1082	U to C	Binding of both L11 and thiostrepton is weakened in RNA fragments b	22
	U1082C/A1086G	Both L11 and thiostrepton bind RNA fragments with about wild-type affinity b	22
	U1082A/A1086U	Both L11 and thiostrepton bind RNA fragments with about wild-type affinity b	22
1086	A to G	Binding of both L11 and thiostrepton is weakened in RNA fragments. b	22
	A1086G/U1082C	Both L11 and thiostrepton bind RNA fragments with about wild-type affinity b	22
	A1086U/U1082A	Both L11 and thiostrepton bind RNA fragments with about wild-type affinity b	22
1206	G to A	Erythromycin sensitive a	3
	G1206A/G1228A	Erythromycin sensitive a	3
1207	C to U	Erythromycin sensitive a	3
	C1207U/C1243U	Erythromycin resistant a	3
1208	C to U	Erythromycin sensitive a	3
	C1208U/C1211U	Erythromycin sensitive a	3
	C1208U/C1243U	Erythromycin resistant a	3
1211	C1211U/C1208U	Erythromycin sensitive a	3
1215	G to A	Erythromycin sensitive a	3
1218	G1218A/G1245A	Erythromycin sensitive a	3
1220	G1220A/G1239A	Erythromycin resistant a	3
1221	C1221U/C1229U	Erythromycin resistant a	3
	C1221U/C1233U	Erythromycin resistant a	3
	C1221U/C1243U	Erythromycin sensitive a	3
1225	G to A	Erythromycin sensitive a	3
1227	G1227A/G1236A	Erythromycin sensitive a	3
1228	G1228A/G1206A	Erythromycin sensitive a	3
1229	C to U	Erythromycin sensitive a	3
1232	G1232A/G1238A	Erythromycin sensitive a	3
1233	C to U	Erythromycin sensitive a	3
1235	G to A	Erythromycin sensitive a	3
1236	G to A	Erythromycin sensitive a	3
	G1236A/G1227A	Erythromycin sensitive a	3
1238	G to A	Erythromycin sensitive a	3
	G1238A/G1232A	Erythromycin sensitive a	3
1239	G1239A/G1220A	Erythromycin resistant a	3
1243	C1243U/C1207U	Erythromycin resistant a	3
	C1243U/C1208U	Erythromycin resistant a	3
	C1243U/C1221U	Erythromycin sensitive a	3
1245	G1245A/G1218A	Erythromycin sensitive a	3
1248	G to A	Erythromycin sensitive a	3
2654	A to C	Mildly restrictive effect on fidelity a	19
	A to U	Minor increase in stop codon readthrough and frameshifting a	19
	A to G	Significant increase in stop codon readthrough and frameshifting a	19
	A2654G/C2666U	Significant increase in stop codon readthrough and frameshifting a	19
	A2654G/C2666G	Increased stop codon readthrough and frameshifting a	19
	A2654C/C2666U	Minor increase in stop codon readthrough and frameshifting a	19
	A2654C/C2666G	Minor increase in stop codon readthrough and frameshifting a	19
	A2654U/C2666A	Minor increase in stop codon readthrough and frameshifting a	19
	A2654U/C2666G	Minor increase in stop codon readthrough and frameshifting a	19
	A2654U/C2666U	Minor increase in stop codon readthrough and frameshifting a	19
	A2654C/C2666A	Minor increase in stop codon readthrough and frameshifting a	19
	A2654G/C2666A	Minor increase in stop codon readthrough and frameshifting a	19
2666	C to U	Increased stop codon readthrough and frameshifting a	19
	C to G	No effect on stop codon readthrough or frameshifting a	19
	C to A	No effect on stop codon readthrough or frameshifting a	19

^a In vivo . ^b In vitro .

Table 3 16SNDBexp: examples of mutations in 16S and 16S-like ribosomal RNA

Position	Alteration	Phenotype	Reference(s)
13 a	U to A or C	Reduction of both streptomycin-induced
		misreading and streptomycin binding c	20
*	U to G	Intermediate level streptomycin resistance
		in Chlamydomonas reinhardtii chloroplast.	11
517 a	G to A,C or U	Increased translational error rate b
		Increased level of chemical modification
		at positions 530, 531 and 532 in 70S ribosomes c	17,18,31
*	G to A	Ochre nonsense suppressor in yeast mitochondria	23
523	A to C	Streptomycin r . b	15
*	A to C	Streptomycin resistance in chloroplast of Chlamydomonas reinhardtii	9,11
525	C to U	Streptomycin r ; (with U1192) slightly Spc ts b	21
*	C to U	Streptomycin resistance in tobacco chloroplast	8

^a Highly conserved among the 16S-like rRNAs in all three primary kingdoms. ^b in vivo ; ^c in vitro ; *organisms other than E.coli.

Table 4 23S-likeMDB: examples of mutations in 23S-like ribosomal RNA

Position	Alteration	Phenotype	Reference
1067	A to G or U	Thiostrepton resistance in Halobacterium sp.	12
2032	G to A	Lincomycin resistance in tobacco chloroplasts.	2
2058	A to G	Erythromycin resistance in yeast mitochondria.	25
	A to G	Lincomycin resistance in tobacco chloroplasts.	2
2059	A to G	Lincomycin resistance in tobacco chloroplasts.	2
2447	G to A	Chloramphenicol resistance in yeast mitochondria.	4
	G to C	Anisomycin resistance in Halobacterium sp.	13
2451	A to U	Chloramphenicol resistance in mouse mitochondria	14
2452	C to U	Chloramphenicol resistance in mouse mitochondria	24
	C to U	Anisomycin resistance in Halobacterium sp.	13
2453	A to C	Anisomycin resistance in Halobacterium sp.	13
2503	A to C	Chloramphenicol resistance in yeast mitochondria	4
2504	U to C	Chloramphenicol resistance in human mitochondria.	14
	U to C	Chloramphenicol resistance in mouse mitochondria.	1
2611	C to U	Spiramycin resistance in yeast mitochondria.	26
	C to G	Erythromycin and spiramycin resistance in yeast mitochondria	26
	C to G	Erythromycin and spiramycin resistance in Chlamydomonas chloroplasts	9

Expanded versions of each database are currently available as text files only. The expanded versions include data from E.coli and from other organisms; these files are entitled 16SMDBexp and 23SMDBexp. Table 3 illustrates the format of 16SMDBexp and provides examples of some mutations included in this file. Files containing only the data from organisms other than E.coli are entitled 16S-likeMDB and 23S-likeMDB. Table 4 illustrates the format of 23S-likeMDB and provides examples of some mutations included in this file.

In summary, there are now four new text files available, in addition to 16SMDB and 23SMDB. The four new files are: (i) 16SMDBexp; (ii) 23SMDBexp; (iii) 16S-likeMDB; and (iv) 23S-likeMDB. Ultimately, the goal of this work is to provide a database that can be queried for specific kinds of information. Our plan is to organize the data, so that one can access, for example: (i) all the data from one specific organism; (ii) all the data for one specific nucleotide position; or (iii) all the data for one specific phenotype.

AVAILABILITY

Individuals with access to the Internet telecommunications network may obtain text files of 16SMDB or 23SMDB by anonymous file transfer protocol.

The ftp site is: Acad.FandM.edu

The directory is: /NAR

The database is also available on the World Wide Web at the following URL:

http://www.fandm.edu/Departments/Biology/Databases/RNA.html

Email inquiries should be addressed as follows:

K_Triman@Acad.FandM.edu.

Inquiries may also be directed to K. Triman at Fax +1 717 399 4548. I would welcome any suggested revisions to the database, as well as information about newly characterized 16S or 23S rRNA mutations.

ACKNOWLEDGEMENTS

I am grateful to Janan Eppig from the Bioinformatics Group at the Jackson Laboratory for her expert advice on the use of appropriate database software. Steven Vavoulis assisted in the preparation of the manuscript. This work was supported by the National Science Foundation (MCB-9315443).

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*To whom correspondence should be addressed. Tel: +1 717 291 3948; Fax: +1 717 399 4548; Email: k_triman@acad.fandm.edu
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