Expanded versions of the 16S and 23S ribosomal RNA mutation databases (16SMDBexp and 23SMDBexp) [published erratum appears in Nucleic Acids Res 1998 Feb 15;26(4):following 1134]

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Nucleic Acids Research Pages 280-284

Expanded versions of the 16S and 23S Ribosomal RNA Mutation Databases (16SMDBexp and 23SMDBexp)
Description
Availability
Acknowledgements
References

Expanded versions of the 16S and 23S Ribosomal RNA Mutation Databases (16SMDBexp and 23SMDBexp)

Kathleen L. Triman*, Alexandra Peister, Raven A. Goel

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

Received September 30, 1997; Accepted October 3, 1997

ABSTRACT

Expanded versions of the Ribosomal RNA Mutation Databases provide lists of mutated positions in 16S and 16S-like ribosomal RNA (16SMDBexp) and 23S and 23S-like ribosomal RNA (23SMDBexp) and the identity of each alteration. Alterations from organisms other than Escherichia coli are reported at positions according to the E.coli numbering system. 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 at the following URL: http://www.fandm.edu/Departments/Biology/Databases/RNA.html

DESCRIPTION

The expanded version of the 16S Ribosomal RNA Mutation Database (16SMDBexp), currently at Franklin and Marshall College, consists of an annotated list of 295 alterations distributed over 157 positions in 16S ribosomal RNA from Escherichia coli and in 16S-like rRNA from other organisms. Table 1 illustrates the format for presentation of the data and includes 62 new alterations added to the 16SMDBexp database since the previous announcement (32). Mutated positions are arranged in order beginning with the 5[prime] end of 16S rRNA and ending with the 3[prime] 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 (29).

The 23S Ribosomal RNA Mutation Database (23SMDB), currently at Franklin and Marshall College, consists of an annotated list of 271 alterations distributed over 143 positions in 23S ribosomal RNA from E.coli and in 23S-like rRNA from other organisms. Table 2 includes 36 new alterations added to the 23SMDBexp database since the previous announcement (32). A review of the data and genetic methods employed in the detection of 23S rRNA mutant phenotypes will be published elsewhere (33).

There are currently six text files of ribosomal RNA mutations available: (i) 16SMDBexp and (ii) 23SMDBexp, both described above, (iii) 16SMDB and (iv) 23SMDB, files containing only the data from E.coli, and (v) 16S-likeMDB and (vi) 23S-likeMDB, files containing only the data from organisms other than E.coli (28,30-32). 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 the ribosomal RNA mutation databases by anonymous file transfer protocol. The ftp site is: Acad.FandM.edu; the directory is: /NAR .

The databases are 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{at}Acad.FandM.edu. Inquiries may also be directed to K. Triman at Fax: (717) 399 4548. The authors welcome any suggested revisions to the database, as well as information about newly characterized 16S or 23S rRNA mutations.

Table 1. 16SMDBexp: single and double mutations in 16S and 16S-like ribosomal RNA

Position Alteration Phenotype Ref(s)

13 U->9A Impaired growth 17

13 U13A/A914U Impaired growth 17

18 C18A Inhibits translation. Mutant 30S particles are impaired in forming 70S tight couples 17

23 C23U Dominant cold-sensitive phenotype and a defective maturation of the 16S rRNA 5[prime] end 18

517 G->A Increased sensitivity to streptomycin in S.cerevisiae 3

517 U->A Polysome formation severely inhibited while tight couple formation was not disturbed 17

526 C->U Extra PvuII site in region coding for 530-loop in N.plumbaginifolia 37

527 G->U Lethal, found in all ribosome fractions 21

527 G527U/A1492C Lethal, found in polysome 21

527 G527U/A1492G Like G527U 21

527 G527U/A1492U Lethal, found in polysome 21

527 G527U/A1493C Like G527U 21

527 G527U/A1493G Lethal, found in polysome 21

527 G527U/A1493U Like G527U 21

529 G->U Stimulates initiation from a non-AUG initiation codon 14

530 G530A/A531G No increase in initiation from non-AUG codons 14

597 G597A/C643U Slightly decreased affinity for S8 binding 13

597 G597C/U641A/ C643G No effect on S8 binding 13

597 G597U/C643G No binding of S8 13

597 G597U/U641A/C643G No binding of S8 13

597 G597U/U641C/C643G No effect on S8 binding 13

653 nU No effect on B.stearothermophilus S15 binding 1

665 A665C/A668C No effect on B.stearothermophilus S15 binding 1

740 U->C Slight reduction in S15 binding 1

748 nA 30-fold reduction in S15 affinity 1

749 C->A Little effect on S15 binding 1

752 G->C Severely reduced affinity for S15 1

787 A->C Produces ribosomes that are highly functional 8

787 A->G Strongly inhibits ribosome function 8

787 A->U Moderately inhibits ribosome function 8

787 A787C/C795A Moderately inhibits ribosome function 8

787 A787C/C795G Strongly inhibits ribosome function 8

787 A787C/C795U Produces ribosomes that are highly functional 8

787 A787G/C795A Moderately inhibits ribosome function 8

787 A787G/C795G Moderately inhibits ribosome function 8

787 A787G/C795U Produces ribosomes that are highly functional 8

787 A787U/C795A Strongly inhibits ribosome function 8

787 A787U/C795G Strongly inhibits ribosome function 8

787 A787U/C795U Produces ribosomes that are highly functional 8

795 C->A Produces ribosomes that are highly functional 8

795 C->G Moderately inhibits ribosome function 8

795 C->U Produces ribosomes that are highly functional 8

885 G->C Interfere with 912·885 base pair and favored 912·888 conformation 10

885 G->A Novel mutation for streptomycin resistance. Creates a StyI recognition sequence. Affects binding of S12. In N.plumbaginifolia 37

885 G->U Favored the 912·885 conformation. Increases rates of readthrough errors and in-frame stop codons 10

888 G->A Antisuppressor phenotype in Yeast. Increased base pairing in the 912·888 conformation 10

910 C->G Favored the 912·888 conformation, but without cold-sensitivity. Lowers stop codon read-through rates, and elevated rate of frame-shifting. 10

910 C910G/G887C Favored the 912·885 conformation. Increases rates of readthrough errors and in-frame stop codons 10

911 U->C Favored the 912·885 conformation. Increases rates of readthrough errors and in-frame stop codons 10

912 C->G Favored the 912·888 conformation, but without cold-sensitivity. Lowers stop codon read-through rates, and elevated rate of frame-shifting. 10

912 C->U High-level streptomycin resistance in N.plumbaginifolia 37

912 C912G/G885C Favored the 912·885 conformation. Increases rates of readthrough errors and in-frame stop codons 10

Table 1. continued

Position Alteration Phenotype Ref(s)

912 C912G/G885C Favored the 912·885 conformation. Increases rates of readthrough errors and in-frame stop codons 10

912 C912G/G885U Allowed base pairing at 912·885 but interfered with 912·888 base pairing 10

912 C912G/G888C Favored the 912·888 conformation and cold sensitivity, but does not increase reactivity to kethoxal 10

912 C912G/G888U Favored 912·888 conformation but cold-sensitive 10

912 U->C Decreases resistance to streptomycin and increases resistance to paromomycin and inhibits nonsense suppression induced by paromomycin in S.cerevisiae 3

913 A->G Moderate effect of streptomycin binding in N.plumbaginifolia 37

914 A->U Impaired growth 17

915 A->G Increased streptomycin binding in N.plumbaginifolia 37

1054 C->A Lethal above 37°C or high expression. UGA suppression 15

1054 C->G Slight defect in subunit association. Suppresses all three termination codons 15

1054 C->U Temperature sensitive lethality; slow growth rate at 37°C and when highly expressed. Defective ability to enter polysome 15

1054 nC Lethal at 31°C, No suppression of trpA nonsense mutation. Affects 30S subunit assembly and subunit association 15

1065 U1065C/A1191G Inhibits translation, increased level of acetylation, and does not allow S5 to bind. Causes an accumulation of free 30S subunits 18

1192 C->G Gain resistance to spectinomycin and macrolides in Mycobacterium smegmatis 20

1192 C->U Spectinomycin resistance, but no effect on stop codon, readthrough, frameshifting, or initiation events 14

1199 U1199C/C1200U Stimulates initiation from a non-AUG initiation codon 14

1199 U1199G/C1200G Stimulates initiation from a non-AUG initiation codon 14

1341 U->C No effect on growth rate 4

1341 U1341C/C1192U No effect on growth rate 4

1351 A1351C/C1192U Counteracts mutation C1192U and restores spectinomycin binding. No cell growth 4

1351 U->C No effect on growth rate 4

1357 A->C No effect on growth rate 4

1357 A1357C/C1192U Severely decreased growth rate due to defect in elongation 4

1386 G->A Spectinomycin resistance in N.tabacum 25

1395 C1395U/G1505U Viable cells, suppresses lethality. Stimulates initiation from a non-AUG initiation codon. Increased growth rate over C1395U alone 14

1400 nC1400/G1505U Viable cells, suppresses lethality. Stimulates initiation from a non-AUG initiation codon. Increased growth rate over nC1400 alone 14

1405 G->C Significantly reduced interaction with Paromomycin at positions 1491 and 1494 12

1405 G1405C/C1496G No affect on Paromomycin binding 12

1406 U->A or C No affect on Paromomycin binding 12

1406 U1406G/U1495G No effect on Paromomycin binding 12

1407 C->G Severely impaired Paromomycin binding 12

1407 C1407G/G1494C Severely impaired Paromomycin binding 12

1407 C1407U/G1494G Severely impaired Paromomycin binding 12

1407 C1407U/G1494A Severely impaired Paromomycin binding 12

1407 C1407U/G1505U Viable cells, suppresses lethality. Stimulates initiation from a non-AUG initiation codon. Increased growth rate over C1407U alone 14

1408 A->C Moderate reduction of Paromomycin binding 12

1408 A->G Gain resistance to gentamicin, amikacin, or tobramycin in Mycobacterium smegmatis 20

1408 A->G High level neamine and kanamycin resistance in C.reinhardtii 6

1408 A->G Weak reduction of Paromomycin binding 12

1408 A->U Large reduction of Paromomycin binding 12

1409 C->U Low level neamine and kanamycin resistance in C.reinhardtii 6

1409 C1409A/G1491U Slightly reduced interaction with Paromomycin 12

1409 C1409G/G1491C Slightly reduced interaction with Paromomycin 12

1491 G->U Weakened interaction with Paromomycin 12

1492 A1492C/A1493C No effect on Paromomycin binding 12

1494 G->C Severely impaired Paromomycin binding 12

1495 U->A or C Greatly reduced affinity for Paromomycin binding 12

1495 U->G No effect on Paromomycin binding 12

1495 U1495G/U1406G No effect on Paromomycin binding 12

1496 C->G Significant reduction of paromomycin binding at positions 1405 and 1491. Slight reduction of Paromomycin binding at position 1494 12

1505 G1505U/G791A Slower growth rate than G791A alone 14

Table 2. 23SMDBexp: single and double mutations in 23S and 23S-like ribosomal RNA

Position Alteration Phenotype Ref(s)

1067 A1067U Normal growth 22,23

1093 G->U trpA UGA suppressor; temperature sensitive 36

G->C trpA UGA suppressor; temperature sensitive 36

G->A trpA UGA suppressor; temperature sensitive 36

G1093A/A1098G trpA UGA suppressor; temperature sensitive 36

1098 A->U Normal growth phenotpye 36

A->G Normal growth phenotpye 36

A->C trpA UGA suppressor; temperature sensitive 36

A1098G/G1093A trpA UGA suppressor; temperature sensitive 36

2057 G->A Ery^r in Chlamydomonas chloroplasts 6

2058 A->G Ery^r, Lincomycin and clindamycin resistance in Chlamydomonas chloroplasts 6

A->G Lincomycin resistance in Solanum nigrum chloroplasts 7

A->G Clarithromycin resistance in Helicobacter pylori 34

2059 A->G Clarithromycin resistance in H.pylori 34

2061 G->A Chloramphenicol resistance in rat mitochondria 35

2062 A->C Chloramphenicol resistance in Halobacterium halobium 11

2249 U2249C Normal growth 22,23

2250 G2250A Normal growth 22,23

G2250A/C2254U Normal growth 22,23

2251 G->A Dominant lethal; Abolished both binding of tRNA and peptidyl transferase activity 5

G->U Dominant lethal; Abolished both binding of tRNA and peptidyl transferase activity 5

2252 G->A, C or U Less than 5% of control level peptidyl transferase activity 19

2253 G2253A 19% of control level peptidyl transferase activity 19

G2253C 42% control level peptidyl transferase activity 19

G2253U Less than 5% control level peptidyl transferase activity 19

2254 C2254U Normal growth 22,23

2438 U->C Amicetin resistance in H.halobium 9

U->A Amicetin resistance and reduced growth rate in H.halobium 9

U->G Unstable in presence or absence of amicetin in H.halobium 9

2452 C->A Chloramphenicol resistance in human mitochondria 2

C->U Anisomycin resistance in Tetrahymena thermophila 26

C->U Chloramphenicol resistance in H.halobium

C->U Low level sparsomycin resistance in H.halobium 27

2499 C->U Sparsomycin resistance in H.halobium 27

2505 G->A 14% activity of 70S ribosomes 19

G->C Excluded from 70S ribosomes; 17% activity of 70S ribosomes 19

G->U <5% activity of 70S ribosomes 19

2506 U->A Dominant lethal; 5% activity of 70S ribosomes 19

U->C 20% activity of 70S ribosomes 19

U->G <5% activity of 70S ribosomes 19

2507 C2507U Dominant lethal 22,23

C2507U/G2581A Dominant lethal; Inhibition of puromycin in reaction 22,23

[Delta]507/G2581A Dominant lethal; Inhibition of puromycin in reaction 22,23

2508 G2508U Control level peptidyl transferase activity 18,19

2580 U2580A Deleterious; <5% activity of 70S ribosomes 19

U2580C Dominant lethal; 12% activity of 70S ribosomes 19

U2580G Deleterious; 6% activity of 70S ribosomes 19

Table 2. continued

Position Alteration Phenotype Ref(s)

U2580C Reduced growth 22,23

2581 G2581A Deleterious; 22% activity of 70S ribosomes 22,23

G2581A Dominant lethal inhibition of puromycin in reaction 22,23

G2581C Deleterious; 13% activity of 70S ribosomes 22,23

G2581U Deleterious; 18% activity of 70S ribosomes 22,23

2582 G2582A <5% of control level peptidyl transferase activity 22,23

G2582C <5% of control level peptidyl transferase activity 22,23

G2582U <5% of control level peptidyl transferase activity 22,23

2583 G->A <5% of control level peptidyl transferase activity 19

G->C <5% of control level peptidyl transferase activity 19

G->U Dominant lethal; <5% of control level peptidyl transferase activity 19

2584 U->A Deleterious; 20% activity of 70S ribosomes 19

U->C Deleterious; 20% activity of 70S ribosomes 19

U->G Dominant lethal 19

2585 U->A Dominant lethal; <6% of control level peptidyl transferase activity; disrupted binding of tRNA fragment, Decreased peptidyl transferase activity 19, 5

U->C Dominant lethal; <6% of control level peptidyl transferase activity; disrupted binding of tRNA fragment, Decreased peptidyl transferase activity 19, 5

U->G Dominant lethal;36% of control level peptidyl transferase activity; disrupted binding of tRNA fragment, Decreased peptidyl transferase activity 19, 5

2611 C->U or G Ery^r and low level lincomycin and clindamycin resistance in Chlamydomonas chloroplasts 6

ACKNOWLEDGEMENTS

We are 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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<11>

*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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Position	Alteration	Phenotype	Ref(s)
13	U->9A	Impaired growth	17
13	U13A/A914U	Impaired growth	17
18	C18A	Inhibits translation. Mutant 30S particles are impaired in forming 70S tight couples	17
23	C23U	Dominant cold-sensitive phenotype and a defective maturation of the 16S rRNA 5[prime] end	18
517	G->A	Increased sensitivity to streptomycin in S.cerevisiae	3
517	U->A	Polysome formation severely inhibited while tight couple formation was not disturbed	17
526	C->U	Extra PvuII site in region coding for 530-loop in N.plumbaginifolia	37
527	G->U	Lethal, found in all ribosome fractions	21
527	G527U/A1492C	Lethal, found in polysome	21
527	G527U/A1492G	Like G527U	21
527	G527U/A1492U	Lethal, found in polysome	21
527	G527U/A1493C	Like G527U	21
527	G527U/A1493G	Lethal, found in polysome	21
527	G527U/A1493U	Like G527U	21
529	G->U	Stimulates initiation from a non-AUG initiation codon	14
530	G530A/A531G	No increase in initiation from non-AUG codons	14
597	G597A/C643U	Slightly decreased affinity for S8 binding	13
597	G597C/U641A/ C643G	No effect on S8 binding	13
597	G597U/C643G	No binding of S8	13
597	G597U/U641A/C643G	No binding of S8	13
597	G597U/U641C/C643G	No effect on S8 binding	13
653	nU	No effect on B.stearothermophilus S15 binding	1
665	A665C/A668C	No effect on B.stearothermophilus S15 binding	1
740	U->C	Slight reduction in S15 binding	1
748	nA	30-fold reduction in S15 affinity	1
749	C->A	Little effect on S15 binding	1
752	G->C	Severely reduced affinity for S15	1
787	A->C	Produces ribosomes that are highly functional	8
787	A->G	Strongly inhibits ribosome function	8
787	A->U	Moderately inhibits ribosome function	8
787	A787C/C795A	Moderately inhibits ribosome function	8
787	A787C/C795G	Strongly inhibits ribosome function	8
787	A787C/C795U	Produces ribosomes that are highly functional	8
787	A787G/C795A	Moderately inhibits ribosome function	8
787	A787G/C795G	Moderately inhibits ribosome function	8
787	A787G/C795U	Produces ribosomes that are highly functional	8
787	A787U/C795A	Strongly inhibits ribosome function	8
787	A787U/C795G	Strongly inhibits ribosome function	8
787	A787U/C795U	Produces ribosomes that are highly functional	8
795	C->A	Produces ribosomes that are highly functional	8
795	C->G	Moderately inhibits ribosome function	8
795	C->U	Produces ribosomes that are highly functional	8
885	G->C	Interfere with 912·885 base pair and favored 912·888 conformation	10
885	G->A	Novel mutation for streptomycin resistance. Creates a StyI recognition sequence. Affects binding of S12. In N.plumbaginifolia	37
885	G->U	Favored the 912·885 conformation. Increases rates of readthrough errors and in-frame stop codons	10
888	G->A	Antisuppressor phenotype in Yeast. Increased base pairing in the 912·888 conformation	10
910	C->G	Favored the 912·888 conformation, but without cold-sensitivity. Lowers stop codon read-through rates, and elevated rate of frame-shifting.	10
910	C910G/G887C	Favored the 912·885 conformation. Increases rates of readthrough errors and in-frame stop codons	10
911	U->C	Favored the 912·885 conformation. Increases rates of readthrough errors and in-frame stop codons	10
912	C->G	Favored the 912·888 conformation, but without cold-sensitivity. Lowers stop codon read-through rates, and elevated rate of frame-shifting.	10
912	C->U	High-level streptomycin resistance in N.plumbaginifolia	37
912	C912G/G885C	Favored the 912·885 conformation. Increases rates of readthrough errors and in-frame stop codons	10

				S. J. Schroeder, G. Blaha, and P. B. Moore Negamycin Binds to the Wall of the Nascent Chain Exit Tunnel of the 50S Ribosomal Subunit Antimicrob. Agents Chemother., December 1, 2007; 51(12): 4462 - 4465. [Abstract] [Full Text] [PDF]

				S. T. Gregory, J. F. Carr, D. Rodriguez-Correa, and A. E. Dahlberg Mutational Analysis of 16S and 23S rRNA Genes of Thermus thermophilus J. Bacteriol., July 15, 2005; 187(14): 4804 - 4812. [Abstract] [Full Text] [PDF]

				S. T. Gregory, J. F. Carr, and A. E. Dahlberg A Mutation in the Decoding Center of Thermus thermophilus 16S rRNA Suggests a Novel Mechanism of Streptomycin Resistance J. Bacteriol., March 15, 2005; 187(6): 2200 - 2202. [Abstract] [Full Text] [PDF]