EcoGene

EcogeneTopic Page

TopicPage for TLR Repeats of Escherichia coli K-12

Intergenic Repeat Families

Description:

tRNA-linked repeats (TLRs) have 18-19 bp of 3' tRNA sequences at their 3' ends.
TLRA1-17 (68-178 bp) and TRLB1-5 (49-181 bp) are proposed here as alternative name for these two families of tRNA-linked repeat sequences.

Details:

A nomenclature for the 22 TLR repeats was proposed for some newfound members (Rudd, 1998) based upon the well characterized tyrT-linked rtT (repeat of tyrT) naming convention (Bosl, 1991).

All 22 names start with "r" for repeat. The second letter corresponds to the first letter of the tRNA gene or 5S rRNA gene immediately upstream of the tRNA-linked repeat.The last capitalized letter of the TLR name is the fourth capital letter of the linked tRNA or 5S rRNA gene. This nomenclature is used in EcoGene, but an alternative TLRA1-17 and TLRB1-5 nomenclature is also presented to distinguish the two sequence-related families. The 5 member TLRB intergenic repeat family include rsW, downstream of serW and rsX1-4, four tandem copies of the TLRB repeat downstream of serX.

The TLR repeats may be remnants of repeated utilization of tRNA genes for phage or plasmid integrations and excisions, which can leave small regions of duplicated tRNA gene ends behind as debris from horizontal gene transmissions (Rudd, 1998).

rsW' and rsX4' appear to be partial TLRB repeat sequences, as do most of the TLRA sequences, which vary in length.

The tRNA-linked repeats TLRA and TLRB.

TLR	Gene	Centisome	TLR code	Left End	Right End	Length (bp)	Orientation

rlT	lysT	16.81	TLRA1	779849	779952	104	Clockwise
rlW	lysW	16.82	TLRA2	780172	780239	68	Clockwise
rlY	lysY	16.82	TLRA3	780476	780543	68	Clockwise
rlZ	lysZ	16.83	TLRA4	780680	780766	87	Clockwise
rlQ	lysQ	16.83	TLRA5	780951	781031	81	Clockwise
rtV3	tyrV	27.72	TLRA6	1285933	1286110	178	Counterclockwise
rtV2	tyrV	27.72	TLRA7	1286111	1286288	178	Counterclockwise
rtV1	tyrV	27.72	TLRA8	1286289	1286466	178	Counterclockwise
rtT	tyrT	27.73	TLRA9	1286586	1286716	131	Counterclockwise
rlV	lysV	54.30	TLRA10	2519426	2519506	81	Clockwise
raQ	argQ	60.69	TLRA11	2815673	2815758	86	Counterclockwise
raZ	argZ	60.69	TLRA12	2815946	2816033	88	Counterclockwise
raV	argV	60.70	TLRA13	2816361	2816447	87	Counterclockwise
rrF	rrfF	73.74	TLRA14	3421282	3421385	104	Counterclockwise
rpK	proK	79.89	TLRA15	3706471	3706606	136	Counterclockwise
rrA	rrfA	87.05	TLRA16	4038719	4038822	104	Counterclockwise
rrB	rrfB	89.87	TLRA17	4169839	4169942	104	Clockwise

rsW'	serW	19.94	TLRB1	925058	925106	49	Counterclockwise
rsX4'	serX	23.63	TLRB2	1096182	1096244	63	Counterclockwise
rsX3	serX	23.63	TLRB3	1096245	1096425	181	Counterclockwise
rsX2	serX	23.63	TLRB4	1096426	1096606	181	Counterclockwise
rsX1	serX	23.64	TLRB5	1096607	1096787	181	Counterclockwise

17 TLRA and 5 TLRB DNA sequences

FASTA format sequence library file TLR.lib

Multiple Alignment and Repeat Tree The multiple alignment data, the multiple alignment figure, and the neighbor-joining tree data were created using ClustalX locally. Only aligned positions without gaps were used to generate the Repeat Tree. The TLRA clustering reflects the clustering of the adjacent duplicated tRNA and 5S rRNA sequences. The TLRA tree figure was drawn using the Phylodendron server at Indiana University .

TRLA Alignment
TRLB Alignment
TRLA Repeat Tree

The rtV TLR Repeats

rtV1 encodes the Tpr small protein of uncertain function and its poorly characterized sRNA/mRNA called rttR (Counterclockwise). ychS is a probably spuriously annotated ORF encoding a 91 aa protein sequence that is hypothetically translated from rtV3 and part of rtV2. A simliar spurious translation of the serX-linked repeats, ycdV (b1031) has already been removed from the E. coli K-12 genome annotation.

The tyrTV operon ends at the 178 bp rtV1 sequence; rtV repeats are rho-dependent transcriptional terminators (Madden, 1889).

The tyrTV operon and rtV123 are immediately followed (Counterclockwise) by the REP108ab cluster, then the TERM21 repeat, which appear to be transcription signals for the convergent (Clockwise) narGHJI operon.