TLR Repeats


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.


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.