Listeria monocytogenes is a gram positive bacterium and causes many food-borne infections such as Listeriosis. This bacteria is ubiquitous in the environment where it can act as either a saprophyte when free living within the environment or as a pathogen when entering a host organism. Many non-coding RNAs have been identified within the bacteria genome where several of these have been classified as novel non-coding RNAs and may contribute to pathogenesis.

Tiling arrays and mutagenesis identified many non-coding RNAs within the L. monocytogenes genome and the location of these non-coding RNAs within the bacterial genome was confirmed by RACE (rapid amplification of cDNA ends) analysis. These studies showed that the expression of many non-coding RNAs was dependent on the environment and that several of these non-coding RNAs act as cis-regulatory elements. Comparisons between previously characterized non-coding RNAs and those present in the L. monocyotogenes genome identified 50 novel non-coding RNAs in L. monocyotogenes. An additional comparative study between the pathogenic L. monocytogenes strain and the non pathogenic L. innocua strain identified several non-coding RNAs that are only present within L. monocytogenes which suggests that these ncRNAs may have a role in pathogenesis. The tables below summarizes the location, flanking genes and also the characteristics of the novel small non-coding RNAs identified and the previously characterized non-coding RNAs present in L. monocytogenes

Novel Non-coding RNAs ID Start Stop Size 5′ flanking gene sense of the gene on the genomea 3′ flanking gene Characteristic Rfam rli22 31997 32107 110 lmo0028 -> -> -> lmo0029 sRNA rli23 172171 172268 97 lmo0172 <- -> sRNA Antisense to lmo0172 transposase Homolog of rli25 and rli35. rli24 271029 271186 157 lmo0256 -> -> -> lmo0257 sRNA rli25 357618 357516 102 lmo0330 -> <- sRNA Antisense to lmo0330: transposase. Homolog of rli23 and rli35 rli26 388707 388520 187 lmo0360 -> <- <- lmo0361 sRNA rli27 434831 434929 98 lmo0411 <- -> <- lmo0412 sRNA rli28 507394 507206 188 lmo0470 -> <- -> lmo0471 sRNA Homolog of rli50 rli29 507643 507450 193 lmo0470 -> <- -> lmo0471 sRNA Antisense to the 5'UTR of lmo0471 rli30 540785 540670 115 lmo0506 -> <- sRNA Antisense to lmo0506 rli31 597812 597926 114 lmo0558 <- -> -> lmo0559 Required for lysozyme resistance and pathogenesis. Structure characterized as two long hairpins. Interacts with the RNA binding global regulator SpoVG. rli32 600750 600604 147 lmo0560 <- <- <- lmo0561 sRNA rli33 708326 708860 534 lmo0671 -> -> -> lmo0672 sRNA rli34 803031 802948 83 lmo0777 -> <- -> lmo0778 sRNA rli35 855495 855393 102 lmo0828 -> <- sRNA Antisense to lmo0828: transposase. Homolog of rli23 and rli25 rli36 859527 859444 83 nifJ -> <- <- fbp sRNA rli37 907576 907832 256 lmo0866 -> -> -> lmo0867 ORF ORF of 58aa. RBS region: TGATACGGGAGTGTGGTGCTAGTTATG rli38 1152549 1152917 369 lmo1115 <- -> -> lmo1116 sRNA role in virulence rli39 1179807 1179993 187 lmo1149 -> -> <- lmo1150 sRNA Annotated as a cobalamin riboswitch in Rfam rli40 1275810 1275547 264 lmo1251 -> <- <- lmo1252 ORF ORF of 64 aa. RBS region: AGTGAGGCGTCCTTATG rli41 1277207 1276713 495 lmo1252 <- <- -> lmo1253 Two ORFs ORF of 45 aa. RBS region: AGAGGAGGTATTTTCTATG ORF of 35 aa. RBS region:AAGGAGGAAAACAAATTG rli42 1399617 1399447 171 lmo1374 -> <- -> lmo1375 sRNA rli43 1861630 1861377 253 inlC <- <- <- rplS ORF ORF of 35aa. RBS region: AGAGTGAGGTGTAATATG rli44 2039087 2039375 289 lmo1964 <- -> <- lmo1965 ORF ORF of 28aa. RBS region: GGAAAGGATAACCCATG rli45 2154775 2154852 77 lmo2074 -> -> <- lmo2075 sRNA Antisense to rli46 rli46 2155058 2154765 294 lmo2074 -> <- <- lmo2075 sRNA Antisense to rli45 rli47 2226024 2226532 508 lmo2141 -> -> <- lmo2142 sRNA rli48 2361423 2361274 149 lmo2271 <- <- -> lmo2272 sRNA rli49 2660179 2660364 185 lmo2579 -> -> <- lmo2580 sRNA rli50 2783274 2783098 176 lmo2709 -> <- <- lmo2710 sRNA Homolog of rli28 rli51 207589 207709 120 hly -> -> -> mpl 5′-UTR-derived Increased in intestinal lumen rli52 552421 552327 94 lmo0517 <- <- <- lmo0518 5′-UTR-derived Putative riboswitch. rli53 955829 956001 172 lmo0918 -> -> -> lmo0919 5′-UTR-derived Putative riboswitch. rli54 1078584 1079111 527 lmo1051 <- -> -> pdhA 5′-UTR-derived Putative riboswitch. rli55 1198107 1198389 282 lmo1170 -> -> -> pduQ 5′-UTR-derived Putative riboswitch. rli56 1199859 1199958 99 pduQ -> -> -> lmo1172 5′-UTR-derived Putative riboswitch. rli57 ? 1216658 ? lmo1190 -> -> -> cbiA 3′-UTR-derived Annotated as a cobalamin riboswitch in Rfam lmo1190-rli57 transcript levelncreasedinintestinal lumen rli58 ? 1639974 ? rpsD -> <- <- lmo1597 rli59 1702553 1702373 180 lmo1652 <- <- <- lmo1653 5′-UTR-derived rli60 2054124 2054308 184 lmo1982 <- -> -> ilvD 5′-UTR-derived Putative riboswitch. rli6122753632275258106lmo2187<-<-<-lmo21885′-UTR-derived Putative riboswitch rli6223645082364337172lmo2277<-<-<-lmo22785′-UTR-derived Putative riboswitch. rli632613301??atpI<-<-<-lmo25375′-UTR-derived Putative riboswitch rliA513584513807224lmo0476<->->-lmo0477 snRNArliB544357544716360lmo0509 -> -> ->lmo0510sRNArliC11543091154671363lmo1117->-><-lmo1118sRNArliD13595291359202 328 rpsO -> <- ->pnpAsRNA antisenserliE15845861584808223comC <- -> <-folCsRNA antisense to comC mRNArliF21062922106073220nadA -> <- <-lmo2026snRNArliG23869922386715278 lmo2302 <- <- <-lmo2303sRNArliH1180826 1181254429 lmo1150 <- -> ->lmo1151sRNA antisenserliI 28422002841962239lmo2760 <- <- ->lmo2761 sRNAsbrA 1399363 1399433 70 lmo1374 -> -> ->lmo1375 sRNA aArrows indicate the sense of the gene on the genome. Bold arrows indicate gene absent from L. innocua.

Listeria monocytogenes EGD-e strain was used in these studies EMBL accession AL591824.1

Characterised non-coding RNAs ID Rfam SAM RF00162 LhrC RF00616 TPP RF00059 glmS RF00234 PreQ1 RF00522 T-box RF00230 SsrS RF00013 ID Rfam LhrB RF00558 FMN RF00050 ssrA RF00023 SRP RF00169 PrfA RF00038 L10 leader RF00557 Purine RF00167 ID Rfam lysine RF00168 yybP-ykoY RF00080 glycine RF00504 L21 RF00559 RyrR RF00515 LhrA RF00615 L13 RF00555

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