Listeria monocytogenes non-coding RNA
Introduction '''''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 '''->''' ''' '''''' ''' '''''' lmo0471 sRNA Homolog of rli50  rli29 507643 507450 193 lmo0470 '''->''' '''''' lmo0471 sRNA Antisense to the 5'UTR of lmo0471  rli30 540785 540670 115 lmo0506 ->  -> 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  -> -> lmo0672 sRNA   rli34 803031 802948 83 lmo0777 ->  lmo0778 sRNA   rli35 855495 855393 102 lmo0828 '''->''' '''  -> -> lmo0867 ORF ORF of 58aa. RBS region: TGATACGGGAGTGTGGTGCTAGTTATG   rli38 1152549 1152917 369 lmo1115 '''''' '''->''' lmo1116 sRNA role in virulence   rli39 1179807 1179993 187 lmo1149 -> ->   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 '''  '''->'''  ''' -> ''' lmo2272 sRNA   rli49 2660179 2660364 185 lmo2579 -> '''->'''  '''''' '''->''' '''->''' mpl 5′-UTR-derived Increased in intestinal lumen   rli52 552421 552327 94 lmo0517  -> -> 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 -> ''' -> ilvD 5′-UTR-derived Putative riboswitch. rli6122753632275258106lmo2187'''>-'''lmo0477 snRNArliB544357544716360lmo0509 -> '''->''' ->lmo0510sRNArliC11543091154671363lmo1117'''->''''''->'''''' pnpAsRNA antisenserliE15845861584808223comC   ''' ->lmo1151sRNA antisenserliI 28422002841962239lmo2760 lmo2761 sRNAsbrA 1399363 1399433 70 lmo1374 -> -> ->lmo1375 sRNAaArrows 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
References
External links *  Rfam database