19638370, Genes Dev. 2009 Sep 1;23(17):2004-15. doi: 10.1101/gad.541609. Epub 2009 Jul 28.

Characterization method

Northern Blot

Genomic accession number


Nucelotide position range







Salmonella enterica/28901

Degradation or Biosynthesis


Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

nadE STM1310 AAL20235.1 0 - 839 (-) AE006468.2:1390110-1390949
osmE STM1311 AAL20236.1 1046 - 1388 (+) AE006468.2:1391156-1391498 -
celA STM1312 AAL20237.1 1688 - 2009 (+) AE006468.2:1391798-1392119 -
celB STM1313 AAL20238.1 2091 - 3450 (+) AE006468.2:1392201-1393560 -
celC STM1314 AAL20239.1 3500 - 3848 (+) AE006468.2:1393610-1393958 -
celD STM1315 AAL20240.1 3858 - 4701 (+) AE006468.2:1393968-1394811 -
celF STM1316 AAL20241.1 4825 - 6181 (+) AE006468.2:1394935-1396291
celG STM1317 AAL20242.1 6193 - 6952 (+) AE006468.2:1396303-1397062 -

Cluster number


Gene name

Gene position

Gene type

Found by CGCFinder?

nadE 1 - 828 (-) CDS No
osmE 1047 - 1388 (+) CDS No
celA 1689 - 2009 (+) TC: gnl|TC-DB|C4X744|4.A.3.2.7 Yes
celB 2092 - 3450 (+) TC: gnl|TC-DB|P17334|4.A.3.2.1 Yes
celC 3501 - 3848 (+) TC: gnl|TC-DB|P69791|4.A.3.2.1 Yes
celD 3859 - 4701 (+) TF: DBD-Pfam|HTH_AraC,DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
celF 4826 - 6181 (+) CAZyme: GH4 Yes
celG 6194 - 6952 (+) CDS No




19638370, Genes Dev. 2009 Sep 1;23(17):2004-15. doi: 10.1101/gad.541609. Epub 2009 Jul 28.


Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target.


Figueroa-Bossi N, Valentini M, Malleret L, Fiorini F, Bossi L


A relevant, yet little recognized feature of antisense regulation is the possibility of switching roles between regulatory and regulated RNAs. Here we show that induction of a Salmonella gene relies on the conversion of a small RNA from effector to regulatory target. The chiP gene (formerly ybfM), identified and characterized in the present study, encodes a conserved enterobacterial chitoporin required for uptake of chitin-derived oligosaccharides. In the absence of inducer, chiP is kept silent by the action of a constitutively made small RNA, ChiX (formerly SroB, RybC), which pairs with a sequence at the 5' end of chiP mRNA. Silencing is relieved in the presence of chitooligosaccharides due to the accumulation of an RNA that pairs with ChiX and promotes its degradation. Anti-ChiX RNA originates from an intercistronic region of the chb operon, which comprises genes for chitooligosaccharide metabolism and whose transcription is activated in the presence of these sugars. We present evidence suggesting that the chb RNA destabilizes ChiX sRNA by invading the stem of its transcription terminator hairpin. Overall, our findings blur the distinction between effector and target in sRNA regulation, raising the possibility that some of the currently defined targets could actually be inhibitors of sRNA function.