User:M2bioinfo-Orsay/sandbox/team8

SQ1002 regulatory sRNA family
R-Scape Predicted Secondary Structure of SQ1002 sRNA
Identifiers
Symbol	SQ1002
Other data
RNA type	Gene;
Domain(s)	Bacteria; Firmicutes
PDB structures	PDBe

SQ1002 regulatory sRNA family

CD630_SQ1002 sRNA

In molecular biology, the CD630_SQ1002 putative regulatory sRNA was discovered in a large-scale analysis of Clostridium difficile 630. Its size is between 200 and 250 nucleotides long (exactly 237). Its extremities were identified by 5'RACE and 3'RACE. This ncRNA, candidate sRNA in an intergenic region (IGR ncRNA), was first in silico predicted in Clostridium difficile 630 on the antisense strand then experimentally validated by Northern Blot and RT-PCR analysis with probes specific for this candidate sequence. Its expression is growth phase-dependent.

SQ002 regulatory sRNA family

General informations

This family is a putative trans-encoded sRNA family. Trans-encoded sRNAs regulate mRNA stability by regulating their level of expression at different locus, the function or mRNA and gene family expression regulated by this family of sRNA is yet unknown. These sRNAs are produced in Gram positive bacteria from the Firmicutes phylum, mostly in Clostridium difficile and possibly in some Bacillales.

Synteny

In term of synteny, all of the Clostridium difficile sRNA gene sequences were in the vicinity of the same family of genes encoding for proteins having an acyl or amino-acyl transfer activity (such as Acyltransferase or Tryptophanyl-tRNA synthetase) and genes encoding for ferrous ions transport proteins, leading to the conclusion that these sRNAs might be independant trans-encoded sRNAs. Moreover, these sRNAs seem to either bind to the positive or negative strand of the mRNAs that need to be regulated during bacterial growth phase since these sRNA seem to be induced at the onset of the Stationnary phase<ref name=OlgaSoutourina>/>. Only the Bacillales species do not have the same family of genes in the vicinity of the sRNA sequence. These sRNA sequences are all located in intergenic regions (repeat region) and are not overlapping any mRNA sequence on any of their UTR.