Regulation by small non-coding
RNAs in bacteria
Regulation of gene expression in prokaryotes can occur at different levels
DNA Modification
Transcriptional
Posttranscriptional
Translational
Posttranslational
Translation
Transcription
DNA
mRNA
Protein
RNA
Non-coding
Coding
mRNA
rRNA
tRNA
Small noncoding
RNA
cisencoded
sRNAs
transencoded
sRNAs
sRNA encoding Region
Intergenig Region
Lacks obvious start and stop codons
3’ UTR
5’ UTR
ATG
TGA
CTAGCTATGCGTAGCGTA
GCTCGATACGCATCGCAT
3´-UTR
ORF
5´-UTR
Intergenic region
5´-UTR
ORF
3´-UTR
sRNAs exert their regulatory action
either as positive or negative regulators
Lalaouna et al (2013). Biochimica et Biophysica Acta 1829, 742 - 747
RIBOSWITCHES
The Spot42 example
Møller T et al. Genes Dev. 2002;16:1696-1706
The E. coli galactose operon
Møller T et al. Genes Dev. 2002;16:1696-1706
galE
SPOT 42
Permease
galT
galK
Gal K
Galactose (out)
Galactose (in)
Gal K
Gal T
Gal E
Galactose-1-P
UDP-Galactose
UDP-Glucose
Glucose-1-P
galM
Central carbohydrate metabolic pathways controlled by small RNAs for uptake and
metabolism of galactose, glucose, and amino sugars
Görke B, Vogel J. Genes Dev. 2008;22:2914-2925
Görke B, Vogel J. Genes Dev. 2008;22:2914-2925
Exploiting Hfq proteins to identify sRNAs from Bcc bacteria
CG Ramos, AM Grilo, PJ da Costa, JH Leitão. 2013.
Genomics 101(2):139-148
24 novel sRNAs were identified in B. cenocepacia J2315
Distribution of the Bcj sRNAs in sequenced strains of the B. cepacia complex
sRNAs at IST….
MtvR is a trans-encoded sRNA
CG Ramos, AM Grilo, PJP da
Costa, JR Feliciano, JH Leitão
(2013). Journal of Bacteriology 195
(16) 3514–3523
h2cR is a cis encoded sRNA
CG Ramos, PJ da Costa, G
Döring, JH Leitão. 2012.
PLoS ONE 7(10): e47896.
h2cR regulates Hfq2 at the mRNA and protein level
The sRNAs Bcj8 and Bcj14 are activated by acidic pH
RNA chaperones and biofilm formation in Bcc
Fazli et al., Environ Microbiol, in press
Hfq is a small protein acting as a major posttranscriptional regulator
of bacterial gene expression
Promote
RNA-RNA duplex formation
Promote
Rnase attack
Hfq
Functions
on mRNA
Promote
Polyadenylation and
3´-5´degradation
Protection
From RNases
Searching for virulence-related genes from Bcc bacteria
B. cenocepacia J2315 harbors two functional hfq-like genes
Ramos et. al., J. Bacteriol. (2011) 193:1515-1526
hfq and hfq2 patterns of transcription and protein relative abundance
Mutations in each RNA chaperone affect resistance to stresses
Both chaperones are required for full virulence to the nematode C. elegans
Colonization and virulence
to C. elegans
Flagella
mediated motility
Acidic stress
B. cenocepacia
hfq and hfq2 mutants
Exopolysaccharide
production
Growth under
stress conditions
Sousa S et al. Microbiology 2010;156:896-908
Ramos C G et al. J. Bacteriol. 2011;193:1515-1526