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Phylogenetic signatures of RNA-RNA contacts in bacteria. Daniel Gautheret Institut de Génétique et Microbiologie CNRS-Université Paris-Sud. RNA-based gene regulation. In eukaryotes: RNAi, microRNA (1990’s). RNAi and miRNA function. ds RNA. Dicer. Ago. Regulatory RNA. Target mRNA.

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Phylogenetic signatures of rna rna contacts in bacteria
Phylogenetic signatures of RNA-RNA contacts in bacteria

Daniel Gautheret

Institut de Génétique et Microbiologie

CNRS-Université Paris-Sud


Rna based gene regulation
RNA-based gene regulation

  • In eukaryotes: RNAi, microRNA (1990’s)


Rnai and mirna function
RNAi and miRNA function

ds RNA

Dicer

Ago

Regulatory RNA

Target mRNA

Degradation or

Translation stop



Rna the ideal information based regulator
RNA: the ideal information-based regulator

Universal

G

C

C

A

G

U

U

G

A

U

C

C

A

G

Regulatorysequencesdictatetargets


Rna absent from regulation networks
RNA absent from regulation networks

KEGG regulation network for actin biosyntesis, modified by Clement & Zucker


Target prediction
Target prediction

Mixed results, lots of False Positives



Srna tend to bind via accessible regions
sRNA tend to bind via accessible regions

ryhB

oxyS

dsrA

Bind to targets


Target prediction with accessibility
Target prediction with accessibility

Improvedresults, but far fromperfect


Obstacles to correct target prediction

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  • Drag image to reposition. Double click to magnify further.

Obstacles to correct target prediction

The Hfqchaperone

Chevalier et al. 2010


Using srna conservation
Using sRNA conservation

Pairwise Blast vs. all completegenomes

Escherichia coli k12 MG1655 ACGAGUGCGGCACG

Escherichia coli O157H7 EDL933 AACGGAGCGGCACC

Shigella flexneri 2a -ACGAAGCTGCACC

Yersinia pestis Antiqua AACGAAG--GCACC

reference

1 x 0,01

0 x 0,2

1 x 0,6

Weighted by evolutionary distance

conservation

dsrA

Sequence


dsrA

rpoS

Accessibilité

hns

Conservation

Résultante


arcZ

Accessibilité

STM3216

tpx

Conservation

sdaC

Résultante


micC

ompC

Accessibilité

Conservation

Résultante


ryhB

sdhC

Accessibilité

Conservation

Résultante


oxyS

fhlA

Hfq binding site

fhlA

Accessibilité

Conservation

Résultante


Constraints on srna vs mrna
Constraints on sRNA vs. mRNA

sRNA

Target 1

Target 2

Target 3

Target 4


Srna vs target conservation
sRNA vs. Target conservation

142

140

120

110

100

99

# species with homology

80

69

60

40

24

20

14

13

11

9

ryhB

oxyS

dsrA

ompC

hns

rpoS

fhlA

sdhC

micC


Mrna conservation
mRNA conservation

AveragetargettedmRNAs

Average E. coli mRNAs

-1


Profile clustering 5 regions of mrnas
Profile clustering: 5’ regions of mRNAs

4/50 vs 35/2097 Pvalue : 0.014

3/45 vs 35/2097 Pvalue : 0.049

2/63 vs 35/2097 Pvalue : 0.030


Next developments
Next developments

sRNA

mRNA1

mRNA2

Covariation


Combine with phylogenetic profiling
Combine with phylogenetic profiling

1070 bacterialgenomes

Genes and RNA elements

Cluster of co-evolvingRNAs and genes


Acknowledgements
Acknowledgements

Alban Ott

Antonin Marchais

RNA sequence, structure & function lab


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