Phylogenetic signatures of RNA-RNA contacts in bacteria

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Daniel Gautheret

Institut de Génétique et MicrobiologieCNRS-Université Paris-Sud

RNA-based gene regulation

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

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RNAi and miRNA function

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Dicer

ds RNA

Regulatory RNA

Ago

Target mRNA

Degradation orTranslation stop

Bacterial sRNA (1980’s)

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RNA: the ideal information-based regulator

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G

GG

GA

AA

C

CU

C

C UU

Regulatory sequences dictate targets

Universal

RNA absent from regulation networks

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

Target prediction

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Mixed results, lots of False Positives

Taking accessibility into account

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Hofacker 2007

sRNA tend to bind via accessible regions

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dsrA ryhB oxyS

Bind to targets

Target prediction with accessibility

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Improved results, but far from perfect

Obstacles to correct target prediction

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Chevalier et al. 2010

The Hfq chaperone

Using sRNA conservation

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Sequence

Escherichia coli k12 MG1655 ACGAGUGCGGCACG

Escherichia coli O157H7 EDL933 AACGGAGCGGCACC

Shigella flexneri 2a -ACGAAGCTGCACC

Yersinia pestis Antiqua AACGAAG--GCACC

1 x 0,010 x 0,21 x 0,6

dsrA

reference

conservation

Weighted by evolutionary distance

Pairwise Blast vs. all complete genomes

13 / 23

dsrArpoS

hns

Accessibilité

Conservation

Résultante

arcZ

sdaC

STM3216tpx

Accessibilité

Conservation

Résultante

micC ompC

Accessibilité

Conservation

Résultante

ryhBsdhC

Accessibilité

Conservation

Résultante

oxySHfq binding sitefhlA fhlA

Accessibilité

Conservation

Résultante

Constraints on sRNA vs. mRNA

Target 1

Target 2

Target 3

Target 4

sRNA

sRNA vs. Target conservation

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0

20

40

60

80

100

120

140

160

dsrAoxyS fhlA hns

rpoSompC

micCryhB sdhC

69

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110

99

142

14 139

24# species with homology

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40

60

80

100

120

140

mRNA conservation

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-1

Average E. coli mRNAs

Average targetted mRNAs

Profile clustering: 5’ regions of mRNAs

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3/45 vs 35/2097 Pvalue : 0.049

2/63 vs 35/2097 Pvalue : 0.030

4/50 vs 35/2097 Pvalue : 0.014

Next developments

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sRNA mRNA1 mRNA2

Covariation

Combine with phylogenetic profiling

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1070 bacterial genomes

Genes and RNA elements

Cluster of co-evolving RNAs and genes

Acknowledgements

Alban OttAntonin Marchais

RNA sequence, structure & function lab

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