New Roles for Old ncRNAs in Archaeas ? Revisiting the Structure/Function

Relationships of H/ACA guide RNAs from Transcriptomics and Computational RNomics

Fabrice LeclercIGM - Orsay

fabrice.leclerc@igmors.u-psud.fr

H/ACA & H/ACA-like motifsin Archaea

rRNA (tRNA)

Euryarchaea/Crenarchea (E/C)

C: PyrobaculumC: Thermoprotea

E: PyrococcusE: ThermococcusE: MethanococcusE: ArchaeoglobusE: Haloferax

C: SulfolobusC: Aeropyrum

H/ACA H/ACA-like

Outline

✤ H/ACA(-like) structure function relationships (structural determinants for RNA guide & target)

✤ Archaea: H/ACA (Euryarchaea + Crenarchaea) & H/ACA-like (Crenarchaea): variations on the same theme ?

✤ Alternative function(s) in Archaea ?

“Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in rRNAs”

7 K-turn,4 K-loop

Muller et al., 2008

7 H/ACA Genes, 11 H/ACA Motifs

23 rRNA targets

10 H/ACA sRNA Genes,

10 H/ACA Motifs10 rRNA targets2 tRNA targets

“Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features”

Bernick et al., 2012

10 K-turn

Structures of H/ACA RNAs & RNPs

(Pyrococcus furiosus)

5’

G

AA

GC

UGGG

GC

GGA

3’

stem H1

stem H2

K-loop

targetrRNA (tRNA)

guide

L7Ae

Nop10

Cbf5

ACA

PDB ID: 3LWO

Zhou et al., 2010

7-1

0b

p

14-1

6b

p9

-10

bp

Structures of H/ACA RNAsfamily 10/5/9 (Pyrococcus)

10bp

9bp

5nt

10

5

9

PDB ID: 3LWO

Structures of H/ACA RNAsfamily 10/6/9 (Pyrococcus)

10bp

9bp

6nt

10

6

9

PDB ID: 3HAX

Subfamilies of H/ACA Motifs in Pyrococcus

Representations of RNA guide/target pairs

“Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in rRNAs”

Muller et al., NAR, 2008

non-productive

productive15 productive8 non-productive

“Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in rRNAs”

Muller et al., NAR, 2008

Structural Determinants in “Productive” H/ACA RNPs

(1)

productive

non-productive

Structural Determinants in “Productive” H/ACA RNPs

(2)

productive

non-productive

10 H/ACA sRNA Genes,

10 H/ACA Motifs10 K-turn Motifs

ANA Motif (?)

“Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features”

Bernick et al., RNA, 2012

H/ACA Motifs (sR201, sR202) in Pyrobaculum

H/ACA-like Motifs (sR203-206, sR208-210) in Pyrobaculum (1)

10

9

≥5}≥14

H/ACA-like Motifs (sR203-206, sR208-210) in Pyrobaculum (2)

10 H/ACA sRNA Genes,

10 H/ACA Motifs10 K-turn Motifs

ANA Motif (?)

“Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features”

Bernick et al., RNA, 2012

non-productive

productive

H/ACA-like Motif sR207 in Pyrobaculum: RNA fold

non-productive

12

9

4 }13

H/ACA-like Motif sR207 in Pyrobaculum: RNA target

H/ACA-like Motifs in Pyrococcus ?

H/ACA-(like) Motifs in Pyrococcus

Toffano-Nioche et al., 2013

Conclusions

✤ H/ACA-like guide RNAs are expected to work in the same way with a few specificities (ANA box,...)

✤ H/ACA-like motifs present in both Euryarchaea and Crenarchaea

✤ productive H/ACA & H/ACA-like guide RNAs in Pyrobaculum

✤ non-productive(?) H/ACA-like guide RNAs in Pyrococcus

Pyrococcus, Thermococcus, Archaeoglobus, Haloferax, Methanocaldococcus

Pyrobaculum, Sulfolobus, Aeropyrum, Metalloshaera

Acknowledgments

✤ Claire Toffano-Nioche

✤ Daniel Gautheret

Institut de Génétique & Microbiologie, Orsay