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Ribosome biogenesis and nucleocytoplasmic transport
Ecm1 - a new pre-60S nuclear export factor
in S. cerevisiae
Unité de Génétique des Interactions MacromoléculairesURA CNRS2171, Institut Pasteur
Yanhua YAO
Supervisor: Micheline FROMONT-RACINE
Rentrée doctorale 20081015-17
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Why study ribosome biogenesis?
• Essential Pathway • Very expensive for the cell (2000 ribosomes/min.)
• Highly regulated (stress, cell cycle ….)
• Highly conserved across the evolution
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Ribosome biogenesis in eucaryotes
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Identification of45 new pre-60S factors
(Mass Spectrometry)
Saveanu et al. 2003, M. C. B.
Ribosomal proteins
Erb1Noc2, Mak5Nop2, Sda1, Puf6Dbp7, Nop7, Yhr197w, Nog1Arx1, Nug1, Dbp9Fpr3, Nop12, Ssf1Fpr4, Nog2Ycr072c, Ytm1, Mak11, Cic1Mak16, Rlp7, Rpf2Nop1, Rrp1Vps75, Brx1, Nsa2, Nop16
Tif6
Yor252w
Pre-ribosomal proteins
Rlp24
-TAP
Nog1-TAP
Mtr4*
*
Since 2000......
Rigaut et al. 1999, Nat. Biotechnol.
Tandem Affinity Purification
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Pre-60S factors’ Recycling
Lebreton et al. 2006, J.C.B.
?
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Question:
How the pre-60S particles are exported?
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Pre-60S factors’ Recycling
Lebreton et al. 2006, J.C.B.
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•Not essential (Gavin et al., 2002, Nature)•Synthetic Lethality with nug1-1 and mtr2-33 (Bassler et al., 2001, Mol. Cell)
Genetic Interactions Network
ARX1
Nuclear Pore
ComplexeECM1
N
M
X
Z
YBCA
N
M
X
Z
YCA
(Decourty et al. 2008, P.N.A.S.)
B
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Validation of genetic interactions
Double mutant: Slow growth or sick growth
Conclusion 1: When the NPC (nuclear pore complex) is compromised, Ecm1 is essential.
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The depletion of Ecm1 affecte 60S biognesis
Conclusion 2: When the NPC is affected, Ecm1 becomes
essential for pre-60S nuclear export.
Rpl25-GFP
WT
ecm1∆
pom34∆
PGAL1-ECM1 pom34∆
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Ecm1- a pre-60S factor
1 Kap1212 Kap1083 Nog14 Fpr45 Nog2Rpl
Conclusion 3: Ecm1 is conditionally associated with pre-60S particles.
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Binding domain
onX
Y
(Brent and Ptashne 1985; Fields and Song, 1989) Activating domain
Two-hybid Yeast Screen
X: Ecm1
Y: Nup192
Conclusion 4: Ecm1 binds physically to NPC.
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adapted from Bradatsch et al., 2007
Gadal et al., 2001Ho et al., 2000
Bradatschet al., 2007Hung et al., 2008
Yao et al., 2007
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Ecm1 overlaps with other export pathway
Conclusion 5: Ecm1, Arx1 and Mex67 show subtle functional interactions involved in the same export process, but each protein has additional important cellular roles.
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Ecm1
Conclusions and Perspectives:
A novel additional pre-60S nuclear export factor.
adapted from Bradatsch et al., 2007
• Ecm1 and Arx1 in the same complexe ?
• How is pre-60S export regulated ?
But…
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Micheline Fromont-Racine
Alain Jacquier
Cosmin Saveanu
Laurence Decourty
Emilie Demoinet
Helen Neil
Odile Labouise
Christophe Malabat
Acknowledgements:
GIM’s Lab: Plateforme protéomique:
Pascal Lenormand
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Combining gene deletions (synthetic lethality, epistasy, suppression):
- neutral
- aggravating
- alleviating
N
M
X
Z
YBCA
N
B
M
X
Z
YBCA
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5,000 systematic deletion strains
MATαQuery mutation∆X
MAT A
MATAMAT A
Diploidsobtention Meiosis
Competitivegrowth of doublemutants (1 tube)
Genetic Interactions Mapping (GIM)
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Query population
Reference population
barcodes PCR amplification
barcodes PCR amplification
potential aggravating int.
~ 26.000 duplicated spots Yeast BarCode 13.5kmicroarray (SLRI, Toronto)
potential alleviating int.
-> log2(Query/Reference) for ~5 000 double mut.
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20
Principe du double-hybridePrincipe du double-hybride
Domaine deliaison a l’ADN
on
off
onXY
XY
off
Brent and Ptashne 1985; Fields and Song (1989)
Domaine
D'activation