Publications

Selected Publications

Rabut, G., Le Dez, G., Verma, R., Makhnevych, T., Knebel, A., Kurz, T.,
Boone, C., Deshaies, R., and Peter, M. (2011)
The TFIIH subunit Tfb3 regulates cullin neddylation.
Mol. Cell, 43, 488-495

Pelet, S., Rudolf, F., Nadal-Ribelles, M., de Nadal, E., Posas, F. and Peter, M.
(2011) Transient activation of the HOG MAPK pathway regulates bimodal
gene expression.
Science, 332, 732-735.

Piwko, W., Olma, M.H., Held, M., Bianco, J., Pedrioli, P., Hofmann, K.,
Pasero, P., Gerlich, D.W., and Matthias Peter (2010) RNAi-based screening
identifies the Mms22L – Nfkbil2 complex as a novel regulator of DNA
replication in human cells.
EMBO J., 29, 4210-4222.

Kijanska, M., Dohnal, I., Reiter, W., Kaspar, S., Stoffel, I., Ammerer, G.,
Kraft, C., and Peter, M. (2010) Activation of Atg1 kinase in autophagy
by regulated phosphorylation.
Autophagy, 6, 1168-1178.

Dechant, R., Binda, M., Lee, SS., Pelet, S., Winderickx, J., and Peter, M. (2010)
Cytosolic pH is a second messenger for glucose and regulates the PKA pathway
via V-ATPase.
EMBO J., 29 (15), 2515-2526.

Siergiejuk, E., Scott, D.C., Schulman, B.A., Hofmann, K., Kurz, T., Peter, M.
(2009) Cullin neddylation and substrate-adaptors counteract SCF inhibition
by the CAND1-like protein Lag2 in Saccharamyces cerevisiae.
EMBO J., 28, 3845-56.

Maerki, S., Olma, M.H., Staubli, T., Steigemann, P., Gerlich D.W., Quadroni,
M., Sumara, I., Peter, M. (2009) The Cul3-KLHL21 E3 ubiquitin ligase targets
Aurora B to midzone microtubules in anaphase and is required for cytokinesis.
J. Cell Biol., 187, 791-800.

Meyer-Schaller, N., Chou, Y.C., Sumara, I., Martin, D.D., Kurz, T., Katheder, N.,
Hofmann, K., Berthiaume, L.G., Peter, M. (2009) The human Dcn1-like protein
DCNL3 promotes Cul3 neddylation at membranes.
PNAS, 106, 12365-12370.

Leidel, S.*, Pedrioli, P.G.A.*, Bucher, T., Brost, R., Costanzo, M., Schmidt, A.,
Aebersold, R., Boone, C., Hofmann, K. and Peter, M. (2009) Ubiquitin-related
modifier Urm1 acts as a sulfur-carrier in thiolation of eukaryotic tRNA.
Nature, 458, 228-232. *equal contribution

Kraft, C., Deplazes, A., Sohrmann, M., Peter, M. (2008) Mature ribosomes are
selectively degraded upon starvation by an autophagy pathway requiring the
Ubp3p/Bre5p ubiquitin protease.
Nature Cell Biology, 10, (5), 602-610.

Kurz, T., Chou, Y.-C., Willems, A., Meyer-Schaller, N., Hecht, M.-L., Tyers,
M., Peter, M. and Sicheri, F. (2008) Dcn1 Functions as a Scaffold-Type E3
Ligase for Cullin Neddylation.
Mol. Cell, 29, 23-35.

Sumara, I., Quadroni, M., Frei, C., Olma, M., Sumara, G., Ricci, R., and Peter,
M., (2007) A Cul3-based E3-ligase is required to remove Aurora B from
mitotic chromosomes, thereby regulating mitotic progression and completion
of cytokinesis in human cells.
Developmental Cell, 12, 887-900.

Selected Reviews

Kraft, C., Peter, M., and Hofmann, K. (2010) Selective autophagy: ubiquitin
recognition and beyond.
Nature Cell Biology, 12, 836-841.

Kraft, C., Reggiori, F. and Peter, M. (2009) Selective types of autophagy in
yeast.
Biochim Biophys Acta, 1793, 1404-1412.

Dechant, R., and Peter, M. (2008) Nutrient signals driving cell growth.
Current Opinion of Cell Biology, 20, 678-687.

Rabut, G. and Peter, M. (2008) Function and regulation of protein neddylation.
EMBO Reports, 9, 969-976.

Rudolf, F., Pelet, S., and Peter, M., (2008) Regulation of MAPK signalling in
yeast.
Topics in Current Genetics, 20, Stress-Activated Protein Kinases, Posas, F.,
and Nebrada, A.R. (Eds)

Sumara, I., Maerki, S. and Peter, M. (2008) E3 ubiquitin ligases and mitosis:
embracing the complexity.
Trends Cell Biology, 18, (2), 84-94.

Chang, F., and Peter, M. (2003) Yeasts make their mark.
Nat. Cell. Biol., 4, 294-9.

Peter Lab Publications 2003 – present

2011

Huotari, J. , Meyer-Schaller, N., Hubner, M., Stauffer, S., Katheder, N.,
Horvath, P., Mancini, R., Helenius, A., and Peter, M. (2011) Cullin-3
regulates late endosome maturation.
PNAS – in press.

Lee, S. S., Horvath, P., Pelet, S., Hegemann, B., Lee, L. P., and Peter, M. (2011)
Quantitative and Dynamic Assay of Single Cell Chemotaxis.
Integrative Biology -in press.

Pelet, S., and Peter, M. (2011) Dynamic processes at stress promoters
regulate the bimodal expression of HOG response genes.
Commun. Integr. Biol. , 4, 6.

Sole, C., Nadal-Ribelles, M., Kraft, C., Peter, M., Posas, F., and de Nadal, E. (2011)
Control of Ubp3 ubiquitin protease activity by the Hog1 SAPK modulates transcription
upon osmostress.
EMBO J., 30, 16, 3274-3283

Zechner, C., Ganguly, A., Pelet, S., Peter, M., and Koeppl, H. (2011)
Accounting for extrinsic variability in the estimation of stochastic rate constants.
Int. J. Robust. Nonlinear Control - in press.

Rabut, G., Le Dez, G., Verma, R., Makhnevych, T., Knebel, A., Kurz, T.,
Boone, C., Deshaies, R., and Peter, M. (2011)
The TFIIH subunit Tfb3 regulates cullin neddylation.
Mol. Cell, 43, 488-495

Piwko, W., Buser, R., and Peter, M. (2011) Rescuing stalled replication forks
MMS22L-TONSL, a novel complex for DNA replication fork repair in human cells.
Cell Cycle, 10, 1703-1705

Pelet, S., Rudolf, F., Nadal-Ribelles, M., de Nadal, E., Posas, F. and Peter, M.
(2011) Transient activation of the HOG MAPK pathway regulates bimodal
gene expression.
Science, 332, 732-735.

Pelet, S., and Peter M. (2011) Fluorescent-based quantitative
measurements of signal transduction in single cells.
Chapter 17 of Koeppl, H. et al. (eds.) Design and Analysis of
Biomolecular Circuits: Engineering Approaches to Systems and
Synthetic Biology, Springer, 369-393

Dechant, R., and Peter, M. (2011) The N-terminal domain of the V-ATPase
subunit "a" is regulated by pH in vitro and in vivo.
Channels, 5, 1, 1-5.

2010

Bodenmiller, B., Wanka, S., Kraft, C., Urban, J., Campbell, D., Pedrioli, P.,
Gerrits, B., Picotti, P., Lam, H., Vitek, O., Brusniak, M.Y., Roschitzki, B.,
Zhang, C., Schlapbach, R., Shokat, K., Colman-Lerner, A., Nesviszskii, A.I.,
Peter, M., Loewith, R., Mering, C.v., Aebersold, R. (2010) Phosphoproteomic
Analysis Reveals Interconnected System-Wide Responses to Pertubations of
Kinases and Phosphatases in Yeast.
Science Signaling, 3, rs4

Piwko, W., Olma, M.H., Held, M., Bianco, J., Pedrioli, P., Hofmann, K.,
Pasero, P., Gerlich, D.W., and Matthias Peter (2010) RNAi-based screening
identifies the Mms22L – Nfkbil2 complex as a novel regulator of DNA
replication in human cells.
EMBO J., 29, 4210-4222.

Kijanska, M., Dohnal, I., Reiter, W., Kaspar, S., Stoffel, I., Ammerer, G.,
Kraft, C., and Peter, M. (2010) Activation of Atg1 kinase in autophagy
by regulated phosphorylation.
Autophagy, 6, 1168-1178.

Burschowsky, D., Rudolf, F., Rabut, G., Herrmann, T., Peter, M., and Wider, G.
(2010) Structural analysis of the conserved ubiquitin-binding motifs (UBMS)
of the translation polymerase IOTA in complex with ubiquitin.
J. Biol. Chem.,286 (2), 1364-1373

Kraft, C., Peter, M., and Hofmann, K. (2010) Selective autophagy: ubiquitin
recognition and beyond.
Nature Cell Biology, 12, 836-841.

Maerki, S., Beck, J., Sumara, I., and Peter, M., (2010)
Finding the midzone: the role of ubiquitination for CPC localization
during anaphase.
Cell Cycle - 9 (15), 2921-2922.

Held, M., Schmitz, M.H.A., Fischer, B., Walter, T., Neumann, B., Olma, M.H.,
Peter, M., Ellenberg, J., and Gerlich, D.W. (2010) CellCognition: time-resolved
phenotype annotation in high-throughput live cell imaging.
Nature Methods - 7 (9), 747-754.

Dechant, R., Binda, M., Lee, SS., Pelet, S., Winderickx, J., and Peter, M. (2010)
Cytosolic pH is a second messenger for glucose and regulates the PKA pathway
via V-ATPase.
EMBO J. , 29 (15), 2515-2526.

Schaber, J., Adrover, M.A., Eriksson E., Pelet, S., Petelenz, E., Klein, D., Posas, F.,
Goksör, M., Peter, M., Hohmann, S., Klipp, E. (2010) Biophysical properties of
Saccharomyces cerevisiae and their relation to HOG pathway activation.
European Biophysics Journal - 39 (11), 1547-56.

2009

Chang, M., Luke, B., Kraft, C., Li, Z., Peter, M., Lingner, J., and Rothstein R.,
(2009) Telomerase is essential to alleviate Pif1-induced replication stress at
telomeres.
Genetics , 183, 779-79

Siergiejuk, E., Scott, D.C., Schulman, B.A., Hofmann, K., Kurz, T., Peter, M.
(2009) Cullin neddylation and substrate-adaptors counteract SCF inhibition
by the CAND1-like protein Lag2 in Saccharamyces cerevisiae.
EMBO J., 28, 3845-56.

Maerki, S., Olma, M.H., Staubli, T., Steigemann, P., Gerlich D.W., Quadroni, M.,
Sumara, I., Peter, M. (2009) The Cul3-KLHL21 E3 ubiquitin ligase targets
Aurora B to midzone microtubules in anaphase and is required for cytokinesis.
J. Cell Biol., 187, 791-800.

Meyer-Schaller, N., Chou, Y.C., Sumara, I., Martin, D.D., Kurz, T., Katheder, N.,
Hofmann, K., Berthiaume, L.G., Peter, M. (2009) The human Dcn1-like protein
DCNL3 promotes Cul3 neddylation at membranes.
PNAS, 106, 12365-12370.

Deplazes, A., Möckli, N, Luke B., Auerbach, D., and Peter M. (2009) Yeast
Uri1p promotes translation initiation and may provide a link to cotranslational
quality control.
EMBO J., 28, 1429-41

Kraft, C., Reggiori, F. and Peter, M. (2009) Selective types of autophagy in
yeast.
Biochim Biophys Acta, 1793, 1404-1412

Leidel, S.*, Pedrioli, P.G.A.*, Bucher, T., Brost, R., Costanzo, M., Schmidt, A.,
Aebersold, R., Boone, C., Hofmann, K. and Peter, M. (2009) Ubiquitin-related
modifier Urm1 acts as a sulfur-carrier in thiolation of eukaryotic tRNA.
Nature, 458, 228-232. *equal contribution

Olma, M. H.*, Roy, M.*, Le Bihan, T., Sumara, I., Maerki, S., Larsen, B., M.
Quadroni, M., Peter, M., Tyers, M., and L. Pintard (2009) An interaction
network of the mammalian Cop9/signalosome identifies DDA1 as a core
subunit of multiple CUL4-based E3-ligases.
J. Cell Science, 122, 1035-1044. *equal contribution.

2008

Pedrioli, P.G., Leidel, S., Hofmann, K. (2008) Urm1 at the crossroad of modifications.
‘Protein Modifications: Beyond the Usual Sespects’ Review Series.
EMBO Rep., 12, 1196-202.

Dechant, R., and Peter, M. (2008) Nutrient signals driving cell growth.
Current Opinion of Cell Biology, 20, 678-687.

Rabut, G. and Peter, M. (2008) Function and regulation of protein neddylation.
EMBO Rep., 9, 969-976.

Kraft, C. and Peter, M. (2008) Is Rsp5p involved in the regulation of
ribophagy?
Autophagy, 4, 838-840.

Zaidi, I.W.*, Rabut, G.*, Poveda, A., Scheel, H., Malmström, J., Ulrich, H.,
Hofmann, K., Pasero, P., Peter, M., and Luke, B. (2008) Rtt101p and Mms1p
form a Cul4Ddb1-like ubiquitin ligase, which promotes replication through
damaged DNA.
EMBO Rep., 10, 1034-40. *equal contribution

Kraft, C., Deplazes, A., Sohrmann, M., Peter, M. (2008) Mature ribosomes are
selectively degraded upon starvation by an autophagy pathway requiring the
Ubp3p/Bre5p ubiquitin protease.
Nature Cell Biology, 10, (5), 602-610.

Kurz, T., Chou, Y.-C., Willems, A., Meyer-Schaller, N., Hecht, M.-L., Tyers,
M., Peter, M. and Sicheri, F. (2008) Dcn1 Functions as a Scaffold-Type E3
Ligase for Cullin Neddylation.
Mol. Cell, 29, 23-35.

Rudolf, F., Pelet, S., and Peter, M., (2008) Regulation of MAPK signalling in
yeast.
Topics in Current Genetics, 20, Stress-Activated Protein Kinases, Posas, F.,
and Nebrada, A.R. (Eds).

Demmel, L., Gravert, M., Ercan, E., Habermann, B., Müller-Reichert, T.,
Kukhtina, V., Haucke, V., Baust, T., Sohrmann, M., Kalaidzidis, Y., Klose, Ch.,
Beck, M., Peter, M. and Walch-Solimena, Ch. (2008) The Clathrin Adaptor
Gga2p Is a Phosphatidylinositol 4-phosphate Effector at the Golgi Exit.
Mol Biol Cell, 19, 1991-2002.

Sumara, I., Maerki, S. and Peter, M. (2008) E3 ubiquitin ligases and mitosis:
embracing the complexity.
Trends Cell Biology, 18, (2), 84-94.

2007

Luke, B., Azzalin, C., Hug, N., Deplazes, A., Peter, M. and Lingner, J. (2007)
Saccharomyces cerevisiae Ebs1p is a putative ortholog of human Smg7 and
promotes nonsense-mediated mRNA decay.
Nucleic Acids Res, 35, (22), 7688-7697.

Sumara, I. and Peter, M., (2007) A Cul3-Based E3 Ligase Regulates Mitosis
and is Required to Maintain the Spindle Assembly Checkpoint in Human Cells.
Cell Cycle, 6, 24.

Roberts, T., Waris Zaidi I., Vaisica, J., Peter, M. and Brown, G. (2007) Regulation
of Rtt107 Recruitment to Stalled DNA Replication Forks by the Cullin Rtt101
and the Rtt109 Acetyltransferase.
Mol Biol Cell, 19, 171.180.

Knaus, M., Pelli-Gulli, M., van Drogen, F., Springer, S., Jaquenoud, M., and
Peter, M. (2007) Phosphorylation of Bem2p and Bem3p may contribute to
local activation of Cdc42p at bud emergence.
EMBO J., 26, 4501-4513.

Luke-Glaser, S., Pintard, L., Tyers, M. and Peter, M. (2007) The AAA-ATPase
FIGL-1 controls mitotic progression, and its levels are regulated in the C.
elegans germ line by the CUL-3MEL-26 E3-ligase.
J. Cell Science, 120, 3179-87.

Kuepfer, L., Peter, M., Sauer, U., and Stelling J., (2007) Ensemble modeling
for analysis of cell signaling dynamics.
Nature Biotechnology, 25, 9, 1001-6.

Moeckli N., Deplazes, A., Hassa P.O., Zhang Z., Peter, M., Hottiger, M.O.,
Stagljar, I., and Auerbach D. (2007) A yeast split-ubiquitin based cytosolic
screening system (cytoY2H) to detect interactions between transcriptionally
active proteins.
Biotechniques, 42, 1-5.

Sumara, I., Quadroni, M., Frei, C., Olma, M., Sumara, G., Ricci, R., and Peter,
M., (2007) A Cul3-based E3-ligase is required to remove Aurora B from
mitotic chromosomes, thereby regulating mitotic progression and completion
of cytokinesis in human cells.
Developmental Cell, 12, 887-900.

Zapater, M., Sohrmann, M., Peter, M., Posas, F., de Nadal, E., (2007)
Selective requirement for SAGA in Hog1-mediated gene expression
depending on the severity of the external osmostress conditions.
Mol. Cell. Biol., 27, 3900-10.

Luke-Glaser, S., Roy, M., Larsen, B., Le Bihan, T., Metalnikov, P., Tyers, M.,
Peter, M., and Pintard, L. (2007) CIF-1, a shared subunit of the
COP9/Signalosome and eIF3 complexes regulates MEL-26 levels in the C.
elegans embryo.
Mol. Cell. Biol., 27, 4526-40.

Zumbuehl, A., Stano, P., Sohrmann, M., Peter, M., Walde, P. and Carreira
E.M., (2007), A novel strategy for bioconjugation: synthesis and preliminary
evaluation with amphotericin B.
Org. Biomol. Chem., 5, 1339-42.

2006

Blake, D., Luke, B., Kanellis, P., Jorgensen, P., Goh, Th., Penfold,
S.,Breitkreutz, B.-J., Durocher, D., Peter, M. and Tyers, M., (2006) The F-box
protein Dia2 overcomes replication impedance to promote genome stability in
Saccharamyces cerevisiae.
Genetics, 174, 1709-27.

Luke, B., Versini, G., Jaquenoud, M., Zaidi, I.W., Kurz, T., Pintard, L., Pasero,
Ph. and Peter, M. (2006) The cullin Rtt101p Promotes Replication Fork
Progression through Damaged DNA and Natural Pause Sites.
Curr.Biol., 16, 786-792.

Dard, N. and Peter, M. (2006) Scaffold proteins in MAP kinase signaling:
more than simple passive activation platforms.
BioEssays, 28, 146-156.

2005

Bienko, M., Green, C.M., Crosetto, N., Rudolf, F., Zapart, G., Coull, B.,
Kannouche, P., Wider, G., Peter, M., Lehmann, A.R., Hofmann, K. and Dikic, I.
(2005) Ubiquitin-binding domains in Y-family polymerases regulate translesion
synthesis.
Science, 310, 1821-1824.

Luke-Glaser, S., Pintard, L., Lu, Ch., Mains, P.E., and Peter, M., (2005) The
BTB-Protein MEL-26 Promotes Cytokinesis in C. elegans by a CUL-3-
Independent Mechanism.
Curr. Biol., 15, 1605-1615.

Knaus, M., Cameroni, E., Pedruzzi, I., Tatchell, K., De Virgilio, and Peter, M.
(2005) The Bud14p-Glc7p complex functions as a cortical regulator of dynein
in budding yeast.
EMBO J., 24, 3000-3011.

Kurz, T., Ozlü, N., O’Rourke, S., Rudolf, F., Luke, B., Hyman, A.A.,
Bowerman, B., and Peter, M. (2005) The conserved protein DCN-1/Dcn1p is
required for cullin neddylation in C. elegans and S. cerevisiae.
Nature, 435, 1257-61.

Blondel, M., Bach, S. Bamps, S., Dobbelaere, J., Wiget, P., Longaretti, C.,
Barral, Y., Meijer, M., and Peter, M. (2005) Degradation of the PCH-protein
Hof1 by SCFGrr1 is important for proper actomyosin ring contraction during
cytokinesis in yeast.
EMBO J., 24, 1440-1452.

2004

Pintard, L., Willems, A., and Peter, M. (2004) Cullin-based ubiquitin ligases:
Cul3-BTB complexes join the family.
EMBO J., 23, 1681-7.

Lafourcade, L., Galan, J.-M., Gloor, Y., Hagenauer-Tsapis, R., and Peter, M.
(2004) The GAP Gyp1p is required for recycling of internalized membrane
material by inactivation of the Rab/Ypt-GTPase Ypt1p.
Mol. Cell. Biol., 24, 3815-3826.

VanDrogen, F., and Peter, M. (2004) Revealing protein dynamics by
photobleaching techniques.
Methods in Mol. Biol. 284, 289-308.

Shimada, Y., Wiget, P., Gulli, M.-P., Bi, E. and Peter, M. (2004) Regulation of
the nucleotide exchange factor Cdc24p by auto-inhibition.
EMBO J., 23, 1051-62.

Wiget, P., Shimada, Y., Butty, A.C. and Peter, M. (2004) Site-specific
activation of the nucleotide exchange factor Cdc24p by the scaffold protein
Far1p during yeast mating.
EMBO J., 23, 1063-74.

VanDrogen-Petit, A., Zwahlen, C., Peter, M., and Bovin, A. (2004). Insight into
molecular interactions between two PB1 domains.
J. Mol. Biol., 336, 1195-1210.

Aouida M, Pagé, N, Peter, M., and Dindial, R. (2004) A genome-wide screen
in Saccharomyces cerevisiae reveals altered transport as a mechanism of
resistance to anticancer drug bleomycin.
Cancer Research, 64, 1102-1109.

Tong, A.H., Lesage, G., Bader, G.D., Ding, H., Xu, H., Xin, X., Young, J.,
Berriz, G.F., Brost, R.L., Chang, M., Chen, Y., Cheng, X., Chua, G., Friesen,
H., Goldberg, D.S., Haynes, J., Humphries, C., He, G., Hussein, S., Ke, L.,
Krogan, N., Li Z., Levinson, J.N., Lu, H., Menard, P., Munyana, C., Parsons,
A.B., Ryan, O., Tonikian, R., Roberts, T., Sdicu, A.M., Shapiro, J., Sheikh, B.,
Suter, B., Wong, S.L., Zhang, L.V., Zhu, H., Burd, C.G., Munro, S., Sander,
C., Rine, J., Greenblatt, J., Peter, M., Bretscher, A., Bell, G., Roth, F.P.,
Brown, G.W., Andrews, B., Bussey, H., Boone, C., (2004) Global mapping of
the yeast genetic interaction network.
Science, 303, 808-813.

2003

Sohrmann, M. and Peter, M. (2003) Polarising without a C(l)ue.
Trends Cell Biol., 13, 526-533.

Pintard, L. and Peter, M. (2003) Cdc34: cycling on and off the SCF.
Nat. Cell. Biol., 5, 856-857.

Gstaiger, M., Luke, B., Hess, D., Oakeley, E., Wirbelauer, C., Blondel, M.,
Mestan, J., Vigneron, M., Peter, M. and Krek, W. (2003) Control of nutrientsensitive
transcription programs by the unconventional prefoldin URI1.
Science, 302, 1208-1212.

Pintard, L. Willis, J., Willems, A., Johnson, J., Srayko, M., Kurz, T., Glaser, S.,
Mains, P., Tyers, M., Bowerman, B. and Peter, M. (2003) The BTB-containing
protein MEL-26 functions as a substrate-specific adapter of the CUL-3
ubiquitin ligase.
Nature, 425, 311-316.

Pintard, L., Kurz, T., Glaser, S., Willis, J.H., Peter, M. and Bowerman, B.
(2003) Neddylation and deneddylation of CUL-3 is required to target MEI-
1/Katanin for degradation at the meiosis-to-mitosis transition in C.elegans.
Curr. Biol. 13, 911-921.

Chang, F., and Peter, M. (2003) Yeasts make their mark.
Nat. Cell. Biol., 4, 294-9.

Lafourcade, C., Galan, J.-M., and Peter, M. (2003) The F-box protein Rcy1p is
required to activate the GTPase Ypt6p during recycling of membrane proteins
in yeast.
Genetics, 164, 469-477.