Kraft Lab

Publications

Selected Publications

Barz S*, Kriegenburg F*, Henning A, Bhattacharya A, Mancilla H, Sánchez-Martín P, and Kraft C (2020). Atg1 kinase regulates autophagosome-vacuole fusion by controlling SNARE bundling. EMBO Reports 217, DOI: 10.15252/embr.202051869

Hollenstein D, Gómez‐Sánchez R, Ciftci A, Kriegenburg F, Mari M, Torggler R, Licheva M, Reggiori F  and Kraft C (2019). Vac8 establishes an autophagosome formation site between the vacuole and the ER. Journal of Cell Science DOI: 10.1242/jcs.235002  

Bas L, Papinski D, Licheva M, Torggler R, Rohringer S, Schuschnig M, and Kraft C (2018). Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome-vacuole fusion. Journal of Cell Biology 217: DOI: 10.1083/jcb.201804028

Torggler R*, Papinski D*, Brach T*, Bas L, Schuschnig M, Pfaffenwimmer T, Rohringer S, Matzhold T, Schweida D, Brezovich A and Kraft C (2016). Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole. Molecular Cell 64: 221-235. DOI: 10.1016/j.molcel.2016.09.008

Brezovich A, Schuschnig M, Ammerer G and Kraft C (2015). An in vivo detection system for transient and low abundant protein interactions and their kinetics in budding yeast. Yeast 32: 355-365. DOI: 10.1002/yea.3063

Pfaffenwimmer T, Reiter W, Brach T, Nogellova V, Papinski D, Schuschnig M, Abert C, Ammerer G, Martens S and Kraft C (2014). The Hrr25 kinase promotes selective autophagy by phosphorylating the cargo-receptor Atg19. EMBO Reports 15: 862-870. DOI: 10.15252/embr.201438932

Papinski D, Schuschnig M, Reiter W, Wilhelm L, Barnes C, Majolica A, Hansmann I, Pfaffenwimmer T, Kijanska M, Stoffel I, Lee SS, Brezovich A, Lou HJ, Turk BE, Aebersold R, Ammerer G, Peter M and Kraft C (2014). Early steps in autophagy depend on direct phosphorylation of Atg9 by the Atg1 kinase. Molecular Cell 53: 471-483. DOI: 10.1016/j.molcel.2013.12.011



All Publications

2021

Morgenstern M, Peikert CD, Lübbert P, Suppanz I, Klemm C, Alka O, Steiert C, Naumenko N, Schendzielorz A, Melchionda L, Mühlhäuser WWD, Knapp B, Busch JD, Stiller SB, Dannenmaier S, Lindau C, Licheva M, Eickhorst C, Galbusera R, Zerbes R, Ryan MT, Kraft C, Kozjak-Pavlovic V, Drepper F, Dennerlein S, Oeljeklaus S, Pfanner N, Wiedemann N and Warscheid B (2021). Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. Cell Metabolism 33, DOI: 10.1016/j.cmet.2021.11.001

Walter C, Marada A, Suhm T, Ernsberger R, Muders V, Kücükköse C, Sanchez-Martin P, Hu Z, Aich A, Loroch S, Solari FA, Poveda-Huertes D, Schwierzok A, Pommerening H, Matic S, Brix J, Sickmann A, Kraft C, Dengjel J, Dennerlein S, Brummer T, Vögtle FN and Meisinger C (2021). Global kinome profiling reveals DYRK1A as critical activator of the human mitochondrial import machinery. Nature Communications 12, DOI: 10.1038/s41467-021-24426-9

Barz S*, Kriegenburg F*, Sánchez-Martín P, and Kraft C (2021). Small but mighty: Atg8 and Rabs in Membrane Dynamics during Autophagy. BBA DOI: 10.1016/j.bbamcr.2021.119064

Licheva M*, Raman B*, Kraft C and Reggiori F (2021) Phosphoregulation of the autophagy machinery by kinases and phosphatases. Autophagy DOI: 10.1080/15548627.2021.1909407


2020

Barz S*, Kriegenburg F*, Henning A, Bhattacharya A, Mancilla H, Sánchez-Martín P, and Kraft C (2020). Atg1 kinase regulates autophagosome-vacuole fusion by controlling SNARE bundling. EMBO Reports 217, DOI: 10.15252/embr.202051869

Hollenstein D and Kraft C (2020). Autophagosomes are formed at a distinct cellular structure. Current Opinion in Cell Biology DOI: 10.1016/j.ceb.2020.02.012

Eickhorst C*, Licheva M*, Kraft C (2020). Scaffold proteins in autophagy. Progress in Molecular Biology and Translational Science. DOI: 10.1016/bs.pmbts.2020.01.009

Steinberg R, Origi A, Natriashvili A, Sarmah P, Licheva M, Walker P, Kraft C, High S, Luirink J, Shi W, Helmstädter M, Ulbrich M and Koch H (2020). Post-translational insertion of small membrane proteins by the bacterial signal recognition particle. Plos Biology. DOI: 10.1371/journal.pbio.3000874


2019

Hollenstein D, Gómez‐Sánchez R, Ciftci A, Kriegenburg F, Mari M, Torggler R, Licheva M, Reggiori F  and Kraft C (2019). Vac8 establishes an autophagosome formation site between the vacuole and the ER. Journal of Cell Science DOI: 10.1242/jcs.235002  

Poveda-Huertes D, Matic S, Marada A, Habernig L, Licheva M, Myketin L, Gilsbach R, Tosal Castano S, Papinski D, Mulica P, Kretz O, Kücükkose C, Aras Taskin A, Hein L, Kraft C, Büttner S, Meisinger C and Vögtle F-N (2019). An Early mtUPR: Redistribution of the Nuclear Transcription Factor Rox1 to Mitochondria Protects against Intramitochondrial Proteotoxic Aggregates. Molecular Cell DOI: 10.1016/j.molcel.2019.09.026

Kriegenburg F, Bas L, Gao J, Ungermann C and Kraft C (2019) The multi-functional SNARE protein Ykt6 in autophagosomal fusion processes. Cell Cycle DOI: 10.1080/15384101.2019.1580488


2018

Bas L, Papinski D and Kraft C (2018) Ykt6 mediates autophagosome-vacuole fusion. Molecular and Cellular Oncology: DOI: 10.1080/23723556.2018.1526006

Kraft C, Boya P, Codogno P, Elazar Z, Eskelinen E, Farrés J, Kirkin V, Jungbluth H, Martinez A, Pless O, Primard C, Proikas-Cezanne T, Simonsen A, Reggiori F (2018) Driving next generation autophagy researchers towards translation (DRIVE), an international PhD training program on autophagy. Autophagy : DOI: 10.1080/15548627.2018.1515532

Bas L, Papinski D, Licheva M, Torggler R, Rohringer S, Schuschnig M, and Kraft C (2018). Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome-vacuole fusion. Journal of Cell Biology 217: DOI: 10.1083/jcb.201804028

Gómez-Sánchez R, Rose J, Guimarães R, Mari M, Painski D, Rieter E, Geerts W, Hardenberg R, Kraft C, Ungermann C, and Reggiori F (2018). Atg9 establishes Atg2-dependent contact sites between the ER and phagophores. Journal of Cell Biology 217: DOI: 10.1083/jcb.201710116


2017

Sánchez-Wandelmer J, Kriegenburg F, Rohringer S, Schuschnig M, Gomez-Sanchez R, Zens B, Abreu S, Hardenberg R, Hollenstein D, Gao J, Ungermann C, Martens S, Kraft C and Reggiori F (2017). Atg4 proteolytic activity can be inhibited by Atg1 phosphorylation. Nature Communications 8: 295. DOI: 10.1038/s41467-017-00302-3

Abreu S, Kriegenburg F, Gomez-Sanchez R, Mari M, Sanchez-Wandelmer J, Rasmussen M, Soares Guimaraes R, Zens B, Schuschnig M, Hardenberg R, Peter M, Johansen T, Kraft C, Martens S and Reggiori F (2017). A conserved LIR motif mediates Atg4 association to autophagosomal membranes and Atg8 deconjugation. EMBO Reports 18: 765-780. DOI: 10.15252/embr.201643146

Torggler R, Papinski D and Kraft C (2017). Assays to Monitor Autophagy in Saccharomyces cerevisiae. Cells 6: 23. DOI:10.3390/cells6030023

Galluzzi L, ..., Kraft C, ..., Kroemer G (2017). Molecular definitions of autophagy and related processes. The EMBO journal 36:1811-1836. DOI: 10.15252/embj.201796697


2016

Fracchiolla D, Sawa-Makarska J, Zens B, de Ruiter A, Brezovich A, Romanov J, Runggatscher K, Kraft C, Zagrovic B and Martens S (2016). Mechanism of cargo-directed Atg8 conjugation during selective autophagy. Elife 5, e18544. DOI: 10.7554/eLife.18544

Papinski D and Kraft C (2016). Regulation of autophagy by signalling through the Atg1/ULK1 complex. Journal of Molecular Biology 428: 1725-1741. DOI: 10.1016/j.jmb.2016.03.030

Torggler R, Papinski D, Brach T, Bas L, Schuschnig M, Pfaffenwimmer T, Rohringer S, Matzhold T, Schweida D, Brezovich A and Kraft C (2016). Two Independent Pathways within Selective Autophagy Converge to Activate Atg1 Kinase at the Vacuole. Molecular Cell 64: 221-235. DOI: 10.1016/j.molcel.2016.09.008

Klionsky DJ, Abdelmohsen K, Abe A, Abedin M, ..., Kraft C, ..., Zughaier S (2016). Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy 8: 445-544. DOI: 10.4161/auto.19496


2015

Müller M, Schmidt O, Angelova M, Faserl K, Kremser L, Pfaffenwimmer T, Kraft C, Trajanoski Z, Lindner H and Teis D (2015). The sequential action of the MVB pathway and autophagy ensures cell survival during starvation. Elife 4: e07736. DOI: 10.7554/eLife.07736.

Brezovich A, Schuschnig M, Ammerer G and Kraft C (2015). An in vivo detection system for transient and low abundant protein interactions and their kinetics in budding yeast. Yeast 32: 355-365. DOI: 10.1002/yea.3063

Rebsamen M, Pochini L, Stasyk T, Araujo M, Galluccio M, Kandasamy R, Snijder B, Fauster A, Fudashevskaya E, Bruckner M, Scorzoni S, Filipek P, Huber K, Bigenzahn J, Heinz L, Kraft C, Bennett K, Indiveri C, Huber L and Superti-Furga G (2015). SLC38A9 is a component of the lysosomal amino acid sensing machinery that controls mTORC1. Nature 519: 477-481. DOI: 10.1038/nature14107


2014

Wilson-Zbinden C, Xavier da Silveira dos Santos A, Stoffel-Studer I, van der Vaart A, Hofmann K, Reggiori F, Riezman H, Kraft C and Peter M (2014). A common phosphatidylethanolamine pool is used for autophagy, and for phosphatidylcholine and glycosylphosphatidylinositol anchor synthesis in Saccharomyces cerevisiae. Genetics 2: 475-485. DOI: 10.1534/genetics.114.169797

Pfaffenwimmer T, Reiter W, Brach T, Nogellova V, Papinski D, Schuschnig M, Abert C, Ammerer G, Martens S and Kraft C (2014). The Hrr25 kinase promotes selective autophagy by phosphorylating the cargo-receptor Atg19. EMBO Reports 15: 862-870. DOI: 10.15252/embr.201438932

Papinski D and Kraft C (2014). Atg1 kinase organizes autophagosome formation by phosphorylating Atg9. Autophagy 10: 1338-1340. DOI: 10.4161/auto.28971

Papinski D, Schuschnig M, Reiter W, Wilhelm L, Barnes C, Majolica A, Hansmann I, Pfaffenwimmer T, Kijanska M, Stoffel I, Lee SS, Brezovich A, Lou HJ, Turk BE, Aebersold R, Ammerer G, Peter M and Kraft C (2014). Early steps in autophagy depend on direct phosphorylation of Atg9 by the Atg1 kinase. Molecular Cell 53: 471–483. DOI: 10.1016/j.molcel.2013.12.011


2013

Martens S, Rusten TE, Kraft C (2013). Autophagy at Sea. Autophagy 9: 1286-1291. DOI: 10.4161/auto.25838


2012

Romanov J, Walczak M, Ibiricu I, Schüchner S, Ogris E, Kraft C, Martens S (2012). Mechanism and functions of membrane binding by the Atg5-Atg12/Atg16 complex during autophagosome formation. EMBO journal 31: 4304-4317. DOI: 10.1038/emboj.2012.278

Kraft C*, Kijanska M, Kalie E, Siergiejuk E, Lee S, Semplicio G, Stoffel I, Brezovich A, Verma M, Hansmann I, Ammerer G, Hofmann K, Tooze S and Peter M* (2012). Binding of the Atg1/ULK1 kinase to the ubiquitin-like protein Atg8 regulates autophagy. The EMBO journal 31: 3691-3703 (* corresponding authors). DOI: 10.1038/emboj.2012.225

Klionsky DJ, Abdalla FC, Abeliovich H, Abraham RT, ..., Kraft C, ..., Zuckerbraun B (2012). Guidelines for the use and interpretation of assays for monitoring autophagy. Autophagy 8: 445-544. DOI: 10.4161/auto.19496

Kraft C* and Martens S* (2012). Mechanisms and regulation of autophagosome formation. Current opinion in cell biology 24: 1-6. DOI: 10.1016/j.ceb.2012.05.001

Cebollero E, Reggiori F, Kraft C (2012). Reticulophagy and ribophagy: regulated degradation of protein production factories. Int J Cell Biol 2012: 182834. DOI: 10.1155/2012/182834


2011

Buschhorn BA, Petzold G, Galova M, Dube P, Kraft C, Herzog F, Stark H, Peters JM (2011). Substrate binding on the APC/C occurs between the coactivator Cdh1 and the processivity factor Doc1. Nature Struct Mol Biol 18: 6-13. DOI: 10.1038/nsmb.1979

Sole C, Nadal-Ribelles M, Kraft C, Peter M, Posas F, de Nadal E (2011). Control of Ubp3 ubiquitin protease activity by the Hog1 SAPK modulates transcription upon osmostress. The EMBO journal 30: 3274-3284. DOI: 10.1038/emboj.2011.227


2010

Kijanska M, Dohnal I, Reiter W, Kaspar S, Stoffel I, Ammerer G, Kraft C*, Peter M* (2010). Activation of Atg1 kinase in autophagy by regulated phosphorylation. Autophagy 6: 1168-1178  (* corresponding authors). DOI: 10.4161/auto.6.8.13849

Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R (2010). Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal 3: rs4. DOI: 10.1126/scisignal.2001182

Kraft C, Peter M, Hofmann K (2010). Selective autophagy: ubiquitin-mediated recognition and beyond. Nature Cell Biol 12: 836-841. DOI: 10.1038/ncb0910-836


2009

Kraft C*, Reggiori F and Peter M* (2009). Selective types of autophagy in yeast. Biochim Biophys Acta 1793: 1404-1412 (* corresponding authors). DOI: 10.1016/j.bbamcr.2009.02.006

Chang M, Luke B, Kraft C, Li Z, Peter M, Lingner J, Rothstein R (2009). Telomerase is essential to alleviate pif1-induced replication stress at telomeres. Genetics 183: 779-791. DOI: 10.1534/genetics.109.107631


2008

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 Biol 10: 602-610 (* corresponding authors). DOI: 10.1038/ncb1723

Kraft C*and Peter M* (2008). Is the Rsp5 ubiquitin ligase involved in the regulation of ribophagy? Autophagy 4: 838-840. DOI: doi.org/10.4161/auto.6603


2006

Kraft C, Gmachl M, Peters JM (2006). Methods to measure ubiquitin-dependent proteolysis mediated by the anaphase-promoting complex. Methods 38: 39. DOI: 10.1016/j.ymeth.2005.07.005


2005

Kraft C, Vodermaier HC, Maurer-Stroh S, Eisenhaber F and Peters JM (2005). The WD40 propeller domain of Cdh1 functions as a destruction box receptor for APC/C substrates. Molecular Cell 18: 543-553. DOI: 10.1016/j.molcel.2005.04.023

Wilson CM, Kraft C, Duggan C, Ismail N, Crawshaw SG and High S (2005). Ribophorin I associates with a subset of membrane proteins after their integration at the sec61 translocon. J Biol Chem 280: 4195-4206. DOI: 10.1074/jbc.M410329200


2004

Acquaviva C, Herzog F, Kraft C and Pines J (2004). The anaphase promoting complex/cyclosome is recruited to centromeres by the spindle assembly checkpoint. Nature Cell Biol 6: 892-898. DOI: 10.1038/ncb1167

Sumara I, Gimenez-Abian JF, Gerlich D, Hirota T, Kraft C, de la Torre C, Ellenberg J and Peters JM (2004). Roles of polo-like kinase 1 in the assembly of functional mitotic spindles. Curr Biol 14: 1712-1722. DOI: 10.1016/j.cub.2004.09.049

Mathe E, Kraft C, Giet R, Deak P, Peters JM and Glover DM (2004). The E2-C vihar is required for the correct spatiotemporal proteolysis of cyclin B and itself undergoes cyclical degradation. Curr Biol 14: 1723-1733. DOI: 10.1016/j.cub.2004.09.023


2003

Kraft C, Herzog F, Gieffers C, Mechtler K, Hagting A, Pines J and Peters JM (2003). Mitotic regulation of the human anaphase-promoting complex by phosphorylation. The EMBO journal 22: 6598-6609. DOI: 10.1093/emboj/cdg627

Kraft C (2003). Mitotic entry: tipping the balance. Curr Biol 13: R445-446. DOI: 10.1016/S0960-9822(03)00367-1