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Items: 1 to 20 of 61

1.
An APEX2-based proximity-dependent biotinylation assay with temporal specificity to study protein interactions during autophagy in the yeast Saccharomyces cerevisiae
Yasmina Filali-Mouncef, Alexandre Leytens, Prado Vargas Duarte, Mattia Zampieri, Jörn Dengjel, Fulvio Reggiori
Autophagy. 2024; 20(10): 2323–2337. Published online 2024 Jul 3. doi: 10.1080/15548627.2024.2366749
PMCID:
PMC11423678
ArticlePDF–1.7M
2.
Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle
Michael J. O’Brien, Athar Ansari
Biochim Biophys Acta Proteins Proteom. Author manuscript; available in PMC 2024 Feb 16.
Published in final edited form as: Biochim Biophys Acta Proteins Proteom. 2024 Jan 1; 1872(1): 140968. Published online 2023 Oct 19. doi: 10.1016/j.bbapap.2023.140968
PMCID:
PMC10872477
ArticlePDF–1.7M
3.
The social and structural architecture of the yeast protein interactome
André C. Michaelis, Andreas-David Brunner, Maximilian Zwiebel, Florian Meier, Maximilian T. Strauss, Isabell Bludau, Matthias Mann
Nature. 2023; 624(7990): 192–200. Published online 2023 Nov 15. doi: 10.1038/s41586-023-06739-5
PMCID:
PMC10700138
ArticlePDF–20M
4.
Profiling and verifying the substrates of E3 ubiquitin ligase Rsp5 in yeast cells
Shuai Fang, Geng Chen, Yiyang Wang, Rakhee Ganti, Tatiana A. Chernova, Li Zhou, Savannah E. Jacobs, Duc Duong, Hiroaki Kiyokawa, Yury O. Chernoff, Ming Li, Natalia Shcherbik, Bo Zhao, Jun Yin
STAR Protoc. 2023 Sep 15; 4(3): 102489. Published online 2023 Aug 9. doi: 10.1016/j.xpro.2023.102489
PMCID:
PMC10440593
ArticlePDF–5.4M
5.
A systematic proximity ligation approach to studying protein‐substrate specificity identifies the substrate spectrum of the Ssh1 translocon
Nir Cohen, Naama Aviram, Maya Schuldiner
EMBO J. 2023 Jun; 42(11): e113385. Published online 2023 Apr 19. doi: 10.15252/embj.2022113385
PMCID:
PMC10233368
ArticlePDF–1.2M
6.
Ubiquitin-Conjugating Enzymes Ubc1 and Ubc4 Mediate the Turnover of Hap4, a Master Regulator of Mitochondrial Biogenesis in Saccharomyces cerevisiae
Denise Capps, Arielle Hunter, Mengying Chiang, Tammy Pracheil, Zhengchang Liu
Microorganisms. 2022 Dec; 10(12): 2370. Published online 2022 Nov 30. doi: 10.3390/microorganisms10122370
PMCID:
PMC9787919
ArticlePDF–2.3M
7.
A balancing act: interactions within NuA4/TIP60 regulate picNuA4 function in Saccharomyces cerevisiae and humans
Phoebe Y T Lu, Alyssa C Kirlin, Maria J Aristizabal, Hilary T Brewis, Nancy Lévesque, Dheva T Setiaputra, Nikita Avvakumov, Joris J Benschop, Marian Groot Koerkamp, Frank C P Holstege, Nevan J Krogan, Calvin K Yip, Jacques Côté, Michael S Kobor
Genetics. 2022 Nov; 222(3): iyac136. Published online 2022 Sep 6. doi: 10.1093/genetics/iyac136
PMCID:
PMC9630986
ArticlePDF–2.2M
8.
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources
Stacia R Engel, Edith D Wong, Robert S Nash, Suzi Aleksander, Micheal Alexander, Eric Douglass, Kalpana Karra, Stuart R Miyasato, Matt Simison, Marek S Skrzypek, Shuai Weng, J Michael Cherry
Genetics. 2022 Apr; 220(4): iyab224. Published online 2021 Dec 13. doi: 10.1093/genetics/iyab224
PMCID:
PMC9209811
ArticlePDF–818K
9.
Ubc1 turnover contributes to the spindle assembly checkpoint in Saccharomyces cerevisiae
Heather E Arsenault, Julie M Ghizzoni, Cassandra M Leech, Anne R Diers, Stephane Gesta, Vivek K Vishnudas, Niven R Narain, Rangaprasad Sarangarajan, Jennifer A Benanti
G3 (Bethesda) 2021 Dec; 11(12): jkab346. Published online 2021 Sep 29. doi: 10.1093/g3journal/jkab346
PMCID:
PMC8664427
ArticlePDF–909K
10.
Regulation of the Endocytosis and Prion Chaperoning Machineries by Yeast E3 Ubiquitin Ligase Rsp5 as Revealed by Orthogonal Ubiquitin Transfer
Yiyang Wang, Shuai Fang, Geng Chen, Rakhee Ganti, Tatiana A. Chernova, Li Zhou, Duc Duong, Hiroaki Kiyokawa, Ming Li, Bo Zhao, Natalia Shcherbik, Yury O. Chernoff, Jun Yin
Cell Chem Biol. Author manuscript; available in PMC 2022 Sep 16.
Published in final edited form as: Cell Chem Biol. 2021 Sep 16; 28(9): 1283–1297.e8. Published online 2021 Mar 4. doi: 10.1016/j.chembiol.2021.02.005
PMCID:
PMC8380759
ArticlePDF–2.9M
11.
The UBA domain of conjugating enzyme Ubc1/Ube2K facilitates assembly of K48/K63‐branched ubiquitin chains
Lukas Pluska, Ernst Jarosch, Henrik Zauber, Andreas Kniss, Anita Waltho, Katrin Bagola, Maximilian von Delbrück, Frank Löhr, Brenda A Schulman, Matthias Selbach, Volker Dötsch, Thomas Sommer
EMBO J. 2021 Mar 15; 40(6): e106094. Published online 2021 Feb 12. doi: 10.15252/embj.2020106094
PMCID:
PMC7957398
ArticlePDF–2.9M
12.
Dosage suppression genetic interaction networks enhance functional wiring diagrams of the cell
Leslie Magtanong, Cheuk Hei Ho, Sarah L Barker, Wei Jiao, Anastasia Baryshnikova, Sondra Bahr, Andrew M Smith, Lawrence E Heisler, John S Choy, Elena Kuzmin, Kerry Andrusiak, Anna Kobylianski, Zhijian Li, Michael Costanzo, Munira A Basrai, Guri Giaever, Corey Nislow, Brenda Andrewa, Charles Boone
Nat Biotechnol. Author manuscript; available in PMC 2020 Jul 28.
Published in final edited form as: Nat Biotechnol. 2011 May 15; 29(6): 505–511. Published online 2011 May 15. doi: 10.1038/nbt.1855
PMCID:
PMC7386433
ArticlePDF–1.0M
13.
Proteasome Activity Is Influenced by the HECT_2 Protein Ipa1 in Budding Yeast
Anne P. Lutz, Sarah Schladebeck, Christian Renicke, Roberta Spadaccini, Hans-Ulrich Mösch, Christof Taxis
Genetics. 2018 May; 209(1): 157–171. Published online 2018 Mar 8. doi: 10.1534/genetics.118.300744
PMCID:
PMC5937183
ArticlePDF–2.1M
14.
A global interaction network maps a wiring diagram of cellular function
Michael Costanzo, Benjamin VanderSluis, Elizabeth N. Koch, Anastasia Baryshnikova, Carles Pons, Guihong Tan, Wen Wang, Matej Usaj, Julia Hanchard, Susan D. Lee, Vicent Pelechano, Erin B. Styles, Maximilian Billmann, Jolanda van Leeuwen, Nydia van Dyk, Zhen-Yuan Lin, Elena Kuzmin, Justin Nelson, Jeff S. Piotrowski, Tharan Srikumar, Sondra Bahr, Yiqun Chen, Raamesh Deshpande, Christoph F. Kurat, Sheena C. Li, Zhijian Li, Mojca Mattiazzi Usaj, Hiroki Okada, Natasha Pascoe, Bryan-Joseph San Luis, Sara Sharifpoor, Emira Shuteriqi, Scott W. Simpkins, Jamie Snider, Harsha Garadi Suresh, Yizhao Tan, Hongwei Zhu, Noel Malod-Dognin, Vuk Janjic, Natasa Przulj, Olga G. Troyanskaya, Igor Stagljar, Tian Xia, Yoshikazu Ohya, Anne-Claude Gingras, Brian Raught, Michael Boutros, Lars M. Steinmetz, Claire L. Moore, Adam P. Rosebrock, Amy A. Caudy, Chad L. Myers, Brenda Andrews, Charles Boone
Science. Author manuscript; available in PMC 2017 Oct 30.
Published in final edited form as: Science. 2016 Sep 23; 353(6306): aaf1420. doi: 10.1126/science.aaf1420
PMCID:
PMC5661885
ArticlePDF–2.6M
15.
Architecture and dynamics of overlapped RNA regulatory networks
Christopher P. Lapointe, Melanie A. Preston, Daniel Wilinski, Harriet A.J. Saunders, Zachary T. Campbell, Marvin Wickens
RNA. 2017 Nov; 23(11): 1636–1647. doi: 10.1261/rna.062687.117
PMCID:
PMC5648032
ArticlePDF–6.6M
16.
Identification of karyopherins involved in the nuclear import of RNA exosome subunit Rrp6 in Saccharomyces cerevisiae
Fernando A. Gonzales-Zubiate, Ellen K. Okuda, Julia P. C. Da Cunha, Carla Columbano Oliveira
J Biol Chem. 2017 Jul 21; 292(29): 12267–12284. Published online 2017 May 24. doi: 10.1074/jbc.M116.772376
PMCID:
PMC5519375
ArticlePDF–3.2M
17.
A novel translational control mechanism involving RNA structures within coding sequences
Jennifer Jungfleisch, Danny D. Nedialkova, Ivan Dotu, Katherine E. Sloan, Neus Martinez-Bosch, Lukas Brüning, Emanuele Raineri, Pilar Navarro, Markus T. Bohnsack, Sebastian A. Leidel, Juana Díez
Genome Res. 2017 Jan; 27(1): 95–106. doi: 10.1101/gr.209015.116
Correction in:
Genome Res. 2017 Apr; 27(4): 663.
PMCID:
PMC5204348
ArticlePDF–1.3M
18.
The San1 Ubiquitin Ligase Functions Preferentially with Ubiquitin-conjugating Enzyme Ubc1 during Protein Quality Control
Rebeca Ibarra, Daniella Sandoval, Eric K. Fredrickson, Richard G. Gardner, Gary Kleiger
J Biol Chem. 2016 Sep 2; 291(36): 18778–18790. Published online 2016 Jul 12. doi: 10.1074/jbc.M116.737619
PMCID:
PMC5009252
ArticlePDF–2.1M
19.
One library to make them all: Streamlining yeast library creation by a SWAp-Tag (SWAT) strategy
Ido Yofe, Uri Weill, Matthias Meurer, Silvia Chuartzman, Einat Zalckvar, Omer Goldman, Shifra Ben-Dor, Conny Schütze, Nils Wiedemann, Michael Knop, Anton Khmelinskii, Maya Schuldiner
Nat Methods. Author manuscript; available in PMC 2016 Sep 22.
Published in final edited form as: Nat Methods. 2016 Apr; 13(4): 371–378. Published online 2016 Feb 29. doi: 10.1038/nmeth.3795
PMCID:
PMC4869835
ArticlePDF–2.7M
20.
An inter‐species protein–protein interaction network across vast evolutionary distance
Quan Zhong, Samuel J Pevzner, Tong Hao, Yang Wang, Roberto Mosca, Jörg Menche, Mikko Taipale, Murat Taşan, Changyu Fan, Xinping Yang, Patrick Haley, Ryan R Murray, Flora Mer, Fana Gebreab, Stanley Tam, Andrew MacWilliams, Amélie Dricot, Patrick Reichert, Balaji Santhanam, Lila Ghamsari, Michael A Calderwood, Thomas Rolland, Benoit Charloteaux, Susan Lindquist, Albert‐László Barabási, David E Hill, Patrick Aloy, Michael E Cusick, Yu Xia, Frederick P Roth, Marc Vidal
Mol Syst Biol. 2016 Apr; 12(4): 865. Published online 2016 Apr 23. doi: 10.15252/msb.20156484
PMCID:
PMC4848758
ArticlePDF–2.1M

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