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Select item 108724771.

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

Abstract Article PDF–1.7M

Select item 106000072.

Structures illustrate step-by-step mitochondrial transcription initiation

Quinten Goovaerts, Jiayu Shen, Brent De Wijngaert, Urmimala Basu, Smita S. Patel, Kalyan Das

Nature. 2023; 622(7984): 872–879. Published online 2023 Oct 11. doi: 10.1038/s41586-023-06643-y

PMCID:: PMC10600007

Abstract Article PDF–13M

Select item 92098113.

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

Abstract Article PDF–818K

Select item 80447124.

Assembly and Cryo-EM structure determination of yeast mitochondrial RNA polymerase initiation complex intermediates

Sergio E. Martinez, Anupam Singh, Brent De Wijngaert, Shemaila Sultana, Chhaya Dharia, Hans Vanbuel, Jiayu Shen, Daniel Vasilchuk, Smita S. Patel, Kalyan Das

STAR Protoc. 2021 Jun 18; 2(2): 100431. Published online 2021 Mar 31. doi: 10.1016/j.xpro.2021.100431

PMCID:: PMC8044712

Abstract Article PDF–1.9M

Select item 78554935.

Cryo-EM structures reveal transcription initiation steps by yeast mitochondrial RNA polymerase

Brent De Wijngaert, Shemaila Sultana, Anupam Singh, Chhaya Dharia, Hans Vanbuel, Jiayu Shen, Daniel Vasilchuk, Sergio E. Martinez, Eaazhisai Kandiah, Smita S. Patel, Kalyan Das

Mol Cell. Author manuscript; available in PMC 2022 Jan 21.

Published in final edited form as: Mol Cell. 2021 Jan 21; 81(2): 268–280.e5. Published online 2020 Dec 4. doi: 10.1016/j.molcel.2020.11.016

PMCID:: PMC7855493

Abstract Article PDF–2.9M

Select item 72426946.

The C-terminal tails of the mitochondrial transcription factors Mtf1 and TFB2M are part of an autoinhibitory mechanism that regulates DNA binding

Urmimala Basu, Nandini Mishra, Mohammed Farooqui, Jiayu Shen, Laura C. Johnson, Smita S. Patel

J Biol Chem. 2020 May 15; 295(20): 6823–6830. Published online 2020 Apr 2. doi: 10.1074/jbc.RA120.013338

PMCID:: PMC7242694

Abstract Article PDF–1.5M

Select item 70496857.

The C-terminal tail of the yeast mitochondrial transcription factor Mtf1 coordinates template strand alignment, DNA scrunching and timely transition into elongation

Urmimala Basu, Seung-Won Lee, Aishwarya Deshpande, Jiayu Shen, Byeong-Kwon Sohn, Hayoon Cho, Hajin Kim, Smita S Patel

Nucleic Acids Res. 2020 Mar 18; 48(5): 2604–2620. Published online 2020 Jan 25. doi: 10.1093/nar/gkaa040

PMCID:: PMC7049685

Abstract Article PDF–6.6M

Select item 63471708.

Effect of Sec61 interaction with Mpd1 on endoplasmic reticulum-associated degradation

Fabio Pereira, Mandy Rettel, Frank Stein, Mikhail M. Savitski, Ian Collinson, Karin Römisch

PLoS One. 2019; 14(1): e0211180. Published online 2019 Jan 25. doi: 10.1371/journal.pone.0211180

PMCID:: PMC6347170

Abstract Article PDF–16M

Select item 57653599.

Genome-Wide Mapping of Decay Factor–mRNA Interactions in Yeast Identifies Nutrient-Responsive Transcripts as Targets of the Deadenylase Ccr4

Jason E. Miller, Liye Zhang, Haoyang Jiang, Yunfei Li, B. Franklin Pugh, Joseph C. Reese

G3 (Bethesda) 2018 Jan; 8(1): 315–330. Published online 2017 Nov 20. doi: 10.1534/g3.117.300415

PMCID:: PMC5765359

Abstract Article PDF–2.2M

Select item 575387310.

Protein Moonlighting Revealed by Noncatalytic Phenotypes of Yeast Enzymes

Adriana Espinosa-Cantú, Diana Ascencio, Selene Herrera-Basurto, Jiewei Xu, Assen Roguev, Nevan J. Krogan, Alexander DeLuna

Genetics. 2018 Jan; 208(1): 419–431. Published online 2017 Nov 10. doi: 10.1534/genetics.117.300377

PMCID:: PMC5753873

Abstract Article PDF–1.5M

Select item 564803211.

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

Abstract Article PDF–6.6M

Select item 556293712.

Exploring Genetic Suppression Interactions on a Global Scale

Jolanda van Leeuwen, Carles Pons, Joseph C. Mellor, Takafumi N. Yamaguchi, Helena Friesen, John Koschwanez, Mojca Mattiazzi Ušaj, Maria Pechlaner, Mehmet Takar, Matej Ušaj, Benjamin VanderSluis, Kerry Andrusiak, Pritpal Bansal, Anastasia Baryshnikova, Claire Boone, Jessica Cao, Atina Cote, Marinella Gebbia, Gene Horecka, Ira Horecka, Elena Kuzmin, Nicole Legro, Wendy Liang, Natascha van Lieshout, Margaret McNee, Bryan-Joseph San Luis, Fatemeh Shaeri, Ermira Shuteriqi, Song Sun, Lu Yang, Ji-Young Youn, Michael Yuen, Michael Costanzo, Anne-Claude Gingras, Patrick Aloy, Chris Oostenbrink, Andrew Murray, Todd R. Graham, Chad L. Myers, Brenda J. Andrews, Frederick P. Roth, Charles Boone

Science. Author manuscript; available in PMC 2017 Aug 19.

Published in final edited form as: Science. 2016 Nov 4; 354(6312): aag0839. doi: 10.1126/science.aag0839

PMCID:: PMC5562937

Abstract Article PDF–2.5M

Select item 548454413.

The yeast protein kinase Sch9 adjusts V-ATPase assembly/disassembly to control pH homeostasis and longevity in response to glucose availability

Tobias Wilms, Erwin Swinnen, Elja Eskes, Laura Dolz-Edo, Alice Uwineza, Ruben Van Essche, Joëlle Rosseels, Piotr Zabrocki, Elisabetta Cameroni, Vanessa Franssens, Claudio De Virgilio, Gertien J. Smits, Joris Winderickx

PLoS Genet. 2017 Jun; 13(6): e1006835. Published online 2017 Jun 12. doi: 10.1371/journal.pgen.1006835

PMCID:: PMC5484544

Abstract Article PDF–14M

Select item 505508314.

Functional Metabolomics Describes the Yeast Biosynthetic Regulome

Michael Mülleder, Enrica Calvani, Mohammad Tauqeer Alam, Richard Kangda Wang, Florian Eckerstorfer, Aleksej Zelezniak, Markus Ralser

Cell. 2016 Oct 6; 167(2): 553–565.e12. doi: 10.1016/j.cell.2016.09.007

PMCID:: PMC5055083

Abstract Article PDF–3.9M

Select item 497439415.

The Yeast Mitochondrial RNA Polymerase and Transcription Factor Complex Catalyzes Efficient Priming of DNA Synthesis on Single-stranded DNA

Aparna Ramachandran, Divya Nandakumar, Aishwarya P. Deshpande, Thomas P. Lucas, Ramanagouda R-Bhojappa, Guo-Qing Tang, Kevin Raney, Y. Whitney Yin, Smita S. Patel

J Biol Chem. 2016 Aug 5; 291(32): 16828–16839. Published online 2016 Jun 16. doi: 10.1074/jbc.M116.740282

PMCID:: PMC4974394

Abstract Article PDF–2.2M

Select item 470795216.

Protein-RNA networks revealed through covalent RNA marks

Christopher P. Lapointe, Daniel Wilinski, Harriet A. J. Saunders, Marvin Wickens

Nat Methods. Author manuscript; available in PMC 2016 May 18.

Published in final edited form as: Nat Methods. 2015 Dec; 12(12): 1163–1170. Published online 2015 Nov 2. doi: 10.1038/nmeth.3651

PMCID:: PMC4707952

Abstract Article PDF–856K

Select item 466488217.

Saccharomyces cerevisiae Is Dependent on Vesicular Traffic between the Golgi Apparatus and the Vacuole When Inositolphosphorylceramide Synthase Aur1 Is Inactivated

Natalia S. Voynova, Carole Roubaty, Hector M. Vazquez, Shamroop K. Mallela, Christer S. Ejsing, Andreas Conzelmann

Eukaryot Cell. 2015 Dec; 14(12): 1203–1216. Prepublished online 2015 Oct 2. Published online 2015 Nov 30. doi: 10.1128/EC.00117-15

PMCID:: PMC4664882

Abstract Article PDF–2.3M

Select item 461603918.

Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p

Christopher J. Kershaw, Joseph L. Costello, David Talavera, William Rowe, Lydia M. Castelli, Paul F. G. Sims, Christopher M. Grant, Mark P. Ashe, Simon J. Hubbard, Graham D. Pavitt

Sci Rep. 2015; 5: 15518. Published online 2015 Oct 23. doi: 10.1038/srep15518

PMCID:: PMC4616039

Abstract Article PDF–2.2M

Select item 461581319.

The thumb subdomain of yeast mitochondrial RNA polymerase is involved in processivity, transcript fidelity and mitochondrial transcription factor binding

Gilberto Velazquez, Rui Sousa, Luis G Brieba

RNA Biol. 2015 May; 12(5): 514–524. Published online 2015 Feb 5. doi: 10.1080/15476286.2015.1014283

PMCID:: PMC4615813

Abstract Article PDF–1.1M

Select item 460890920.

ATP-binding cassette transporters and sterol O-acyltransferases interact at membrane microdomains to modulate sterol uptake and esterification

Sonia Gulati, Dina Balderes, Christine Kim, Zhongmin A. Guo, Lisa Wilcox, Estela Area-Gomez, Jamie Snider, Heimo Wolinski, Igor Stagljar, Juliana T. Granato, Kelly V. Ruggles, Joseph A. DeGiorgis, Sepp D. Kohlwein, Eric A. Schon, Stephen L. Sturley

FASEB J. 2015 Nov; 29(11): 4682–4694. Published online 2015 Jul 28. doi: 10.1096/fj.14-264796

PMCID:: PMC4608909

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