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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
...(Thermo Fisher Scientific) against 15 mL methylation buffer with 200 µM freshly added SAM at 25°C for M.SssI or 37°C for M.CviPI. Next, 0.5–1 µg fully assembled pUC19-601-25mer plasmid (pFMP233) (Lowary and Widom 1998; Lieleg et al. 2015a) and Saccharomyces Genome Database (SGD) assembled Escherichia coli...
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Resource: Global analysis of protein homomerization in Saccharomyces cerevisiae
- Yeonsoo Kim,
- Jong Pil Jung,
- Chan-Gi Pack,
- and Won-Ki Huh
Genome Res. January 2019 29: 135-145; Published in Advance December 19, 2018, doi:10.1101/gr.231860.117
..., cells can build up large protein complexes by homomerization with a relatively small number of genes (Goodsell and Olson 2000). Third, proteins can go through functional transitions depending on their homomeric states. For example, Escherichia coli UvrD acts as either a helicase or a translocase...
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Research: Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method
- Koji Makanae,
- Reiko Kintaka,
- Takashi Makino,
- Hiroaki Kitano,
- and Hisao Moriya
Genome Res. February 2013 23: 300-311; Published in Advance December 28, 2012, doi:10.1101/gr.146662.112
...plasmids with those genes in Escherichia coli and confirmed that they were too toxic for the transformants to form colonies (data not shown).We thus concluded that theywere very low limit genes. In addition, for TUB2, we created a promoter-deletion series and obtained a TUB2 allele with a 100-bp promoter...
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Method: High resolution mapping of modified DNA nucleobases using excision repair enzymes
- D. Suzi Bryan,
- Monica Ransom,
- Biniam Adane,
- Kerri York,
- and Jay R. Hesselberth
Genome Res. September 2014 24: 1534-1542; Published in Advance July 11, 2014, doi:10.1101/gr.174052.114
...cancer. Nat Rev Cancer 1: 22–33. Gadsden MH, McIntosh EM, Game JC, Wilson PJ, Haynes RH. 1993. dUTP pyrophosphatase is an essential enzyme in Saccharomyces cerevisiae. EMBO J 12: 4425–4431. Gallagher PE, Duker NJ. 1986. Detection of UV purine photoproducts in a defined sequence of human DNA. Mol Cell...
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LETTER: Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model
- Natalie C. Duarte,
- Markus J. Herrgård,
- and Bernhard Ø. Palsson
Genome Res. July 2004 14: 1298-1309; Published in Advance June 14, 2004, doi:10.1101/gr.2250904
...for several microorganisms, including Escherichia coli ( Pramanik and Keasling 1997 ; Edwards and Palsson 2000 ; Reed et al. 2003 ), Helicobacter pylori ( Schilling et al. 2002 ), Haemophilus influenzae ( Edwards and Palsson 1999 ), and Saccharomyces cerevisiae ( Förster et al. 2003a ). These models have been...
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RESOURCE: Large-scale identification of protein–protein interaction of Escherichia coli K-12
- Mohammad Arifuzzaman,
- Maki Maeda,
- Aya Itoh,
- Kensaku Nishikata,
- Chiharu Takita,
- Rintaro Saito,
- Takeshi Ara,
- Kenji Nakahigashi,
- Hsuan-Cheng Huang,
- Aki Hirai,
- Kohei Tsuzuki,
- Seira Nakamura,
- Mohammad Altaf-Ul-Amin,
- Taku Oshima,
- Tomoya Baba,
- Natsuko Yamamoto,
- Tomoyo Kawamura,
- Tomoko Ioka-Nakamichi,
- Masanari Kitagawa,
- Masaru Tomita,
- Shigehiko Kanaya,
- Chieko Wada,
- and Hirotada Mori
Genome Res. May 2006 16: 686-691; Published in Advance April 10, 2006, doi:10.1101/gr.4527806
...in . Escherichia coli. Curr. Top. Cell. Regul. 33 : 231 – 247 . ↵ Ho Y. , Gruhler A. , Heilbut A. , Bader G.D. , Moore L. , Adams S.L. , Millar A. , Taylor P. , Bennett K. , Boutilier K. , et al. ( 2002 ) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415...
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LETTER: Divergence of Function in Sequence-Related Groups of Escherichia coli Proteins
- Laila Alves Nahum and
- Monica Riley
Genome Res. August 1, 2001 11: 1375-1381; doi:10.1101/gr.180901
...-chain amino acid biosynthetic pathway. J. Bacteriol. 170 : 3937 – 3945 . ↵ Chang Y.Y. , Wang A.Y. , Cronan J.E. , Jr. ( 1993 ) Molecular cloning, DNA sequencing, and biochemical analyses of Escherichia coli glyoxylate carboligase. An enzyme of the acetohydroxy acid synthase–pyruvate oxidase family. J. Biol...
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LETTER: Principles of transcriptional regulation and evolution of the metabolic system in E. coli
- Aswin S.N. Seshasayee,
- Gillian M. Fraser,
- M. Madan Babu,
- and Nicholas M. Luscombe
Genome Res. January 2009 19: 79-91; Published in Advance October 3, 2008, doi:10.1101/gr.079715.108
...to investigate the evolutionary trends and transcriptional control of metabolism in Escherichia coli K12. Globally, the regulatory system is organized in a clear hierarchy of general and specific transcription factors (TFs) that control differing ranges of metabolic functions. Further, catabolic, anabolic...
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RESEARCH: Analogous Enzymes: Independent Inventions in Enzyme Evolution
- Michael Y. Galperin,
- D. Roland Walker,
- and Eugene V. Koonin
Genome Res. August 1, 1998 8: 779-790; doi:10.1101/gr.8.8.779
...was followed by a shift in the substrate specificity. A similar mechanism is likely to account for the origin of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase from an alkaline phosphatase-like enzyme and of the second phosphofructokinase of Escherichia coli (PfkB) from an enzyme...
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RESOURCE: Inferring genome-wide functional linkages in E. coli by combining improved genome context methods: Comparison with high-throughput experimental data
- Sailu Yellaboina,
- Kshama Goyal,
- and Shekhar C. Mande
Genome Res. April 2007 17: 527-535; Published in Advance March 5, 2007, doi:10.1101/gr.5900607
.... Here, we report an interaction network of Escherichia coli , obtained by training a Support Vector Machine on the high quality of interactions in the EcoCyc database, and with the assumption that the periplasmic and cytoplasmic proteins may not interact with each other. The data features included...
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