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Items: 1 to 50 of 192

1.

Mechanisms of Transcriptional Pausing in Bacteria.

Kang JY, Mishanina TV, Landick R, Darst SA.

J Mol Biol. 2019 Jul 13. pii: S0022-2836(19)30446-2. doi: 10.1016/j.jmb.2019.07.017. [Epub ahead of print] Review.

PMID:
31310765
2.

Systems metabolic engineering of Escherichia coli improves co-conversion of lignocellulose-derived sugars.

Kim J, Tremaine M, Grass JA, Purdy HM, Landick R, Kiley PJ, Reed JL.

Biotechnol J. 2019 Jul 12:e1800441. doi: 10.1002/biot.201800441. [Epub ahead of print]

PMID:
31297978
3.

Transcription of Bacterial Chromatin.

Shen BA, Landick R.

J Mol Biol. 2019 May 31. pii: S0022-2836(19)30325-0. doi: 10.1016/j.jmb.2019.05.041. [Epub ahead of print] Review.

PMID:
31153903
4.

Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription.

Stumper SK, Ravi H, Friedman LJ, Mooney RA, Corrêa IR, Gershenson A, Landick R, Gelles J.

Elife. 2019 Feb 5;8. pii: e40576. doi: 10.7554/eLife.40576. [Epub ahead of print]

5.

A Regulatory NADH/NAD+ Redox Biosensor for Bacteria.

Liu Y, Landick R, Raman S.

ACS Synth Biol. 2019 Feb 15;8(2):264-273. doi: 10.1021/acssynbio.8b00485. Epub 2019 Jan 23.

PMID:
30633862
6.

RNA Polymerase Clamp Movement Aids Dissociation from DNA but Is Not Required for RNA Release at Intrinsic Terminators.

Bellecourt MJ, Ray-Soni A, Harwig A, Mooney RA, Landick R.

J Mol Biol. 2019 Feb 15;431(4):696-713. doi: 10.1016/j.jmb.2019.01.003. Epub 2019 Jan 8.

PMID:
30630008
7.

The elemental mechanism of transcriptional pausing.

Saba J, Chua XY, Mishanina TV, Nayak D, Windgassen TA, Mooney RA, Landick R.

Elife. 2019 Jan 8;8. pii: e40981. doi: 10.7554/eLife.40981.

8.

OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate.

Ghosh IN, Martien J, Hebert AS, Zhang Y, Coon JJ, Amador-Noguez D, Landick R.

Metab Eng. 2019 Mar;52:324-340. doi: 10.1016/j.ymben.2018.12.008. Epub 2018 Dec 27.

9.

Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein.

Lawson MR, Ma W, Bellecourt MJ, Artsimovitch I, Martin A, Landick R, Schulten K, Berger JM.

Mol Cell. 2018 Sep 20;71(6):911-922.e4. doi: 10.1016/j.molcel.2018.07.014. Epub 2018 Aug 16.

PMID:
30122535
10.

In Vitro Transcription Assay to Quantify Effects of H-NS Filaments on RNA Chain Elongation by RNA Polymerase.

Boudreau BA, Kotlajich MV, Landick R.

Methods Mol Biol. 2018;1837:351-386. doi: 10.1007/978-1-4939-8675-0_18.

PMID:
30109619
11.

Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast.

Higgins DA, Young MKM, Tremaine M, Sardi M, Fletcher JM, Agnew M, Liu L, Dickinson Q, Peris D, Wrobel RL, Hittinger CT, Gasch AP, Singer SW, Simmons BA, Landick R, Thelen MP, Sato TK.

Genetics. 2018 Sep;210(1):219-234. doi: 10.1534/genetics.118.301161. Epub 2018 Jul 25.

12.

Structural Basis for Transcript Elongation Control by NusG Family Universal Regulators.

Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA.

Cell. 2018 Jun 14;173(7):1650-1662.e14. doi: 10.1016/j.cell.2018.05.017. Epub 2018 Jun 7.

13.

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032.

Yang S, Vera JM, Grass J, Savvakis G, Moskvin OV, Yang Y, McIlwain SJ, Lyu Y, Zinonos I, Hebert AS, Coon JJ, Bates DM, Sato TK, Brown SD, Himmel ME, Zhang M, Landick R, Pappas KM, Zhang Y.

Biotechnol Biofuels. 2018 May 2;11:125. doi: 10.1186/s13068-018-1116-x. eCollection 2018.

14.

StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments.

Boudreau BA, Hron DR, Qin L, van der Valk RA, Kotlajich MV, Dame RT, Landick R.

Nucleic Acids Res. 2018 Jun 20;46(11):5525-5546. doi: 10.1093/nar/gky265.

15.

Life times of metastable states guide regulatory signaling in transcriptional riboswitches.

Helmling C, Klötzner DP, Sochor F, Mooney RA, Wacker A, Landick R, Fürtig B, Heckel A, Schwalbe H.

Nat Commun. 2018 Mar 5;9(1):944. doi: 10.1038/s41467-018-03375-w.

16.

RNA Polymerase Accommodates a Pause RNA Hairpin by Global Conformational Rearrangements that Prolong Pausing.

Kang JY, Mishanina TV, Bellecourt MJ, Mooney RA, Darst SA, Landick R.

Mol Cell. 2018 Mar 1;69(5):802-815.e5. doi: 10.1016/j.molcel.2018.01.018.

17.

Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts.

Boyaci H, Chen J, Lilic M, Palka M, Mooney RA, Landick R, Darst SA, Campbell EA.

Elife. 2018 Feb 26;7. pii: e34823. doi: 10.7554/eLife.34823.

18.

Chemical genomic guided engineering of gamma-valerolactone tolerant yeast.

Bottoms S, Dickinson Q, McGee M, Hinchman L, Higbee A, Hebert A, Serate J, Xie D, Zhang Y, Coon JJ, Myers CL, Landick R, Piotrowski JS.

Microb Cell Fact. 2018 Jan 12;17(1):5. doi: 10.1186/s12934-017-0848-9.

19.

Trigger loop dynamics can explain stimulation of intrinsic termination by bacterial RNA polymerase without terminator hairpin contact.

Ray-Soni A, Mooney RA, Landick R.

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):E9233-E9242. doi: 10.1073/pnas.1706247114. Epub 2017 Oct 16.

20.

The Battle of RNA Synthesis: Virus versus Host.

Harwig A, Landick R, Berkhout B.

Viruses. 2017 Oct 21;9(10). pii: E309. doi: 10.3390/v9100309. Review.

21.

Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments.

Welch R, Chung D, Grass J, Landick R, Keles S.

Nucleic Acids Res. 2017 Sep 6;45(15):e145. doi: 10.1093/nar/gkx594.

22.

Trigger loop of RNA polymerase is a positional, not acid-base, catalyst for both transcription and proofreading.

Mishanina TV, Palo MZ, Nayak D, Mooney RA, Landick R.

Proc Natl Acad Sci U S A. 2017 Jun 27;114(26):E5103-E5112. doi: 10.1073/pnas.1702383114. Epub 2017 Jun 12.

23.

RNA polymerase motions during promoter melting.

Feklistov A, Bae B, Hauver J, Lass-Napiorkowska A, Kalesse M, Glaus F, Altmann KH, Heyduk T, Landick R, Darst SA.

Science. 2017 May 26;356(6340):863-866. doi: 10.1126/science.aam7858.

24.

Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation.

Steinert H, Sochor F, Wacker A, Buck J, Helmling C, Hiller F, Keyhani S, Noeske J, Grimm S, Rudolph MM, Keller H, Mooney RA, Landick R, Suess B, Fürtig B, Wöhnert J, Schwalbe H.

Elife. 2017 May 25;6. pii: e21297. doi: 10.7554/eLife.21297.

25.

Architecture of a transcribing-translating expressome.

Kohler R, Mooney RA, Mills DJ, Landick R, Cramer P.

Science. 2017 Apr 14;356(6334):194-197. doi: 10.1126/science.aal3059.

26.

Dynamics of GreB-RNA polymerase interaction allow a proofreading accessory protein to patrol for transcription complexes needing rescue.

Tetone LE, Friedman LJ, Osborne ML, Ravi H, Kyzer S, Stumper SK, Mooney RA, Landick R, Gelles J.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1081-E1090. doi: 10.1073/pnas.1616525114. Epub 2017 Jan 30.

27.

Correction: Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Narasimhan RA, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Piotrowski JS, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R.

PLoS Genet. 2016 Nov 9;12(11):e1006447. doi: 10.1371/journal.pgen.1006447. eCollection 2016 Nov.

28.

Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae.

Sato TK, Tremaine M, Parreiras LS, Hebert AS, Myers KS, Higbee AJ, Sardi M, McIlwain SJ, Ong IM, Breuer RJ, Avanasi Narasimhan R, McGee MA, Dickinson Q, La Reau A, Xie D, Tian M, Reed JL, Zhang Y, Coon JJ, Hittinger CT, Gasch AP, Landick R.

PLoS Genet. 2016 Oct 14;12(10):e1006372. doi: 10.1371/journal.pgen.1006372. eCollection 2016 Oct. Erratum in: PLoS Genet. 2016 Nov 9;12 (11):e1006447.

29.
30.

Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research.

McIlwain SJ, Peris D, Sardi M, Moskvin OV, Zhan F, Myers KS, Riley NM, Buzzell A, Parreiras LS, Ong IM, Landick R, Coon JJ, Gasch AP, Sato TK, Hittinger CT.

G3 (Bethesda). 2016 Jun 1;6(6):1757-66. doi: 10.1534/g3.116.029389.

31.

Mechanisms of Bacterial Transcription Termination: All Good Things Must End.

Ray-Soni A, Bellecourt MJ, Landick R.

Annu Rev Biochem. 2016 Jun 2;85:319-47. doi: 10.1146/annurev-biochem-060815-014844. Epub 2016 Mar 17. Review.

PMID:
27023849
32.

A Two-Way Street: Regulatory Interplay between RNA Polymerase and Nascent RNA Structure.

Zhang J, Landick R.

Trends Biochem Sci. 2016 Apr;41(4):293-310. doi: 10.1016/j.tibs.2015.12.009. Epub 2016 Jan 25. Review.

33.

Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain.

Dickinson Q, Bottoms S, Hinchman L, McIlwain S, Li S, Myers CL, Boone C, Coon JJ, Hebert A, Sato TK, Landick R, Piotrowski JS.

Microb Cell Fact. 2016 Jan 20;15:17. doi: 10.1186/s12934-016-0417-7.

34.

P1 Ref Endonuclease: A Molecular Mechanism for Phage-Enhanced Antibiotic Lethality.

Ronayne EA, Wan YC, Boudreau BA, Landick R, Cox MM.

PLoS Genet. 2016 Jan 14;12(1):e1005797. doi: 10.1371/journal.pgen.1005797. eCollection 2016 Jan.

35.

Bacterial RNA polymerase can retain σ70 throughout transcription.

Harden TT, Wells CD, Friedman LJ, Landick R, Hochschild A, Kondev J, Gelles J.

Proc Natl Acad Sci U S A. 2016 Jan 19;113(3):602-7. doi: 10.1073/pnas.1513899113. Epub 2016 Jan 5.

36.

Controlling microbial contamination during hydrolysis of AFEX-pretreated corn stover and switchgrass: effects on hydrolysate composition, microbial response and fermentation.

Serate J, Xie D, Pohlmann E, Donald C Jr, Shabani M, Hinchman L, Higbee A, Mcgee M, La Reau A, Klinger GE, Li S, Myers CL, Boone C, Bates DM, Cavalier D, Eilert D, Oates LG, Sanford G, Sato TK, Dale B, Landick R, Piotrowski J, Ong RG, Zhang Y.

Biotechnol Biofuels. 2015 Nov 14;8:180. doi: 10.1186/s13068-015-0356-2. eCollection 2015.

37.

Structure of a bacterial RNA polymerase holoenzyme open promoter complex.

Bae B, Feklistov A, Lass-Napiorkowska A, Landick R, Darst SA.

Elife. 2015 Sep 8;4. doi: 10.7554/eLife.08504.

38.

CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.

Bae B, Nayak D, Ray A, Mustaev A, Landick R, Darst SA.

Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4178-87. doi: 10.1073/pnas.1502368112. Epub 2015 Jul 20.

39.

Plant-derived antifungal agent poacic acid targets β-1,3-glucan.

Piotrowski JS, Okada H, Lu F, Li SC, Hinchman L, Ranjan A, Smith DL, Higbee AJ, Ulbrich A, Coon JJ, Deshpande R, Bukhman YV, McIlwain S, Ong IM, Myers CL, Boone C, Landick R, Ralph J, Kabbage M, Ohya Y.

Proc Natl Acad Sci U S A. 2015 Mar 24;112(12):E1490-7. doi: 10.1073/pnas.1410400112. Epub 2015 Mar 9.

40.

H-NS and RNA polymerase: a love-hate relationship?

Landick R, Wade JT, Grainger DC.

Curr Opin Microbiol. 2015 Apr;24:53-9. doi: 10.1016/j.mib.2015.01.009. Epub 2015 Jan 30. Review.

PMID:
25638302
41.

Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria.

Kotlajich MV, Hron DR, Boudreau BA, Sun Z, Lyubchenko YL, Landick R.

Elife. 2015 Jan 16;4. doi: 10.7554/eLife.04970.

42.

Trigger-helix folding pathway and SI3 mediate catalysis and hairpin-stabilized pausing by Escherichia coli RNA polymerase.

Windgassen TA, Mooney RA, Nayak D, Palangat M, Zhang J, Landick R.

Nucleic Acids Res. 2014 Nov 10;42(20):12707-21. doi: 10.1093/nar/gku997. Epub 2014 Oct 21.

43.

Engineering and two-stage evolution of a lignocellulosic hydrolysate-tolerant Saccharomyces cerevisiae strain for anaerobic fermentation of xylose from AFEX pretreated corn stover.

Parreiras LS, Breuer RJ, Avanasi Narasimhan R, Higbee AJ, La Reau A, Tremaine M, Qin L, Willis LB, Bice BD, Bonfert BL, Pinhancos RC, Balloon AJ, Uppugundla N, Liu T, Li C, Tanjore D, Ong IM, Li H, Pohlmann EL, Serate J, Withers ST, Simmons BA, Hodge DB, Westphall MS, Coon JJ, Dale BE, Balan V, Keating DH, Zhang Y, Landick R, Gasch AP, Sato TK.

PLoS One. 2014 Sep 15;9(9):e107499. doi: 10.1371/journal.pone.0107499. eCollection 2014.

44.

Aromatic inhibitors derived from ammonia-pretreated lignocellulose hinder bacterial ethanologenesis by activating regulatory circuits controlling inhibitor efflux and detoxification.

Keating DH, Zhang Y, Ong IM, McIlwain S, Morales EH, Grass JA, Tremaine M, Bothfeld W, Higbee A, Ulbrich A, Balloon AJ, Westphall MS, Aldrich J, Lipton MS, Kim J, Moskvin OV, Bukhman YV, Coon JJ, Kiley PJ, Bates DM, Landick R.

Front Microbiol. 2014 Aug 13;5:402. doi: 10.3389/fmicb.2014.00402. eCollection 2014.

45.

RNA polymerase pausing and nascent-RNA structure formation are linked through clamp-domain movement.

Hein PP, Kolb KE, Windgassen T, Bellecourt MJ, Darst SA, Mooney RA, Landick R.

Nat Struct Mol Biol. 2014 Sep;21(9):794-802. doi: 10.1038/nsmb.2867. Epub 2014 Aug 10.

47.

Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria.

Haft RJ, Keating DH, Schwaegler T, Schwalbach MS, Vinokur J, Tremaine M, Peters JM, Kotlajich MV, Pohlmann EL, Ong IM, Grass JA, Kiley PJ, Landick R.

Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):E2576-85. doi: 10.1073/pnas.1401853111. Epub 2014 Jun 9.

48.

A pause sequence enriched at translation start sites drives transcription dynamics in vivo.

Larson MH, Mooney RA, Peters JM, Windgassen T, Nayak D, Gross CA, Block SM, Greenleaf WJ, Landick R, Weissman JS.

Science. 2014 May 30;344(6187):1042-7. doi: 10.1126/science.1251871. Epub 2014 May 1.

49.

Mycobacterial RNA polymerase requires a U-tract at intrinsic terminators and is aided by NusG at suboptimal terminators.

Czyz A, Mooney RA, Iaconi A, Landick R.

MBio. 2014 Apr 8;5(2):e00931. doi: 10.1128/mBio.00931-14.

50.

Death by a thousand cuts: the challenges and diverse landscape of lignocellulosic hydrolysate inhibitors.

Piotrowski JS, Zhang Y, Bates DM, Keating DH, Sato TK, Ong IM, Landick R.

Front Microbiol. 2014 Mar 14;5:90. doi: 10.3389/fmicb.2014.00090. eCollection 2014.

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