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Items: 1 to 50 of 113

1.

Systems and synthetic biology tools for advanced bioproduction hosts.

Chen Y, Banerjee D, Mukhopadhyay A, Petzold CJ.

Curr Opin Biotechnol. 2020 Jan 8;64:101-109. doi: 10.1016/j.copbio.2019.12.007. [Epub ahead of print] Review.

PMID:
31927061
2.

Production of tetra-methylpyrazine using engineered Corynebacterium glutamicum.

Eng T, Sasaki Y, Herbert RA, Lau A, Trinh J, Chen Y, Mirsiaghi M, Petzold CJ, Mukhopadhyay A.

Metab Eng Commun. 2019 Dec 2;10:e00115. doi: 10.1016/j.mec.2019.e00115. eCollection 2020 Jun.

3.

Structural Mechanism of Regioselectivity in an Unusual Bacterial Acyl-CoA Dehydrogenase.

Blake-Hedges JM, Pereira JH, Cruz-Morales P, Thompson MG, Barajas JF, Chen J, Krishna RN, Chan LJG, Nimlos D, Alonso-Martinez C, Baidoo EEK, Chen Y, Gin JW, Katz L, Petzold CJ, Adams PD, Keasling JD.

J Am Chem Soc. 2020 Jan 15;142(2):835-846. doi: 10.1021/jacs.9b09187. Epub 2020 Jan 2.

PMID:
31793780
4.

Development of Container Free Sample Exposure for Synchrotron X-ray Footprinting.

Gupta S, Chen Y, Petzold CJ, DePonte DP, Ralston CY.

Anal Chem. 2020 Jan 7;92(1):1565-1573. doi: 10.1021/acs.analchem.9b04849. Epub 2019 Dec 16.

PMID:
31790200
5.

Comparative ultrafast spectroscopy and structural analysis of OCP1 and OCP2 from Tolypothrix.

Kuznetsova V, Dominguez-Martin MA, Bao H, Gupta S, Sutter M, Kloz M, Rebarz M, Přeček M, Chen Y, Petzold CJ, Ralston CY, Kerfeld CA, Polívka T.

Biochim Biophys Acta Bioenerg. 2020 Feb 1;1861(2):148120. doi: 10.1016/j.bbabio.2019.148120. Epub 2019 Nov 14.

6.

Omics-driven identification and elimination of valerolactam catabolism in Pseudomonas putida KT2440 for increased product titer.

Thompson MG, Valencia LE, Blake-Hedges JM, Cruz-Morales P, Velasquez AE, Pearson AN, Sermeno LN, Sharpless WA, Benites VT, Chen Y, Baidoo EEK, Petzold CJ, Deutschbauer AM, Keasling JD.

Metab Eng Commun. 2019 Aug 10;9:e00098. doi: 10.1016/j.mec.2019.e00098. eCollection 2019 Dec.

7.

Mevalonate Pathway Promiscuity Enables Noncanonical Terpene Production.

Eiben CB, de Rond T, Bloszies C, Gin J, Chiniquy J, Baidoo EEK, Petzold CJ, Hillson NJ, Fiehn O, Keasling JD.

ACS Synth Biol. 2019 Oct 18;8(10):2238-2247. doi: 10.1021/acssynbio.9b00230. Epub 2019 Oct 2.

8.

Automated "Cells-To-Peptides" Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes.

Chen Y, Guenther JM, Gin JW, Chan LJG, Costello Z, Ogorzalek TL, Tran HM, Blake-Hedges JM, Keasling JD, Adams PD, García Martín H, Hillson NJ, Petzold CJ.

J Proteome Res. 2019 Oct 4;18(10):3752-3761. doi: 10.1021/acs.jproteome.9b00455. Epub 2019 Aug 30.

9.

Water molecules mediate zinc mobility in the bacterial zinc diffusion channel ZIPB.

Gupta S, Merriman C, Petzold CJ, Ralston CY, Fu D.

J Biol Chem. 2019 Sep 6;294(36):13327-13335. doi: 10.1074/jbc.RA119.009239. Epub 2019 Jul 18.

10.

Separating Golgi Proteins from Cis to Trans Reveals Underlying Properties of Cisternal Localization.

Parsons HT, Stevens TJ, McFarlane HE, Vidal-Melgosa S, Griss J, Lawrence N, Butler R, Sousa MML, Salemi M, Willats WGT, Petzold CJ, Heazlewood JL, Lilley KS.

Plant Cell. 2019 Sep;31(9):2010-2034. doi: 10.1105/tpc.19.00081. Epub 2019 Jul 2.

11.

Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning.

Opgenorth P, Costello Z, Okada T, Goyal G, Chen Y, Gin J, Benites V, de Raad M, Northen TR, Deng K, Deutsch S, Baidoo EEK, Petzold CJ, Hillson NJ, Garcia Martin H, Beller HR.

ACS Synth Biol. 2019 Jun 21;8(6):1337-1351. doi: 10.1021/acssynbio.9b00020. Epub 2019 May 24.

PMID:
31072100
12.

Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism.

Thompson MG, Blake-Hedges JM, Cruz-Morales P, Barajas JF, Curran SC, Eiben CB, Harris NC, Benites VT, Gin JW, Sharpless WA, Twigg FF, Skyrud W, Krishna RN, Pereira JH, Baidoo EEK, Petzold CJ, Adams PD, Arkin AP, Deutschbauer AM, Keasling JD.

mBio. 2019 May 7;10(3). pii: e02577-18. doi: 10.1128/mBio.02577-18.

13.

Methyl ketone production by Pseudomonas putida is enhanced by plant-derived amino acids.

Dong J, Chen Y, Benites VT, Baidoo EEK, Petzold CJ, Beller HR, Eudes A, Scheller HV, Adams PD, Mukhopadhyay A, Simmons BA, Singer SW.

Biotechnol Bioeng. 2019 Aug;116(8):1909-1922. doi: 10.1002/bit.26995. Epub 2019 Apr 29.

PMID:
30982958
14.

X-ray radiolytic labeling reveals the molecular basis of orange carotenoid protein photoprotection and its interactions with fluorescence recovery protein.

Gupta S, Sutter M, Remesh SG, Dominguez-Martin MA, Bao H, Feng XA, Chan LG, Petzold CJ, Kerfeld CA, Ralston CY.

J Biol Chem. 2019 May 31;294(22):8848-8860. doi: 10.1074/jbc.RA119.007592. Epub 2019 Apr 12.

15.

Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptor.

Luu DD, Joe A, Chen Y, Parys K, Bahar O, Pruitt R, Chan LJG, Petzold CJ, Long K, Adamchak C, Stewart V, Belkhadir Y, Ronald PC.

Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8525-8534. doi: 10.1073/pnas.1818275116. Epub 2019 Apr 4.

16.

Engineering Corynebacterium glutamicum to produce the biogasoline isopentenol from plant biomass hydrolysates.

Sasaki Y, Eng T, Herbert RA, Trinh J, Chen Y, Rodriguez A, Gladden J, Simmons BA, Petzold CJ, Mukhopadhyay A.

Biotechnol Biofuels. 2019 Feb 27;12:41. doi: 10.1186/s13068-019-1381-3. eCollection 2019.

17.

Complete biosynthesis of cannabinoids and their unnatural analogues in yeast.

Luo X, Reiter MA, d'Espaux L, Wong J, Denby CM, Lechner A, Zhang Y, Grzybowski AT, Harth S, Lin W, Lee H, Yu C, Shin J, Deng K, Benites VT, Wang G, Baidoo EEK, Chen Y, Dev I, Petzold CJ, Keasling JD.

Nature. 2019 Mar;567(7746):123-126. doi: 10.1038/s41586-019-0978-9. Epub 2019 Feb 27.

PMID:
30814733
18.

A rapid methods development workflow for high-throughput quantitative proteomic applications.

Chen Y, Vu J, Thompson MG, Sharpless WA, Chan LJG, Gin JW, Keasling JD, Adams PD, Petzold CJ.

PLoS One. 2019 Feb 14;14(2):e0211582. doi: 10.1371/journal.pone.0211582. eCollection 2019.

19.

Recent Advances in X-Ray Hydroxyl Radical Footprinting at the Advanced Light Source Synchrotron.

Morton SA, Gupta S, Petzold CJ, Ralston CY.

Protein Pept Lett. 2019;26(1):70-75. doi: 10.2174/0929866526666181128125725.

20.

Heterohexamers Formed by CcmK3 and CcmK4 Increase the Complexity of Beta Carboxysome Shells.

Sommer M, Sutter M, Gupta S, Kirst H, Turmo A, Lechno-Yossef S, Burton RL, Saechao C, Sloan NB, Cheng X, Chan LG, Petzold CJ, Fuentes-Cabrera M, Ralston CY, Kerfeld CA.

Plant Physiol. 2019 Jan;179(1):156-167. doi: 10.1104/pp.18.01190. Epub 2018 Nov 2.

21.

Renewable production of high density jet fuel precursor sesquiterpenes from Escherichia coli.

Liu CL, Tian T, Alonso-Gutierrez J, Garabedian B, Wang S, Baidoo EEK, Benites V, Chen Y, Petzold CJ, Adams PD, Keasling JD, Tan T, Lee TS.

Biotechnol Biofuels. 2018 Oct 20;11:285. doi: 10.1186/s13068-018-1272-z. eCollection 2018.

22.

Viscous control of cellular respiration by membrane lipid composition.

Budin I, de Rond T, Chen Y, Chan LJG, Petzold CJ, Keasling JD.

Science. 2018 Dec 7;362(6419):1186-1189. doi: 10.1126/science.aat7925. Epub 2018 Oct 25.

PMID:
30361388
23.

Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC.

Eng T, Demling P, Herbert RA, Chen Y, Benites V, Martin J, Lipzen A, Baidoo EEK, Blank LM, Petzold CJ, Mukhopadhyay A.

Microb Cell Fact. 2018 Oct 8;17(1):159. doi: 10.1186/s12934-018-1006-8.

24.

Probing the Flexibility of an Iterative Modular Polyketide Synthase with Non-Native Substrates in Vitro.

Curran SC, Hagen A, Poust S, Chan LJG, Garabedian BM, de Rond T, Baluyot MJ, Vu JT, Lau AK, Yuzawa S, Petzold CJ, Katz L, Keasling JD.

ACS Chem Biol. 2018 Aug 17;13(8):2261-2268. doi: 10.1021/acschembio.8b00422. Epub 2018 Jun 26.

PMID:
29912551
25.

Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B2 Biosynthesis.

Barajas JF, Zargar A, Pang B, Benites VT, Gin J, Baidoo EEK, Petzold CJ, Hillson NJ, Keasling JD.

Chembiochem. 2018 Jul 4;19(13):1391-1395. doi: 10.1002/cbic.201800169. Epub 2018 May 14.

26.

Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer.

Denby CM, Li RA, Vu VT, Costello Z, Lin W, Chan LJG, Williams J, Donaldson B, Bamforth CW, Petzold CJ, Scheller HV, Martin HG, Keasling JD.

Nat Commun. 2018 Mar 20;9(1):965. doi: 10.1038/s41467-018-03293-x.

27.

Discovery of enzymes for toluene synthesis from anoxic microbial communities.

Beller HR, Rodrigues AV, Zargar K, Wu YW, Saini AK, Saville RM, Pereira JH, Adams PD, Tringe SG, Petzold CJ, Keasling JD.

Nat Chem Biol. 2018 May;14(5):451-457. doi: 10.1038/s41589-018-0017-4. Epub 2018 Mar 19.

28.

Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli.

George KW, Thompson MG, Kim J, Baidoo EEK, Wang G, Benites VT, Petzold CJ, Chan LJG, Yilmaz S, Turhanen P, Adams PD, Keasling JD, Lee TS.

Metab Eng. 2018 May;47:60-72. doi: 10.1016/j.ymben.2018.03.004. Epub 2018 Mar 9.

PMID:
29530749
29.

Improving methyl ketone production in Escherichia coli by heterologous expression of NADH-dependent FabG.

Goh EB, Chen Y, Petzold CJ, Keasling JD, Beller HR.

Biotechnol Bioeng. 2018 May;115(5):1161-1172. doi: 10.1002/bit.26558. Epub 2018 Mar 1.

PMID:
29411856
30.

Toward industrial production of isoprenoids in Escherichia coli: Lessons learned from CRISPR-Cas9 based optimization of a chromosomally integrated mevalonate pathway.

Alonso-Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS.

Biotechnol Bioeng. 2018 Apr;115(4):1000-1013. doi: 10.1002/bit.26530. Epub 2018 Feb 7.

31.

A bacterial pioneer produces cellulase complexes that persist through community succession.

Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW.

Nat Microbiol. 2018 Jan;3(1):99-107. doi: 10.1038/s41564-017-0052-z. Epub 2017 Nov 6.

32.

Heterologous Gene Expression of N-Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N-terminus of Modular Polyketide Synthase.

Yuzawa S, Bailey CB, Fujii T, Jocic R, Barajas JF, Benites VT, Baidoo EEK, Chen Y, Petzold CJ, Katz L, Keasling JD.

ACS Chem Biol. 2017 Nov 17;12(11):2725-2729. doi: 10.1021/acschembio.7b00714. Epub 2017 Oct 17.

33.

Multiple marker abundance profiling: combining selected reaction monitoring and data-dependent acquisition for rapid estimation of organelle abundance in subcellular samples.

Hooper CM, Stevens TJ, Saukkonen A, Castleden IR, Singh P, Mann GW, Fabre B, Ito J, Deery MJ, Lilley KS, Petzold CJ, Millar AH, Heazlewood JL, Parsons HT.

Plant J. 2017 Dec;92(6):1202-1217. doi: 10.1111/tpj.13743. Epub 2017 Nov 20.

34.

Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme.

de Rond T, Stow P, Eigl I, Johnson RE, Chan LJG, Goyal G, Baidoo EEK, Hillson NJ, Petzold CJ, Sarpong R, Keasling JD.

Nat Chem Biol. 2017 Nov;13(11):1155-1157. doi: 10.1038/nchembio.2471. Epub 2017 Sep 11.

35.

The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization.

Morrell WC, Birkel GW, Forrer M, Lopez T, Backman TWH, Dussault M, Petzold CJ, Baidoo EEK, Costello Z, Ando D, Alonso-Gutierrez J, George KW, Mukhopadhyay A, Vaino I, Keasling JD, Adams PD, Hillson NJ, Garcia Martin H.

ACS Synth Biol. 2017 Dec 15;6(12):2248-2259. doi: 10.1021/acssynbio.7b00204. Epub 2017 Sep 8.

36.

The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface.

Fukushima T, Gupta S, Rad B, Cornejo JA, Petzold CJ, Chan LJG, Mizrahi RA, Ralston CY, Ajo-Franklin CM.

J Am Chem Soc. 2017 Sep 13;139(36):12647-12654. doi: 10.1021/jacs.7b06560. Epub 2017 Aug 31.

37.

Engineering glucose metabolism of Escherichia coli under nitrogen starvation.

Chubukov V, Desmarais JJ, Wang G, Chan LJG, Baidoo EE, Petzold CJ, Keasling JD, Mukhopadhyay A.

NPJ Syst Biol Appl. 2017 Jan 5;3:16035. doi: 10.1038/npjsba.2016.35. eCollection 2017.

38.

Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks.

d'Espaux L, Ghosh A, Runguphan W, Wehrs M, Xu F, Konzock O, Dev I, Nhan M, Gin J, Reider Apel A, Petzold CJ, Singh S, Simmons BA, Mukhopadhyay A, García Martín H, Keasling JD.

Metab Eng. 2017 Jul;42:115-125. doi: 10.1016/j.ymben.2017.06.004. Epub 2017 Jun 10.

PMID:
28606738
39.

Programming mRNA decay to modulate synthetic circuit resource allocation.

Venturelli OS, Tei M, Bauer S, Chan LJG, Petzold CJ, Arkin AP.

Nat Commun. 2017 Apr 26;8:15128. doi: 10.1038/ncomms15128.

40.

Production of jet fuel precursor monoterpenoids from engineered Escherichia coli.

Mendez-Perez D, Alonso-Gutierrez J, Hu Q, Molinas M, Baidoo EEK, Wang G, Chan LJG, Adams PD, Petzold CJ, Keasling JD, Lee TS.

Biotechnol Bioeng. 2017 Aug;114(8):1703-1712. doi: 10.1002/bit.26296. Epub 2017 May 18.

41.

Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments.

Daly P, van Munster JM, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Pullan ST, Delmas S, Waldron PR, Grigoriev IV, Tucker GA, Simmons BA, Archer DB.

Biotechnol Biofuels. 2017 Feb 7;10:35. doi: 10.1186/s13068-017-0700-9. eCollection 2017.

42.

Synchrotron X-ray footprinting as a method to visualize water in proteins.

Gupta S, Feng J, Chan LJ, Petzold CJ, Ralston CY.

J Synchrotron Radiat. 2016 Sep 1;23(Pt 5):1056-69. doi: 10.1107/S1600577516009024. Epub 2016 Jul 27.

43.

In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community.

Zargar K, Saville R, Phelan RM, Tringe SG, Petzold CJ, Keasling JD, Beller HR.

Sci Rep. 2016 Aug 10;6:31362. doi: 10.1038/srep31362.

44.

Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.

Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L, O'Brien EJ, Batth TS, Martin HG, Feist A, Adams PD, Keasling JD, Palsson BO, Lee TS.

Cell Syst. 2016 May 25;2(5):335-46. doi: 10.1016/j.cels.2016.04.004. Epub 2016 May 19.

45.

Synthetic and systems biology for microbial production of commodity chemicals.

Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Martín HG.

NPJ Syst Biol Appl. 2016 Apr 7;2:16009. doi: 10.1038/npjsba.2016.9. eCollection 2016. Review.

46.

Investigation of Proposed Ladderane Biosynthetic Genes from Anammox Bacteria by Heterologous Expression in E. coli.

Javidpour P, Deutsch S, Mutalik VK, Hillson NJ, Petzold CJ, Keasling JD, Beller HR.

PLoS One. 2016 Mar 14;11(3):e0151087. doi: 10.1371/journal.pone.0151087. eCollection 2016.

47.

Free-Flow Electrophoresis of Plasma Membrane Vesicles Enriched by Two-Phase Partitioning Enhances the Quality of the Proteome from Arabidopsis Seedlings.

de Michele R, McFarlane HE, Parsons HT, Meents MJ, Lao J, González Fernández-Niño SM, Petzold CJ, Frommer WB, Samuels AL, Heazlewood JL.

J Proteome Res. 2016 Mar 4;15(3):900-13. doi: 10.1021/acs.jproteome.5b00876. Epub 2016 Feb 4.

PMID:
26781341
48.

A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection.

Schwessinger B, Li X, Ellinghaus TL, Chan LJ, Wei T, Joe A, Thomas N, Pruitt R, Adams PD, Chern MS, Petzold CJ, Liu CC, Ronald PC.

Integr Biol (Camb). 2016 Apr 18;8(4):542-5. doi: 10.1039/c5ib00232j. Epub 2015 Nov 27.

49.

The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium.

Pruitt RN, Schwessinger B, Joe A, Thomas N, Liu F, Albert M, Robinson MR, Chan LJ, Luu DD, Chen H, Bahar O, Daudi A, De Vleesschauwer D, Caddell D, Zhang W, Zhao X, Li X, Heazlewood JL, Ruan D, Majumder D, Chern M, Kalbacher H, Midha S, Patil PB, Sonti RV, Petzold CJ, Liu CC, Brodbelt JS, Felix G, Ronald PC.

Sci Adv. 2015 Jul 24;1(6):e1500245. doi: 10.1126/sciadv.1500245. eCollection 2015 Jul.

50.

Engineering a Polyketide Synthase for In Vitro Production of Adipic Acid.

Hagen A, Poust S, Rond Td, Fortman JL, Katz L, Petzold CJ, Keasling JD.

ACS Synth Biol. 2016 Jan 15;5(1):21-7. doi: 10.1021/acssynbio.5b00153. Epub 2015 Nov 10.

PMID:
26501439

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