Author

C. J. Petzold

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 11 Biochemistry· 2 Biophysics· 2 Bioengineering· 1 Physiology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 10 Organism:bacteria (other)· 8 Assay:proteomics· 8 Research Focus:cell type annotation· 5 Research Focus:gene regulatory network inference· 4 Assay:metabolomics· 4 Research Focus:drug response / drug discovery· 3 Organism:E. coli· 3

Frequent Co-Authors

Y. Chen· 13 shared J. D. Keasling· 8 shared J. W. Gin· 5 shared A. Mukhopadhyay· 4 shared B. A. Simmons· 4 shared M. G. Thompson· 4 shared P. D. Adams· 4 shared J. F. Barajas· 3 shared

Activity by Year

2018-2024 · peak 6/yr

Co-Author Collaboration Network

10 top collaborators · 39 mutual co-author links

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13 shared papersMicrobiology

Y. Chen

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Author profile →

17 papers

Recent·Most cited

Bottlenecks in the Implementation of Genome Scale Metabolic Model Based Designs for Bioproduction from Aromatic Carbon Sources

D. Banerjee, J. Menasalvas, Y. Chen, J. W. Gin, E. E. Baidoo, C. J. Petzold, T. Eng, A. Mukhopadhyay

This study identifies fumarate hydratase activity as a bottleneck in a genome-scale metabolic model design for bioproduction from para-coumarate, requiring optimization for growth and product formation.

bioRxiv · Mar 15, 2024Microbiology

Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells

S. Raza, D. Sarkar, L. J. G. Chan, J. Mae, M. Sutter, C. J. Petzold, C. A. Kerfeld, C. Y. Ralston, S. Gupta, J. V. Vermaas

The paper compares pore structure and dynamics in bacterial microcompartment shell proteins under different geometries using molecular modeling and simulations.

bioRxiv · Mar 12, 2024Biophysics

Genetically refactored Agrobacterium-mediated transformation

M. Thompson, L. D. Kirkpatrick, G. M. Geiselman, L. M. Waldburger, A. N. Pearson, M. Szarzanowicz, K. M. Vuu, K. Markel, N. F. Hummel, D. D. Suazo, C. Tahmin, R. Cui, S. Liu, J. Cevallos, H. Pannu, , P. M. Shih

This paper refactors the Agrobacterium tumor-inducing plasmid into a minimal set of genes for plant and fungal transformation, demonstrating a bottom-up engineering approach.

bioRxiv · Oct 13, 2023 · PreprintMicrobiology

Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2

S. Shrestha, D. Awasthi, Y. Chen, J. W. Gin, C. J. Petzold, P. D. Adams, B. A. Simmons, S. Singer

This study investigates carbon catabolite repression in Pseudomonas putida M2 during simultaneous sugar and aromatic co-utilization, revealing simultaneous repression by sugars and aromatics and the role of crc and small RNAs.

bioRxiv · May 23, 2023 · PreprintMicrobiology

Revealing Pentose Catabolism in Pseudomonas putida

M.-R. Park, R. Gauttam, B. Fong, Y. Chen, H. G. Lim, A. Feist, A. Mukhopadhyay, C. J. Petzold, B. A. Simmons, S. W. Singer

The paper identifies three Pseudomonas putida isolates with diverse pentose catabolism capabilities and characterizes their genes and pathways for xylose and arabinose oxidation.

bioRxiv · Oct 5, 2022 · PreprintMicrobiology

Mixed Heavy Metals Stress Induces Global Iron Starvation as Revealed by System Level Multi-Omic Analyses

J. L. Goff, Y. Chen, M. P. Thorgersen, L. T. Hoang, F. L. Poole, E. G. Szink, G. Siuzdak, C. J. Petzold, M. W. W. Adams

The paper investigates the combined effects of eight heavy metals on Bacillus cereus, revealing global iron starvation responses not observed with individual metals.

bioRxiv · Aug 5, 2022 · PreprintMicrobiology

Allosteric priming of E. coli CheY by the flagellar motor protein FliM

P. Wheatley, A. Pandini, S. Gupta, Y. Chen, C. J. Petzold, C. Y. Ralston, D. F. Blair, S. M. Khan

This study uses molecular dynamics and experimental methods to show that phosphorylation of CheY increases its affinity for FliMN by altering conformational dynamics and sidechain burial.

Biophysical Journal · Sep 1, 2020Peer-reviewedBiophysics

Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida

M. R. Incha, M. G. Thompson, J. M. Blake-Hedges, Y. Liu, A. N. Pearson, M. Schmidt, J. Gin, C. J. Petzold, A. Deutschbauer, J. D. Keasling

This study identifies bottlenecks in T3PKS product production in Pseudomonas putida and shows that deleting a catabolic enzyme increases bisdemethoxycurcumin yield.

Metabolic Engineering Communications · Jun 1, 2020Peer-reviewedMicrobiology

Chemoinformatic-guided engineering of polyketide synthases

A. Zargar, R. Lal, L. Valencia, J. Wang, T. Backman, P. Cruz-Morales, A. Kothari, M. Werts, A. Wong, C. B. Bailey, A. Loubat, Y. Liu, Y. Chen, V. Benites, S. Chang, , J. D. Keasling

This study uses chemoinformatics to engineer polyketide synthases for producing saturated β-carbon compounds, finding a correlation between chemical similarity and product titers.

bioRxiv · May 10, 2020Biochemistry

Genome-scale metabolic rewiring to achieve predictable titers rates and yield of a non-native product at scale

D. Banerjee, T. T. Eng, A. K. Lau, B. Wang, Y. Sasaki, R. A. Herbert, Y. Chen, Y. Liu, J.-P. Prahl, V. R. Singan, D. Tanjore, C. J. Petzold, J. D. Keasling, A. Mukhopadhyay

This study engineers Pseudomonas putida to produce indigoidine with high titer, rate, and yield by coupling product formation with growth through metabolic rewiring and CRISPRi knockdowns.

bioRxiv · Feb 21, 2020Bioengineering

Structural mechanism of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase

J. M. Blake-Hedges, J. Henrique Pereira, P. Cruz-Morales, M. G. Thompson, J. F. Barajas, J. Chen, R. N. Krishna, L. J. G. Chan, D. Nimlos, C. Alonso-Martinez, E. Baidoo, Y. Chen, J. W. Gin, L. Katz, C. J. Petzold, , J. D. Keasling

This paper investigates the structural mechanism of regioselectivity in a bacterial acyl-CoA dehydrogenase, identifying key residues and structural features responsible for its unique substrate specificity.

bioRxiv · Oct 22, 2019Biochemistry

Succession of physiological stages hallmarks the transcriptomic response of fungus Aspergillus niger to lignocellulose

J. M. van Munster, P. Daly, M. J. Blythe, R. Ibbett, M. Kokolski, S. Gaddipati, E. Lindquist, V. R. Singan, K. W. Barry, A. M. Lipzen, C. Y. Ngan, C. J. Petzold, L. J. G. Chan, M. Arvas, R. Raulo, , D. B. Archer

This study identifies physiological stages in Aspergillus niger's transcriptomic response to lignocellulose substrates, showing conserved metabolic patterns and substrate-specific adaptations.

bioRxiv · Oct 17, 2019Microbiology

The response of Pseudomonas putida to a complex lignolysate

M.-R. Park, Y. Chen, M. G. Thompson, V. Benites, B. Fong, C. J. Petzold, E. E. K. Baidoo, J. Gladden, P. D. Adams, J. D. Keasling, B. A. Simmons, S. Singer

This paper shows that Pseudomonas putida can grow on lignolysate from sorghum, using aromatic monomers and other unknown factors like amino acids and ionic liquid.

bioRxiv · Sep 10, 2019 · PreprintMicrobiology

The metabolic response of Pseudomonas taiwanensis to NADH dehydrogenase deficiency

S. C. Nies, R. Dinger, Y. Chen, G. G. Wordofa, M. Kristensen, K. Schneider, J. Büchs, C. J. Petzold, J. D. Keasling, L. Blank, B. E. Ebert

This paper investigates the metabolic response of Pseudomonas taiwanensis to NADH dehydrogenase deficiencies, finding high metabolic flexibility that enables phenotypic stability but complicates metabolic engineering.

bioRxiv · May 2, 2019Physiology

Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism

M. G. Thompson, J. M. Blake-Hedges, P. Cruz-Morales, J. F. Barajas, S. C. Curran, C. B. Eiben, N. C. Harris, V. T. Benites, J. W. Gin, W. A. Sharpless, F. F. Twigg, W. Skyrud, R. N. Krishna, J. H. Pereira, E. Baidoo, , J. D. Keasling

This paper uses RB-TnSeq to identify novel enzymes in Pseudomonas putida lysine metabolism, revealing new biochemical pathways and functions for DUF1338 proteins.

bioRxiv · Mar 18, 2019Microbiology

Large-scale chemical-genetics of the human gut bacterium Bacteroides thetaiotaomicron

H. Liu, M. N. Price, H. K. Carlson, Y. Chen, J. Ray, A. L. Shiver, C. J. Petzold, K. C. Huang, A. P. Arkin, A. Deutschbauer

This study systematically measures mutant phenotypes for genes in Bacteroides thetaiotaomicron to uncover gene functions and improve understanding of gut microbiota physiology.

bioRxiv · Mar 9, 2019Microbiology

Sulfated RaxX, which represents an unclassified group of ribosomally synthesized post-translationally modified peptides, binds a host immune receptor

D. D. Luu, A. Joe, Y. Chen, K. Parys, O. Bahar, R. Pruitt, L. J. G. Chen, C. J. Petzold, K. Long, C. Adamchak, V. Stewart, Y. Belkhadir, P. C. Ronald

The paper identifies RaxX as a sulfated RiPP that binds the rice immune receptor XA21, revealing its role in bacterial immune activation.

bioRxiv · Oct 13, 2018Microbiology