This paper introduces a membrane-free spot-plating protocol for Agrobacterium-mediated transformation of diverse yeasts, improving efficiency and reducing costs.

PLoS ONE · Oct 8, 2026Peer-reviewedMicrobiology

Binary vector origin predictably determines Agrobacterium-mediated transformation outcome across eukaryotic kingdoms

Matthew J. Szarzanowicz, Michael Busche, Ziyu Dai, Nathan Lapp, Gina M. Geiselman, Jiayuan Jia, Lucas M. Waldburger, Yan Liang, Guoliang Yuan, Rylan D. Duong, Kyle R. Pomraning, Nathan J. Hillson, Jacob O. Brunkard, Blake Alexander Simmons, John M. Gladden, , Patrick M. Shih

This study shows that binary vector origin of replication family, not copy number, determines Agrobacterium-mediated transformation outcomes across plants and fungi.

bioRxiv · Nov 18, 2025 · PreprintPlant Biology

Ensemble and Iterative Engineering for Maximized Bioconversion to the Blue Pigment, Indigoidine from Non-Canonical Sustainable Carbon Sources

Thomas Eng, Deepanwita Banerjee, Javier Menasalvas, Yan Chen, Jennifer W. Gin, Hemant Choudhary, Edward E. K. Baidoo, Jian-Hua Chen, Axel A. Ekman, Ramu D. Kakumanu, Yuzhong Liu Diercks, Alex Codik, Carolyn A. Larabell, John M. Gladden, Blake Alexander Simmons, , Aindrila Mukhopadhyay

The paper develops growth-coupled microbial strains for high-yield indigoidine production using iterative engineering and computational evaluation.

Cell Reports · Sep 1, 2023Peer-reviewedSystems Biology

Engineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical production

Luis E. Valencia, Matthew R. Incha, Matthias Schmidt, Allison N. Pearson, Mitchell G. Thompson, Jacob B. Roberts, Marina Mehling, Kevin Yin, Ning Sun, Asun M. Oka, Patrick M. Shih, Lars M. Blank, John M. Gladden, Jay D. Keasling

This paper engineers Pseudomonas putida KT2440 to produce medium- and long-chain free fatty acids and oleochemicals, achieving titers up to 670 mg/L.

Communications Biology · Dec 12, 2022Peer-reviewedSynthetic Biology

A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages

Uri Neri, Yuri I. Wolf, Simon Roux, Antônio Pedro Camargo, Benjamin Lee, Darius Kazlauskas, I. Min Chen, Natalia Ivanova, Lisa Zeigler Allen, David Páez-Espino, Donald A. Bryant, Devaki Bhaya, Adrienne B. Narrowe, Alexander J. Probst, Alexander Sczyrba, , Vincent J. Denef

The paper expands the global RNA virome by five-fold, identifying new clades of RNA bacteriophages and revealing novel virus-host interactions.

Cell · Sep 28, 2022Peer-reviewedGenomics

Toward sustainable jet fuels: bioconversion of cellulose into isoprenoid biojet candidates using rumen bacteria and non-conventional yeast

Laura Ellen Walls, Peter B. Otoupal, Rodrigo Ledesma‐Amaro, Sharon B. Velasquez‐Orta, John M. Gladden, Leonardo Rios‐Solis

This paper demonstrates the bioconversion of cellulose into bisabolene, a biojet fuel candidate, using rumen bacteria and non-conventional yeast in a sequential bioprocess.

bioRxiv · Jul 15, 2022 · PreprintSynthetic Biology

A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides

Luísa Czamanski Nora, Maren Wehrs, Joonhoon Kim, Jan‐Fang Cheng, Angela Tarver, Blake Alexander Simmons, Jon Karl Magnuson, Miranda Harmon‐Smith, Rafael Silva‐Rocha, John M. Gladden, Aindrila Mukhopadhyay, Jeffrey M. Skerker, James Kirby

The paper identifies and characterizes 20 constitutive promoters in Rhodosporidium toruloides for use in genetic engineering and metabolic pathway optimization.

Microbial Cell Factories · Jun 29, 2019Peer-reviewedSynthetic Biology

Multiplexed CRISPR-Cas9 based genome editing of Rhodosporidium toruloides

Peter B. Otoupal, Masakazu Ito, Adam P. Arkin, Jon Karl Magnuson, John M. Gladden, Jeffrey M. Skerker

This paper demonstrates the first use of CRISPR-Cas9 for targeted gene disruption in Rhodosporidium toruloides, achieving efficient multiplexed genome editing for bioproduct engineering.

mSphere · Mar 19, 2019Peer-reviewedSynthetic Biology

Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides

Samuel T. Coradetti, Dominic Pinel, Gina M. Geiselman, Masakazu Ito, Stephen James Mondo, Morgann C. Reilly, Ya-Fang Cheng, Štefan Bauer, Igor V. Grigoriev, John M. Gladden, Blake Alexander Simmons, Rachel B. Brem, Adam P. Arkin, Jeffrey M. Skerker

The paper develops a high-throughput genetics method for Rhodosporidium toruloides, identifies essential genes, and reveals key processes in lipid metabolism.

eLife · Mar 9, 2018Peer-reviewedSystems Biology