Article
Agricultural Engineering
Saddam Hussain Mohammad, Bhima Bhukya
Summary: This study successfully utilized Pseudomonas putida KT2440 to valorize lignin and its derivatives, and synthesized bio-polymers without any genetic manipulation.
BIORESOURCE TECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Si Liu, Tanja Narancic, Jia-Lynn Tham, Kevin E. E. O'Connor
Summary: Through studying Pseudomonas putida KT2440, it was found that PhaJ4 is the main supplier of monomers for PHA synthesis, while PhaJ1 has preference for C6 substrate. Even when all PhaJ homologues were deleted, the mutant still accumulated PHA. Further proteome analysis revealed PedE and PedH as potential monomer suppliers, but even with their deletion, PHA levels remained unchanged. Therefore, PHA metabolism exhibits redundancy.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Zhangyang Xu, Chunmei Pan, Xiaolu Li, Naijia Hao, Tong Zhang, Matthew J. Gaffrey, Yunqiao Pu, John R. Cort, Arthur J. Ragauskas, Wei-Jun Qian, Bin Yang
Summary: Co-feeding lignin derivatives with glycerol was shown to increase cell dry weight and PHA content in P. putida KT2440. The addition of lignin derivatives altered the distribution of PHA monomers and benzoate acted as an independent factor in PHA synthesis. Proteomics and metabolomics analysis revealed that benzoate stimulated oxidative-stress responses and altered intracellular NADH/NADPH ratios, increasing energy generation and storage processes for enhanced PHA biosynthesis.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
Article
Chemistry, Multidisciplinary
Henrik Almqvist, Henrique Veras, Kena Li, Javier Garcia Hidalgo, Christian Hulteberg, Marie Gorwa-Grauslund, Nadia Skorupa Parachin, Magnus Carlquist
Summary: This study developed a process for depolymerization of industrial lignin and conversion of guaiacol to muconic acid, providing an effective pathway for bioconversion.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2021)
Article
Agricultural Engineering
Jin Li, Cheng Yue, Wenping Wei, Yanzhe Shang, Ping Zhang, Bang-Ce Ye
Summary: This study successfully developed an auto-regulatory system to address the challenging issues in lignin valorization, demonstrating its effectiveness and economic advantages.
BIORESOURCE TECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Ayumu Wada, Erica T. Prates, Ryo Hirano, Allison Z. Werner, Naofumi Kamimura, Daniel A. Jacobson, Gregg T. Beckham, Eiji Masai
Summary: Pseudomonas putida KT2440 is a well-studied bacterium capable of utilizing lignin-related monomers for growth. This study reveals that PcaK and HcnK play a major role in the uptake of PCA/4HBA and FA/4CA, respectively, while VanK acts as a transporter for VA/PCA.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Kevin J. McNaught, Eugene Kuatsjah, Michael Zahn, Erica T. Prates, Huiling Shao, Gayle J. Bentley, Andrew R. Pickford, Josephine N. Gruber, Kelley V. Hestmark, Daniel A. Jacobson, Brenton C. Poirier, Chen Ling, Myrsini San Marchi, William E. Michener, Carrie D. Nicora, Jacob N. Sanders, Caralyn J. Szostkiewicz, Dusan Velickovic, Mowei Zhou, Nathalie Munoz, Young-Mo Kim, Jon K. Magnuson, Kristin E. Burnum-Johnson, K. N. Houk, John E. McGeehan, Christopher W. Johnson, Gregg T. Beckham
Summary: Deciphering the mechanisms of bacterial fatty acid biosynthesis is crucial for both engineering bacterial hosts and developing antibiotics. This study reveals that Pseudomonas putida KT2440 has three distinct pathways for initiating fatty acid biosynthesis, with the third pathway being a novel alternative. The findings provide new opportunities for various biotechnological and biomedical applications.
METABOLIC ENGINEERING
(2023)
Article
Environmental Sciences
Yuxin Zhao, You Che, Fang Zhang, Jiacheng Wang, Weixia Gao, Tong Zhang, Chao Yang
Summary: In this study, an efficient pathway construction strategy for integrating synthetic biodegradation pathways into the chromosome of Pseudomonas putida KT2440 was developed. The strategy resulted in improved chromosomal integration efficiencies and highlighted the potential for in situ bioremediation. Additionally, the strategy can be expanded to a broad range of bacterial species for widespread applications in bioremediation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biotechnology & Applied Microbiology
Austine O. Ehibhatiomhan, Rahman Rahman Pour, Sebastien Farnaud, Timothy D. H. Bugg, Sharon Mendel-Williams
Summary: Expression of lignin-oxidising Pseudomonas fluorescens Dyp1B in the periplasm of Pseudomonas putida KT2440 enhances oxidation activity for DCP and polymeric lignin substrates. Mutagenesis studies reveal that specific amino acid mutations can increase oxidation activity for manganese ions and polymeric lignin. Expression of mutant genes as tat fusion proteins also enhances lignin oxidation by P. putida KT2440.
ENZYME AND MICROBIAL TECHNOLOGY
(2023)
Article
Agricultural Engineering
Jin Li, Bang-Ce Ye
Summary: In this study, a method for biosynthesis of protocatechuic acid (PCA) in Pseudomonas putida KT2440 was developed with high yield. By using constitutive promoters and metabolic engineering strategies, the engineered strain achieved the highest reported titer of PCA from glucose. Further bioprocess engineering efforts led to significant improvements in PCA production, demonstrating the potential for metabolically engineered microbial cell factories.
BIORESOURCE TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Linh Thanh Nguyen, Dung Hoang Anh Mai, Arslan Sarwar, Eun Yeol Lee
Summary: This study constructed a production pathway for short-chain-length polyhydroxyalkanoates (PHAs) in P. putida KT2440 and enhanced the product yield by reconstructing the ethanol catabolic pathway. Transcriptome analysis was conducted to gain insights into central metabolic pathways and gene expression patterns in response to substrate changes. Furthermore, the potential of P. putida KT2440 for producing copolymers from different carbon sources was demonstrated.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Yiting Zhang, Honglu Liu, Yujie Liu, Kaiyue Huo, Shufang Wang, Ruihua Liu, Chao Yang
Summary: This study successfully increased the PHA yield by screening endogenous strong promoters from P. putida KT2440, demonstrating the potential of this strategy for enhanced production of secondary metabolites and heterologous proteins in P. putida KT2440.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biotechnology & Applied Microbiology
Gerald N. Presley, Allison Z. Werner, Rui Katahira, David C. Garcia, Stefan J. Haugen, Kelsey J. Ramirez, Richard J. Giannone, Gregg T. Beckham, Joshua K. Michener
Summary: This study identified a pathway for cleavage of a specific lignin structure in Novosphingobium aromaticivorans DSM12444, and demonstrated the engineering of Pseudomonas putida KT2440 for microbial lignin valorization. This work expands the biological funnel of P. putida and has the potential to discover new enzymatic reactions in N. aromaticivorans.
METABOLIC ENGINEERING
(2021)
Article
Agricultural Engineering
Arslan Sarwar, Linh Thanh Nguyen, Eun Yeol Lee
Summary: This study demonstrates the efficient upgrading of ethanol to fatty acid ethyl esters (FAEEs) using Pseudomonas putida KT2440, achieving high yields through gene expression and culture optimization. It provides a basis for integrating bioethanol production with the efficient conversion of ethanol to biodiesel.
BIORESOURCE TECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Hyun Gyu Lim, Kevin Rychel, Anand Sastry, Gayle J. Bentley, Joshua Mueller, Heidi S. Schindel, Peter E. Larsen, Philip D. Laible, Adam M. Guss, Wei Niu, Christopher W. Johnson, Gregg T. Beckham, Adam M. Feist, Bernhard O. Palsson
Summary: This study applies a machine-learning approach to uncover the genome-scale transcriptional regulatory network in Pseudomonas putida KT2440, providing a basis for understanding its physiological processes and engineering it for practical use.
METABOLIC ENGINEERING
(2022)
Article
Plant Sciences
Niaz Bahar Chowdhury, Wheaton L. Schroeder, Debolina Sarkar, Nardjis Amiour, Isabelle Quillere, Bertrand Hirel, Costas D. Maranas, Rajib Saha
Summary: The genome-scale metabolic model for maize roots accurately predicts metabolic reprogramming under nitrogen stress conditions and identifies key metabolites regulating root biomass growth. Additionally, it reveals specific phosphatidylcholine and phosphatidylglycerol metabolites playing a crucial role in increased biomass production under nitrogen-deficient conditions. This integrated model shows promise as a tool for analyzing stress conditions in maize roots and engineering stress-tolerant maize genotypes.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Multidisciplinary Sciences
Suresh V. Kuchipudi, Meera Surendran-Nair, Rachel M. Ruden, Michele Yon, Ruth H. Nissly, Kurt J. Vandegrift, Rahul K. Nelli, Lingling Li, Bhushan M. Jayarao, Costas D. Maranas, Nicole Levine, Katriina Willgert, Andrew J. K. Conlan, Randall J. Olsen, James J. Davis, James M. Musser, Peter J. Hudson, Vivek Kapur
Summary: White-tailed deer, particularly in Iowa, have been found to be susceptible to SARS-CoV-2 infection and show evidence of human-to-deer transmission. This discovery highlights the need for a One Health approach to better understand the ecology, molecular evolution, and dissemination of the virus.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biotechnology & Applied Microbiology
Patrick F. Suthers, Costas D. Maranas
Summary: Computational design of growth-coupled production strains for Issatchenkia orientalis yeast was studied in this research, aiming to produce a variety of organic acids. The study identified strategies for 37 substrate-product pairs, with 15 pairs achieving production at any growth rate. This approach can potentially align industrial goals with biological fitness and improve strain stability.
BIOTECHNOLOGY PROGRESS
(2022)
Article
Multidisciplinary Sciences
Chunliu Zhuo, Xin Wang, Maite Docampo-Palacios, Brian C. Sanders, Nancy L. Engle, Timothy J. Tschaplinski, John Hendry, Costas D. Maranas, Fang Chen, Richard A. Dixon
Summary: The factors controlling the composition of lignin are still unknown. C-lignin, a homopolymer of caffeyl alcohol, has unique properties as a biomaterial and a precursor of industrial chemicals. In the seed coat of Cleome hassleriana, lignin switches from guaiacyl (G)- to C-lignin at around 12 to 14 days after pollination, which is associated with changes in the monolignol pathway.
Article
Virology
Abhinay Gontu, Erika A. Marlin, Santhamani Ramasamy, Sabarinath Neerukonda, Gayatri Anil, Jasmine Morgan, Meysoon Quraishi, Chen Chen, Veda Sheersh Boorla, Ruth H. Nissly, Padmaja Jakka, Shubhada K. Chothe, Abirami Ravichandran, Nishitha Kodali, Saranya Amirthalingam, Lindsey LaBella, Kathleen Kelly, Pazhanivel Natesan, Allen M. Minns, Randall M. Rossi, Jacob R. Werner, Ernest Hovingh, Scott E. Lindner, Deepanker Tewari, Vivek Kapur, Kurt J. Vandegrift, Costas D. Maranas, Meera Surendran Nair, Suresh Kuchipudi
Summary: Multiple animal species are susceptible to SARS-CoV-2 infection, and the transmission and adaptation in livestock may have significant impacts on food security and public health. The developed iELISA method can effectively detect antibodies in cattle, swine, and chickens, facilitating the monitoring and screening of cross-species transmission.
Article
Biochemistry & Molecular Biology
Veda Sheersh Boorla, Ratul Chowdhury, Ranjani Ramasubramanian, Brandon Ameglio, Rahel Frick, Jeffrey J. Gray, Costas D. Maranas
Summary: This study focuses on the computational design of neutralizing antibodies for emerging SARS-CoV-2 variants. By recombining VDJ genes and optimizing amino acid substitutions, high-affinity antibody variable regions were designed. Computational evaluation identified a promising candidate for experimental testing.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Editorial Material
Chemistry, Physical
Veda Sheersh Boorla, Vikas Upadhyay, Costas D. Maranas
Summary: Constraining metabolic models by enzyme capacities greatly improves predictions of genotype-phenotype relationships. A new method based on deep learning has been developed to estimate enzyme turnovers and used to reconstruct enzyme-constrained genome-scale metabolic models for over 300 yeast species.
Article
Virology
Kurt J. Vandegrift, Michele Yon, Meera Surendran Nair, Abhinay Gontu, Santhamani Ramasamy, Saranya Amirthalingam, Sabarinath Neerukonda, Ruth H. Nissly, Shubhada K. Chothe, Padmaja Jakka, Lindsey LaBella, Nicole Levine, Sophie Rodriguez, Chen Chen, Veda Sheersh Boorla, Tod Stuber, Jason R. Boulanger, Nathan Kotschwar, Sarah Grimke Aucoin, Richard Simon, Katrina L. Toal, Randall J. Olsen, James J. Davis, Dashzeveg Bold, Natasha N. Gaudreault, Krishani Dinali Perera, Yunjeong Kim, Kyeong-Ok Chang, Costas D. Maranas, Juergen A. Richt, James M. Musser, Peter J. Hudson, Vivek Kapur, Suresh V. Kuchipudi
Summary: There is growing evidence of SARS-CoV-2 spillover from humans to various animal species, including deer. This study investigated the active and asymptomatic infection of the Omicron variant in free-ranging deer in New York City. The findings revealed that a small number of deer had been exposed to SARS-CoV-2, with two deer showing evidence of reinfection or early seroconversion. This suggests that variants of concern are still circulating and may reestablish transmission cycles in US deer populations, highlighting the need for a coordinated One Health response.
Article
Biotechnology & Applied Microbiology
Mengqi Hu, Hoang Dinh, Yihui Shen, Patrick F. Suthers, Catherine M. Call, Xuanjia Ye, Jimmy Pratas, Zia Fatma, Huimin Zhao, Joshua D. Rabinowitz, Costas D. Maranas
Summary: The parameterization of kinetic models requires measurement of fluxes and/or metabolite levels for a base strain and genetic perturbations. It remains unclear whether kinetic models constructed for different strains of the same species have similar or significantly different kinetic parameters. In this study, two separate large-scale kinetic models were parameterized using K-FIT for different strains of Saccharomyces cerevisiae, and the results showed strain-specific differences in key metabolic pathways.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Hoang Dinh, Costas D. Maranas
Summary: In this study, a compact and tractable genome-scale resource balance analysis (RBA) model called scRBA was reconstructed to analyze metabolic fluxes and proteome allocation efficiently. The model helps to identify bottlenecks in biosynthetic pathways and estimates parameter values that vary with environmental conditions. It reveals the enhancing effect of substrate channeling and post-translational activation on in vivo enzyme efficiency, and explains the Crabtree effect by specific limitations in mitochondrial proteome capacity.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Wheaton L. Schroeder, Teun Kuil, Antonius J. A. van Maris, Lee R. Lynd, Costas D. Maranas
Summary: Lignocellulosic biomass is a potential carbon source for chemical manufacturing, and the thermophilic anaerobe Clostridium thermocellum shows promise in bioprocessing this biomass. A new genome-scale model, iCTH669, was constructed and analyzed to understand pyrophosphate metabolism in C. thermocellum. The model showed no direct energetic advantage for substituting ATP with pyrophosphate in C. thermocellum, but identified possible sources of pyrophosphate production.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Zong-Yen Wu, Wan Sun, Yihui Shen, Jimmy Pratas, Patrick F. Suthers, Ping-Hung Hsieh, Sudharsan Dwaraknath, Joshua D. Rabinowitz, Costas D. Maranas, Zengyi Shao, Yasuo Yoshikuni
Summary: Through genetic engineering, Issatchenkia orientalis was modified to produce 2.0 g/L of citramalate, showcasing its potential as a promising strain for citramalate production due to its ability to survive at extremely low pH levels.
METABOLIC ENGINEERING COMMUNICATIONS
(2023)
Article
Plant Sciences
Soyeon Choi, Pradeep K. Prabhakar, Ratul Chowdhury, Thomas H. Pendergast IV, Breeanna R. Urbanowicz, Costas Maranas, Katrien M. Devos
Summary: We have identified a key gene that can control the flowering time and biomass accumulation in switchgrass, a bioenergy crop native to North America, by showing how a single variant can significantly alter protein functionality. In this study, we mapped a robust flowering time quantitative trait locus (QTL) on chromosome 4K and identified the transcription factor gene PvHd1 as the underlying causal gene. Protein modeling and in vitro experiments demonstrated that a substitution at position 35 in the PvHd1 protein greatly changed its structure and functionality.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biotechnology & Applied Microbiology
Vikas Upadhyay, Veda Sheersh Boorla, Costas D. Maranas
Summary: Retro-biosynthetic approaches have been improved with the EnzRank algorithm, which uses a convolutional neural network to rank existing enzymes based on their suitability for directed evolution or de novo design of specific substrate activity. The algorithm is trained on enzyme-substrate pairs from the BRENDA database and achieves high accuracy in predicting enzyme-substrate activity. A web-based user interface has also been developed for easy access to EnzRank using SMILES strings of substrates and enzyme sequences.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Deepro Banerjee, Michael A. Jindra, Alec J. Linot, Brian F. Pfleger, Costas D. Maranas
Summary: In this study, the researchers proposed a machine learning-based enzyme classification method called EnZymClass, which aims to address the difficulties and challenges in predicting the function of plant acyl-ACP thioesterases (TEs). By applying EnZymClass, the researchers successfully classified TEs into different substrate specificity categories and identified two enzymes with previously uncharacterized activity in experimental testing.
CURRENT RESEARCH IN BIOTECHNOLOGY
(2022)