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
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
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
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
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
Biochemistry & Molecular Biology
Dorota Dabrowska, Justyna Mozejko-Ciesielska, Tomasz Pokoj, Slawomir Ciesielski
Summary: This study investigated the transcriptome adjustment of Pseudomonas putida for mcl-PHA synthesis under nitrogen limitation. The results showed that key genes were co-regulated under N-limiting conditions, while potential regulators may play important roles in this process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(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
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
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
Biochemical Research Methods
Xinyuan He, Tianyu Gao, Yan Chen, Kun Liu, Jiantao Guo, Wei Niu
Summary: In this study, we successfully achieved genetic code expansion in Pseudomonas putida KT2440, introducing non-natural amino acids into proteins. By optimizing the decoding system, we successfully incorporated four non-natural amino acids into proteins and demonstrated the utility of genetic code expansion in protein-protein interaction studies.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Microbiology
Tania Henriquez, Heinrich Jung
Summary: The MxtR/ErdR system is essential for acetate utilization in Pseudomonas putida KT2440, stimulating the expression of specific genes, but does not play a role in regulating siderophore production and the expression of RND transporters.
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
Biotechnology & Applied Microbiology
Philipp Demling, Andreas Ankenbauer, Bianca Klein, Stephan Noack, Till Tiso, Ralf Takors, Lars M. Blank
Summary: The study demonstrated that Pseudomonas putida KT2440 can withstand repeated oxygen limitations encountered in large-scale bioreactors, with slowed growth and production but maintained stability. Intracellular ATP concentrations can be restored, and minimal changes in the proteome were observed under oscillations in dissolved oxygen tensions.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
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
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
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)