Article
Agriculture, Multidisciplinary
Bai-Feng Zheng, Zhi-Zheng Wang, Jin Dong, Jin-Yi Ma, Yang Zuo, Qiong-You Wu, Guang-Fu Yang
Summary: A new compound, 8aj, was discovered to be a potent inhibitor of Nicotiana tabacum PPO enzyme. It showed 71-fold higher activity than the commercial herbicide oxadiazon and has the potential to be developed as a new herbicide for weed control.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Plant Sciences
Ryoya Kohata, HyunSeok Lim, Yuki Kanamoto, Akio Murakami, Yuichi Fujita, Ayumi Tanaka, Wesley Swingley, Hisashi Ito, Ryouichi Tanaka
Summary: The pathways for synthesizing tetrapyrroles, including heme and chlorophyll, are conserved among organisms, despite the divergence of several enzymes in these pathways. Cyanobacteria show mosaic phylogenetic distribution of three types of homologues encoding Protoporphyrinogen IX oxidase (PPOX). This study provides experimental evidence for the functionality of cyanobacterial PPOX homologues and demonstrates the presence of two types of functional PPOX in G. violaceus.
JOURNAL OF PLANT RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Baifan Wang, Zijuan Zhang, Hao Zhu, Congwei Niu, Xin Wen, Zhen Xi
Summary: This study found that the hydrogen-bonding network around Arg59 in protoporphyrinogen IX oxidase is crucial for enzyme activity, maintaining the substrate binding chamber and stabilizing the micro-environment of the FAD isoalloxazine ring to enhance substrate-FAD interaction.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Agriculture, Multidisciplinary
Da-Wei Wang, Lu Liang, Zhi-Yuan Xue, Shu-Yi Yu, Rui-Bo Zhang, Xia Wang, Han Xu, Xin Wen, Zhen Xi
Summary: A novel series of N-phenylaminomethylthioacetylpyrimidine-2,4-diones were discovered as promising PPO inhibitors, with compound 2c showing excellent post-emergence herbicidal activity in paddy fields. Compound 2c has the potential to be developed as a new herbicide for weed management.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Agriculture, Multidisciplinary
Da-Wei Wang, Hang Zhang, Shu-Yi Yu, Rui-Bo Zhang, Lu Liang, Xia Wang, Huang-Ze Yang, Zhen Xi
Summary: This study successfully designed and synthesized a new series of compounds with improved bioactivity against weeds through in silico structure-guided optimization. One highly potent compound, 6g, was discovered with excellent weed control and relative safety on maize. Molecular simulations indicated that compound 6g exhibited higher potency and more favorable interactions with the target enzyme, suggesting that this approach is effective for obtaining enzyme inhibitors with enhanced performance.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Martijn F. L. Derks, Christian Gross, Marcos S. Lopes, Marcel J. T. Reinders, Mirte Bosse, Arne B. Gjuvsland, Dick de Ridder, Hendrik-Jan Megens, Martien A. M. Groenen
Summary: The genotype-phenotype link is complex and important in life sciences. Pigs are a valuable model for studying causal variations and molecular pathways underlying important phenotypes, and a new approach has been proposed in this study to accelerate the discovery of novel causal variants and molecular mechanisms affecting these phenotypes.
Review
Agronomy
Abigail L. Barker, John Pawlak, Stephen O. Duke, Roland Beffa, Patrick J. Tranel, Joe Wuerffel, Bryan Young, Aimone Porri, Rex Liebl, Raphael Aponte, Douglas Findley, Michael Betz, Jens Lerchl, Stanley Culpepper, Kevin Bradley, Franck E. Dayan
Summary: This article reviews the importance and current state of PPO-inhibiting herbicides, which have been used for 60 years since their first introduction. Recent increased interest in PPO-inhibiting herbicides, due to their increased use and cases of resistance, has led to a better understanding of the mechanism of action of PPO inhibitors. The article discusses the importance of the two isoforms of PPO in plants, current knowledge of target-site resistance mechanisms, non-target site resistance cases, and crop selectivity mechanisms. It emphasizes the need for consistent and reproducible greenhouse screening and target-site mutation assays to effectively study and compare PPO-inhibitor resistance cases.
Article
Soil Science
Yang Ruan, Tingting Wang, Shiwei Guo, Qiwei Huang, Qirong Shen, Ning Ling
Summary: This study investigated rare bacteria in the rhizospheres of natural watermelon and chimeric watermelon to understand the assembling processes of rare rhizobacteria during plant development and their effects on functional stability. The results showed that over 80% of total operational taxonomic units (OTUs) in the rhizosphere were classified as rare taxa, including transient, permanent, and conditionally rare taxa. Transient rare taxa had the highest richness, while conditionally rare taxa showed the largest variations along growth stages and played a significant role in assembling. Pairs of conditionally rare taxa with high asynchrony and similar functional potentials were identified in the rhizobacterial communities, indicating functional stability through redundancy. The number of pairs in the rhizosphere of chimeric plants was approximately two times higher than that in natural watermelon, suggesting that chimeric plants can enhance rhizospheric functions.
BIOLOGY AND FERTILITY OF SOILS
(2022)
Article
Biochemistry & Molecular Biology
Lars L. Santema, Lorenzo Basile, Claudia Binda, Marco W. Fraaije
Summary: A highly thermostable bacterial MAO enzyme, MAO(Tb), has been identified and studied, showing efficient activity towards n-alkylamines with n-heptylamine as the best substrate. The enzyme has a crystal structure highly similar to human MAO A and MAO B, but lacks a C-terminal extension found in the mammalian counterparts. The bacterial MAO also displays a slightly different active site access tunnel, which may explain its specificity towards long aliphatic amines.
Article
Plant Sciences
Xiang Pu, Menghan Chen, Ming Lei, Xinyu Lin, Jiahua Zhang, Zhihui Ai, Jinwei He, Yuke Liu, Shengnan Yang, Hanguang Wang, Jinqiu Liao, Li Zhang, Qianming Huang
Summary: A functional triterpene, C28 oxidase, has been found in C. acuminata, indicating its involvement in triterpene metabolism. Through gene analysis and enzymatic activity evaluation, two gene families, CYP716A and CYP716C, were identified to play roles in triterpene metabolism. CYP716C is mainly involved in oleanane-type triterpene metabolism, while CYP716A is responsible for ursane and lupane-type triterpene metabolism.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Review
Chemistry, Medicinal
Max Cruesemann
Summary: Traditional natural product discovery approaches are limited in terms of dereplication, but recent advances in mass spectrometry, sequencing, and bioinformatics have provided important tools for accelerating and rationalizing natural product discovery. By utilizing signature-based or correlation-based mass spectrometry genome mining approaches, metabolomic and genomic information can be rapidly linked.
Article
Biochemistry & Molecular Biology
Abbas Abou-Hamdan, Roman Mahler, Philipp Grossenbacher, Olivier Biner, Dan Sjostrand, Martin Lochner, Martin Hogbem, Christoph von Ballmoos
Summary: Superoxide anion, produced in large amounts in enzymatic and adventitious reactions, serves various cellular functions but can also lead to the production of more harmful species. Recent findings suggest that the membrane protein CybB from E. coli may function as a superoxide:quinone oxidoreductase.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2022)
Article
Engineering, Biomedical
Yue Huang, Yuan Liu, Shrey Shah, Dongyeop Kim, Aurea Simon-Soro, Tatsuro Ito, Maryam Hajfathalian, Yong Li, Jessica C. Hsu, Lenitza M. Nieves, Faizan Alawi, Pratap C. Naha, David P. Cormode, Hyun Koo
Summary: The study utilized nanotechnology to design a novel treatment that can produce reactive oxygen species under pathological conditions of dental caries in order to target biofilm pathogens, reducing the occurrence of cavities.
Article
Microbiology
Melissa C. Kordahi, Ian B. Stanaway, Marion Avril, Denise Chac, Marie-Pierre Blanc, Benjamin Ross, Christian Diener, Sumita Jain, Paul McCleary, Ana Parker, Vincent Friedman, Jennifer Huang, Wynn Burke, Sean M. Gibbons, Amy D. Willis, Richard P. Darveau, William M. Grady, Cynthia W. Ko, R. William DePaolo
Summary: This study provides fundamental insight into the microbial microenvironment of the pre-neoplastic polyp by highlighting strain-specific genomic and proteomic differences, as well as more broad compositional differences in the microbiome.
CELL HOST & MICROBE
(2021)
Article
Biotechnology & Applied Microbiology
Gang Zhang, Shigang Yao, Yunan Liu, Hailing Fang, Yuqin Song, Chao Wang, Dawei Wei, Jie Feng
Summary: In this study, we identified 530 novel tyrosine-type integrases from bacterial genomic islands. These integrases belong to a distinct evolutionary clade and are affiliated with new integrase groups. The integration functions of six representative novel integrases were validated in a bacterial model system, and their expression patterns were confirmed in Escherichia coli. This study revealed site-specific recombination functions of novel integrases and expands the toolbox for genetic engineering.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Sam J. B. Mallinson, Melodie M. Machovina, Rodrigo L. Silveira, Marc Garcia-Borras, Nathan Gallup, Christopher W. Johnson, Mark D. Allen, Munir S. Skaf, Michael F. Crowley, Ellen L. Neidle, Kendall N. Houk, Gregg T. Beckham, Jennifer L. DuBois, John E. McGeehan
NATURE COMMUNICATIONS
(2018)
Article
Biochemical Research Methods
Amer M. Alanazi, Ellen L. Neidle, Cory Momany
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2013)
Review
Microbiology
Kathryn T. Elliott, Laura E. Cuff, Ellen L. Neidle
FUTURE MICROBIOLOGY
(2013)
Review
Biochemistry & Molecular Biology
Kathryn T. Elliott, Ellen L. Neidle
Article
Microbiology
Laura E. Cuff, Kathryn T. Elliott, Sarah C. Seaton, Maliha K. Ishaq, Nicole S. Laniohan, Anna C. Karls, Ellen L. Neidle
JOURNAL OF BACTERIOLOGY
(2012)
Article
Biochemistry & Molecular Biology
Ajchareeya Ruangprasert, Sarah H. Craven, Ellen L. Neidle, Cory Momany
JOURNAL OF MOLECULAR BIOLOGY
(2010)
Article
Biochemistry & Molecular Biology
Sarah H. Craven, Obidimma C. Ezezika, Sandra Haddad, Ruth A. Hall, Cory Momany, Ellen L. Neidle
MOLECULAR MICROBIOLOGY
(2009)
Article
Biochemistry & Molecular Biology
Sarah C. Seaton, Kathryn T. Elliott, Laura E. Cuff, Nicole S. Laniohan, Poonam R. Patel, Ellen L. Neidle
MOLECULAR MICROBIOLOGY
(2012)
Editorial Material
Biochemistry & Molecular Biology
Cory Momany, Ellen L. Neidle
MOLECULAR MICROBIOLOGY
(2012)
Article
Genetics & Heredity
Melissa P. Tumen-Velasquez, Nicole S. Laniohan, Cory Momany, Ellen L. Neidle
Article
Biochemistry & Molecular Biology
Bradley W. Biggs, Stacy R. Bedore, Erika Arvay, Shu Huang, Harshith Subramanian, Emily A. McIntyre, Chantel Duscent-Maitland, Ellen L. Neidle, Keith E. J. Tyo
NUCLEIC ACIDS RESEARCH
(2020)
Article
Biotechnology & Applied Microbiology
Isabel Pardo, Ramesh K. Jha, Ryan E. Bermel, Felicia Bratti, Molly Gaddis, Emily McIntyre, William Michener, Ellen L. Neidle, Taraka Dale, Gregg T. Beckham, Christopher W. Johnson
METABOLIC ENGINEERING
(2020)
Review
Microbiology
Sarah H. Craven, Ellen L. Neidle
FUTURE MICROBIOLOGY
(2007)
Article
Biochemical Research Methods
Obidimma C. Ezezika, Sandra Haddad, Ellen L. Neidle, Cory Momany
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2007)