Article
Biochemistry & Molecular Biology
Marie Pacoud, Karine Mandon, Julie Cazareth, Olivier Pierre, Pierre Frendo, Genevieve Alloing
Summary: Reactive oxygen species, such as hydrogen peroxide, play a crucial role in controlling the establishment and functioning of Rhizobium-legume symbiosis. This study used biosensors to measure the intracellular redox state of Sinorhizobium meliloti, a bacterium involved in nitrogen-fixing symbiosis. The results revealed an oxidative shift in the redox status of S. meliloti during bacteroid differentiation. These findings provide new opportunities for studying redox dynamics during N2-fixing symbiosis.
FREE RADICAL BIOLOGY AND MEDICINE
(2022)
Article
Microbiology
Quentin Nicoud, Quentin Barriere, Nicolas Busset, Sara Dendene, Dmitrii Travin, Mickael Bourge, Romain Le Bars, Claire Boulogne, Marie Lecroel, Sandor Jenei, Atilla Kereszt, Eva Kondorosi, Emanuele G. Biondi, Tatiana Timchenko, Benoit Alunni, Peter Mergaert
Summary: Various functions in Sinorhizobium meliloti are involved in protecting endosymbionts, including peptide transporters, bacterial envelope structures, and stress response regulators.
Article
Plant Sciences
Ru-Jie Li, Chun-Xiao Zhang, Sheng-Yao Fan, Yi-Han Wang, Jiangqi Wen, Kirankumar S. Mysore, Zhi-Ping Xie, Christian Staehelin
Summary: This study reveals the presence of a second Nod factor cleaving hydrolase (MtCHIT5b) in Medicago truncatula, which degrades Sinorhizobium meliloti Nod factors in the rhizosphere in conjunction with MtNFH1. The expression of MtCHIT5b is induced by purified Nod factors treatment or rhizobia inoculation, and it is localized in the infection pocket of root hairs. The study also demonstrates that overexpression of MtCHIT5b leads to reduced nodule formation, and simultaneous silencing of MtCHIT5b and MtNFH1 results in decreased nodulation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Emmanuelle D'Amours, Annick Bertrand, Jean Cloutier, Annie Claessens, Solen Rocher, Philippe Seguin
Summary: This study reveals a relationship between nodule and shoot regrowth after freezing stress, with a higher proportion of undamaged nodules related to increased shoot biomass. The results demonstrate that choosing stress-adapted alfalfa populations and S. meliloti strains can enhance alfalfa persistence.
Article
Biotechnology & Applied Microbiology
Prithwi Ghosh, Katie N. Adolphsen, Svetlana N. Yurgel, Michael L. Kahn
Summary: It was found that by introducing specific genes from S. medicae into the S. meliloti strain, the symbiotic effect between rhizobia and plants could be enhanced, promoting plant growth and increasing biomass. These genes related to symbiotic effectiveness may play important roles among different rhizobial strains and could potentially provide new contributions to symbiotic relationships.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
MacLean G. Kohlmeier, Ben A. Bailey-Elkin, Brian L. Mark, Ivan J. Oresnik
Summary: Sinorhizobium meliloti 1021 is a Gram-negative alphaproteobacterium with a strong capacity for carbohydrate metabolism. The study of its enzyme SmoS suggests a preference for sorbitol despite a higher affinity for galactitol. X-ray diffraction experiments confirm SmoS as a tetramer, and computational experiments indicate a more energetically favorable binding of tagatose to the protein.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Cintia Soledad Ramirez, Carmien Tolmie, Diederik Johannes Opperman, Pablo Javier Gonzalez, Maria Gabriela Rivas, Carlos Dante Brondino, Felix Martin Ferroni
Summary: This study presents the crystal structure of a copper-containing nitrite reductase (NirK) from Sm and its role in symbiosis, as well as complex structural alignments and docking studies with related proteins. The activity of SmNirK, although lower than classical NirKs, is affected by structural differences and regulation within the symbiotic environment. In vitro kinetics demonstrated similar electron donation performance from SmPaz1 and SmPaz2 to SmNirK, facilitated by conserved residues mediating interprotein electron transfer.
Article
Gastroenterology & Hepatology
Yisheng He, Mai Shi, Xu Wu, Jiang Ma, Kevin Tak-Pan Ng, Qingsu Xia, Lin Zhu, Peter Pi-Cheng Fu, Kwan Man, Stephen Kwok-Wing Tsui, Ge Lin
Summary: This study identified a novel mutational signature associated with pyrrolizidine alkaloids (PAs) exposure in liver cancer, highlighting the potential prevalence of PA-associated liver cancers in Asian populations. The PA mutational signature was validated in patients with PPA-positive liver cancer, establishing its specificity in revealing PA-induced mutations. This research provides important insights for the scientific basis and preventive measures against PA-associated human liver cancers.
Article
Multidisciplinary Sciences
Cindy V. Bui, Curtis W. Boswell, Brian Ciruna, Jonathan V. Rocheleau
Summary: This study develops an in vivo assay to measure endogenous NADPH/NADP+ dynamics in pancreatic beta cells of live zebrafish embryos using the Apollo-NADP+ sensor. Results show that pyruvate cycling is the main source of NADP+ reduction in beta cells, with contributions from folate cycling. Additionally, stress induces an increase in folate cycling in beta cells, which requires increased glycolytic intermediates and cytosolic NAD+.
Article
Microbiology
Lei Sun, Ann Van Loey, Carolien Buve, Chris W. Michiels
Summary: In this study, it was found that mutants of L. monocytogenes with increased tolerance to the plant essential oil component trans-cinnamaldehyde (t-CIN) were obtained through experimental evolution. The mutations were found in the yhfK gene, which encodes an oxidoreductase. The deletion of yhfK conferred increased sensitivity to t-CIN and other alpha,beta-unsaturated aldehydes, but the t-CIN tolerance was restored through genetic complementation. It was proposed that YhfK is an ene reductase that converts t-CIN to 3-phenylpropanal by reducing the C=C double bond of the alpha,beta-unsaturated aldehyde moiety.
MICROBIOLOGY SPECTRUM
(2023)
Article
Agronomy
Juan Hilario Cafiero, Maria Salvetti Casasco, Mauricio Javier Lozano, Carolina Vacca, Silvina Laura Lopez Garcia, Walter Omar Draghi, Antonio Lagares, Maria Florencia Del Papa
Summary: Through the analysis of the S. meliloti LPU63 genome, this study found that this strain has high competitiveness and efficient nitrogen fixation ability. In addition, it has potential plant growth-promoting characteristics and the ability to potentially emit N2O under anaerobic conditions through nitrate ester metabolism. Moreover, LPU63 has a high ability to produce melanin, which enhances its survival in soil environments. Therefore, these characteristics provide the basis for the rational design of a new environmentally friendly alfalfa bioinoculant.
FRONTIERS IN AGRONOMY
(2023)
Article
Biotechnology & Applied Microbiology
Tania Chroumpi, Mao Peng, Maria Victoria Aguilar-Pontes, Astrid Mueller, Mei Wang, Juying Yan, Anna Lipzen, Vivian Ng, Igor V. Grigoriev, Miia R. Makela, Ronald P. deVries
Summary: Pentose catabolism in A. niger is a well-studied pathway with a high level of complexity and redundancy, emphasizing the importance of a comprehensive understanding of metabolic pathways before metabolic engineering for the generation of more efficient fungal cell factories.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ana Rita Oliveira, Cristiano Mota, Kateryna Klymanska, Frederic Biaso, Maria Joao Romao, Bruno Guigliarelli, Ines Cardoso Pereira
Summary: The study investigated the structure and catalytic mechanism of metal-dependent formate dehydrogenases, revealing their high activity and structural stability. Spectroscopic and crystallographic analysis determined the redox characteristics and structural changes of the metal centers.
ACS CHEMICAL BIOLOGY
(2022)
Editorial Material
Biochemistry & Molecular Biology
M. J. Ryan, M. Schloter, G. Berg, T. Kostic, L. L. Kinkel, K. Eversole, J. A. Macklin, B. Schelkle, M. Kazou, I. Sarand, B. K. Singh, D. Fischer, E. Maguin, I. Ferrocino, N. Lima, R. S. McClure, T. C. Charles, R. S. C. de Souza, G. S. Kiran, H. L. Krug, J. Taffner, H. Roume, J. Selvin, D. Smith, D. Rybakova, A. Sessitsch
Summary: The microbiome research field is rapidly advancing and requires a well-established biobanking infrastructure for preserving microbiome samples and their functional potential. There is an urgent need for assessing how biobanks can support research in this rapidly evolving field.
TRENDS IN MICROBIOLOGY
(2021)
Correction
Biochemistry & Molecular Biology
M. J. Ryan, M. Schloter, G. Berg, T. Kostic, L. L. Kinkel, K. Eversole, J. A. Macklin, B. Schelkle, M. Kazou, I. Sarand, B. K. Singh, D. Fischer, E. Maguin, I. Ferrocino, N. Lima, R. S. McClure, T. C. Charles, R. S. C. de Souza, G. S. Kiran, H. L. Krug, J. Taffner, H. Roume, J. Selvin, D. Smith, D. Rybakova, A. Sessitsch
TRENDS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
Gem Thomas-Barry, Chaney C. G. St Martin, Michael D. J. Lynch, Adesh Ramsubhag, Judy Rouse-Miller, Trevor C. Charles
Summary: This study investigated the changes in rhizobacteriome community structure in hyper-seasonal edaphic savannas, showing that soil and season were key determinants influencing the community structure. Plant biomass, root traits, and rhizobacterial community compositions were found to be influenced by seasonal changes and savanna-specific drivers.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Stuart J. Smyth, Trevor C. Charles
Summary: Digital sequence information (DSI), defined as nonphysical genetic resources like genetic sequence data, lacks a clear definition and is not consistent among countries. Restricting the free sharing of DSI may conflict with core principles in fields like microbiology and molecular genetics, potentially impacting international research collaborations.
TRENDS IN BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Tam T. Tran, Trevor C. Charles
Summary: Promoter engineering can enhance bio-product production, but the activity of a promoter may vary in different gene contexts. Inserted genes can affect promoter activity, leading to changes at the transcriptional level, which influence downstream applications.
Article
Biochemistry & Molecular Biology
Mohammed Al Za'abi, Badreldin H. Ali, Yousuf Al Suleimani, Sirin A. Adham, Haytham Ali, Priyadarsini Manoj, Mohammed Ashique, Abderrahim Nemmar
Summary: The study showed that metformin can effectively alleviate renal damage induced by adenine and STZ, especially when given together. This indicates that metformin may have an inhibitory effect on the progression of CKD in both diabetic and non-diabetic rats.
Article
Biodiversity Conservation
Javiera Soto, Trevor C. Charles, Michael D. J. Lynch, Giovanni Larama, Hector Herrera, Cesar Arriagada
Summary: A novel strain of Brevundimonas sp. capable of growing under high doses of arsenic was isolated from metal(loid) contaminated soil in central Chile. Real-time PCR analysis revealed down-regulation of the arsB gene involved in arsenic efflux, while arsR, arsH, and ACR3 genes showed no significant differences in expression levels with the addition of arsenic.
Editorial Material
Microbiology
Vanessa A. Varaljay, Trevor C. Charles, Rolf Daniel
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xueya Zhang, Shuang Liang, Qingnan Wu, Trevor C. Charles, Rui He, Jiakai Wu, Yuhui Zhao, Zhiyi Zhao, Hezhong Wang
Summary: This study investigated the mode of action of nanochitin whisker (NC) against Fusarium pseudograminearum (Fpg), an important pathogenic fungus causing wheat crown rot disease. The results showed that NC significantly reduced hyphal growth and spore germination rate of Fpg. It exerted its effects by disrupting cell wall structure, altering membrane integrity, decreasing enzyme activity related to energy-supply, and reducing mycotoxin production.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Review
Environmental Sciences
Aleksander Cholewinski, Eugenia Dadzie, Cassandra Sherlock, William A. Anderson, Trevor C. Charles, Komal Habib, Steven B. Young, Boxin Zhao
Summary: The resilience and low cost of plastics have led to their widespread use, but also contribute to their abundance and persistence as waste. Plastic pollution is a major concern for global ecosystems and their health. Material flow analysis, previously used in other industries, has been applied to plastics to understand how waste enters the environment. However, research on degradation strategies for microplastics has been limited and material flow analysis lacks data. The variety of plastics, their additives, and contaminants present significant challenges in degrading microplastic particles.
ENVIRONMENTAL POLLUTION
(2022)
Article
Biochemistry & Molecular Biology
Noura Al-Zeheimi, Yan Gao, Peter A. A. Greer, Sirin A. A. Adham
Summary: Breast cancer metastasis is a leading cause of female mortality, and Neuropilin-1 (NRP-1) plays a ligand-dependent role in breast cancer. While clinical studies have shown a link between NRP-1 and metastatic disease, its exact role in breast cancer metastasis remains uncertain. In this study, the NRP-1 gene was knocked out in MDA-MB-231 breast cancer cells using CRISPR-Cas9, and the effects on metastasis were investigated using a mouse engraftment model. Knockout cells showed reduced metastasis to the lungs, and transcriptome analysis revealed altered pathways and changes in genes associated with metastasis. These findings suggest a functional role for NRP-1 in breast cancer metastasis and support further exploration of NRP-1 and the identified genes as potential targets for treating metastatic breast cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Environmental Sciences
Rashmi Chandra, Aranksha Thakor, Tizazu H. Mekonnen, Trevor C. Charles, Hyung-Sool Lee
Summary: The production of polyhydroxyalkanoates (PHAs) with high carboxylate concentration accumulated from solid-state fermentation (SSF) of food waste (FW) was tested using Pseudomonas putida strain KT2440. The mixed-culture SSF of FW supplied in a high carboxylate concentration led to a high PHA production of 0.56 g PHA/g CDM under nutrients control. The dominant PHA building block produced was 3-hydroxybutyrate, followed by 3-hydroxy-2-methylvalerate and 3-hydroxyhexanoate, indicating that acetate, butyrate, and propionate were the main precursors to PHA.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2023)
Article
Microbiology
Meghan Donovan, Calvin S. Mackey, Michael D. J. Lynch, Grayson N. Platt, Amber N. Brown, Brian K. Washburn, Darryl J. Trickey, J. Thomas Curtis, Yan Liu, Trevor C. Charles, Zuoxin Wang, Kathryn M. Jones
Summary: Research on the role of gut microbiota in behavior has advanced significantly. The probiotic L. reuteri can affect social and stress-related behaviors, but the mechanisms behind this are still unclear. Using prairie voles, a socially-monogamous species, the study found that treatment with live L. reuteri led to decreased social affiliation compared to heat-killed L. reuteri in females but not males. There were also differences in neurochemical markers, gut microbiome composition, and behaviors between the sexes and treatments.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Microbiology
Angela Sessitsch, Steve Wakelin, Michael Schloter, Emmanuelle Maguin, Tomislav Cernava, Marie-Christine Champomier-Verges, Trevor C. Charles, Paul D. Cotter, Ilario Ferrocino, Aicha Kriaa, Pedro Lebre, Don Cowan, Lene Lange, Seghal Kiran, Lidia Markiewicz, Annelein Meisner, Marta Olivares, Inga Sarand, Bettina Schelkle, Joseph Selvin, Hauke Smidt, Leo van Overbeek, Gabriele Berg, Luca Cocolin, Yolanda Sanz, Wilson Lemos Fernandes, S. J. Liu, Matthew Ryan, Brajesh Singh, Tanja Kostic
Summary: Microbiomes play crucial roles in ecosystem functioning, supporting planetary health through nutrient cycling, climate regulation, and water filtration. They are closely associated with complex multicellular organisms and contribute to the health of their hosts. However, there is still limited understanding of microbiome transfer and connectivity.
MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS
(2023)
Review
Biotechnology & Applied Microbiology
Nicole LeBlanc, Trevor C. Charles
Summary: Bacterial cells are commonly used for the production of value-added products. However, their own metabolism, genetic instability, and the toxicity of the product often hinder efficient production. Genome reductions have been performed to create strains that can serve as chassis for downstream applications. Despite improvements in cellular characteristics, the construction of these cells efficiently and rapidly remains a major challenge.
FRONTIERS IN GENOME EDITING
(2022)
