Article
Biochemical Research Methods
Francisco Javier Albicoro, Carolina Vacca, Juan Hilario Cafiero, Walter Omar Draghi, Maria Carla Martini, Mark Goulian, Antonio Lagares, Maria Florencia Del Papa
Summary: To adapt to different environmental conditions, Sinorhizobium meliloti relies on finely tuned regulatory networks, most of which are unexplored to date. Deletion of the two-component system ActJK in S. meliloti negatively affects acid tolerance, bacteroid development, nodule occupancy, and the expression of genes involved in exopolysaccharide synthesis and efflux pumps. The study provides insights into the adaptation of rhizobia to acid stress and highlights the importance of ActJK in regulating key components associated with acid tolerance.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Microbiology
Agnese Bellabarba, Giovanni Bacci, Francesca Decorosi, Erki Aun, Elisa Azzarello, Maido Remm, Luciana Giovannetti, Carlo Viti, Alessio Mengoni, Francesco Pini
Summary: The association between leguminous plants and symbiotic nitrogen-fixing rhizobia showcases mutualism between eukaryotic hosts and prokaryotic microbes. While this symbiosis is somewhat species-specific, different rhizobial strains can co-colonize the same nodule. Through a bacterial genome-wide association (GWAS) analysis, the study identified genomic determinants related to competitive capabilities in Sinorhizobium meliloti strains.
Article
Biochemical Research Methods
Tyll Stocker, Lena Altrogge, Caroline Marcon, Yan Naing Win, Frank Hochholdinger, Heiko Schoof
Summary: Insertional mutagenesis is a powerful tool for creating loss-of-function mutations on a genome-wide scale. MuWU is an automated Mutant-seq workflow utility that efficiently identifies insertion sites and handles complex bioinformatic tasks, making it a valuable resource for functional genomics studies.
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
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
Robin Klein, Jannis Brehm, Juliane Wissig, Ralf Heermann, Gottfried Unden
Summary: This study identified the CRP-like transcriptional regulator Clr and the TetR-like regulator CycR as interacting proteins with the membrane-bound AC CyaC in Sinorhizobium meliloti. The interactions of CycR with Clr and CyaC with Clr are dependent on the presence of cAMP and ATP, respectively, while the interaction of CyaC with CycR is independent of nucleotides.
Article
Biochemistry & Molecular Biology
Martina Slapakova, Domenico Sgambati, Luciano Pirone, Veronica Russo, Gianluca D'Abrosca, Mariangela Valletta, Rosita Russo, Angela Chambery, Gaetano Malgieri, Emilia Maria Pedone, Remus Thei Dame, Paolo Vincenzo Pedone, Ilaria Baglivo
Summary: Proteins of the MucR/Ros family play a crucial role in bacterial infection or symbiosis with eukaryotic hosts. In this study, MucR isolated from Sinorhizobium meliloti was characterized for the first time, showing its ability to bind DNA and recognize specific sequences. The research identified MucR from Sinorhizobium meliloti as a member of a new family of Histone-like Nucleoid Structuring (H-NS) proteins, explaining its multifaceted role in many species of alpha-proteobacteria.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
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
Multidisciplinary Sciences
Franklin Harris, John Dobbs, David Atkins, James A. Ippolito, Jane E. Stewart
Summary: The study found that inoculated groups had greater biomass compared to uninoculated groups, with similar effects of Sinorhizobium meliloti on both potting soil and regolith; additionally, NH4 production in soil was mainly controlled by plant uptake, and the symbiotic plant-bacteria relationships differed slightly between regolith and potting mix.
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
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
Biochemistry & Molecular Biology
Linnea Charlotta Hjelm, Hanna Lindberg, Stefan Stahl, John Lofblom
Summary: Affibody molecules are small affinity proteins with excellent properties. A new type of protein scaffold based on a dimeric form of affibodies has been developed, which has a distinct secondary structure content and mode of binding. The scaffold forms a tunnel-like cavity upon binding, encapsulating the target peptide. Selections from a high-complexity phage-displayed library using this scaffold resulted in the identification of high-affinity binders that effectively inhibit amyloid aggregation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agronomy
Victoria Spartakovna Muntyan, Marina Lvovna Roumiantseva
Summary: This study analyzed the complete genome sequencing data of 26 Sinorhizobium meliloti strains and 25 bacterial strains belonging to 17 genera to investigate the salt-tolerance-related genes. It was found that multiple copies of the genes associated with the first and second stages of salt stress response were present on the pSymA replicon, which is known for its role in nitrogen fixation activity. The closest phylogenetic relatives of the tested genes were identified, providing insights into the evolutionary pathways of stress-related gene pool formation in root nodule nitrogen-fixing bacteria.
Article
Immunology
Zhanning Shen, Bo Liu, Zhen Zhu, Jige Du, Zhiyu Zhou, Chenfan Pan, Yong Chen, Chunsheng Yin, Yufeng Luo, Huanrong Li, Xiaoyun Chen
Summary: This study constructed a new vaccine candidate, ORFV rGS14?CBP?GIF?121, by deleting a third gene. The in vitro growth characteristics, safety, immunogenicity, and protective efficacy were evaluated and showed that the triple-gene deletion mutant had a safety, immunogenicity, and immune protection rate of 100%.
Article
Multidisciplinary Sciences
Abril Luchetti, Lucas G. Castellani, Andres Martin Toscani, Antonio Lagares, Maria Florencia Del Papa, Gonzalo Torres Tejerizo, Mariano Pistorio
Summary: Rhizobia are Gram-negative bacteria that form symbiotic relationships with leguminous plants and can fix atmospheric nitrogen. They often carry multiple plasmids, some of which contain genes for symbiosis or free-living. The pSmeLPU88b plasmid from Sinorhizobium meliloti LPU88 has been studied for its mobilization properties. The full sequence of pSmeLPU88b was obtained and it was found to have two replication modules, high DNA identity with a plasmid from another S. meliloti isolate, and several CDS genes related to recombinases and toxin-antitoxin systems. The cloned replication systems demonstrated different stability behaviors but could coexist.
Article
Biochemistry & Molecular Biology
Sook Jung, Taein Lee, Chun-Huai Cheng, Katheryn Buble, Ping Zheng, Jing Yu, Jodi Humann, Stephen P. Ficklin, Ksenija Gasic, Kristin Scott, Morgan Frank, Sushan Ru, Heidi Hough, Kate Evans, Cameron Peace, Mercy Olmstead, Lisa W. DeVetter, James McFerson, Michael Coe, Jill L. Wegrzyn, Margaret E. Staton, Albert G. Abbott, Dorrie Main
NUCLEIC ACIDS RESEARCH
(2019)
Article
Multidisciplinary Sciences
Ebenezer Oluwaseun Esan, Lord Abbey, Svetlana Yurgel
Letter
Biotechnology & Applied Microbiology
Gavin M. Douglas, Vincent J. Maffei, Jesse R. Zaneveld, Svetlana N. Yurgel, James R. Brown, Christopher M. Taylor, Curtis Huttenhower, Morgan G. I. Langille
NATURE BIOTECHNOLOGY
(2020)
Article
Environmental Sciences
G. W. Price, Morgan G. I. Langille, Svetlana N. Yurgel
Summary: The study found that annual applications of alkaline stabilized biosolid (ATB) had a greater impact on bacterial community structure compared to fungi and eukaryotes. Higher rates of annual ATB applications resulted in lower bacterial alpha-diversity, as well as fungal and eukaryotic Shannon diversity, while single or lower rates of ATB annually showed increased alpha-diversity relative to the control.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Plant Sciences
Ann M. Callahan, Tetyana N. Zhebentyayeva, Jodi L. Humann, Christopher A. Saski, Kelsey D. Galimba, Laura L. Georgi, Ralph Scorza, Dorrie Main, Christopher D. Dardick
Summary: The 'HoneySweet' plum is resistant to Plum pox potyvirus through an RNAi-triggered mechanism. Whole genome sequencing revealed two different transgene insertion events, but the specific locations of the insertions remain undetermined due to potential sequence differences between the two plum cultivars. RNA-seq data confirmed that the insertions did not disrupt any genes or cause significant expression changes in neighboring genes.
HORTICULTURE RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Pramod Rathor, Tudor Borza, Sophia Stone, Thierry Tonon, Svetlana Yurgel, Philippe Potin, Balakrishnan Prithiviraj
Summary: This study successfully expressed an unknown function gene, highly responsive to abiotic stresses in Ectocarpus sp., into Arabidopsis thaliana, leading to enhanced tolerance to salt and temperature stresses. The expression of key genes related to abiotic stress tolerance was significantly up-regulated in the transgenic line.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Austin W. Lloyd, David Percival, Svetlana N. Yurgel
Summary: The study found that fungicide treatment on lowbush blueberries led to a decrease in fungal richness, with certain taxa in the Clavariaceae family increasing under fungicide treatment. Additionally, enzymes associated with soil nutrient cycles showed significant differences between fungicide-treated plots and untreated control plots, implying potential changes to nutrient pathways.
Article
Plant Sciences
Jing Yu, Sook Jung, Chun-Huai Cheng, Taein Lee, Ping Zheng, Katheryn Buble, James Crabb, Jodi Humann, Heidi Hough, Don Jones, J. Todd Campbell, Josh Udall, Dorrie Main
Summary: Over the past eight years, the volume of data generated by the cotton research community has exponentially increased, leading to the creation of the CottonGen online community database which provides access to integrated genetic and breeding data and analysis tools. The data stored in CottonGen includes genes, genotypes, and phenotypes, and the platform facilitates utilization of these resources for research on cotton crop improvement through curation and online tools.
Article
Plant Sciences
Lauren E. Braley, Jeremy B. Jewell, Jose Figueroa, Jodi L. Humann, Dorrie Main, Guadalupe A. Mora-Romero, Natalia Moroz, James W. Woodhall, Richard Allen White, Kiwamu Tanaka
Summary: Early detection of causal pathogens is crucial for preventing crop loss. This study assessed the use of the Oxford Nanopore MinION sequencer as a molecular diagnostic tool for soilborne diseases in potato fields. The results demonstrated the high potential of Nanopore sequencing as a minimally biased method for comprehensive pathogen detection. The GraphMap-based MinION sequencing method could contribute to disease management by identifying pathogens in field soil prior to planting.
Article
Plant Sciences
Lord Abbey, Svetlana N. Yurgel, Ojo Alex Asunni, Raphael Ofoe, Josephine Ampofo, Lokanadha Rao Gunupuru, Nivethika Ajeethan
Summary: The use of municipal solid waste compost has been found to have positive effects on soil health and plant productivity. However, its long-term effects on soil microbial and plant metabolic pathways have not been well understood. This 5-year study investigated the effects of annual, biennial, and no compost application on soil properties, microbiome function, and plant growth and metabolites profile. The results showed that MSW compost increased soil nutrients, organic matter, and water-holding capacity. It also influenced the bacterial community composition and metabolic pathways, leading to increased crop yield and tricarboxylic acid cycle metabolites. Overall, the study suggests that MSW compost can be a valuable solution for improving soil health and plant production in the medium to long term.
Article
Mathematical & Computational Biology
Sook Jung, Taein Lee, Ksenija Gasic, B. Todd Campbell, Jing Yu, Jodi Humann, Sushan Ru, Daniel Edge-Garza, Heidi Hough, Dorrie Main
Summary: In the era of big data, efficient management systems like the Breeding Information Management System (BIMS) are essential for breeders to keep track of and analyze the large amounts of data generated by breeding programs. BIMS allows breeders to integrate their private breeding data with public data, enhancing genetic understanding and utility for marker-assisted breeding. The system also includes tools like the Android App Field Book for easier data collection and analysis.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Mathematical & Computational Biology
Sook Jung, Chun-Huai Cheng, Katheryn Buble, Taein Lee, Jodi Humann, Jing Yu, James Crabb, Heidi Hough, Dorrie Main
Summary: Tripal MegaSearch is a module for querying and downloading biological data stored in Chado, allowing users to select data types and customize fields. Administrators can set example data types, while users can restrict datasets and download desired data accordingly.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Plant Sciences
Pramod Rathor, Tudor Borza, Yanhui Liu, Yuan Qin, Sophia Stone, Junzeng Zhang, Joseph P. M. Hui, Fabrice Berrue, Agnes Groisillier, Thierry Tonon, Svetlana Yurgel, Philippe Potin, Balakrishnan Prithiviraj
Article
Agronomy
Monica Sandepogu, Pushp Sheel Shukla, Samuel Asiedu, Svetlana Yurgel, Balakrishnan Prithiviraj
Article
Mathematical & Computational Biology
Katheryn Buble, Sook Jung, Jodi L. Humann, Jing Yu, Chun-Huai Cheng, Taein Lee, Stephen P. Ficklin, Heidi Hough, Bradford Condon, Margaret E. Staton, Jill L. Wegrzyn, Dorrie Main
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2019)
