Article
Gastroenterology & Hepatology
Helit Cohen, Boaz Adani, Emiliano Cohen, Bar Piscon, Shalhevet Azriel, Prerak Desai, Heike Bahre, Michael McClelland, Galia Rahav, Ohad Gal-Mor
Summary: This study investigates the changes in the DksA regulon during Salmonella evolution, showing that DksA plays a crucial role in the growth, gene expression, and invasion of Salmonella. It regulates multiple metabolic pathways and virulence genes. The study also reveals the assimilation of horizontally acquired virulence genes under the DksA regulon, providing insights into the evolution of virulence gene regulation in Salmonella species.
Article
Biochemistry & Molecular Biology
Can Huang, Wenqian Li, Jingyu Chen
Summary: This study aims to investigate the function of DksA in fatty acid metabolism and cell membrane structure in Yersinia enterocolitica. The results showed that deletion of DksA resulted in decreased expression of fatty acid degradation genes and slower growth at low temperatures. Furthermore, DksA positively regulated the integrity of the inner and outer membranes of Y. enterocolitica under polymyxin B exposure.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Can Huang, Jiao Meng, Wenqian Li, Jingyu Chen
Summary: This study investigated the role of stringent response in Yersinia enterocolitica, a typical foodborne pathogen, and found that (p)ppGpp and DksA have synergistic and independent roles in regulating gene expression and phenotypes of Y. enterocolitica. Gene expression analysis revealed that (p)ppGpp and DksA deficiency reduced the transcription of flagellar synthesis genes and biofilm synthesis genes, which could potentially contribute to changes in motility and biofilm formation.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Alessandra Fortuna, Heike Baehre, Paolo Visca, Giordano Rampioni, Livia Leoni
Summary: DksA1 and DksA2 play critical roles in P. aeruginosa environmental adaptation, largely interchangeable with each other. While most genes' expression levels are restored by either dksA1 or dksA2, a small subset of genes seems to be preferentially complemented by one of them.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ram P. Maharjan, Geraldine J. Sullivan, Felise G. Adams, Bhumika S. Shah, Jane Hawkey, Natasha Delgado, Lucie Semenec, Hue Dinh, Liping Li, Francesca L. Short, Julian Parkhill, Ian T. Paulsen, Lars Barquist, Bart A. Eijkelkamp, Amy K. Cain
Summary: Using functional genomics, we have identified the transcriptional regulator DksA as a master regulator for broad stress protection and virulence in Acinetobacter baumannii. DksA controls various aspects such as ribosomal protein expression, metabolism, mutation rates, desiccation, antibiotic resistance, and host colonization. This study lays the groundwork for understanding the role of DksA as a major regulator in stress response and virulence in this important pathogen.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Infectious Diseases
Gerrit Brandis, Susanna Granstrom, Anna T. Leber, Katrin Bartke, Linnea Garoff, Sha Cao, Douglas L. Huseby, Diarmaid Hughes
Summary: Cip(R) rpoB mutations may contribute to resistance development and induce a ppGpp-independent stringent-Like response. In addition, the resistance development in strains carrying Cip(R) rpoB alleles also depends on other factors, such as mutations in dksA.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Environmental Sciences
Zejia Lu, Weiqi Li, Yiding Xin, Yili Huang
Summary: This study reveals the important roles of rsh in Novosphingobium pentar-omativorans US6-1's metabolism and accommodation to different pollutants. The results show that rsh affects US6-1's multiplication and metabolism, including survival rate, amino acid and nucleotide metabolism, EPS production, and redox homeostasis. The stringent response system based on rsh can help maintain redox homeostasis and improve survival rate when facing oxidative stress. The findings provide valuable data for environmental scientists and engineers to harness bacterial activities for bioremediation purposes.
ENVIRONMENTAL POLLUTION
(2023)
Review
Plant Sciences
Ana G. L. Assuncao
Summary: This review discusses zinc sensing and transcriptional regulation in Arabidopsis and their evolutionary conservation in land plants. It highlights the potential research opportunities in studying zinc deficiency response and modulating F-bZIP activity to enhance zinc accumulation in crops.
Article
Biochemistry & Molecular Biology
Satarupa Bhaduri, Analine Aguayo, Yusuke Ohno, Marco Proietto, Jasmine Jung, Isabel Wang, Rachel Kandel, Narinderbir Singh, Ikran Ibrahim, Amit Fulzele, Eric J. Bennett, Akio Kihara, Sonya E. Neal
Summary: This study reveals the association between the pseudoprotease Dfm1 and the SPOTS complex, highlighting their roles in sphingolipid metabolism. Additionally, Dfm1 is found to play a crucial role in the ER export and degradation of Orm2. These findings provide insights into the molecular mechanisms underlying sphingolipid metabolism and its implications in disease.
Article
Microbiology
Giacomo Baruzzo, Agnese Serafini, Francesca Finotello, Tiziana Sanavia, Laura Cioetto-Mazzabo, Francesca Boldrin, Enrico Lavezzo, Luisa Barzon, Stefano Toppo, Roberta Provvedi, Riccardo Manganelli, Barbara Di Camillo
Summary: Bacteria respond to nutrient starvation by implementing the stringent response, which leads to metabolic remodeling and decreased growth rate. SigE is not directly involved in initiating the stringent response, but it plays a key role in protecting the cell from stress and maintaining metabolic homeostasis.
MICROBIOLOGY SPECTRUM
(2023)
Review
Microbiology
Eleanor C. Saunders, Marijke F. Sernee, Julie E. Ralton, Malcolm J. McConville
Summary: Leishmania parasites can survive long-term in the mature phagolysosome compartment of host cells by switching to a slow growth state and activating a stringent metabolic response. The heterogeneous expression of this response in vivo reflects temporal and spatial differences in lesion tissues, including dormant stages.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Review
Microbiology
Sophie E. Irving, Naznin R. Choudhury, Rebecca M. Corrigan
Summary: This Review delves into the diverse metabolic pathways regulated in bacterial cells and emphasizes the importance of alarmones in the stringent response and bacterial pathogenesis. It highlights the complexity and broad range of functions controlled by these alarmones, providing an update on the enzymes involved in their turnover and discussing their role in virulence and chronic infection.
NATURE REVIEWS MICROBIOLOGY
(2021)
Article
Plant Sciences
Olga Petrova, Olga Parfirova, Yuri Gogolev, Vladimir Gorshkov
Summary: The study revealed that the stringent response mechanism exhibits different responses in different host plants during plant-bacteria interactions, affecting the resistance of plants to bacterial infection.
Article
Multidisciplinary Sciences
Surya D. Aggarwal, Adrian J. Lloyd, Saigopalakrishna S. Yerneni, Ana Rita Narciso, Jennifer Shepherd, David Roper, Christopher G. Dowson, Sergio R. Filipe, N. Luisa Hiller
Summary: In response to unfavorable conditions, the Gram-positive pathogen Streptococcus pneumoniae relies on cell wall biosynthesis proteins MurM and MurN. MurM modulates stress response by decreasing the pool of mischarged tRNAs, while enhanced lysis in the absence of MurM may be caused by LytA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Plant Sciences
Styliani N. Chorianopoulou, Dimitris L. Bouranis
Summary: Sulfur is an essential macronutrient for plant growth and metabolism, and it plays diverse roles in their life cycles. It is connected to the homeostasis of essential micronutrients, such as iron, copper, zinc, and manganese. Sulfur is involved in the uptake, transportation, and distribution of these micronutrients, and it interacts with them in functional ways.
Article
Microbiology
Christine Tara Peterson, Josue Perez Santiago, Stanislav N. Iablokov, Deepak Chopra, Dmitry A. Rodionov, Scott N. Peterson
Summary: This study evaluated the potential of short-chain fatty acids (SCFAs) to modulate the structure and function of the human gut microbiota. Each SCFA displayed unique modulatory potential, altering the fitness of specific bacterial strains through cross-feeding. These findings are important for the identification of prebiotics that can enhance the therapeutic effects of specific SCFAs.
CURRENT MICROBIOLOGY
(2022)
Article
Cell Biology
Michael J. Barratt, Sharika Nuzhat, Kazi Ahsan, Steven A. Frese, Aleksandr A. Arzamasov, Shafiqul Alam Sarker, M. Munirul Islam, Parag Palit, Md Ridwan Islam, Matthew C. Hibberd, Swetha Nakshatri, Carrie A. Cowardin, Janaki L. Guruge, Alexandra E. Byrne, Siddarth Venkatesh, Vinaik Sundaresan, Bethany Henrick, Rebbeca M. Duar, Ryan D. Mitchell, Giorgio Casaburi, Johann Prambs, Robin Flannery, Mustafa Mahfuz, Dmitry A. Rodionov, Andrei L. Osterman, David Kyle, Tahmeed Ahmed, Jeffrey Gordon
Summary: Disrupted development of the gut microbiota is a contributing cause of childhood malnutrition. An experiment found that giving B. infantis combined with LNT can increase the abundance of B. infantis subspecies in infants with severe acute malnutrition and promote weight gain, but the effect is still much lower than in healthy controls. A B. infantis strain, Bg_2D9, with superior fitness may have potential in treating malnourished infants.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Irina A. Rodionova, Ye Gao, Jonathan Monk, Ying Hefner, Nicholas Wong, Richard Szubin, Hyun Gyu Lim, Dmitry A. Rodionov, Zhongge Zhang, Milton H. Saier, Bernhard O. Palsson
Summary: In this study, researchers elucidated the regulatory functions of seven out of the 19 LysR-type transcription factors in Escherichia coli K-12, establishing the functions for four LTFs and identifying the target genes for three LTFs.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
James S. Weagley, Mark Zaydman, Siddarth Venkatesh, Yo Sasaki, Neha Damaraju, Alex Yenkin, William Buchser, Dmitry A. Rodionov, Andrei Osterman, Tahmeed Ahmed, Michael J. Barratt, Aaron DiAntonio, Jeffrey Milbrandt, Jeffrey Gordon
Summary: This study characterized bacterial TIR protein domains and found that TIR NADases activity in bacterial strains resulted in a specific metabolite, v-cADPR-x. The research highlighted the correlation between acute malnutrition and decreased fecal levels of TIR genes encoding the generation of v-cADPR-x as well as decreased levels of the metabolite itself.
Article
Microbiology
German A. Ashniev, Sergey N. Petrov, Stanislav N. Iablokov, Dmitry A. Rodionov
Summary: The study focuses on the impact of human gut microbiota (HGM) on host health and disease. Through genome analysis of over 2800 genomes representing 823 cultured HGM species, the researchers reconstructed biosynthetic pathways for proteinogenic amino acids. The findings provide insights into the conservation of amino acid biosynthetic phenotypes and demonstrate the potential of metabolic phenotype profiling for predicting the overall metabolic properties of HGM microbiomes.
Correction
Biochemistry & Molecular Biology
Nathan D. Han, Jiye Cheng, Omar Delannoy-Bruno, Daniel Webber, Nicolas Terrapon, Bernard Henrissat, Dmitry A. Rodionov, Aleksandr A. Arzamasov, Andrei L. Osterman, David K. Hayashi, Alexandra Meynier, Sophie Vinoy, Chandani Desai, Stacey Marion, Michael J. Barratt, Andrew C. Heath, Jeffrey I. Gordon
Article
Ecology
Miriam N. Ojima, Lin Jiang, Aleksandr A. Arzamasov, Keisuke Yoshida, Toshitaka Odamaki, Jinzhong Xiao, Aruto Nakajima, Motomitsu Kitaoka, Junko Hirose, Tadasu Urashima, Toshihiko Katoh, Aina Gotoh, Douwe van Sinderen, Dmitry A. Rodionov, Andrei L. Osterman, Mikiyasu Sakanaka, Takane Katayama
Summary: This study applied assembly theory to investigate the formation of bifidobacterial communities in the infant gut. The results showed that arrival order and sugar consumption phenotypes significantly affected community formation. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis dominated through inhibitory priority effects, while Bifidobacterium breve benefited from facilitative priority effects and utilized a specific degradant to dominate. This study highlights the importance of initial community assembly and its impact on the maturation trajectory of the infant gut microbiota.
Article
Biochemistry & Molecular Biology
Rory J. Craig, Sean D. Gallaher, Shengqiang Shu, Patrice A. Salome, Jerry W. Jenkins, Crysten E. Blaby-Haas, Samuel O. Purvine, Samuel O'Donnell, Kerrie Barry, Jane Grimwood, Daniela Strenkert, Janette Kropat, Chris Daum, Yuko Yoshinaga, David M. Goodstein, Olivier Vallon, Jeremy Schmutz, Sabeeha S. Merchant
Summary: The article presents a major update to the Chlamydomonas reference genome and structural annotations, revealing large genomic changes in laboratory culture. The authors improved assembly quality and annotations, generated chromosome-level assemblies for two laboratory strains, and validated their results through linkage analyses. They also updated gene symbols and textual annotation of functionally characterized genes, and discovered genomic instability in the classical reference strain. The resources presented in this article will pave the way for further research in Chlamydomonas genomics.
Article
Biotechnology & Applied Microbiology
Jason L. Vailionis, Weishu Zhao, Ke Zhang, Dmitry A. Rodionov, Gina L. Lipscomb, Tania N. N. Tanwee, Hailey C. O'Quinn, Ryan G. Bing, Robert M. Kelly, Michael W. W. Adams, Ying Zhang
Summary: A genome-scale metabolic model was developed for the growth of Pyrococcus furiosus, an archaeon that ferments carbohydrates and peptides at 100 degrees C. The model investigates the energy balance of P. furiosus and reveals the importance of acetate production and the coupling of ATP synthase and hydrogenase in generating a sodium gradient. The model is used to guide genetic engineering designs for ethanol production and provides valuable insights for bio-based chemical and fuel production.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Microbiology
Christine Tara Peterson, Josue Perez-Santiago, Stanislav N. Iablokov, Dmitry A. Rodionov, Scott N. Peterson
Summary: This study examined the impact of prebiotics and medicinal herbs on gut microbiota composition and host physiology using in vitro cultivation and 16S rRNA sequencing. By analyzing the relationship between sugar composition and microbiota composition, the study found that restructuring microbial communities with glycan substrates can alter community metabolism and influence host physiological changes. The combination of genome-wide metabolic reconstruction and 16S rRNA sequence-based community profiles provides valuable insights into community metabolism.
Article
Multidisciplinary Sciences
Bahia Khalfaoui-Hassani, Crysten E. Blaby-Haas, Andreia Verissimo, Fevzi Daldal
Summary: Heme-copper oxygen reductases are crucial membrane-bound complexes in cellular respiration. This study identified potential MFS transporters as missing copper transporters and found their importance in the biogenesis of E. coli bo(3)-Qox.
Article
Multidisciplinary Sciences
Lital Davidi, Sean D. Gallaher, Eyal Ben-David, Samuel O. Purvine, Thomas L. Fillmore, Carrie D. Nicora, Rory J. Craig, Stefan Schmollinger, Sanja Roje, Crysten E. Blaby-Haas, Robert P. Auber, Jennifer H. Wisecaver, Sabeeha S. Merchant
Summary: This article investigates the adaptation mechanisms of two marine algae species under iron-deficient conditions. The study reveals multiple iron uptake routes in these species and their ability to adjust protein expression and structure to cope with iron deficiency.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Plant Sciences
Lifang Zhang, Janeen Braynen, Audrey Fahey, Kriti Chopra, Paolo Cifani, Dimiru Tadesse, Michael Regulski, Fangle Hu, Hubertus J. J. van Dam, Meng Xie, Doreen Ware, Crysten E. Blaby-Haas
Summary: Metal homeostasis is important for maintaining metal availability within cells, and low bioavailability of essential metal nutrients can negatively affect crop health and yield. Understanding the function of metallochaperones in plants provides an opportunity to improve metal-use efficiency and develop plant food with higher concentrations of bioavailable metals.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Christine Tara Peterson, Stanislav N. Iablokov, Dmitry A. Rodionov, Scott N. Peterson
Summary: Parkinson's disease is a neurodegenerative disease characterized by the loss of dopaminergic neurons. Research indicates that initial dysregulation may occur in the gastrointestinal tract and gut barrier defects may accompany it. A study evaluated the effect of Ayurvedic herbs on fecal microbiota from Parkinson's disease patients and found that each participant showed unique changes, suggesting personalized response and potential for selecting individualized medicinal herbs.
Article
Biochemistry & Molecular Biology
Nathan D. Han, Jiye Cheng, Omar Delannoy-Bruno, Daniel Webber, Nicolas Terrapon, Bernard Henrissat, Dmitry A. Rodionov, Aleksandr A. Arzamasov, Andrei L. Osterman, David K. Hayashi, Alexandra Meynier, Sophie Vinoy, Chandani Desai, Stacey Marion, Michael J. Barratt, Andrew C. Heath, Jeffrey Gordon
Summary: Plant fibers in byproduct streams produced by non-harsh food processing methods contain diverse and naturally occurring biomolecules with physiological activities. It has been found that human gut microbiota can release N-methylserotonin from orange fibers, and certain strains of Bacteroides ovatus have the ability to specifically liberate this compound. Orally administered N-methylserotonin has various effects on mice and its fecal accumulation in humans is positively correlated with microbial genes encoding enzymes that digest pectic glycans.