Article
Biology
Josiah C. Kratz, Shiladitya Banerjee
Summary: A quantitative theory is developed to explain the relationship between bacterial growth and division rates and proteome allocation in time-varying nutrient environments. The theory shows that in such environments, cell size and growth are regulated by trade-offs between biomass accumulation and division. The study also finds that bacteria exhibit a transient memory of previous metabolic states, allowing for faster adaptation to previously encountered environments.
COMMUNICATIONS BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Yeonoh Shin, M. Zuhaib Qayyum, Danil Pupov, Daria Esyunina, Andrey Kulbachinskiy, Katsuhiko S. Murakami
Summary: The study reveals the cryo-EM structures of E. coli RNA polymerase and rRNA promoter complex with DksA/ppGpp during open complex formation, providing insights into the key steps of promoter recognition and opening.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Chao-Chieh Lin, Chien-Kuang Cornelia Ding, Tianai Sun, Jianli Wu, Kai-Yuan Chen, Pei Zhou, Jen-Tsan Chi
Summary: All organisms have developed stress adaptive strategies to maintain homeostasis. Bacteria rely on the stringent response triggered by (p)ppGpp, while metazoans possess MESH1 as a ppGpp hydrolase. Knockdown of MESH1 in human cancer cells induces ER stress and ISR, with ATF4 playing a key role in mediating the stress survival response and ferroptosis regulation.
CELL DEATH & DISEASE
(2021)
Article
Microbiology
Katia Ospino, Beny Spira
Summary: This study investigated the effects of glyphosate on the resistance, tolerance, or persistence of bacteria towards antibiotics, as well as the role of (p)ppGpp in this process. The results showed that glyphosate did not affect the minimum inhibitory concentration of tested antibiotics, but it enhanced bacterial tolerance and/or persistence towards them. The increase in ciprofloxacin and kanamycin tolerance was partially dependent on the presence of relA, while the strong increase in ampicillin tolerance caused by glyphosate was independent of relA. The study concluded that glyphosate contributes to the temporary increase in E. coli tolerance or persistence by inducing aromatic amino acid starvation, but does not affect antibiotic resistance.
Article
Microbiology
Xu Qiu, Xiaorong Cao, Huahua Jian, Huangming Wu, Guangxin Xu, Xixiang Tang
Summary: This study examined the transcriptomic data of deep-sea bacteria Microbacterium sediminis YLB-01 under different temperature and pressure conditions, revealing its adaptive mechanism in high-pressure and low-temperature environments. The bacterium responds to the environment by upregulating genes related to transport system, DNA repair, metabolic pathways, and down-regulating genes involved in division, energy production, and cell wall synthesis. Seven key genes specifically expressed under low temperature and high pressure conditions were identified. This study provides insights into the transcription-level tolerance mechanisms of M. sediminis YLB-01 in a simulated deep-sea in situ environment.
CURRENT MICROBIOLOGY
(2022)
Article
Microbiology
Viktoriya Shyp, Badri Nath Dubey, Raphael Bohm, Johannes Hartl, Jutta Nesper, Julia A. Vorholt, Sebastian Hiller, Tilman Schirmer, Urs Jenal
Summary: This study demonstrates that the small signaling molecules (p)ppGpp and c-di-GMP reciprocally regulate the growth of Caulobacter crescentus by converging on the small-molecule-binding protein SmbA. (p)ppGpp promotes growth on glucose, while c-di-GMP inhibits glucose consumption, with SmbA playing a role in this metabolic switch and quenching redox stress associated with growth on glucose. The identification of SmbA as a central regulatory hub for these two global second messengers suggests potential for future studies on specific crosstalk between small-molecule-based regulatory networks.
NATURE MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Tatsuaki Kurata, Tetiana Brodiazhenko, Sofia Raquel Alves Oliveira, Mohammad Roghanian, Yuriko Sakaguchi, Kathryn Jane Turnbull, Ondrej Bulvas, Hiraku Takada, Hedvig Tamman, Andres Ainelo, Radek Pohl, Dominik Rejman, Tanel Tenson, Tsutomu Suzuki, Abel Garcia-Pino, Gemma Catherine Atkinson, Vasili Hauryliuk
Summary: Multiple families of SAS RSH enzymes have been discovered to inhibit bacterial growth by specifically inhibiting protein synthesis, establishing RSHs as RNA-modifying enzymes.
Article
Multidisciplinary Sciences
Puhua Niu, Maria J. Soto, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian
Summary: Extensive research has been done on predictive modeling of genome-scale metabolic reaction networks. Living systems involve complex stochastic processes, and for more accurate predictions, both metabolic reactions and genetic regulatory relationships should be modeled. TRIMER is a new modeling and simulation pipeline that integrates transcription regulation with metabolic regulation, demonstrating applicability to both simulated and experimental data.
Article
Microbiology
Dariusz Nowicki, Klaudyna Krause, Patrycja Szamborska, Adrianna Zukowska, Grzegorz M. Cech, Agnieszka Szalewska-Palasz
Summary: Bacterial resistance to known antibiotics poses a serious threat to public health, motivating the search for new therapeutic strategies utilizing compounds from nature. Specific plant metabolites, such as isothiocyanates, have been found to exhibit significant antibacterial effects by inducing the stringent response and amino acid starvation in pathogenic bacteria. Synergistic effects between different isothiocyanates have been observed, leading to a lower minimal inhibitory concentration for bacterial growth inhibition. This unique mode of action also inhibits prophage induction and toxin production in pathogenic strains, suggesting potential therapeutic applications for plant secondary metabolites.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Laura Meyer, Elsa Germain, Etienne Maisonneuve
Summary: The small protein YtfK was identified as a key regulator of SpoT-mediated stringent response in E. coli, regulated by the cAMP-CRP complex. YtfK contributes to SpoT-dependent accumulation of (p)ppGpp and cell survival under glucose starvation.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Nicola Pellicciotta, Matteo Paoluzzi, Dario Buonomo, Giacomo Frangipane, Luca Angelani, Roberto Di Leonardo
Summary: By modulating bacterial motility with light, researchers have found a way to control the transport direction and speed of microscopic particles by adjusting the active pressure gradients. This discovery provides new insights into the potential use of active pressure for controlled transport of microscopic objects.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Prathitha Kar, Sriram Tiruvadi-Krishnan, Jaana Mannik, Jaan Mannik, Ariel Amir
Summary: How cells regulate their cell cycles is a central question for cell biology. This paper presents a study on cell size regulation in Escherichia coli, using conditional independence tests and data on cell size at key cell cycle events. The results suggest that the division event is controlled by the onset of constriction at midcell, and that replication-related processes and additional cues beyond DNA replication play roles in this control.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Alaksh Choudhury, Benoit Gachet, Zoya Dixit, Roland Faure, Ryan T. Gill, Olivier Tenaillon
Summary: Mutations in RNA polymerase can promote growth or maintenance by altering molecular functions, and these mutations can cluster in two modules. Combining mutations from both modules enhances adaptive evolution.
NATURE COMMUNICATIONS
(2023)
Article
Mathematical & Computational Biology
Travis A. Ahn-Horst, Luis Santiago Mille, Gwanggyu Sun, Jerry H. Morrison, Markus W. Covert
Summary: Growth and environmental responses are crucial for organisms' survival and adaptation. A study on a whole-cell model of E. coli found that small molecule feedback inhibition pathways and dysregulated amino acid synthesis pathways play important roles in growth regulation and concentration fluctuations at the single-cell level, respectively.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Hanwen Li, Jinqiang Nian, Shuang Fang, Meng Guo, Xiahe Huang, Fengxia Zhang, Qing Wang, Jian Zhang, Jiaoteng Bai, Guojun Dong, Peiyong Xin, Xianzhi Xie, Fan Chen, Guodong Wang, Yingchun Wang, Qian Qian, Jianru Zuo, Jinfang Chu, Xiaohui Ma
Summary: Nitrogen is a crucial nutrient for plants, but the regulation of nitrogen metabolism and starvation responses in plants is not well understood. This study identifies ARE2 as a key regulator of nitrogen starvation responses in rice.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Article
Multidisciplinary Sciences
Yeonoh Shin, M. Zuhaib Qayyum, Danil Pupov, Daria Esyunina, Andrey Kulbachinskiy, Katsuhiko S. Murakami
Summary: The study reveals the cryo-EM structures of E. coli RNA polymerase and rRNA promoter complex with DksA/ppGpp during open complex formation, providing insights into the key steps of promoter recognition and opening.
NATURE COMMUNICATIONS
(2021)
Article
Immunology
Stefan Tukaj, Jagoda Mantej, Michal Sobala, Katarzyna Potrykus, Zbigniew Tukaj, Detlef Zillikens, Ralf J. Ludwig, Katja Bieber, Michael Kasperkiewicz
Summary: The study found that Hsp70 immunization and anti-Hsp70 antibody treatment can decrease disease severity in a psoriasis-like skin inflammation mouse model by affecting T cell populations. This suggests that Hsp70 may be a promising therapeutic target for psoriasis and other autoimmune dermatoses.
FRONTIERS IN IMMUNOLOGY
(2021)
Editorial Material
Endocrinology & Metabolism
Helen R. Murphy
Editorial Material
Microbiology
Katarzyna Potrykus, Michael Cashel, Gert Bange
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Grzegorz M. Cech, Agnieszka Szalewska-Palasz, Katarzyna Potrykus, Anna Kloska
Summary: The development of P1vir is enhanced in the dksA mutant due to improvements in replication, virion assembly, and less efficient lysis, as shown by RNA sequencing analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Anna Kloska, Grzegorz M. Cech, Dariusz Nowicki, Monika Maciag-Dorszynska, Aleksandra E. Bogucka, Stephanie Markert, Doerte Becher, Katarzyna Potrykus, Paulina Czaplewska, Agnieszka Szalewska-Palasz
Summary: This study investigates the molecular adaptation mechanisms of marine bacteria to osmotic stress, focusing on adjustment at the proteome level. The results show that bacteria adjust at all levels of their biological processes in response to salinity challenges. The accumulation of DNA-binding proteins and increased polyamine uptake are suggested to play a role in protecting the nucleoid against changes in DNA topology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biology
Anoop Narayanan, Manju Narwal, Sydney A. Majowicz, Carmine Varricchio, Shay A. Toner, Carlo Ballatore, Andrea Brancale, Katsuhiko S. Murakami, Joyce Jose
Summary: In this study, a screening strategy for antiviral drugs against SARS-CoV-2 was developed, which involves in-cell protease assay, antiviral and biochemical activity assessments, as well as structural determinations. Several protease inhibitors with low cytotoxicity were identified and their mechanisms of action were examined.
COMMUNICATIONS BIOLOGY
(2022)
Article
Health Care Sciences & Services
Madeleine Benton, Iklil Iman, Kimberley Goldsmith, Angus Forbes, Siew Mooi Ching, Iliatha Papachristou Nadal, Nicola Guess, Helen R. Murphy, Barakatun-Nisak Mohd Yusof, Anisah Baharom, Nur Hafizah Mahamad Sobri, Nurul Iftida Basri, Mazatulfazura Sf Salim, Irmi Zarina Ismail, Faezah Hassan, Khalida Ismail, Boon How Chew
Summary: This study aims to test the feasibility of a digital intervention for type 2 diabetes (T2D) prevention among women with a history of gestational diabetes mellitus (GDM) in Malaysia. The intervention includes a smartphone app and group support, providing tailored information and support to encourage weight loss through adapted dietary intake and physical activity. This will be the first study in Malaysia focusing on T2D prevention among women with GDM using a digital intervention.
JMIR RESEARCH PROTOCOLS
(2022)
Review
Biochemistry & Molecular Biology
Magda Teixeira-Nunes, Pascal Retailleau, Martine Comisso, Vincent Deruelle, Undine Mechold, Louis Renault
Summary: Many pathogens manipulate host cell cAMP signaling pathways to survive and multiply. ExoY toxins, belonging to the nucleotidyl cyclase family, become potent, unregulated enzymes in host cells. This article reviews the common and distinct functional characteristics of different members of the nucleotidyl cyclase family, highlighting the need for further research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
James R. Portman, M. Zuhaib Qayyum, Katsuhiko S. Murakami, Terence R. Strick
Summary: It has been found that the RapA protein can dislodge stalled RNA polymerase from DNA via backtracking, and this process is influenced by supercoiling and torque, inhibited by GreB, and depends on the length of RNA.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Lidiya Lisitskaya, Yeonoh Shin, Aleksei Agapov, Anna Olina, Ekaterina Kropocheva, Sergei Ryazansky, Alexei A. Aravin, Daria Esyunina, Katsuhiko S. Murakami, Andrey Kulbachinskiy
Summary: This study identifies a new class of pAgos that use DNA guides to process RNA targets and can sense mismatches and modifications in the target. The findings broaden our understanding of prokaryotic defense systems and expand the potential application of programmable nucleases in RNA technology.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
Lidiya Lisitskaya, Yeonoh Shin, Aleksei Agapov, Anna Olina, Ekaterina Kropocheva, Sergei Ryazansky, Alexei A. Aravin, Daria Esyunina, Katsuhiko S. Murakami, Andrey Kulbachinskiy
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Zachary F. Mandell, Rishi K. Vishwakarma, Helen Yakhnin, Katsuhiko S. Murakami, Mikhail Kashlev, Paul Babitzke
Summary: The contributions of Rho-dependent and intrinsic transcription termination mechanisms in bacteria were investigated. It was found that NusA and NusG stimulate a significant portion of intrinsic terminators and participate in Rho-dependent termination. Rho was also found to stimulate termination at some intrinsic terminators in vivo. Computational analyses and in vitro experiments provided insights into how Rho stimulates intrinsic terminators.
NATURE MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Monika Karczewska, Patryk Strzelecki, Krystyna Bogucka, Katarzyna Potrykus, Agnieszka Szalewska-Palasz, Dariusz Nowicki
Summary: Urinary tract infections are common bacterial diseases worldwide, with UPECs being the most prominent group among the pathogens responsible. In this study, we examined 118 UPEC isolates to determine their genetic background, antibiotic resistance, and their ability to form biofilms and induce stress responses. Our findings showed that these UPEC strains expressed unique attributes and had a significant ability to form biofilms and accumulate multi-resistance traits, which were crucial for the development of severe infections in a Galleria mellonella model.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Endocrinology & Metabolism
Claire L. Meek, Zoe A. Stewart, Denice S. Feig, Samuel Furse, Sandra L. Neoh, Albert Koulman, Helen R. Murphy
Summary: This study found that maternal hyperglycemia and offspring hyperinsulinism in women with type 1 diabetes during pregnancy are associated with perinatal complications and suboptimal pregnancy outcomes. Metabolomic analysis revealed distinct metabolite profiles for different complications, such as increased carnitines and lipid metabolites in large for gestational age infants, and changes in triacylglycerols or dietary phenols in neonatal hypoglycemia and offspring hyperinsulinism. Altered lipid metabolism is a key feature in type 1 diabetes pregnancy, suggesting the need for new strategies to optimize maternal diet and insulin dosing from the first trimester.