Article
Biochemical Research Methods
Stephanie L. Brumwell, Katherine D. Van Belois, Daniel J. Giguere, David R. Edgell, Bogumil J. Karas
Summary: Deinococcus radiodurans has been established as an attractive microbial platform for extremophile biology and industrial bioproduction. The development of a simple and robust conjugation-based DNA transfer method has improved the genomic manipulation and tractability of this species, allowing for the introduction of stable plasmids and successful cloning of a large megaplasmid.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Jordan K. Villa, Runhua Han, Chen-Hsun Tsai, Angela Chen, Philip Sweet, Gabriela Franco, Respina Vaezian, Rok Tkavc, Michael J. Daly, Lydia M. Contreras
Summary: This study identified an sRNA called PprS as a post-transcriptional coordinator of ionizing radiation (IR) recovery in the bacterium Deinococcus radiodurans, playing a crucial role in regulating post-radiation recovery. Knockdown of PprS resulted in reduced survival and growth under IR, highlighting its importance in this process. PprS was found to stabilize transcripts involved in various pathways, presenting an additional layer of sRNA-based control in DNA repair pathways associated with bacterial radioresistance.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Domenica Farci, Patrycja Haniewicz, Dario Piano
Summary: The study found that the S-layer in Deinococcus radiodurans has crystalline regularity in all layers of the cell envelope, indicating its importance as a structural and functional scaffold.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Yi-Chih Chiu, Ting-Syuan Hsu, Chen-Yu Huang, Chun-Hua Hsu
Summary: The study characterized a thermostable urate oxidase, DrUox, with high catalytic efficiency and thermal stability, further enhancing its potential for medical applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Shihao Liu, Fei Wang, Heye Chen, Zhixiang Yang, Yifan Ning, Cheng Chang, Dong Yang
Summary: This study investigated the dynamic changes of protein expression and phosphorylation in Deinococcus radiodurans under heavy ion irradiation using label-free (phospho)proteomics. The results showed significant changes in a large number of proteins and phosphorylation sites, with phosphorylation levels being more sensitive to irradiation. Furthermore, pathways related to RNA metabolism and antioxidation were activated after irradiation, indicating their importance in radiation response. This study provides a basis for subsequent functional and applied studies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Ganesh K. Maurya, Hari S. Misra
Summary: The cisII and cisMP elements in Deinococcus radiodurans contain both origin of replication and parS-like functions, and the secondary genome replicons (chrII and MP) are maintained independent of chrI and play important roles in the radioresistance of the bacterium.
LIFE SCIENCE ALLIANCE
(2021)
Article
Microbiology
Yining Chen, Qing Zhang, Deyu Wang, Yao-Gen Shu, Hualin Shi
Summary: Earth's near space is an extreme environment with high radiation and extreme cold, but many studies have shown that microbes can still survive here. Investigating the factors that affect the survival of microorganisms in near space after exposure to radiation is important for understanding radioresistance mechanisms and long-distance microbial transfer. The results of the study suggest that the growth condition before radiation has a memory effect on the survival of microorganisms.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biochemistry & Molecular Biology
Min-Kyu Kim, Lei Zhao, Soyoung Jeong, Jing Zhang, Jong-Hyun Jung, Ho Seong Seo, Jong-il Choi, Sangyong Lim
Summary: Thioredoxin is a crucial protein in cellular redox control and oxidative stress response, forming part of the Trx system with Trx, TrxR, and NADPH. Bacterial Trx1 and Trx2 have different active sites and structural domains, essential for the redox activity in bacteria.
Review
Biochemistry & Molecular Biology
Aman Kumar Ujaoney, Narasimha Anaganti, Mahesh Kumar Padwal, Bhakti Basu
Summary: Desiccation and ionizing radiation are common environmental stresses that organisms have evolved resistance to. The evolution of desiccation resistance may be linked to ionizing radiation resistance, though evidence is lacking. Additionally, the presence of radiation resistance in hyperthermophiles suggests multiple pathways to radiation resistance.
MOLECULAR MICROBIOLOGY
(2023)
Article
Environmental Sciences
T. Manobala, Sudhir K. Shukla, T. Subba Rao, M. Dharmendira Kumar
Summary: This study focuses on the kinetic modeling of uranium biosorption by Deinococcus radiodurans biofilm biomass, indicating the process is spontaneous and exothermic. The sorption of U(VI) by D. radiodurans biofilm biomass is suggested to follow a pseudosecond-order reaction. Chemical modifications in surface functional groups of the biofilm biomass significantly impact uranium binding capacity.
Article
Microbiology
Elena K. Gaidamakova, Ajay Sharma, Vera Y. Matrosova, Olga Grichenko, Robert P. Volpe, Rok Tkavc, Isabel H. Conze, Polina Klimenkova, Irina Balygina, William H. Horne, Cene Gostincar, Xiao Chen, Kira S. Makarova, Igor Shuryak, Chandra Srinivasan, Belinda Jackson-Thompson, Brian M. Hoffman, Michael J. Daly
Summary: The oxidative damage theory by Denham Harman suggests that superoxide radicals play a central role in aging and radiation injury, with Mn2+-dependent superoxide dismutase (MnSOD) being the main scavenger. However, research on radiation-resistant organisms like Caenorhabditis elegans and Deinococcus radiodurans shows that MnSOD may not be essential for longevity or radiation resistance. Instead, these organisms accumulate small-molecule Mn2+-antioxidant complexes which could be the primary defense against reactive oxygen species, potentially complementing or even replacing MnSOD.
Article
Microbiology
Reema Chaudhary, Swathi Kota, Hari S. Misra
Summary: This study reveals that the Ser/Thr protein kinase RqkA in Deinococcus radiodurans can phosphorylate the cell division protein DivIVA, thereby regulating its activity and cellular dynamics. This finding contributes to our understanding of the cell cycle regulation mechanism in this bacterium.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
M. Sudharsan, N. Rajendra Prasad, G. Kanimozhi, B. S. Rishiikeshwer, G. R. Brindha, Anindita Chakraborty
Summary: This study investigates the survival mechanism of the gram-positive bacterium Deinococcus radiodurans in a radiation environment. The results show that the redox status, antioxidant enzyme activities, and metabolite content play crucial roles in the radiation survival of D. radiodurans.
MICROBIOLOGICAL RESEARCH
(2022)
Article
Genetics & Heredity
Sun-Wook Jeong, Min-Kyu Kim, Lei Zhao, Seul-Ki Yang, Jong-Hyun Jung, Heon-Man Lim, Sangyong Lim
Summary: Deinococcus radiodurans is highly resistant to ionizing radiation and has exceptional DNA repair abilities. RecG helicase plays important roles in DNA repair, recombination, and replication. The QPW residues in DrRecG facilitate its association with DNA junctions, enhancing its DNA repair efficiency.
FRONTIERS IN GENETICS
(2021)
Article
Biology
Anna Seck, Salvatore De Bonis, Christine Saint-Pierre, Didier Gasparutto, Jean-Luc Ravanat, Joanna Timmins
Summary: This study investigates the nucleotide excision repair (NER) pathway in Deinococcus radiodurans, a radiation resistant bacterium. By reconstituting an in vitro NER system using UvrABC proteins, the authors were able to determine the kinetics of repair on different DNA substrates and the order and precise sites of incisions. This newly developed assay provides valuable insights into the mechanisms of DNA damage recognition and repair in bacteria.
COMMUNICATIONS BIOLOGY
(2022)
Article
Evolutionary Biology
Kathryn M. Stevens, Antoine Hocher, Tobias Warnecke
Summary: Histones play important roles in eukaryotes by regulating chromatin states and DNA accessibility. Histone variants also exist in archaea, but their functions are poorly understood. Studying the archaeon Thermococcus kodakarensis, researchers have found that the histones HTkA and HTkB exhibit different DNA-binding behaviors and elicit unique transcriptional responses. Evolutionary analysis reveals the conservation of these two paralogs throughout the Thermococcales order. The findings support the idea of convergent evolution between archaea and eukaryotes and suggest the presence of diverged histone-fold proteins in some Thermococcales genomes.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Biophysics
Jacob B. Swadling, Tobias Warnecke, Kyle L. Morris, Alexis R. Barr
Summary: Balanced proliferation-quiescence decisions are crucial for normal development and tissue homeostasis, but dysregulation can lead to tumorigenesis. Cyclin/Cyclin-dependent kinases (Cdks) play a key role in driving cell proliferation cycles. Cdk inhibitors (CKIs) p21(Cip1)(/Waf1), p27(Ki)(p1), and p57(Kip2) bind to Cyclin/Cdks and inhibit Cdk activity. Tyrosine phosphorylation of CKIs, in response to mitogenic signaling, affects the activation of specific Cyclin/Cdks. However, the impact of CKI tyrosine phosphorylation on Cdk activity varies among different CKIs.
BIOPHYSICAL JOURNAL
(2022)
Review
Medicine, Research & Experimental
David Mas-Ponte, Marcel McCullough, Fran Supek
Summary: Genome sequencing is a powerful tool for detecting DNA repair failures in tumors and understanding their underlying mechanisms. Computational studies have revealed different mutation patterns resulting from failed DNA repair pathways, which can vary across different cancer types and genetic backgrounds. Deficiencies in DNA mismatch repair (MMR) can impact both cancer evolution and treatment outcomes.
Article
Multidisciplinary Sciences
Miguel M. Alvarez, Josep Biayna, Fran Supek
Summary: Research indicates that TPS3-associated break toxicity is higher in genomic regions with active chromatin, while DSB repair pathway choice and DNA sequence context also play a role in toxicity. The differential toxicity of sgRNA-targeted sites can reduce the power of genetic screens to detect conditional essentiality.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Isidoro Feliciello, Edyta Dermic, Helena Malovic, Sinisa Ivankovic, Davor Zahradka, Sven Ljubic, Alfredo Procino, Damir Dermic
Summary: Bacterial SSB proteins play an essential role in DNA metabolism, and their gene expression is SOS-dependent under radiation and stress conditions. However, under normal bacterial growth, the expression of the ssb gene is not linked to SOS induction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Antoine Hocher, Guillaume Borrel, Khaled Fadhlaoui, Jean-Francois Brugere, Simonetta Gribaldo, Tobias Warnecke
Summary: The study reveals that growth temperature is a significant determinant of nucleoid-associated protein abundance, with different organisms having diverse compositions of these proteins. High levels of chromatinization have evolved as a mechanism to prevent uncontrolled helix denaturation at higher temperatures.
NATURE MICROBIOLOGY
(2022)
Article
Biology
Bruno Fito-Lopez, Marina Salvadores, Miguel-Martin Alvarez, Fran Supek
Summary: TP53 is a tumor suppressor gene that is mutated in approximately half of all human cancers. In this study, a large-scale statistical analysis was conducted on transcriptomes of around 7,000 tumors and 1,000 cell lines, revealing that 12% of tumors and 8% of cancer cell lines phenocopy TP53 loss. The study also identified USP28 gene deletions as a likely cause of TP53 functional impairment in various types of tumors.
Article
Fisheries
Ines Haberle, Lav Bavcevic, Tin Klanjscek
Summary: Individual performance determines population dynamics. The condition index, a measure of individual performance, has been recommended as a tool in fisheries management and conservation. However, the lack of understanding of the relationship between individual-level processes and population-level responses hinders its adoption. In this study, we use composite modeling to link individual condition to population status and explore the effects of fishing pressure on the condition index.
FISH AND FISHERIES
(2023)
Article
Biology
Ksenija Zahradka, Jelena Repar, Damir Dermic, Davor Zahradka
Summary: This study investigated the postsynaptic stage of transductional recombination, particularly in the less well-studied RecFOR pathway, through transduction experiments and mutant analysis. It was found that RecG and RadA proteins have a redundant role in transductional recombination via the RecFOR pathway, and they functionally interact with PriA during initiation of recombination-dependent replication.
PERIODICUM BIOLOGORUM
(2022)
Article
Microbiology
Ksenija Zahradka, Jelena Repar, Damir Dermic, Davor Zahradka
Summary: Homologous recombination repairs potentially lethal DNA lesions, such as double-strand DNA breaks (DSBs) and single-strand DNA gaps (SSGs). In Escherichia coli, DSB repair is initiated by the RecBCD enzyme, which resects double-strand DNA ends and loads RecA recombinase onto the emerging single-strand (ss) DNA tails. SSG repair is mediated by the RecFOR protein complex, which loads RecA onto the ssDNA segment of gaped duplex. The study characterised cytological changes in various recombination mutants of E. coli after three different DNA-damaging treatments: I-SceI endonuclease expression, gamma-irradiation, and UV-irradiation. The results show the importance of chromosome morphology as a valuable marker in genetic analyses of recombinational repair in E. coli.
Meeting Abstract
Biochemistry & Molecular Biology
David Mas-Ponte, Fran Supek
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
Meeting Abstract
Biochemistry & Molecular Biology
Marina Salvadores, Francisco Fuster-Tormo, Fran Supek
EUROPEAN JOURNAL OF HUMAN GENETICS
(2022)
