Article
Biochemistry & Molecular Biology
Jegadheeswari Venkadakrishnan, Ganesh Lahane, Arti Dhar, Wei Xiao, Krishna Moorthi Bhat, Tej K. Pandita, Audesh Bhat
Summary: DNA damage tolerance (DDT) pathway suppresses replication fork arrest-induced DNA double strand breaks (DSBs) through translesion DNA synthesis (TLS) and homology-directed DDT mechanisms, with TLS polymerases playing a crucial role. Defects in TLS pathway can lead to various diseases. Apart from their role in DDT pathway, noncanonical functions of TLS polymerases are also important for maintaining genomic stability.
MOLECULAR AND CELLULAR BIOLOGY
(2023)
Article
Microbiology
Mari Tagel, Heili Ilves, Margus Leppik, Karl Jurgenstein, Jaanus Remme, Maia Kivisaar
Summary: The study demonstrates a link between tRNA pseudouridylation and mutation frequency in Pseudomonas species, showing that deficiency in TruA-dependent pseudouridylation increases mutation frequency. This mutagenic effect is not attributed to error-prone DNA polymerases or malfunctioning of DNA repair pathways. It suggests that the elevated mutation frequency in the absence of tRNA pseudouridylation could be due to a more specific response or a cumulative effect of several small effects.
Article
Engineering, Environmental
Xiao-Yang Liu, Shuxia Guo, Thomas Bocklitz, Petra Roesch, Juergen Popp, Han-Qing Yu
Summary: This study developed an approach based on confocal Raman mapping and non-negative matrix factorization analysis to probe the hydrated biofilm matrix in situ. The method was able to resolve the chemical components of the biofilm and visualize their spatial organization. The study found diverse chemical components within different Pseudomonas spp. biofilm matrices and identified their relationship with specific physiological functions and microenvironments.
Article
Environmental Sciences
Huizhong Liu, Sujuan Li, Xiaobao Xie, Qingshan Shi
Summary: This study showed that tetracycline could dose-dependently stimulate biofilm formation in Pseudomonas putida, increasing the bacteria's tolerance to the antibiotic. Additionally, various other antibiotics were found to promote biofilm formation in P. putida, except aminoglycosides. Biofilm formation conferred higher tolerance to specific antibiotics such as tetracyclines and fluoroquinolones in P. putida cells.
ENVIRONMENTAL POLLUTION
(2021)
Article
Environmental Sciences
Mourad Fedeila, Zohra Hachaichi-Sadouk, Luis Fernando Bautista, Raquel Simarro
Summary: Two bacterial strains, Pseudomonas aeruginosa and Pseudomonas putida, isolated from industrial effluents in El-Harrach, Algeria, were able to degrade clopidogrel bisulfate under aerobic conditions. The consortium showed high efficiency in removing clopi-dogrel bisulfate at concentrations ranging from 5 to 1500 mg/L within 96 hours. The study also demonstrated the influence of pH, temperature, and supplemental sources of carbon and nitrogen on the biodegradation of clopidogrel bisulfate.
JOURNAL OF CONTAMINANT HYDROLOGY
(2023)
Article
Microbiology
Eveline-Marie Lammens, Daniel Christophe Volke, Kaat Schroven, Marleen Voet, Alison Kerremans, Rob Lavigne, Hanne Hendrix
Summary: The development of CRISPR-Cas-based engineering technologies has revolutionized the microbial biotechnology field. The alternative Class I Type I-C CRISPR-Cas3 system has been utilized as a highly efficient genome editing tool for Pseudomonas hosts.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
Andrew J. Borchert, Alissa Bleem, Gregg T. Beckham
Summary: By using RB-TnSeq technology, this study identified genes in Pseudomonas putida KT2440 that influenced stress tolerance against lignin-derived compounds, providing promising engineering targets for improving feedstock tolerance in lignin valorization strains.
METABOLIC ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Chelsey M. VanDrisse, Rosalie Lipsh-Sokolik, Olga Khersonsky, Sarel J. Fleishman, Dianne K. Newman
Summary: This study demonstrates that by engineering the structure of PodA protein and combining it with tobramycin, the killing effect on P. aeruginosa can be enhanced, especially on biofilms that are resistant to conventional antibiotic treatment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Jan de Witt, Philipp Ernst, Jochem Gaetegens, Stephan Noack, Davina Hiller, Benedikt Wynands, Nick Wierckx
Summary: In recent years, there has been increasing interest in branched short-chain dicarboxylates (BSCD) such as itaconic acid in medicine and biotechnology. They are used as building blocks for plastics and there is a need for microbial upcycling strategies to provide sustainable solutions. BSCDs also exhibit antibacterial properties and immunomodulatory effects, making them potentially valuable in the medical field. This study focused on understanding the microbial metabolism of BSCDs, specifically the degradation pathway in Pseudomonas aeruginosa PAO1 and its transfer to Pseudomonas putida. The study identified new genes and discovered a potential antimicrobial candidate, 2-hydroxyparaconate (2-HP). This study expands the substrate range of P. putida and highlights the potential applications of BSCDs.
METABOLIC ENGINEERING
(2023)
Article
Multidisciplinary Sciences
Fatemeh Saadati, Shahab Shahryari, Naeema Mohseni Sani, Davoud Farajzadeh, Hossein Shahbani Zahiri, Hojatollah Vali, Kambiz Akbari Noghabi
Summary: The study demonstrates that rhamnolipid biosurfactants extracted from Pseudomonas aeruginosa have good antibacterial and antibiofilm activity against MRSA ATCC6538 bacterial cells, making them promising candidates for therapeutic applications.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Daniel C. Volke, Roman A. Martino, Ekaterina Kozaeva, Andrea M. Smania, Pablo I. Nikel
Summary: The authors developed an enhanced cytidine base editor for efficient genome editing of Gram-negative bacteria. With optimized CRISPR/Cas technologies and streamlined guide RNA processing, they achieved single-nucleotide resolution manipulations and multiplex base editing with high efficiency. The toolset was successfully applied to construct and deconstruct complex phenotypes in Pseudomonas putida, demonstrating its versatility.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Vladyslava Liudkovska, Pawel S. Krawczyk, Aleksandra Brouze, Natalia Guminska, Tomasz Wegierski, Dominik Cysewski, Zuzanna Mackiewicz, Jonathan J. Ewbank, Krzysztof Drabikowski, Seweryn Mroczek, Andrzej Dziembowski
Summary: This study reveals that cytoplasmic polyadenylation is a previously unknown component of the posttranscriptional regulation of innate immunity in animals, enhancing the expression of secreted innate immunity effector proteins.
Article
Immunology
Maria Canive, Gerard Badia-Bringue, Patricia Vazquez, Joseba M. Garrido, Ramon A. Juste, Almudena Fernandez, Oscar Gonzalez-Recio, Marta Alonso-Hearn
Summary: Although the genetic susceptibility to diseases has been extensively studied, the genetic loci and mechanisms that control disease tolerance are still largely unknown. In this study, the associations between host genetics and paratuberculosis (PTB) tolerance in cattle were investigated. The researchers found several single nucleotide polymorphisms associated with PTB tolerance, shedding light on the mechanisms underlying this trait.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Genetics & Heredity
Justin A. Ling, Zach Frevert, M. Todd Washington
Summary: DNA damage can cause replication forks to stall, but cells have evolved translesion synthesis polymerases to incorporate nucleotides opposite DNA lesions. Recent methodological developments, including time-lapse X-ray crystallography, full-ensemble hybrid methods, and cryo-electron microscopy, have enhanced our understanding of the structures and mechanisms of these polymerases.
Article
Infectious Diseases
Seryoung Kim, Satomi Masai, Keiji Murakami, Momoyo Azuma, Keiko Kataoka, Mayu Sebe, Kazuya Shimizu, Tomoaki Itayama, Niwooti Whangchai, Kanda Whangchai, Ikko Ihara, Hideaki Maseda
Summary: This study established an isolation method to evaluate the infection risk of Pseudomonas aeruginosa in the environment using specific culture conditions and primers. The results showed clear differences between environmental and clinical strains, but both had a high potential resistance risk for non-resistant strains.
Article
Biotechnology & Applied Microbiology
Julia Sidorenko, Tatjana Jatsenko, Maia Kivisaar
MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS
(2017)
Article
Multidisciplinary Sciences
Jaleal S. Sanjak, Julia Sidorenko, Matthew R. Robinson, Kevin R. Thornton, Peter M. Visscher
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2018)
Article
Genetics & Heredity
Jian Zeng, Ronald de Vlaming, Yang Wu, Matthew R. Robinson, Luke R. Lloyd-Jones, Loic Yengo, Chloe X. Yap, Angli Xue, Julia Sidorenko, Allan F. McRae, Joseph E. Powell, Grant W. Montgomery, Andres Metspalu, Tonu Esko, Greg Gibson, Naomi R. Wray, Peter M. Visscher, Jian Yang
Article
Genetics & Heredity
James J. Lee, Robbee Wedow, Aysu Okbay, Edward Kong, Omeed Maghzian, Meghan Zacher, Tuan Anh Nguyen-Viet, Peter Bowers, Julia Sidorenko, Richard Karlsson Linner, Mark Alan Fontana, Tushar Kundu, Chanwook Lee, Hui Li, Ruoxi Li, Rebecca Royer, Pascal N. Timshel, Raymond K. Walters, Emily A. Willoughby, Loic Yengo, Maris Alver, Yanchun Bao, David W. Clark, Felix R. Day, Nicholas A. Furlotte, Peter K. Joshi, Kathryn E. Kemper, Aaron Kleinman, Claudia Langenberg, Reedik Magi, Joey W. Trampush, Shefali Setia Verma, Yang Wu, Max Lam, Jing Hua Zhao, Zhili Zheng, Jason D. Boardman, Harry Campbell, Jeremy Freese, Kathleen Mullan Harris, Caroline Hayward, Pamela Herd, Meena Kumari, Todd Lencz, Jian'an Luan, Anil K. Malhotra, Andres Metspalu, Lili Milani, Ken K. Ong, John R. B. Perry, David J. Porteous, Marylyn D. Ritchie, Melissa C. Smart, Blair H. Smith, Joyce Y. Tung, Nicholas J. Wareham, James F. Wilson, Jonathan P. Beauchamp, Dalton C. Conley, Tonu Esko, Steven F. Lehrer, Patrik K. E. Magnusson, Sven Oskarsson, Tune H. Pers, Matthew R. Robinson, Kevin Thom, Chelsea Watson, Christopher F. Chabris, Michelle N. Meyer, David I. Laibson, Jian Yang, Magnus Johannesson, Philipp D. Koellinger, Patrick Turley, Peter M. Visscher, Daniel J. Benjamin, David Cesarini
Letter
Multidisciplinary Sciences
Chloe X. Yap, Julia Sirodenko, Riccardo E. Marioni, Loic Yengo, Naomi R. Wray, Peter M. Visscher
NATURE COMMUNICATIONS
(2018)
Article
Biochemistry & Molecular Biology
Loic Yengo, Julia Sidorenko, Kathryn E. Kemper, Zhili Zheng, Andrew R. Wood, Michael N. Weedon, Timothy M. Frayling, Joel Hirschhorn, Jian Yang, Peter M. Visscher
HUMAN MOLECULAR GENETICS
(2018)
Article
Multidisciplinary Sciences
Angli Xue, Yang Wu, Zhihong Zhu, Futao Zhang, Kathryn E. Kemper, Zhili Zheng, Loic Yengo, Luke R. Lloyd-Jones, Julia Sidorenko, Yeda Wu, Allan F. McRae, Peter M. Visscher, Jian Zeng, Jian Yang
NATURE COMMUNICATIONS
(2018)
Article
Multidisciplinary Sciences
Chloe X. Yap, Julia Sidorenko, Yang Wu, Kathryn E. Kemper, Jian Yang, Naomi R. Wray, Matthew R. Robinson, Peter M. Visscher
NATURE COMMUNICATIONS
(2018)
Correction
Multidisciplinary Sciences
Chloe X. Yap, Julia Sidorenko, Riccardo E. Marioni, Loic Yengo, Naomi R. Wray, Peter M. Visscher
NATURE COMMUNICATIONS
(2018)
Article
Genetics & Heredity
Maciej Trzaskowski, Divya Mehta, Wouter J. Peyrot, David Hawkes, Daniel Davies, David M. Howard, Kathryn E. Kemper, Julia Sidorenko, Robert Maier, Stephan Ripke, Manuel Mattheisen, Bernhard T. Baune, Hans J. Grabe, Andrew C. Heath, Lisa Jones, Ian Jones, Pamela A. F. Madden, Andrew M. McIntosh, Gerome Breen, Cathryn M. Lewis, Anders D. Borglum, Patrick F. Sullivan, Nicholas G. Martin, Kenneth S. Kendler, Douglas F. Levinson, Naomi R. Wray
AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS
(2019)
Article
Multidisciplinary Sciences
Luke R. Lloyd-Jones, Jian Zeng, Julia Sidorenko, Loic Yengo, Gerhard Moser, Kathryn E. Kemper, Huanwei Wang, Zhili Zheng, Reedik Magi, Tonu Esko, Andres Metspalu, Naomi R. Wray, Michael E. Goddard, Jian Yang, Peter M. Visscher
NATURE COMMUNICATIONS
(2019)
Article
Psychiatry
Maria Niarchou, Enda M. Byrne, Maciej Trzaskowski, Julia Sidorenko, Kathryn E. Kemper, John J. McGrath, Michael C. O' Donovan, Michael J. Owen, Naomi R. Wray
TRANSLATIONAL PSYCHIATRY
(2020)
Article
Multidisciplinary Sciences
Joana A. Revez, Tian Lin, Zhen Qiao, Angli Xue, Yan Holtz, Zhihong Zhu, Jian Zeng, Huanwei Wang, Julia Sidorenko, Kathryn E. Kemper, Anna A. E. Vinkhuyzen, Julanne Frater, Darryl Eyles, Thomas H. J. Burne, Brittany Mitchell, Nicholas G. Martin, Gu Zhu, Peter M. Visscher, Jian Yang, Naomi R. Wray, John J. McGrath
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Qian Zhang, Julia Sidorenko, Baptiste Couvy-Duchesne, Riccardo E. Marioni, Margaret J. Wright, Alison M. Goate, Edoardo Marcora, Kuan-lin Huang, Tenielle Porter, Simon M. Laws, Perminder S. Sachdev, Karen A. Mather, Nicola J. Armstrong, Anbupalam Thalamuthu, Henry Brodaty, Loic Yengo, Jian Yang, Naomi R. Wray, Allan F. McRae, Peter M. Visscher
NATURE COMMUNICATIONS
(2020)