Article
Multidisciplinary Sciences
An N. T. Nguyen, Laura C. Woods, Rebecca Gorrell, Shamitraa Ramanan, Terry Kwok, Michael J. McDonald
Summary: Horizontal gene transfer is vital for microbial evolution, yet we have limited knowledge about the fitness effects and dynamics of these transferred genetic variants. Through evolutionary experiments on laboratory populations of Helicobacter pylori, which naturally take up DNA from their environment, we measured the fitness effects of thousands of transferred genetic variants. Our findings reveal that natural transformation increases the rate of adaptation but comes with a significant genetic load. However, recombination bypasses this cost by enhancing selection efficiency through separating harmful and beneficial genetic variants. Our results demonstrate that adaptation with horizontal gene transfer, which is pervasive in natural microbial populations, is influenced by a combination of selection, recombination, and genetic drift that existing evolutionary models fail to account for.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Biochemistry & Molecular Biology
Gordon Rix, Chang C. Liu
Summary: Traditional approaches to gene evolution have limitations in scale and depth, but engineered genetic systems that enhance mutation rates provide new strategies for exploring gene sequence space and adaptability. Different architectures for in vivo hypermutation can facilitate evolutionary search scale and depth, offering new opportunities in protein evolution and engineering.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Alita R. Burmeister, Eddy Tzintzun-Tapia, Carli Roush, Ivan Mangal, Roxanna Barahman, Robert D. Bjornson, Paul E. Turner
Summary: Bacteriophages have potential for treating antibiotic-resistant bacterial infections by evolving to better infect bacterial cells. The phage U136B can induce bacteria to lose or modify the TolC protein, reducing antibiotic resistance. This study found that U136B can evolve to higher adsorption rates, improving its infection ability. Understanding phage evolution is crucial for developing effective phage therapies.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Xing-ping Lai, Shuai Zhang, Peng-fei Shan, Feng Cui, Yan-bin Yang, Rui Bai
Summary: By using different in-situ modification measures, the properties of rocks can be effectively controlled, and hard-rock softening or soft-rock hardening can be achieved by changing the physical and mechanical parameters of rock samples. In rock burst prevention, filling materials such as non newtonian fluid can increase the energy of the post-peaking phase of rocks and slow down the intensity of energy release.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Brian Iaffaldano, Jakob Reiser
Summary: Directed evolution is a powerful method for protein engineering, but translating results from bacterial and yeast systems to higher organisms can be challenging. Recent advancements in hypermutation tools now allow for targeted mutations in plant and animal cells, which opens up new possibilities for evolving biological molecules such as proteins in relevant cellular contexts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Medicinal
Melissa Standley, Vincent Blay, Violeta Beleva Guthrie, Jay Kim, Audrey Lyman, Andres Moya, Rachel Karchin, Manel Camps
Summary: Multiple mutations often have non-additive (epistatic) phenotypic effects and adaptive evolution is rich in epistatic interactions. The relationship between thermodynamic stability and epistasis, as well as the coupling between protein positions, has been explored.
ACS INFECTIOUS DISEASES
(2022)
Article
Chemistry, Medicinal
Melissa Standley, Vincent Blay, Violeta Beleva Guthrie, Jay Kim, Audrey Lyman, Andres Moya, Rachel Karchin, Manel Camps
Summary: This study investigates the role of epistasis in genetic adaptation using the evolution of cefotaxime resistance in TEM-1 beta-lactamase variants as a model. The results demonstrate that gain-of-function mutations are enriched in sign and reciprocal sign epistasis, which can be inferred solely based on sequence data. Additionally, there is a significant relationship between epistasis and the structural and dynamic coupling of protein positions.
ACS INFECTIOUS DISEASES
(2022)
Article
Multidisciplinary Sciences
Fabienne Benz, Alex R. Hall
Summary: Antibiotic resistance on plasmids is a pressing global health problem. The stability of plasmids varies among clinical plasmids and bacteria, and this variability can rapidly change the likelihood of different bacterium-plasmid combinations spreading.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Genetics & Heredity
Laura Veschetti, Angela Sandri, Cristina Patuzzo, Paola Melotti, Giovanni Malerba, Maria M. Lleo
Summary: Achromobacter species exhibit different adaptive mechanisms in establishing chronic infections in cystic fibrosis patients, with occasional isolates lacking functional genes and chronic isolates showing high rates of hypermutation. Some mechanisms may be more useful for chronic colonization.
MICROBIAL GENOMICS
(2021)
Article
Biology
Kenneth B. Hoehn, Jackson S. Turner, Frederick Miller, Ruoyi Jiang, Oliver G. Pybus, Ali H. Ellebedy, Steven H. Kleinstein
Summary: The study found that after seasonal influenza vaccination, GC B cell lineages often exhibit measurable evolution, suggesting that the poor efficacy of seasonal influenza vaccines is not solely due to the inhibition of vaccine-specific B cell evolution.
Article
Genetics & Heredity
Semen A. Leyn, Jaime E. Zlamal, Oleg V. Kurnasov, Xiaoqing Li, Marinela Elane, Lourdes Myjak, Mikolaj Godzik, Alban de Crecy, Fernando Garcia-Alcalde, Martin Ebeling, Andrei L. Osterman
Summary: Understanding the dynamics and mechanisms of acquired drug resistance is crucial for optimizing current therapies and developing novel ones. Through experimental evolution and genomic sequencing, it was found that E. coli develops robust resistance to triclosan mainly through missense mutations in the fabI gene, with other mutations occurring at earlier stages.
MICROBIAL GENOMICS
(2021)
Article
Multidisciplinary Sciences
Qian Li, Shang Chen, Kui Zhu, Xiaoluo Huang, Yucheng Huang, Zhangqi Shen, Shuangyang Ding, Danxia Gu, Qiwen Yang, Hongli Sun, Fupin Hu, Hui Wang, Jiachang Cai, Bing Ma, Rong Zhang, Jianzhong Shen
Summary: Acquisition of resistance to one antibiotic can sometimes increase susceptibility to a second antibiotic. In this study, it was found that vancomycin-resistant Enterococcus faecium strains showed remarkable increase in susceptibility to pleuromutilin antibiotics (such as lefamulin). The trade-off between vancomycin and pleuromutilins is mediated by epistasis between van gene cluster and msrC, suggesting pleuromutilins may be useful in treating vancomycin-resistant E. faecium infections.
NATURE COMMUNICATIONS
(2022)
Review
Microbiology
John P. Pribis, Yin Zhai, P. J. Hastings, Susan M. Rosenberg
Summary: This article reviews recent advances in antibiotic-induced mutagenesis, discussing the roles of ROS, SOS and general stress responses, and multichromosome cells in stress-response-induced repair of DNA breaks. It also explores other evolvable subpopulations and potential targets for drugs to slow down the evolution of antibiotic resistance.
Article
Biotechnology & Applied Microbiology
Bailey A. A. Fitzgerald, Ayman Wadud, Zachary Slimak, Joan L. L. Slonczewski
Summary: This study investigated the adaptive response of E. faecalis strains to different pH conditions. It was found that acid-adapted strains had mutations in the fusA gene which resulted in decreased resistance to fusidic acid. High pH-adapted strains had mutations in genes related to phosphate transport and pyrimidine biosynthesis, leading to enhanced growth at high pH but decreased growth at low pH.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Joao Botelho
Summary: This study summarizes over 13,000 chromosomally integrated mobile genetic elements (ciMGEs) from more than 20,000 bacterial and archaeal genomes. It reveals that although integrative and conjugative/mobilizable elements (ICEs) are the most important ciMGEs for defense systems, virulence, and antimicrobial resistance genes, integrative mobilizable elements (IMEs) outnumber ICEs. Furthermore, it shows that defense systems, antimicrobial resistance, and virulence genes are negatively correlated in both ICEs and IMEs. Additionally, multiple ciMGEs form heterogeneous communities and challenge inter-phylum barriers.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Amy G. Prater, Heer H. Mehta, Abigael J. Kosgei, William R. Miller, Truc T. Tran, Cesar A. Arias, Yousif Shamoo
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2019)
Article
Biochemical Research Methods
Stephanie D. Cole, Kathryn Beabout, Kendrick B. Turner, Zachary K. Smith, Vanessa L. Funk, Svetlana V. Harbaugh, Alvin T. Liem, Pierce A. Roth, Brian A. Geier, Peter A. Emanuel, Scott A. Walper, Jorge L. Chavez, Matthew W. Lux
ACS SYNTHETIC BIOLOGY
(2019)
Article
Microbiology
Heer H. Mehta, Yousif Shamoo
Article
Microbiology
Amy G. Prater, Heer H. Mehta, Kathryn Beabout, Adeline Supandy, William R. Miller, Truc T. Tran, Cesar A. Arias, Yousif Shamoo
Summary: The LiaFSR signaling pathway plays a crucial role in mediating daptomycin resistance in enterococci, as the lack of a functional pathway can lead to hypersusceptibility. Knocking out LiaFSR signaling significantly delays the onset of resistance, but eventually resistance can emerge through various alternative mechanisms influenced by the environment.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Biochemical Research Methods
Steven M. Blum, Marilyn S. Lee, Glory E. Mgboji, Vanessa L. Funk, Kathryn Beabout, Svetlana Harbaugh, Pierce A. Roth, Alvin T. Liem, Aleksandr E. Miklos, Peter A. Emanuel, Scott A. Walper, Jorge Luis Chavez, Matthew W. Lux
Summary: The performance of cell-free expression systems varies significantly under different matrix materials, highlighting the importance of selecting suitable matrices. Adjusting the rehydration volume of lyophilized reactions can enhance reaction speed, with minimal impact of different matrices. The application of cell-free expression systems holds great potential for on-site practice.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biochemical Research Methods
Kathryn Beabout, Casey B. Bernhards, Meghna Thakur, Kendrick B. Turner, Stephanie D. Cole, Scott A. Walper, Jorge L. Chavez, Matthew W. Lux
Summary: Bacterial mechanisms have been reengineered as sensors for detecting heavy metals, with optimization using cell-free expression systems to achieve improved sensitivity and specificity. Different approaches to sensor optimization may impact specificity and sensitivity, and combining DNA from multiple sensors can enable detection of multiple target substances simultaneously.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Chemistry, Medicinal
Seokju Seo, Saoirse Disney-McKeethen, Ramya Ganiga Prabhakar, Xinhao Song, Heer H. Mehta, Yousif Shamoo
Summary: The use of monodisperse microdroplets in experimental evolution has shown to provide better control over environmental conditions and reveal potential new evolutionary trajectories and dynamics, including large-scale chromosomal rearrangements and amplifications. Microdroplet emulsions, with their advantages in automation and condition control, offer a high-throughput method for biomarker identification and preclinical evaluation.
ACS INFECTIOUS DISEASES
(2022)
Article
Microbiology
Adeline Supandy, Heer H. Mehta, Truc T. Tran, William R. Miller, Rutan Zhang, Libin Xu, Cesar A. Arias, Yousif Shamoo
Summary: Infections caused by vancomycin-resistant Enterococcus faecium (VREfm) are a significant public health threat. The study investigates the potential for VREfm to develop resistance to the combination therapy of daptomycin (DAP) and fosfomycin (FOS), and whether there are genetic drivers that may decrease the efficacy of the combination or delay the onset of resistance. The results show that the combination therapy can effectively inhibit VREfm without substantial cross-drug epistasis, and the addition of FOS can prolong the efficacy of DAP and slow down DAP resistance.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Microbiology
Heer H. Mehta, David Ibarra, Christopher J. Marx, Craig R. Miller, Yousif Shamoo
Summary: Combination antimicrobial therapy has been found to accelerate the evolution of dual resistance in Francisella tularensis, a causative agent of tularemia. This study suggests that the use of non-interacting drugs together may render them ineffective due to mutational switch-backs that enhance the evolution of resistance.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Materials Science, Biomaterials
Kathryn Beabout, Amy M. Ehrenworth Breedon, Steven M. Blum, Aleksandr E. Miklos, Matthew W. Lux, Jorge L. Chavez, Michael S. Goodson
Summary: Bile acids play a crucial role in digestion and human health and can serve as biomarkers for monitoring health and detecting fecal contamination in water sources. By optimizing and transferring the expression of the sensor, its sensitivity and utility have been significantly improved.
ACS BIOMATERIALS SCIENCE & ENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Ukjin Kwon, Hsin-Ho Huang, Jorge L. Chavez, Kathryn Beabout, Svetlana Harbaugh, Domitilla Del Vecchio
Summary: Ratiometric gene expression response is achieved in Escherichia coli bacteria using the incoherent merger network, where one input molecule activates the output protein and the other molecule activates an intermediate protein that enhances the output's degradation. The response is linear to the ratio of input molecules' levels and robust to global perturbations in cellular components.
NUCLEIC ACIDS RESEARCH
(2023)
Meeting Abstract
Chemistry, Multidisciplinary
Casey Bernhards, Kendrick Turner, Kathryn Beabout, Jorge Chavez, Scott Walper, Matthew Lux
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY
(2019)