Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis

B Bosch, MA DeJesus, NC Poulton, W Zhang… - Cell, 2021 - cell.com
Antibacterial agents target the products of essential genes but rarely achieve complete
target inhibition. Thus, the all-or-none definition of essentiality afforded by traditional genetic …

Genetic Surveillance of SARS-CoV-2 Mpro Reveals High Sequence and Structural Conservation Prior to the Introduction of Protease Inhibitor Paxlovid

JT Lee, Q Yang, A Gribenko, BS Perrin Jr, Y Zhu… - Mbio, 2022 - Am Soc Microbiol
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to represent a
global health emergency as a highly transmissible, airborne virus. An important coronaviral …

Analysis of selection in protein-coding sequences accounting for common biases

R Del Amparo, C Branco, J Arenas… - Briefings in …, 2021 - academic.oup.com
The evolution of protein-coding genes is usually driven by selective processes, which favor
some evolutionary trajectories over others, optimizing the subsequent protein stability and …

Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria

AK Simonsen - The ISME Journal, 2022 - academic.oup.com
Bacteria have highly flexible pangenomes, which are thought to facilitate evolutionary
responses to environmental change, but the impacts of environmental stress on pangenome …

Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis

C Bei, J Zhu, PH Culviner, M Gan, EJ Rubin… - Nature …, 2024 - nature.com
Transcriptional regulation is a critical adaptive mechanism that allows bacteria to respond to
changing environments, yet the concept of transcriptional plasticity (TP)–the variability of …

Gene evolutionary trajectories in Mycobacterium tuberculosis reveal temporal signs of selection

A Chiner-Oms, MG López… - Proceedings of the …, 2022 - National Acad Sciences
Genetic differences between different Mycobacterium tuberculosis complex (MTBC) strains
determine their ability to transmit within different host populations, their latency times, and …

A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas

ZY Muñoz-Ramirez, B Pascoe… - The ISME …, 2021 - academic.oup.com
Helicobacter pylori is a common component of the human stomach microbiota, possibly
dating back to the speciation of Homo sapiens. A history of pathogen evolution in allopatry …

Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom

Y Wan, E Mills, RCY Leung, A Vieira… - Microbial …, 2021 - microbiologyresearch.org
Antimicrobial resistance in enteric or urinary Escherichia coli is a risk factor for invasive E.
coli infections. Due to widespread trimethoprim resistance amongst urinary E. coli and …

The global success of Mycobacterium tuberculosis modern Beijing family is driven by a few recently emerged strains

C Zhu, T Yang, J Yin, H Jiang, HE Takiff… - Microbiology …, 2023 - Am Soc Microbiol
Strains of the Mycobacterium tuberculosis complex (MTBC) Beijing family aroused concern
because they were often found in clusters and appeared to be exceptionally transmissible …

Global genomic analysis of SARS-CoV-2 RNA dependent RNA polymerase evolution and antiviral drug resistance

A Mari, T Roloff, M Stange, KK Søgaard, E Asllanaj… - Microorganisms, 2021 - mdpi.com
A variety of antiviral treatments for COVID-19 have been investigated, involving many
repurposed drugs. Currently, the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp …