Bacillus subtilis biofilm formation and social interactions

S Arnaouteli, NC Bamford, NR Stanley-Wall… - Nature Reviews …, 2021 - nature.com
Biofilm formation is a process in which microbial cells aggregate to form collectives that are
embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive …

Evolutionary dynamics of natural product biosynthesis in bacteria

MG Chevrette, K Gutiérrez-García… - Natural product …, 2020 - pubs.rsc.org
Covering: 2008 up to 2019 The forces of biochemical adaptive evolution operate at the level
of genes, manifesting in complex phenotypes and the global biodiversity of proteins and …

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

D Esposito, J Weile, J Shendure, LM Starita… - Genome biology, 2019 - Springer
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …

Mechanisms driving spatial distribution of residents in colony biofilms: an interdisciplinary perspective

L Eigentler, FA Davidson… - Open Biology, 2022 - royalsocietypublishing.org
Biofilms are consortia of microorganisms that form collectives through the excretion of
extracellular matrix compounds. The importance of biofilms in biological, industrial and …

Whole-genome sequences from wild-type and laboratory-evolved strains define the alleleome and establish its hallmarks

EA Catoiu, P Phaneuf, J Monk… - Proceedings of the …, 2023 - National Acad Sciences
The genomic diversity across strains of a species forms the genetic basis for differences in
their behavior. A large-scale assessment of sequence variation has been made possible by …

Mechanisms of protein evolution

V Jayaraman, S Toledo‐Patiño, L Noda‐García… - Protein …, 2022 - Wiley Online Library
How do proteins evolve? How do changes in sequence mediate changes in protein
structure, and in turn in function? This question has multiple angles, ranging from …

Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase

JZ Chen, DM Fowler, N Tokuriki - Elife, 2020 - elifesciences.org
Metallo-β-lactamases (MBLs) degrade a broad spectrum of β-lactam antibiotics, and are a
major disseminating source for multidrug resistant bacteria. Despite many biochemical …

The adaptive landscape of a metallo-enzyme is shaped by environment-dependent epistasis

DW Anderson, F Baier, G Yang, N Tokuriki - Nature Communications, 2021 - nature.com
Enzymes can evolve new catalytic activity when environmental changes present them with
novel substrates. Despite this seemingly straightforward relationship, factors other than the …

Collateral fitness effects of mutations

JD Mehlhoff, FW Stearns, D Rohm… - Proceedings of the …, 2020 - National Acad Sciences
The distribution of fitness effects of mutation plays a central role in constraining protein
evolution. The underlying mechanisms by which mutations lead to fitness effects are …

Interaction between mutation type and gene pleiotropy drives parallel evolution in the laboratory

P Ruelens, T Wynands… - … Transactions of the …, 2023 - royalsocietypublishing.org
What causes evolution to be repeatable is a fundamental question in evolutionary biology.
Pleiotropy, ie the effect of an allele on multiple traits, is thought to enhance repeatability by …