Convergent phenotypic evolution towards fosfomycin collateral sensitivity of Pseudomonas aeruginosa antibiotic‐resistant mutants

P Laborda, JL Martínez… - Microbial …, 2022 - Wiley Online Library
The rise of antibiotic resistance and the reduced amount of novel antibiotics support the
need of developing novel strategies to fight infections, based on improving the use of the …

Active compensation for changes in TDH3 expression mediated by direct regulators of TDH3 in Saccharomyces cerevisiae

P Vande Zande, MA Siddiq, A Hodgins-Davis… - Plos …, 2023 - journals.plos.org
Genetic networks are surprisingly robust to perturbations caused by new mutations. This
robustness is conferred in part by compensation for loss of a gene's activity by genes with …

Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells

IA Mellis, ME Melzer, N Bodkin, Y Goyal - Genome biology, 2024 - Springer
Background Cells and tissues have a remarkable ability to adapt to genetic perturbations via
a variety of molecular mechanisms. Nonsense-induced transcriptional compensation, a form …

Progressive transcriptomic shifts in evolved yeast strains following gene knockout

B Jiang, C Xiao, L Liu - Iscience, 2024 - cell.com
Gene knockout disrupts cellular homeostasis, altering gene expression, and phenotypes.
We investigated whether cells return to their pre-knockout transcriptomic state through …

Design principles of multi-map variation in biological systems

JF Poyatos - Physical biology, 2024 - iopscience.iop.org
Complexity in biology is often described using a multi-map hierarchical architecture, where
the genotype, representing the encoded information, is mapped to the functional level …

The role of the Aspergillus nidulans high mobility group B protein HmbA, the orthologue of Saccharomyces cerevisiae Nhp6p

J Ámon, G Varga, I Pfeiffer, Z Farkas, Z Karácsony… - Scientific Reports, 2022 - nature.com
The mammalian HMGB1 is a high-mobility-group B protein, which is both an architectural
and functional element of chromatin. Nhp6p, the extensively studied fungal homologue of …

Dissecting the fitness costs of complex mutations

P Yubero, JF Poyatos - Molecular Biology and Evolution, 2021 - academic.oup.com
The fitness cost of complex pleiotropic mutations is generally difficult to assess. On the one
hand, it is necessary to identify which molecular properties are directly altered by the …

Impairment of transcription factor Gcr1p binding motif perturbs OPI3 transcription in Saccharomyces cerevisiae

R Chidambaram, G Ramachandran… - Journal of Cellular …, 2022 - Wiley Online Library
In Saccharomyces cerevisiae, the transcription factor GCR1 plays a vital role in
carbohydrate metabolism and in the current study we tried to elucidate its role in lipid …

Role of High Mobility Group B protein HmbA, orthologue of yeast Nhp6p in Aspergillus nidulans

J Ámon, G Varga, I Pfeiffer, Z Karácsony, Z Hegedűs… - bioRxiv, 2022 - biorxiv.org
The mammalian HMGB1 protein belongs to the high-mobility-group B (HMG-B) family, which
is not only architectural but also functional element of the chromatin. The fungal counterpart …

Predicting the fitness costs of complex mutations

P Yubero, JF Poyatos - bioRxiv, 2021 - biorxiv.org
The fitness cost of complex pleiotropic mutations is generally difficult to assess. On the one
hand, it is necessary to identify which molecular properties are directly altered by the …