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Fernandez-Lopez, R.

Publications and source records attributed to Fernandez-Lopez, R..

4 recordsLinked to original sources

HIGH CO2 LEVELS OVERCOME THE NIGHTTIME LETHALITY OF CIRCADIAN MUTANTS IN CYANOBACTERIA

Cyanobacteria have adapted to daily fluctuations in light intensity through a circadian clock that aligns their physiology and metabolism to the external daytime. In the model cyanobacterium Synechococcus elongatus PCC 7942, the rhythm generated by a molecular pacemaker is converted into a global transcriptional oscillation by the central regulator RpaA. Mutants in RpaA and other components have been instrumental in elucidating the clocks molecular architecture and physiological role. Extensive evidence suggests that one of the central functions of circadian regulation is to prevent the accumulation of reactive oxygen species (ROS) during nighttime. However, circadian mutants are unable to grow under natural day/night cycles and require constant illumination, hindering our ability to study the clock function during the night, a phase where circadian regulation is critical for redox homeostasis. Here, we show that the darkness lethality phenotype of circadian mutants can be overcome by high CO2 levels. When grown under a 3% CO2 atmosphere, RpaA-null mutants exhibited growth rates similar to the wt. An analysis of the ROS levels under different CO2 and light intensity conditions revealed carbon scarcity to be the most significant contributor to redox stress. Nighttime ROS accumulation can be modulated by CO2 abundance, an observation that will allow the characterization of heretofore lethal mutants in circadian regulation. The dispensability of the circadian clock in a high CO2 environment suggests that the clock may have evolved as an adaptation to the decrease in atmospheric CO2 levels that occurred after the Great Oxygenation Events, in the Paleoproterozoic era. IMPORTANCECyanobacterial circadian clocks are considered essential for survival under natural day/night conditions, and many circadian mutants are lethal under diel cycles. Results presented here challenge this assumption, showing that these mutants grow normally when CO2 is abundant. This suggests that the major adaptive role of the clock is to manage the redox stress caused by carbon limitation. By separating the effects of carbon availability from circadian control, we identify a key environmental factor that shaped the evolution of biological timekeeping. Using high CO2 to bypass clock dependency will allow the study of circadian function in otherwise lethal mutants. These findings reframe the clock as a specific adaptation to atmospheric carbon, stressing its key role in the regulation of the redox balance.

microbiology↗

Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes

Metabolic dysfunction-associated steatotic liver disease (MASLD) is a multifactorial condition influenced by the gut microbiome (GM). While previous studies have reported inconsistent associations between MASLD and key microbial clades using low-resolution 16S rRNA profiling, we employed high-resolution metagenomic sequencing and multi-marker taxonomic classification across three independent cohorts to identify robust microbial and functional signatures of MASLD. We consistently detected a depletion of Agathobacter rectalis, a known butyrate producer, in MASLD patients. Functionally, MASLD was characterized by a depletion of genes involved in butyrate and methane biosynthesis-particularly within the crotonyl-butyryl-CoA axis-alongside an enrichment of genes driving the production of endogenous alcohols such as ethanol and 1-propanol. Genes encoding these fermentative pathways, often organized in operons like pdu and tor, were more abundant in MASLD samples, indicating a potential shift toward alcohol-producing metabolism. These geno-metabolic changes were accompanied by a broader displacement of beneficial taxa and an increase in accessory gene content across the GM, underscoring the limitations of taxonomy-based disease associations. Many of the differentially abundant genes were also found on plasmids, suggesting that horizontal gene transfer contributes to strain-level metabolic variability relevant to MASLD progression. Our findings support a model in which GM-driven metabolic shifts-rather than taxonomic changes alone-play a central role in MASLD pathogenesis, highlighting the importance of functional and mobile genetic element (MGEs) profiling for uncovering mechanistic links between the microbiome and liver disease.

microbiology↗

Long-term evolution reveals the role of the circadian cycle in the environmental adaptation of cyanobacteria

Circadian clocks synchronize internal cellular states with diurnal rhythms. Widespread in bacteria and eukaryotes, they regulate a variety of physiological processes, from hormone secretion in animals to carbon fixation in photosynthetic organisms. The adaptive role of circadian clocks is assumed to stem from their ability to anticipate environmental change, yet their impact on ecological adaptation remains unclear. Here, we use experimental evolution to study the interplay between fitness and circadian regulation in the model cyanobacterium Synechococcus elongatus PCC 7942. After 1,200 generations under continuous, high-intensity illumination, we obtained a strain that grew six times faster than its ancestral counterpart. Genome sequencing revealed three mutations fixed in the population, two of which replicated the fast-growing phenotype in the wild-type. A deletion in SasA, a key circadian regulator, was essential for fast growth. Transcriptomic and metabolomic analyses revealed that this mutation perturbed the rhythmicity of the cycle, while simultaneously locking the cell in a transcriptomic response to high intensity illumination. A comparison with another fast- growing isolate, UTEX 2973, showed convergent transcriptomic states despite different driving mutations. Our results indicate that the clock acts not only as a timekeeping device, but also as an adaptive mechanism to optimize growth across diverse ecological conditions.

microbiology↗

COPLA, a taxonomic classifier of plasmids

The Plasmid Taxonomic Unit (PTU) concept is an initial step for a natural classification of plasmids. Here we present COPLA, a software for plasmid assignation to existing PTUs. To assess its performance, we used a sample of 1,000 plasmids missing from its current database. Overall, 41% of samples could be assigned an existing PTU (63% within the most abundant order, Enterobacterales), while 4% of samples could help to define new PTUs once COPLA database was updated.

bioinformatics↗