Biology subjects

Chirinos, X.

Publications and source records attributed to Chirinos, X..

3 recordsLinked to original sources

bioRxiv2025

KDM7-mediated oxygen sensing reprograms chromatin to enhance hypoxia tolerance in the root

Roots frequently encounter low oxygen (hypoxia) from soil compaction or water saturation and must adapt to this stress. We investigated how root tip cells sense hypoxia and adjust the meristem epigenome to activate genes that promote tolerance and growth under oxygen limitation. In Arabidopsis root tips, hypoxia tolerance was linked to increased trimethylation of histone H3 at lysine 4 (H3K4me3). We also found that group 7 demethylases (KDM7s) are directly inhibited by hypoxia, and that genetic inactivation of KDM7s, like hypoxia, induces expression of genes essential for meristem survival under oxygen deprivation. We propose that KDM7s function as root-specific oxygen sensors that prime and support hypoxia tolerance.

plant biology↗

bioRxiv2025

Anatomy and habitat shape the oxygen sensing machinery of angiosperms

Hypoxia sensing via the Cys/Arg branch of the N-degron pathway (Cys-NDP) is central for flooding responses in plants, yet how evolutionary and ecological factors have shaped the core oxygen sensing mechanism remains poorly understood. Leveraging the publication of multiple angiosperm genomes, we systematically analysed known Cys-NDP components in 55 angiosperms spanning aquatic, epiphytic, xerophytic, and mesophytic lineages. We also complemented this survey with hypoxia profiling and transcriptomic analyses in a selected panel of plants. This comparative effort revealed variation in Cys-NDP components, with Plant Cysteine Oxidases (PCOs) and group VII Ethylene Response Factors (ERFVIIs) emerging as major sources of diversification. Aquatic monocots displayed complete loss of A-type PCOs and dramatic expansion of a novel clade of ERFVIIs (HREaqua), frequently accompanied by loss or modification of the Cys-degron, uncoupling them from oxygen-dependent turnover. By contrast, xerophytes and epiphytes retained core Cys-NDP elements but showed shared hypoxia-induced gene expression, suggesting endogenous developmental or metabolic pressures for pathway conservation in habitats with limited flooding risk. Across all species, we identified a conserved transcriptional core of 11 orthogroups, including fermentation enzymes and regulatory factors, highlighting the early recruitment of these genes to hypoxia responses. Functional assays confirmed contributions of conserved MYB and LBD transcription factors to hypoxia tolerance in Arabidopsis. Together, our results demonstrate that both habitat and anatomy influence the evolution and deployment of oxygen-sensing networks in angiosperms. While persistent submergence promoted diversification of ERFVIIs and PCOs, retention of the core pathway across lineages points to fundamental roles in coping with endogenous oxygen gradients and fluctuations.

plant biology↗

bioRxiv2025

Manipulating plant oxygen sensing through NCO substitution reveals trade-offs between growth and flooding tolerance

The oxygen-dependent degradation of Ethylene Response Factors VII (ERFVIIs) through the N-degron pathway is central to regulating the transcriptional responses to hypoxia in vascular plants. Plant Cysteine Oxidases (PCOs) control this step by catalysing the oxidation of an N-terminal Cys residue exposed by ERFVIIs. In the present study, we investigated the functional impact of replacing Arabidopsis PCOs with diverse N-terminal cysteine oxidases (NCOs) from across the three eukaryotic kingdoms, hypothesizing that structural and kinetic differences may influence gene regulation of ERFVII targets under hypoxia and thus impact stress tolerance. Combining structural analyses, in vitro biochemical characterisation and in planta complementation assays we observed that not all tested NCOs are functionally equivalent to the endogenous PCOs. In fact, despite the remarkable conservation of catalytic motifs, we identified key differences in enzyme architecture that appear to affect the enzymes capacity to regulate hypoxia responses in plants. Notably, NCO efficiency in oxidising ERFVII peptides inversely correlated with hypoxic gene expression under aerobic conditions and enhanced submergence survival, suggesting that partial ERFVII stabilization primes plants to cope with hypoxia. However, enhanced basal expression of hypoxia-responsive genes in turn correlated negatively with development and biomass accumulation, pointing to a trade-off between growth and stress resilience. Our findings demonstrate that tuning NCO activity can reshape the transcriptional and physiological hypoxia response, suggesting it is possible to enhance plant resilience under fluctuating oxygen conditions through enzyme engineering and precision breeding. Significance statementControl of low oxygen responses to improve crop flooding tolerance is a long-sought objective of molecular plant breeders. The oxygen-dependent oxidation of N-terminal cysteines in transcription factors is thought to be a key step in modulating the transcriptional response to hypoxia. In this study, we tested this hypothesis by substituting endogenous N-terminal cysteine dioxygenases with homologues from different species characterized by highly divergent sequences, structures, and kinetic properties. We show that indeed these variations effectively and predictably influence gene transcription in plants exposed to hypoxia, thereby affecting their tolerance to submergence. However, we also demonstrate that, unexpectedly, these substitutions impact plant growth and development under aerobic conditions, revealing a trade-off between flooding stress resilience and biomass accumulation or yield.

plant biology↗