Biology subjects

Gonzalez-Delgado, A.

Publications and source records attributed to Gonzalez-Delgado, A..

7 recordsLinked to original sources

bioRxiv2026

Cell wall charge gates iron availability in plant roots

Plants acquire essential mineral nutrients from the soil, yet these elements must first traverse the extracellular matrix of the root before reaching the cell surface. How the physical properties of this extracellular compartment influence nutrient distribution and availability remains poorly understood. In plants, this extracellular matrix is formed by the cell wall, which carries a dynamically regulated negative charge that can change during development and in response to environmental cues. Here we demonstrate that cell wall charge functions as a tunable electrostatic gate that determines how iron is partitioned between retention and bioavailability. This decoupling between iron abundance and availability reveals a fundamental tradeoff imposed by extracellular electrostatics. A mechanistic diffusion-binding model shows that increasing wall charge inherently enhances iron sequestration while limiting its mobility at the cell surface. Genetic perturbation of pectin de-methylesterification validates this principle in vivo. Moreover, iron limitation itself triggers active remodeling of cell wall charge, dynamically shifting the balance toward increased iron accessibility. Together, these findings identify the plant cell wall as an active regulator of nutrient homeostasis rather than a passive barrier. By dynamically modulating extracellular electrostatics, roots control iron partitioning and bioavailability, uncovering a new physical layer of regulation in plant mineral nutrition. One-Sentence SummaryThe plant cell wall operates as a tunable electrostatic gate that buffers and releases iron through spatially and environmentally regulated charge dynamics.

plant biology↗

bioRxiv2026

Differential photoperiodic control of morning and evening expressed transcripts in tomato

Photoperiod, the daily duration of light, is a key environmental cue that varies with season and latitude. Photoperiod signals profoundly influence plant growth and development, and play a central role in crop adaptation across latitudes. Deciphering how plants perceive these seasonal light cues at the molecular level is essential for understanding crop evolution and shaping their geographical distribution. In this study, we investigated how photoperiod influences gene expression dynamics in tomato (Solanum lycopersicum) by performing an RNA-seq time-course across three photoperiod regimes, sampling at two-hour intervals. We use isogenic lines segregating for wild alleles of genes involved in circadian rhythm domestication in tomato to describe their contributions to the circadian clock and flowering time pathways. The high temporal resolution of our experiment allowed precise characterization of transcriptional dynamics and their responses to photoperiod, including shifts in phase, amplitude, and waveform. We found that most transcripts time their expression to dawn or approximately 12 hours later, resulting in a systematic misalignment between evening transcripts and the actual timing of dusk. Morning- and evening-phased transcripts differ markedly in expression levels and waveform responses to changes in photoperiod. Together, these patterns suggest that morning transcripts sense photoperiod transcriptionally, and serve as zeitgeber references for evening transcripts, that could measure photoperiod length by coincidence with external cues. Together, our results provide new insight into the molecular basis of photoperiodic adaptation in plants.

plant biology↗

bioRxiv2025

Reverse transcribed ssDNA derepresses translation of a retron antiviral protein

Retrons are bacterial immune systems that prevent the spread of phages by initiating a toxic response within infected hosts. All previously characterized retrons produce high levels of multicopy single-stranded DNA (msDNA) in the cell by reverse transcription, which acts as an antitoxin in the absence of phage infection. However, we describe here a non-canonical mechanism for Type VI retrons, which do not produce detectable msDNA in the absence of phage, yet still provide phage defense. Focusing primarily on Retron-Vpa2, a Type VI retron from Vibrio parahaemolyticus, we show broad defense against phages and identify triggers of the system within phage recombination systems. Within the Retron-Vpa2 operon, we find a highly enriched, structured transcript that we term a hybrid RNA (hyRNA), which contains both the retrons reverse transcription template and a translationally repressed toxic effector coding sequence. We find that phage infection induces the accumulation of high levels of msDNA and that this msDNA is necessary for derepressing translation of the antiviral toxin. These findings present key biological and mechanistic insights into a distinct group of retrons while highlighting the diversity of systems that participate in bacterial immunity.

microbiology↗

bioRxiv2025

Genome editing of phylogenetically distinct bacteria using portable retron-mediated recombineering

Advanced genome editing technologies have enabled rapid and flexible rewriting of the Escherichia coli genome, benefiting fundamental biology and biomanufacturing. Unfortunately, some of the most useful technologies to advance genome editing in E. coli have not yet been ported into other bacterial species. For instance, the addition of bacterial retrons to the genome editing toolbox has increased the efficiency of recombineering in E. coli by enabling sustained, abundant production of ssDNA recombineering donors by reverse transcription that install flexible, precise edits in the prokaryotic chromosome. To extend the utility of this technology beyond E. coli, we surveyed the portability and versatility of retron-mediated recombineering across three different bacterial phyla (Proteobacteria, Bacillota and Actinomycetota) and a total of 15 different species. We found that retron recombineering is functional in all species tested, reaching editing efficiencies above 20% in six of them, above 40% in three of them, and above 90% in two of them. We also tested the extension of the recombitron architecture optimizations and strain backgrounds in a subset of hosts to additionally increase editing rates. The broad recombitron survey carried out in this study forms the basis for widespread use of retron-derived technologies through the whole Bacteria domain.

bioengineering↗

bioRxiv2024

An experimental census of retrons for DNA production and genome editing

Retrons are bacterial immune systems that use reverse transcribed DNA as a detector of phage infection. They are also increasingly deployed as a component of biotechnology. For genome editing, for instance, retrons are modified so that the reverse transcribed DNA (RT-DNA) encodes an editing donor. Retrons are commonly found in bacterial genomes; thousands of unique retrons have now been predicted bioinformatically. However, only a small number have been characterized experimentally. Here, we add substantially to the corpus of experimentally studied retrons. We synthesized >100 previously untested retrons to identify the natural sequence of RT-DNA they produce, quantify their RT-DNA production, and test the relative efficacy of editing using retron-derived donors to edit bacterial genomes, phage genomes, and human genomes. We add 62 new empirically determined, natural RT-DNAs, which are not predictable from the retron sequence alone. We report a large diversity in RT-DNA production and editing rates across retrons, finding that top performing editors outperform those used in previous studies, and are drawn from a subset of the retron phylogeny.

bioengineering↗

bioRxiv2023

Simultaneous multi-site editing of individual genomes using retron arrays

Our understanding of genomics is limited by the scale of our genomic technologies. While libraries of genomic manipulations scaffolded on CRISPR gRNAs have been transformative, these existing approaches are typically multiplexed across genomes. Yet much of the complexity of real genomes is encoded within a genome across sites. Unfortunately, building cells with multiple, non-adjacent precise mutations remains a laborious cycle of editing, isolating an edited cell, and editing again. Here, we describe a technology for precisely modifying multiple sites on a single genome simultaneously. This technology - termed a multitron - is built from a heavily modified retron, in which multiple donor-encoding msds are produced from a single transcript. The multitron architecture is compatible with both recombineering in prokaryotic cells and CRISPR editing in eukaryotic cells. We demonstrate applications for this approach in molecular recording, genetic element minimization, and metabolic engineering.

bioengineering↗

bioRxiv2021

UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions

Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.

evolutionary biology↗