Biology subjects

Arce, A. L.

Publications and source records attributed to Arce, A. L..

7 recordsLinked to original sources

bioRxiv2026

Isogenic reciprocal grafts with transgenic HaHB11 plants dissect shoot and root contributions to yield in field-grown soybean: a multi-omic study

Soybean must coordinate root and shoot signals to optimize yield. Grafting is a powerful tool to study this communication. However, most studies compare contrasting genotypes and cannot separate genotype from graft combination effects. Here we used isogenic soybean lines to dissect root and shoot contributions in the field. These lines differ from controls in a single gene, either HaHB11 or HaHB4, two sunflower HD-Zip I transcription factors associated with increased grain number. Unexpectedly, heterografted plants outperformed homografts in several yield-related traits, an effect not previously documented in soybean. This advantage was reproduced with both HaHB11 and HaHB4 scions, suggesting the effect is not gene-specific. Under non-stress conditions the scion governed yield-related traits, particularly pod number, as well as the leaf transcriptome, whereas both organs left subtle metabolic signatures. The root contribution was minor and confined to the R6-R7 transition, where it was specific to HaHB11. The highest-yielding combination was a control rootstock with an HaHB11 scion (CH11), which increased grain number by [~]30% over the best homograft. CH11 showed higher stomatal conductance and lower leaf temperature; yet CH11 and HaHB11 homografts were remarkably similar, sharing higher stomatal density, differing in only four leaf-expressed genes, and lacking a metabolomic signature. Thus, under non-stress conditions, soybean grain number is governed by the scion and the graft combination, and accompanied by early physiological differences rather than by leaf molecular reprogramming.

plant biology↗

bioRxiv2026

The segregase CDC48 integrates blue light and hormonal cues to regulate photomorphogenesis in Arabidopsis

Photomorphogenesis allows plants to adjust growth to ambient light conditions and relies on protein quality control to ensure the timely turnover of signaling components. The conserved AAA+ ATPase CDC48, along with its cofactors NPL4 and UFD1, is a crucial regulator of proteasomal degradation. While well characterized in other organisms, its role in plant development remains largely unexplored. Here, we show that CDC48 is required for blue light-mediated photomorphogenesis in Arabidopsis. Under blue light, CDC48A accumulates at the plasma membrane and in the nucleus, and cdc48a mutants fail to repress hypocotyl elongation properly. Similar phenotypes are observed upon inhibition of CDC48 or in npl4 and ufd1 mutants. Genetic and biochemical analyses further reveal that CDC48A negatively regulates gibberellin (GA) signaling. Consistently, UFD1 directly interacts with the GA receptor GID1 to promote its degradation. Together, these findings demonstrate that CDC48A integrates light and hormonal cues through protein homeostasis to regulate photomorphogenic development.

plant biology↗

bioRxiv2024

The Nuclear Pore Complex acts as a hub for pri-miRNA transcription and processing in plants

The regulation of miRNA biogenesis and movement is essential for plant development and environmental responses. HASTY (HST), a karyopherin protein, has been implicated in miRNA biogenesis and movement, though its role in non-cell-autonomous miRNA movement remains unclear. Through a genetic screen, we identified that mutations in the HAWAIIAN SKIRT (HWS) gene suppress the developmental defects of hst mutants by restoring miRNA movement. Our findings show that HWS interacts with nuclear transport factors and nuclear pore complex (NPC) components, including NUP1, positioning HWS as a regulator of miRNA nuclear export. Using microscopy and fluorescence in situ hybridization, we showed that pri-miRNA transcription, and likely their co-transcriptional processing, occurs at the nuclear pore. Notably, we uncovered an antagonistic relationship between HST and HWS in regulating MIRNA transcription at the NPC and AGO1 loading, which could explain the observed changes in miRNA movement. HST promotes the association of MIRNA loci with the NPC, likely facilitating co-transcriptional processing, while HWS negatively regulates this process by targeting MEDIATOR complex subunits to degradation detaching, consequently, the processing complex from the NPC. Furthermore, our data provides evidence of spatial coordination of miRNA transcription, biogenesis, and movement highlighting a novel role for the NPC in the miRNA pathway.

plant biology↗

bioRxiv2023

Transposon-triggered epigenetic chromatin dynamics modulate EFR-related pathogen response

Infectious diseases drive the evolution of wild plants and impact yield in crop plants. Like animals, plants can sense biotic threats via conserved pathogen-associated patterns (PAMPs). Since an overly robust immune response can harm plants, understanding the mechanisms for tuning defense responses to the appropriate level is vital as we endeavor to develop pathogen-resistant crops. In this paper, we studied the Arabidopsis pattern recognition receptor (PRR) EFR, which senses bacterial EF-Tu. An inverted-repeat transposon (Ea-IR) between EFR and the neighboring XI-k locus controls local chromatin organization, promoting the formation of a repressive chromatin loop. Upon pathogen infection, the chromatin landscape around EFR and Xl-k dynamically changes to allow for increased EFR transcription. Chromatin opening facilitates the passage of RNA polymerase II across the neighboring XI-k gene termination site, leading to a longer XI-k transcript that includes Ea-IR sequences. Dicer-like (DCL) enzymes process the longer Xl-k transcript into small RNAs (sRNAs), which reset chromatin topology to a repressive state, attenuating, in turn, the immune response, reminiscent of attenuation of receptor signaling in other systems. From an evolutionary point of view, we found that natural Arabidopsis accessions missing Ea-IR have a constitutive "EFR-open" chromatin configuration that correlates with higher basal EFR levels and higher background resistance to pathogens. Collectively, our study offers evidence for a scenario in which a transposon, chromatin organization, and gene expression interact to fine-tune immune responses, both during the course of infection and in the course of evolution. Similar gene-associated IRs in crops could provide valuable non-coding targets for genome editing or assisted plant breeding programs.

plant biology↗

bioRxiv2022

Polymorphic Inverted Repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana

Transposons are mobile elements that are commonly silenced to protect eukaryotic genome integrity. In plants, transposable elements (TEs) can be activated during stress conditions and subsequently insert into gene-rich regions. TE-derived inverted repeats (IRs) are commonly found near plant genes, where they affect host gene expression with potentially positive effects on adaptation. However, the molecular mechanisms by which these IRs control gene expression is unclear in most cases. Here, we identify in the Arabidopsis thaliana genome hundreds of IRs located near genes that are transcribed by RNA Polymerase II, resulting in the production of 24-nt small RNAs that trigger methylation of the IRs. The expression of these IRs is associated with drastic changes in the local 3D chromatin organization, which alter the expression pattern of the hosting genes. Notably, the presence and structure of many IRs differ between A. thaliana accessions. Capture-C sequencing experiments revealed that such variation changes short-range chromatin interactions, which translates into changes in gene expression patterns. CRISPR/Cas9-mediated disruption of two of such IRs leads to a switch in genome topology and gene expression, with phenotypic consequences. Our data demonstrate that the insertion of an IR near a gene provides an anchor point for chromatin interactions that can profoundly impact the activity of neighboring loci. This turns IRs into powerful evolutionary agents that can contribute to rapid adaptation.

plant biology↗

bioRxiv2021

The transcription factor AtHB23 modulates starch turnover for root development and plant survival under salinity

AtHB23 is a homeodomain-leucine zipper I transcription factor, previously characterized as a modulator of lateral root initiation and higher-order roots development. The role of this gene in response to salinity stress was completely unknown. To elucidate the role of AtHB23 in response to salinity stress, we combined histochemical {beta}-glucuronidase (GUS) analysis, root phenotyping, starch staining, optic and electronic transmission microscopy, expression studies by RT-qPCR, and transcriptome analysis of silenced, overexpressor, and crossed plants. We revealed that the expression pattern of AtHB23 is regulated by NaCl in the main and lateral roots, affecting the root phenotype. A severe reduction in primary root length, a significant increment in the initiation of lateral roots, and a low survival rate in salinity conditions were observed in AtHB23-silenced plants, whereas AtHB23 overexpressors showed the opposite phenotype. These developmental defects were explained by the degradation of starch granules and an alteration in starch metabolism. The AtHB23-target gene LAX3 is repressed in the tip of the main root and affected by NaCl. We conclude that AtHB23 is vital for plant survival and adaptation to salt stress conditions, and its function is related to the gravitropic response mediated by starch granule turnover, involving the auxin carrier LAX3. HighlightThe transcription factor AtHB23 is crucial for plant survival and adaptation to salt stress conditions, and its function is related to the gravitropic response mediated by starch-granule turnover, involving LAX3.

plant biology↗

bioRxiv2019

Successful field performance in dry-warm environments of soybean expressing the sunflower transcription factor HaHB4

Soybean yield is limited primarily by abiotic constraints. No transgenic soybean with improved abiotic-stress tolerance is available in the market. We transformed soybean plants with genetic constructs able to express the sunflower transcription factor HaHB4, which confers drought tolerance to Arabidopsis and wheat plants. One line (b10H) carrying the sunflower promoter was chosen among three independent lines because it exhibited the best performance in seed yield (SY). Such line was evaluated in the greenhouse and in twenty-seven field trials developed in different environments of Argentina. In greenhouse experiments, transgenic plants showed increased SY under stress conditions together with wider epycotyl diameter, enlarged xylem area and enhanced water use efficiency than controls. They also exhibited enhanced SY in warm-dry field conditions. This response was accompanied by the increased in seed number that was not compensated by the decreased in individual seed weight. The transcriptome analysis of plants from a field trial with maximum SY difference between genotypes indicated an induction of genes encoding redox and heat shock proteins in b10H. Collectively, our results indicate that soybeans transformed with HaHB4 are expected to have reduced SY penalization when cropped in warm-dry conditions, which constitute the best target environments for this technology. HighlightSoybean transformed with the sunflower gene encoding the transcription factor HaHB4 was evaluated in greenhouse and field trials. Transgenic plants significantly outyielded controls in drought-warm environments due to, at least in part, increased seed number, xylem area, and water use efficiency as well as to the induction of genes encoding redox and heat shock proteins.

plant biology↗