Biology subjects

Nohales, M. A.

Publications and source records attributed to Nohales, M. A..

4 recordsLinked to original sources

bioRxiv2023

A Day in the Life of Arabidopsis: 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms

Functional circadian clock is fundamental to the adaptation and survival of organisms. In land plants, the comprehensive profiling of circadian gene expression at the single-cell level is largely unknown partly due to the challenges in obtaining precisely-timed single cells from plant cells embedded within cell walls. To bridge this gap, we employed single-nucleus RNA sequencing (snRNA-seq) on twelve seedling samples collected at 2-hour intervals over a 24-hour day in Arabidopsis, yielding a total of over 130,000 nuclei. From this data, we found that three cell clusters in the shoot share a coherent rhythm, while more than 3,000 genes display cell-type specific rhythmic expression. Only 19 genes are oscillating in more than ten different cell types, and the majority of them are well-documented core oscillators, suggesting the snRNA-seq circadian data could be used to identify key circadian regulators in a broad range of plant systems. Our data provides the first comprehensive resource for plant circadian rhythms at the single-cell level (hosted at https://zhailab.bio.sustech.edu.cn/sc_circadian).

plant biology↗

bioRxiv2023

DELLA Proteins Recruit the Mediator Complex Subunit MED15 to Co-activate Transcription in Land Plants

DELLA proteins are negative regulators of the gibberellin response pathway in angiosperms, acting as central hubs that interact with hundreds of transcription factors and regulators to modulate their activities. While the mechanism of transcription factor sequestration by DELLAs to prevent DNA binding to downstream targets has been extensively documented, the mechanism that allows them to act as co-activators remains to be understood. Here, we demonstrate that DELLAs directly recruit the Mediator complex to specific loci in Arabidopsis, facilitating transcription. This recruitment involves DELLA amino-terminal domain and the conserved MED15 KIX domain. Accordingly, partial loss of MED15 function mainly disrupted processes known to rely on DELLA co-activation capacity; including cytokinin-dependent regulation of meristem function and skotomorphogenic response, gibberellin metabolism feedback, and flavonol production. We have also found that the single DELLA protein in the liverwort Marchantia polymorpha is capable of recruiting MpMED15 subunits, contributing to transcriptional co-activation. The conservation of Mediator-dependent transcriptional co-activation by DELLA between Arabidopsis and Marchantia implies that this mechanism is intrinsic to the emergence of DELLA in the last common ancestor of land plants. Significance StatementDELLA proteins are plant-specific transcriptional hubs integrating environmental signals with endogenous cues. In order to regulate downstream processes, DELLAs modulate the activity of hundreds of transcription factors and transcriptional regulators in various ways. Here, we describe the molecular mechanism underlying DELLA co-activator function. We show that DELLAs act as transcriptional activators in eukaryotic cells by interacting with the Mediator complex subunit MED15. Mediator function is necessary to regulate a subset of DELLA-regulated responses that are mediated by direct co-activation of DELLA-Transcription factors complexes. We further show that this mechanism is present in bryophyte DELLAs, and thus represents a conserved mechanism of DELLA function in land plants.

plant biology↗

bioRxiv2023

Epidermal GIGANTEA adjusts the response to shade at dusk by directly impinging on PHYTOCHROMEINTERACTING FACTOR 7 function

For plants adapted to bright light, a decrease in the amount of light received can be detrimental to their growth and survival. Consequently, in response to shade from surrounding vegetation, they initiate a suite of molecular and morphological changes known as the shade avoidance response (SAR) through which stems and petioles elongate in search for light. Under sunlight-night cycles, the plants responsiveness to shade varies across the day, being maximal at dusk time. While a role for the circadian clock in this regulation has long been proposed, mechanistic understanding of how it is achieved is incomplete. Here we show that the clock component GIGANTEA (GI) directly interacts with the transcriptional regulator PHYTOCHROME INTERACTING FACTOR 7 (PIF7), a key player in the response to shade. GI represses PIF7 transcriptional activity and the expression of its target genes in response to shade, thereby fine-tuning the magnitude of the response to limiting light conditions. We find that, under light/dark cycles, this function of GI is required to adequately modulate the gating of the response to shade at dusk. Importantly, we also show that GI expression in epidermal cells is sufficient for proper SAR regulation. SIGNIFICANCEPlants have a remarkable capacity to adapt to and cope with changes in environmental conditions. Because of the importance of light to their survival, plants have evolved sophisticated mechanisms to optimize responses to light. An outstanding adaptive response in terms of plant plasticity in dynamic light environments is the shade avoidance response which sun-loving plants deploy to escape canopy and grow towards the light. This response is the result of a complex signaling network in which cues from different pathways are integrated, including light, hormone, and circadian signaling. Within this framework, our study provides a mechanistic model of how the circadian clock contributes to this complex response by temporalizing the sensitivity to shade signals towards the end of the light period. In light of evolution and local adaptation, this work gives insights into a mechanism through which plants may have optimized resource allocation in fluctuating environments.

plant biology↗

bioRxiv2020

COP1 destabilizes DELLA proteins in Arabidopsis

DELLA transcriptional regulators are central components in the control of plant body form in response to the environment. This is considered to be mediated by changes in the metabolism of the hormones gibberellins (GAs), which promote the degradation of DELLAs. However, here we show that warm temperature or shade reduced the stability of a GA-insensitive DELLA allele in Arabidopsis. Furthermore, the degradation of DELLA induced by the warmth anticipated changes in GA levels and depended on the E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1). COP1 enhanced the degradation of normal and GA-insensitive DELLA alleles when co-expressed in N. benthamiana. DELLA proteins physically interacted with COP1 in yeast, mammalian and plant cells. This interaction was enhanced by the COP1 complex partner SUPRESSOR OF phyA-105 1 (SPA1). The level of ubiquitination of DELLA was enhanced by COP1 and COP1 ubiquitinated DELLA proteins in vitro. We propose that DELLAs are destabilized not only by the canonical GA-dependent pathway but also by COP1 and that this control is relevant for growth responses to shade and warm temperature. SignificanceDELLA proteins are plant-specific transcriptional regulators that act as signaling hubs at the interface between the environment and the transcriptional networks that control growth. DELLAs are destabilized by the growth-promoting hormone gibberellin, whose levels are very sensitive to environmental changes. Here we describe an alternative pathway to destabilize these proteins. We show that DELLAs are substrate of COP1, an E3 ubiquitin ligase that increases its nuclear activity to promote growth in response to shade or warmth. Our results also show that the destabilization of DELLAs by COP1 precedes the action of gibberellins, suggesting the existence of a sequential mechanism to control the stability of these proteins.

plant biology↗