Biology subjects

Dehesh, K.

Publications and source records attributed to Dehesh, K..

11 recordsLinked to original sources

bioRxiv2024

Integrated Dual-Channel Retrograde Signaling Directs Stress Responses by Degrading the HAT1/TPL/IMPalpha-9 Suppressor Complex and Activating CAMTA3

The intricate communication between plastids and the nucleus, shaping stress-responsive gene expression, has long intrigued researchers. This study combines genetics, biochemical analysis, cellular biology, and protein modeling to uncover how the plastidial metabolite MEcPP activates the stress-response regulatory hub known as the Rapid Stress Response Element (RSRE). Specifically, we identify the HAT1/TPL/IMP- 9 suppressor complex, where HAT1 directly binds to RSRE and its activator, CAMTA3, masking RSRE and sequestering the activator. Stress-induced MEcPP disrupts this complex, exposing RSRE and releasing CAMTA3, while enhancing Ca2+ influx and raising nuclear Ca2+levels crucial for CAMTA3 activation and the initiation of RSRE- containing gene transcription. This coordinated breakdown of the suppressor complex and activation of the activator highlights the dual-channel role of MEcPP in plastid-to- nucleus signaling. It further signifies how this metabolite transcends its expected biochemical role, emerging as a crucial initiator of harmonious signaling cascades essential for maintaining cellular homeostasis under stress. SummaryThis study uncovers how the stress-induced signaling metabolite MEcPP disrupts the HAT1/TPL/IMP-9 suppressor complex, liberating the activator CAMTA3 and enabling Ca2+ influx essential for CAMTA3 activation, thus orchestrating stress responses via repressor degradation and activator induction.

plant biology↗

bioRxiv2024

Plant U-Box 4 regulates chloroplast stress signaling and programmed cell death via Salicylic acid modulation

BackgroundIn response to environmental stresses, chloroplasts generate reactive oxygen species, including singlet oxygen (1O2), an excited state of oxygen that regulates chloroplast-to-nucleus (retrograde) signaling, chloroplast turnover, and programmed cell death (PCD). Yet, the central signaling mechanisms and downstream responses remain poorly understood. The Arabidopsis thaliana plastid ferrochelatase two (fc2) mutant conditionally accumulates 1O2 and Plant U-Box 4 (PUB4), a cytoplasmic E3 ubiquitin ligase, is involved in propagating 1O2 signals for chloroplast turnover and cellular degradation. Thus, the fc2 and fc2 pub4 mutants are useful genetic tools to elucidate these signaling pathways. Previous studies have focused on the role of 1O2 in promoting cellular degradation in fc2 mutants, but its impact on retrograde signaling from mature chloroplasts (the major site of 1O2 production) is poorly understood. ResultsTo gain mechanistic insights into 1O2 signaling pathways, we compared transcriptomes of adult wt, fc2, and fc2 pub4 plants. The accumulation of 1O2 in fc2 plants broadly repressed genes involved in chloroplast function and photosynthesis, while inducing genes and transcription factors involved in abiotic and biotic stress, the biosynthesis of jasmonic acid (JA) and salicylic acid (SA), microautophagy, and senescence. Elevated JA and SA levels were observed in 1O2-stressed fc2 plants. pub4 reversed most of this 1O2-induced gene expression and reduced the JA content in fc2 plants. The pub4 mutation also blocked JA-induced senescence pathways in the dark. However, fc2 pub4 plants maintained constitutively elevated levels of SA even in the absence of bulk 1O2 accumulation. ConclusionsTogether, this work demonstrates that in fc2 plants, 1O2 leads to a robust retrograde signal that may protect cells by downregulating photosynthesis and ROS production while simultaneously mounting a stress response involving SA and JA. The induction of microautophagy and senescence pathways indicate that 1O2-induced cellular degradation is a genetic response to this stress, and the bulk of this transcriptional response is modulated by the PUB4 protein. However, the effect of pub4 on hormone synthesis and signaling is complex and indicates that an intricate interplay of SA and JA are involved in promoting stress responses and programmed cell death during photo-oxidative damage.

plant biology↗

bioRxiv2024

Mapping protein-metabolite interactions in E. coli by integrating chromatographic techniques and co-fractionation mass spectrometry.

In our pursuit of understanding the protein-metabolite interactome, we introduced PROMIS, a co-fractionation mass spectrometry (CF-MS) technique focusing on biosynthetic and regulatory processes. However, the challenge lies in distinguishing true interactors from coincidental co-elution when a metabolite co-fractionates with numerous proteins. To address this, we integrated two chromatographic techniques-- size exclusion and ion exchange--to enhance the mapping of protein-metabolite interactions (PMIs) in Escherichia coli. This integration aims to refine the PMI network by considering size and charge characteristics, resulting in 994 interactions involving 51 metabolites and 465 proteins. The PMI network is enriched for known and predicted interactions validating our approachs efficacy. Furthermore, the analysis of protein targets for different metabolites revealed novel functional insights, such as the connection between proteinogenic dipeptides and fatty acid biosynthesis. Notably, we uncovered an inhibitory interaction between the riboflavin degradation product lumichrome and orotate phosphoribosyltransferase (PyrE), a key enzyme in de novo pyrimidine synthesis. Lumichrome supplementation mimicked the biofilm formation inhibition observed in a{Delta} pyrE mutant strain, suggesting lumichrome role in integrating pyrimidine and riboflavin metabolism with quorum sensing and biofilm formation. In summary, our integrated chromatographic approach significantly advances PMI mapping, offering novel insights into functional associations and potential regulatory mechanisms in E. coli.

biochemistry↗

bioRxiv2023

ZmPILS6 is an auxin efflux carrier required for maize root morphogenesis

Plant root systems play a pivotal role in plant physiology and exhibit diverse phenotypic traits. Understanding the genetic mechanisms governing root growth and development in model plants like maize is crucial for enhancing crop resilience to drought and nutrient limitations. This study focused on identifying and characterizing ZmPILS6, an annotated auxin efflux carrier, as a key regulator of various crown root traits in maize. ZmPILS6-modified roots displayed reduced network area and suppressed lateral root formation, desirable traits during drought and low phosphate conditions. The research revealed that ZmPILS6 localizes to the endoplasmic reticulum and plays a vital role in controlling the spatial distribution of indole-3-acetic acid (IAA or "auxin") in primary roots. The study also demonstrated that ZmPILS6 can actively efflux IAA when expressed in yeast. Furthermore, the loss of ZmPILS6 resulted in significant proteome remodeling in maize roots, particularly affecting hormone signaling pathways. To identify potential interacting partners of ZmPILS6, a weighted gene co-expression analysis (WGNA) was performed. Altogether, this research contributes to the growing knowledge of essential genetic determinants governing maize root morphogenesis, which is crucial for guiding agricultural improvement strategies. Significance StatementCrop yield and stress resilience are significantly influenced by crown root architecture. A reverse genetic screen aimed at identifying novel regulators of maize root morphogenesis led to the discovery of ZmPILS6, an auxin efflux carrier. The loss of ZmPILS6 negatively impacts numerous root traits that are linked to plant physiology and function. Proteomic characterization of pils6-1 roots revealed that this evolutionarily conserved transporter is required for the proper expression of numerous phytohormone pathways, including abscisic acid, gibberellins, and jasmonic acid. Notably, ZmPILS6 appears to have a contrasting role in regulating root morphogenesis compared to its Arabidopsis ortholog, PILS6. This finding emphasizes the need for functional characterization of candidate genes directly within key crops of interest, which cannot always be correctly inferred from other model plants.

plant biology↗

bioRxiv2022

Dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat primary root growth

Wheat is an essential crop for global food security and is well adapted to a wide variety of soils1. However, the gene networks regulating different root architectures remain poorly understood. We report here the identification of a cluster of a monocot-specific 12-OXOPHYTODIENOATE REDUCTASE genes from subfamily III (OPRIII) that modulate key differences in wheat root architecture associated with grain yield under water-limited conditions. Wheat plants with a loss-of-function mutation in OPRIII showed longer seminal roots, whereas plants with increased OPRIII dosage or transgenic over-expression showed reduced seminal root growth, precocious development of lateral roots and increased jasmonic acid (JA). A JA-biosynthesis inhibitor eliminated the root differences, confirming a JA-mediated mechanism. Multiple transcriptome analysis of transgenic and wild-type lines revealed significant enriched JA-biosynthetic and reactive oxygen species (ROS) pathways that paralleled changes in ROS distribution. The OPRIII genes provide a useful entry point to engineer root architecture in wheat and other cereals.

plant biology↗

bioRxiv2021

ORA47 is a transcriptional regulator of a general stress response hub

Transcriptional regulators of general stress response (GSR) reprogram expression of selected genes to transduce informational signals into cellular events, ultimately manifested in plants ability to cope with environmental challenges. Identification of the core GSR regulatory proteins will uncover the principal modules and their mode of action in the establishment of adaptive responses. To define the GSR regulatory components, we employed a yeast-one-hybrid assay to identify the protein(s) that binds to the previously established functional GSR motif, coined Rapid Stress Response Element (RSRE). This led to the isolation of ORA47 (octadecanoid-responsive AP2/ERF-domain transcription factor 47), a Methyl jasmonate (MeJA) inducible protein. Subsequently, the ORA47 transcriptional activity was confirmed using RSRE-driven Luciferase (LUC) activity assay performed in the ORA47 loss- and gain-of-function lines introgressed into the 4xRSRE::Luc background. In addition, the prime contribution of CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 (CAMTA3) protein in induction of RSRE was reaffirmed by genetic studies. Moreover, exogenous application of MeJA led to enhanced levels of ORA47 and CAMTA3 transcripts, and the induction of RSRE::LUC activity. Metabolic analyses illustrated the reciprocal functional inputs of ORA47 and CAMTA3 in increasing JA levels. Lastly, transient assays identified JASMONATE ZIM-domain1 (JAZ1) as a repressor of RSRE::LUC activity. Collectively, the report provides a fresh insight into the initial mechanistic features of transducing the informational signals into adaptive responses in part via the complex functional interplay between JA biosynthesis/signaling cascade and the transcriptional reprogramming necessary for potentiation of GSR, while offering a window into the role of intraorganellar communication in the establishment of adaptive responses. SignificanceThe work unmasks the initial mechanistic features of adaptive responses that include tight cooperativity between JA biosynthesis and signaling cascade and the nuclear transcriptional machinery comprised of two activators (CAMTA3 and ORA47) and a suppressor JAZ1). The work further identifies CAMTA3 as a functional link between JA signaling and activation of a general stress transcriptional hub.

plant biology↗

bioRxiv2021

Reciprocity between retrograde signal and putative metalloprotease reconfigures plastidial metabolism and structure

Reconfiguration of the plastidial proteome in response to environmental inputs is central to readjustment of its metabolic and structural states. This is necessary for the functionality of this metabolic hub, and the maintenance of organismal integrity. This report establishes the role of the plastidial retrograde signaling metabolite, MEcPP, in increasing the abundance of the putative plastidial metalloprotease (VIR3), and the ensuing decline of VIR3 target enzymes, ascorbate peroxidase and glyceraldehyde 3-phophate dehydrogenase B. The decreased abundance of these enzymes is linked to increased levels of their substrates: H2O2, an elicitor of salicylic acid production and stromule formation; and G3P the substrate for MEcPP synthesis. High-light treatment of wild type plants recapitulated the VIR3-associated reconfiguration of the plastidial metabolic and structural states. These results identify a previously unrecognized link between the stress-induced plastidial retrograde signaling metabolite and a putative zinc-binding metalloprotease. Moreover, the data reveal that the reciprocity between these two components, results in the reconfiguration of the metabolic and structural states of the plastid, deemed necessary to maintain cellular integrity and to shape adaptive responses.

plant biology↗

bioRxiv2021

A plastidial retrograde-signal potentiates biosynthesis of systemic stress response activators

O_LIPlants employ an array of intricate and hierarchical signaling cascades to perceive and transduce informational cues to synchronize and tailor adaptive responses. Systemic stress response (SSR) is a recognized complex signaling and response network quintessential to plants local and distal responses to environmental triggers, however, the identity of the initiating signals has remained fragmented. C_LIO_LIHere, we show that both biotic (aphids and viral pathogens) and abiotic (high-light and wounding) stresses induce accumulation of the plastidial-retrograde-signaling metabolite, methylerythritol cyclodiphosphate (MEcPP), leading to reduction of the phytohormone, auxin, and the subsequent decreased expression of the phosphatase, PP2C.D1. C_LIO_LIThis enables phosphorylation of mitogen-activated protein kinases (MAPK3/6), and the consequential induction of the downstream events ultimately resulting in biosynthesis of the two SSR priming metabolites, pipecolic- and N-hydroxy-pipecolic acid. C_LIO_LIThis work identifies plastids as the initiation site, and the plastidial retrograde-signal, MEcPP as the initiator of a multi-component signaling cascade potentiating the biosynthesis of SSR activators, in response to biotic and abiotic triggers. C_LI

plant biology↗

bioRxiv2021

CamelliA-based simultaneous imaging of Ca2+ dynamics in subcellular compartments

As a universal second messenger, calcium (Ca2+) transmits specific cellular signals via a spatiotemporal signature generated from its extracellular source and internal stores. Our knowledge of the mechanisms underlying generation of a Ca2+ signature is hampered by limited tools enabling simultaneous monitoring of the dynamics of Ca2+ levels in multiple subcellular compartments. To overcome the limitation and to further improve spatiotemporal resolutions, here we have assembled a molecular toolset (the CamelliA lines) in Arabidopsis that enables simultaneous and high-resolution monitoring of Ca2+ dynamics in multiple subcellular compartments through imaging analyses of different single-colored GECIs (Genetically Encoded Calcium Indicators). Indeed, the uncovering of the previously unrecognized Ca2+ signatures in three types of Arabidopsis cells in response to internal and external cues is a testimony to the wide applicability of the newly generated toolset for elucidating the subcellular sources contributing to the Ca2+signatures in plants. One sentence summaryA toolset for simultaneous imaging of Ca2+ dynamics in subcellular compartments has uncovered unrecognized Ca2+ signatures in Arabidopsis cells in response to developmental and external cues.

plant biology↗

bioRxiv2020

Retrograde induction of phyB orchestrates ethylene-auxin hierarchy to regulate growth

Exquisitely regulated plastid-to-nucleus communication by retrograde signaling pathways is essential for fine-tuning of responses to the prevailing environmental conditions. The plastidial retrograde signaling metabolite methylerythritol cyclodiphosphate (MEcPP) has emerged as a stress signal transduced into a diverse ensemble of response outputs. Here we demonstrate enhanced phytochrome B protein abundance in red-light grown MEcPP-accumulating mutant (ceh1) plant relative to wild-type seedlings. We further establish MEcPP-mediated coordination of phytochrome B with auxin and ethylene signaling pathways, and uncover differential hypocotyl growth of red-light grown seedlings in response to these phytohormones. Genetic and pharmacological interference with ethylene and auxin pathways outline the hierarchy of responses, placing auxin epistatic to the ethylene signaling pathway. Collectively, our finding establishes the key role of a plastidial retrograde metabolite in orchestrating the transduction of a repertoire of signaling cascades, and positions plastids at the zenith of relaying information coordinating external signals and internal regulatory circuitry to secure organismal integrity. Two sentence summaryThe plastidial retrograde metabolite, MEcPP, orchestrates coordination of light and hormonal signaling cascade through induction of phytochrome B abundance and modulation of auxin and ethylene levels for optimal adaptive responses to light environment.

plant biology↗

bioRxiv2019

DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs associated with innate immunity and growth inhibition

Gene transcription is counterbalanced by mRNA decay processes that regulate transcript quality and quantity. We show here that the evolutionarily conserved DHH1/DDX6-like RNA HELICASEs of Arabidopsis thaliana control the ephemerality of a subset of cellular mRNAs. These RNA helicases co-localize with key markers of processing bodies and stress granules and contribute to their subcellular dynamics. These RHs function to limit the precocious accumulation and translation of stress-responsive mRNAs associated with autoimmunity and growth inhibition under non-stress conditions. Given the conservation of this RH subfamily, they may control basal levels of conditionally-regulated mRNAs in diverse eukaryotes, accelerating responses without penalty.

plant biology↗