skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato
The evolution of transcriptional regulatory mechanisms is central to how stress response and tolerance differ between species. However, it remains largely unknown how divergence in cis-regulatory sites and, subsequently, transcription factor (TF) binding specificity contribute to stress-responsive expression divergence, particularly between wild and domesticated spe-cies. By profiling wound-responsive gene transcriptomes in wild Solanum pennellii and do-mesticated S. lycopersicum, we found extensive wound-response divergence and identified 493 S. lycopersicum and 278 S. pennellii putative cis-regulatory elements (pCREs) that were predictive of wound-responsive gene expression. Only 24-52% of these wound-response pCREs (depending on wound-response patterns) were consistently enriched in the putative promoter regions of wound-responsive genes across species. In addition, between these two species, their differences in pCRE site sequences were significantly and positively correlated with differences in wound-responsive gene expression. Furthermore, ~11-39% of pCREs were specific to only one of the species and likely bound by TFs from different families. These findings indicate substantial regulatory divergence in these two plant species that di-verged ~3-7 million years ago. Our study provides insights into the mechanistic basis of how the transcriptional response to wounding is regulated and, importantly, the contribution of cis-regulatory components to variation in wound-responsive gene expression between a wild and a domesticated plant species.  more » « less
Award ID(s):
1546617 1655386
PAR ID:
10058048
Author(s) / Creator(s):
Date Published:
Journal Name:
The Plant cell
ISSN:
1040-4651
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; (, PLOS One)
    Irfan, Mohammad (Ed.)
    Drought is a significant environmental stressor that severely impairs plant growth and agricultural productivity. Unraveling the molecular mechanisms underlying plant responses to drought is crucial for developing crops with enhanced resilience. In this study, we investigated the transcriptomic responses of cultivated tomato (Solanum lycopersicum) and its drought-tolerant wild relative,Solanum pennellii, to identify “stress-ready” gene expression patterns associated with pre-adaptation to arid environments. Through RNA-seq analysis, we identified orthologous genes between the two species and compared their transcriptomic profiles under both control and drought conditions. Approximately 43% of the orthologous genes exhibited species-specific expression patterns, while nearly 20% were classified as stress-ready. These stress-ready genes were significantly enriched for functions related to nucleosome assembly, RNA metabolism, and transcriptional regulation. Furthermore, transcription factor binding motif analysis revealed a marked enrichment of ERF family motifs, emphasizing their role in both stress-ready and species-specific responses. Our findings indicate that regulatory mechanisms, particularly those mediated by ERF transcription factors, are pivotal to the drought resilience ofS. pennellii, providing a foundation for future crop improvement strategies. 
    more » « less
  2. ; ; ; ; ; (, The Plant Cell)
    Abstract Plants respond to wounding stress by changing gene expression patterns and inducing the production of hormones including jasmonic acid. This wounding transcriptional response activates specialized metabolism pathways such as the glucosinolate pathways in Arabidopsis thaliana. While the regulatory factors and sequences controlling a subset of wound-response genes are known, it remains unclear how wound response is regulated globally. Here, we how these responses are regulated by incorporating putative cis-regulatory elements, known transcription factor binding sites, in vitro DNA affinity purification sequencing, and DNase I hypersensitive sites to predict genes with different wound-response patterns using machine learning. We observed that regulatory sites and regions of open chromatin differed between genes upregulated at early and late wounding time-points as well as between genes induced by jasmonic acid and those not induced. Expanding on what we currently know, we identified cis-elements that improved model predictions of expression clusters over known binding sites. Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation. Our study provides a global model predictive of wound response and identifies new regulatory sequences important for wounding without requiring prior knowledge of the transcriptional regulators. 
    more » « less
  3. ; ; ; ; ; ; ; ; ; ; et al (, The Plant Cell)
    Abstract Plant roots dynamically respond to nitrogen availability by executing a signaling and transcriptional cascade resulting in altered plant growth that is optimized for nutrient uptake. The NIN-LIKE PROTEIN 7 (NLP7) transcription factor senses nitrogen and, along with its paralog NLP6, partially coordinates transcriptional responses. While the post-translational regulation of NLP6 and NLP7 is well established, their upstream transcriptional regulation remains understudied in Arabidopsis (Arabidopsis thaliana) and other plant species. Here, we dissected a known sub-circuit upstream of NLP6 and NLP7 in Arabidopsis, which was predicted to contain multiple multi-node feedforward loops suggestive of an optimized design principle of nitrogen transcriptional regulation. This sub-circuit comprises AUXIN RESPONSE FACTOR 18 (ARF18), ARF9, DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN 26 (DREB26), Arabidopsis NAC-DOMAIN CONTAINING PROTEIN 32 (ANAC032), NLP6 and NLP7 and their regulation of NITRITE REDUCTASE 1 (NIR1). Conservation and divergence of this circuit and its influence on nitrogen-dependent root system architecture were similarly assessed in tomato (Solanum lycopersicum). The specific binding sites of these factors within their respective promoters and their putative cis-regulatory architectures were identified. The direct or indirect nature of these interactions was validated in planta. The resulting models were genetically validated in varying concentrations of available nitrate by measuring the transcriptional output of the network revealing rewiring of nitrogen regulation across distinct plant lineages. 
    more » « less
  4. ; ; ; ; ; ; (, Molecular Ecology)
    Drought stress is a key limitation for plant growth and colonization of arid habitats. We study the evolution of gene expression response to drought stress in a wild tomato,Solanum chilense,naturally occurring in dry habitats in South America. We conduct a transcriptome analysis under standard and drought experimental conditions to identify drought‐responsive gene networks and estimate the age of the involved genes. We identify two main regulatory networks corresponding to two typical drought‐responsive strategies: cell cycle and fundamental metabolic processes. The metabolic network exhibits a more recent evolutionary origin and a more variable transcriptome response than the cell cycle network (with ancestral origin and higher conservation of the transcriptional response). We also integrate population genomics analyses to reveal positive selection signals acting at the genes of both networks, revealing that genes exhibiting selective sweeps of older age also exhibit greater connectivity in the networks. These findings suggest that adaptive changes first occur at core genes of drought response networks, driving significant network re‐wiring, which likely underpins species divergence and further spread into drier habitats. Combining transcriptomics and population genomics approaches, we decipher the timing of gene network evolution for drought stress response in arid habitats. 
    more » « less
  5. ; ; ; (, Frontiers in Plant Science)
    Switchgrass low-land ecotypes have significantly higher biomass but lower cold tolerance compared to up-land ecotypes. Understanding the molecular mechanisms underlying cold response, including the ones at transcriptional level, can contribute to improving tolerance of high-yield switchgrass under chilling and freezing environmental conditions. Here, by analyzing an existing switchgrass transcriptome dataset, the temporal cis- regulatory basis of switchgrass transcriptional response to cold is dissected computationally. We found that the number of cold-responsive genes and enriched Gene Ontology terms increased as duration of cold treatment increased from 30 min to 24 hours, suggesting an amplified response/cascading effect in cold-responsive gene expression. To identify genomic sequences likely important for regulating cold response, machine learning models predictive of cold response were established using k -mer sequences enriched in the genic and flanking regions of cold-responsive genes but not non-responsive genes. These k -mers, referred to as putative cis -regulatory elements (pCREs) are likely regulatory sequences of cold response in switchgrass. There are in total 655 pCREs where 54 are important in all cold treatment time points. Consistent with this, eight of 35 known cold-responsive CREs were similar to top-ranked pCREs in the models and only these eight were important for predicting temporal cold response. More importantly, most of the top-ranked pCREs were novel sequences in cold regulation. Our findings suggest additional sequence elements important for cold-responsive regulation previously not known that warrant further studies. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email