Plant-environment Interactions Research Articles

Integrating Solar Induced Fluorescence with High Throughput Plant Screening for Advanced Phenotyping of plants

There is an urgent need to address the escalating impacts of climate change, particularly the exacerbation of drought conditions, which pose significant threats to global food security and agricultural sustainability. Innovative solutions are imperative, and one such solution involves integrating advanced technologies like the "PlantArray" system to monitor and enhance plant physiological responses to water scarcity. The "PlantArray" system enables the precise measurement of critical whole-plant physiological traits such as transpiration rate, canopy stomatal conductance (Gs canopy), and growth rate with an exceptional spatiotemporal resolution. Augmenting this system with photosynthesis measurements offers an additional layer of information, facilitating a more focused interpretation of the system parameters. To overcome the limitations of single-leaf photosynthesis measurement techniques, this study employs a remote sensing approach to rapidly scan numerous samples at multiple time points, revealing insights into drought stress responses of S. licopersicum lines. An ultra-spectral spectroradiometer mounted on a mobile cart was positioned above an experimental matrix comprising drought-stressed S. licopersicum obsolete and mutagenic lines. Our findings reveal that the vegetation index PRI exhibited greater sensitivity to drought stress compared to other vegetation and photosynthesis remote sensing indices. Photosynthesis indices demonstrated increased sensitivity to daily biomass accumulation and served as predictors of final plant yield. Interestingly, Solar-Induced Fluorescence (SIF) parameters, solely indicative of photosynthesis-emitted fluorescence, exhibited no correlation with stress levels or final biomass production. This study articulates the potential to monitor plant responses to agricultural stressors through real-time physiological tracking across complete diel cycles, thereby enriching our understanding of plant-environment interactions. Ultimately, this integrated system shows promise in screening and developing crop cultivars with ideal physiological and photosynthetic traits, vital to cultivating resilient crops in extreme droughts and weather conditions.

Temporally resolved growth patterns reveal novel information about the polygenic nature of complex quantitative traits.

Plant height can be an indicator of plant health across environments and used to identify superior genotypes. Typically plant height is measured at a single timepoint when plants reach terminal height. Evaluating plant height using unoccupied aerial vehicles allows for measurements throughout the growing season, facilitating a better understanding of plant-environment interactions and the genetic basis of this complex trait. To assess variation throughout development, plant height data was collected from planting until terminal height at anthesis (14 flights 2018, 27 in 2019, 12 in 2020, and 11 in 2021) for a panel of ~500 diverse maize inbred lines. The percent variance explained in plant height throughout the season was significantly explained by genotype (9-48%), year (4-52%), and genotype-by-year interactions (14-36%) to varying extents throughout development. Genome-wide association studies revealed 717 significant single nucleotide polymorphisms associated with plant height and growth rate at different parts of the growing season specific to certain phases of vegetative growth. When plant height growth curves were compared to growth curves estimated from canopy cover, greater Fréchet distance stability was observed in plant height growth curves than for canopy cover. This indicated canopy cover may be more useful for understanding environmental modulation of overall plant growth and plant height better for understanding genotypic modulation of overall plant growth. This study demonstrated that substantial information can be gained from high temporal resolution data to understand how plants differentially interact with the environment and can enhance our understanding of the genetic basis of complex polygenic traits.

SYNTAXIN OF PLANTS 132 underpins secretion of cargoes associated with salicylic acid signaling and pathogen defense.

Secretory trafficking in plant cells is facilitated by SNARE (soluble N-ethylamide-sensitive factor attachment protein receptor) proteins that drive membrane fusion of cargo-containing vesicles. In Arabidopsis, SYNTAXIN OF PLANTS 132 (SYP132) is an evolutionarily ancient SNARE that functions with syntaxins SYP121 and SYP122 at the plasma membrane. Whereas SYP121 and SYP122 mediate overlapping secretory pathways, albeit with differences in their importance in plant-environment interactions, the SNARE SYP132 is absolutely essential for plant development and survival. SYP132 promotes endocytic traffic of the plasma membrane H+-ATPase AHA1 and aquaporin PIP2;1, and it coordinates plant growth and bacterial pathogen immunity through PATHOGENESIS-RELATED1 (PR1) secretion. Yet, little else is known about SYP132 cargoes. Here, we used advanced quantitative Tandem Mass Tagging (TMT) mass spectrometry (MS) combined with immunoblot assays to track native secreted cargo proteins in the leaf apoplast. We found that SYP132 supports a basal level of secretion in Arabidopsis leaves, and its overexpression influences salicylic acid (SA) and jasmonic acid (JA) defence-related cargoes including PR1, PR2, and PR5 proteins. Impairing SYP132 function also suppressed defence-related secretory traffic when challenged with the bacterial pathogen Pseudomonas syringae. Thus, we conclude that, in addition to its role in hormone-related H+-ATPase cycling, SYP132 influences basal plant immunity.

Functional characterization of a novel terpene synthase GaTPS1 involved in (E)-α-bergamotene biosynthesis in Gossypium arboreum

Terpenoids in plants are mainly synthesized by terpene synthases (TPSs), which play an important role in plant-environment interactions. Gossypium arboreum is one of the important cotton cultivars with excellent pest resistance, however, the biosynthesis of most terpenoids in this plant remains unknown. In this study, we performed a comparative transcriptome analysis of leaves from intact and Helicoverpa armigera-infested cotton plants. The results showed that the H. armigera infestation mainly induced the JA signaling pathway, ten TPS genes were differentially expressed in G. arboreum leaves. Among them, a novel terpene synthase, GaTPS1, was heterologously expressed and functionally characterized in vitro. The enzymatic reaction indicated that recombinant GaTPS1 was primarily responsible for the production of (E)-α-bergamotene. Moreover, molecular docking and site-directed mutagenesis analysis demonstrated that two amino acid residues, A412L and Y535F, distinctly influenced the catalytic activities and product specificity of GaTPS1. The mutants GaTPS1-A412L and GaTPS1-Y535F resulted in a decrease in the proportion of products (E)-α-bergamotene and D-limonene, while an increase in the proportion of products (E)-β-farnesene, α-pinene and β-myrcene. Our findings provide valuable insights into understanding the molecular basis of terpenoid diversity in G. arboreum, with potential applications in plant metabolism regulation and the improvement of resistant cotton cultivars.

Non-linear response of plant caloric value to N addition and mowing treatments in a meadow steppe

BackgroundCaloric value is an important indicator of grassland ecosystem function, but the response of caloric value to nitrogen (N) addition and mowing is still unclear. We explored the adaptive changes of plant caloric value and energy standing crop along a N addition gradient after six-year NH4NO3 addition and mowing treatments in an Inner Mongolian temperate meadow steppe in northern China.ResultsWe found that the response of plant caloric value to N addition at different organizational levels was diverse. The caloric value of legumes increased linearly with N addition rates. The caloric value of grasses exhibited a non-linear response trend, initially increasing followed by saturation or decrease, with a N response threshold present. Due to the dominance of grass species, the caloric value at the community level followed a similar pattern to that of the grasses along the N addition gradient. Under mowing, the caloric value of plants at each organizational level increased and usually mowing enhanced the N response threshold. Amongst these, the N response threshold of Leymus chinensis increased from 3.302 to 5.443 g N m−2 yr−1, grasses increased from 4.414 to 5.746 g N m−2 yr−1, and community increased from 5.373 to 9.216 g N m−2 yr−1. Under non-mowing treatment, the N response thresholds of the most dominant species, Leymus chinensis, and community energy standing crop were 10.001 and 15.119 g N m−2 yr−1, respectively. Under mowing, the energy standing crops showed a linear increasing trend.ConclusionsN response thresholds of plant caloric value and energy standing crop vary at different organizational levels (community > functional group > species). The results reveal varying regulatory capabilities of plants on the ecological environment at different organizational levels. These findings enhance our understanding of plant-environment interactions in grassland ecosystems under N deposition from an energy perspective, which is of great significance to clarify the response mechanism of grassland ecosystem structure and function to N deposition.

Evaluation of Mediterranean perennials for extensive green roofs in water-limited regions: A two-year experiment

Extensive green roofs (EGRs) play a crucial role in urban environments, offering numerous environmental, economic, and social benefits. However, their performance largely depends on plant selection and adaptation to local climatic conditions. This study investigates the suitability of six perennial Euro-Mediterranean species for EGRs in Mediterranean and semi-arid regions, under different water regimes. A two-year experimental analysis was conducted in Rome (Italy) assessing flowering and mortality rates. Results revealed species-specific responses to irrigation levels, with notable performances observed in Thymus serpyllum, Saponaria ocymoides, and Teucrium chamaedrys, showcasing resilience to water stress. Conversely, Lavandula stoechas and Cerastium tomentosum exhibited sensitivity to water availability, emphasizing the importance of species selection for EGRs. No species completely adhered to the expected flowering period, but showed a general tendency of anticipation, and sometimes an extended flowering period, with some differences between the species. The study underscores the complexity of plant-environment interactions and highlights the need for diversified species composition to enhance EGR functionality and resilience.

Artificial intelligence can regulate light and climate systems to reduce energy use in plant factories and support sustainable food production.

Plant factories with artificial lighting (PFALs) can boost food production per unit area but require resources such as carbon dioxide and energy to maintain optimal plant growth conditions. Here we use computational modelling and artificial intelligence (AI) to examine plant-environment interactions across ten diverse global locations with distinct climates. AI reduces energy use by optimizing lighting and climate regulation systems, with energy use in PFALs ranging from 6.42 kWh kg-1 in cooler climates to 7.26 kWh kg-1 in warmer climates, compared to 9.5-10.5 kWh kg-1 in PFALs using existing, non-AI-based technology. Outdoor temperatures between 0 °C and 25 °C favour ventilation-related energy use reduction, with outdoor humidity showing no clear pattern or effect on energy use. Ventilation-related energy savings negatively impact other resource utilization such as carbon dioxide use. AI can substantially enhance energy savings in PFALs and support sustainable food production.

Multi-class plant hormone HILIC-MS/MS analysis coupled with high-throughput phenotyping to investigate plant-environment interactions.

Plant hormones are chemical signals governing almost every aspect of a plant's life cycle and responses to environmental cues. They are enmeshed within complex signaling networks that can only be deciphered by using broad-scale analytical methods to capture information about several plant hormone classes simultaneously. Methods used for this purpose are all based on reversed-phase (RP) liquid chromatography and mass spectrometric detection. Hydrophilic interaction chromatography (HILIC) is an alternative chromatographic method that performs well in analyses of biological samples. We therefore developed and validated a HILIC method for broad-scale plant hormone analysis including a rapid sample preparation procedure; moreover, derivatization or fractionation is not required. The method enables plant hormone screening focused on polar and moderately polar analytes including cytokinins, auxins, jasmonates, abscisic acid and its metabolites, salicylates, indoleamines (melatonin), and 1-aminocyclopropane-1-carboxylic acid (ACC), for a total of 45 analytes. Importantly, the major pitfalls of ACC analysis have been addressed. Furthermore, HILIC provides orthogonal selectivity to conventional RP methods and displays greater sensitivity, resulting in lower limits of quantification. However, it is less robust, so procedures to increase its reproducibility were established. The method's potential is demonstrated in a case study by employing an approach combining hormonal analysis with phenomics to examine responses of three Arabidopsis ecotypes toward three abiotic stress treatments: salinity, low nutrient availability, and their combination. The case study showcases the value of the simultaneous determination of several plant hormone classes coupled with phenomics data when unraveling processes involving complex cross-talk under diverse plant-environment interactions.

Plant Growth Promoting Rhizobacteria (PGPR) induced protection: A plant immunity perspective.

Plant-environment interactions, particularly biotic stress, are increasingly essential for global food security due to crop losses in the dynamic environment. Therefore, understanding plant responses to biotic stress is vital to mitigate damage. Beneficial microorganisms and their association with plants can reduce the damage associated with plant pathogens. One such group is PGPR (Plant growth-promoting rhizobacteria), which influences plant immunity significantly by interacting with biotic stress factors and plant signalling compounds. This review explores the types, metabolism, and mechanisms of action of PGPR, including their enzyme pathways and the signalling compounds secreted by PGPR that modulate gene and protein expression during plant defence. Furthermore, the review will delve into the crosstalk between PGPR and other plant growth regulators and signalling compounds, elucidating the physiological, biochemical, and molecular insights into PGPR's impact on plants under multiple biotic stresses, including interactions with fungi, bacteria, and viruses. Overall, the review comprehensively adds to our knowledge about PGPR's role in plant immunity and its application for agricultural resilience and food security.

The genetic architecture of the pepper metabolome and the biosynthesis of its signature capsianoside metabolites

Capsicum (pepper) is among the most economically important species worldwide, and its fruits accumulate specialized metabolites with essential roles in plant environmental interaction and human health benefits as well as in conferring their unique taste. However, the genetics underlying differences in metabolite presence/absence and/or accumulation remain largely unknown. In this study, we carried out a genome-wide association study as well as generating and characterizing a novel backcross inbred line mapping population to determine the genetic architecture of the pepper metabolome. This genetic analysis provided over 1,000 metabolic quantitative trait loci (mQTL) for over 250 annotated metabolites. We identified 92 candidate genes involved in various mQTLs. Among the identified loci, we described and validated a gene cluster of eleven UDP-glycosyltransferases (UGTs) involved in monomeric capsianoside biosynthesis. We additionally constructed the gene-by-gene-based biosynthetic pathway of pepper capsianoside biosynthesis, including both core and decorative reactions. Given that one of these decorative pathways, namely the glycosylation of acyclic diterpenoid glycosides, contributes to plant resistance, these data provide new insights and breeding resources for pepper. They additionally provide a blueprint for the better understanding of the biosynthesis of species-specific natural compounds in general.

Flavonoids and Derived Anthocyanin Pigments in Plants-Structure, Distribution, Function, and Methods for Quantification and Characterization.

Flavonoids represent a large class of phenolic specialized metabolites and play crucial roles in plant-environment interactions, including responses to biotic and abiotic factors. While the core flavonoid biosynthesis pathway is well known in several plant species, enzymes involved in modifying core flavonoid structures, furnishing them with distinct biological activities, continue to be identified. Anthocyanins, a specific type of flavonoid pigment, serve various functions, including attracting pollinators and seed-dispersing organisms when accumulated in flowers and seeds. Anthocyanins also accumulate in vegetative tissues of many plants, especially under unfavorable conditions. In this review, we present an overview of the diverse structures, various distributions, and multiple functions of flavonoids in plants.

SISTEME VERTICALE HIDROPONICE: INTENSIFICAREA REZISTENȚEI LA CLIMĂ, EFICIENȚEI APEI ȘI AGRICULTURII URBANE

This paper explores hydroponic vertical systems as a sustainable solution to modern agricultural challenges, particularly those posed by climate change. Hydroponics, a method of growing plants without soil using nutrient-rich water solutions, offers significant advantages over traditional farming. Vertical systems maximize space efficiency by growing plants in stacked layers, making them ideal for urban environments with limited space. These systems provide a controlled environment that mitigates the impacts of extreme weather, ensuring consistent crop production. The paper reviews various hydroponic techniques, including deep water culture, nutrient film technique, flood and drain, and drip irrigation. It highlights the efficiency of water use in hydroponics, crucial for areas facing water scarcity. Advanced technologies, such as sensors, automated nutrient delivery, and LED lighting, are employed to optimize growing conditions, enhance resource use efficiency, and improve crop yields. LED lights, in particular, offer energy efficiency, customizable spectra, and low heat output. Mathematical models are used to maximize plant development and resource efficiency, providing a framework for understanding plant-environment interactions. Despite high initial setup costs and the need for technical expertise, hydroponic systems present long-term economic and environmental benefits. This paper underscores hydroponic vertical systems' potential to revolutionize urban agriculture, ensuring food security and sustainability amidst climate change challenges.

Seeing the invisible: Tools to teach and study plant transcriptional responses.

Reporter gene-expressing plants show promoter activity, the stability of transgene expression, and are suitable tools to teach students about plant biotechnology and plant–environment interaction.

How does the life cycle of Clinodiplosis profusa (Cecidomyiidae) adjust to phenological variations of the host plant Eugenia uniflora (Myrtaceae) in sun and shade?

Galls are plant neoformations induced by specialized parasites. Since gall inducers rely on reactive plant sites for gall development, variations in abiotic factors that affect plant phenology are expected to impact the life cycle of gall inducers. To test the hypothesis that different light conditions affect both host plant and gall inducer life cycles, we studied the system Eugenia uniflora (Myrtaceae) - Clinodiplosis profusa (Cecidomyiidae), comparing plants occurring in sunny and shaded environments. We mapped phenological differences among individuals of E. uniflora occurring in the two environments and related them to the influence of luminosity on the life cycle of the gall inducer. Shade plants showed lower intensity of leaf sprouting throughout the year compared to sun-exposed plants, especially during the rainy season. Young and mature galls are synchronized with the peak of leaf sprouting at the beginning of the rainy season, lasting longer in sun-exposed plants - approximately two months longer compared to shade plants. The greater light intensity positively impacts the formation and growth of leaves and galls, with an extended period available for their induction and growth. Thus, light is an important factor for the development of gallers, considering that variations in luminosity influenced not only the phenology of the host plant, but also determined the life cycle of gall inducers. Furthermore, changes in plant-environment interactions are expected to affect the life cycle and richness of other host plant-gall inducer systems.

Attenuated total reflection Fourier-transform infrared spectroscopy reveals environment specific phenotypes in clonal Japanese knotweed

BackgroundJapanese knotweed (Reynoutria japonica var. japonica), a problematic invasive species, has a wide geographical distribution. We have previously shown the potential for attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy and chemometrics to segregate regional differentiation between Japanese knotweed plants. However, the contribution of environment to spectral differences remains unclear. Herein, the response of Japanese knotweed to varied environmental habitats has been studied. Eight unique growth environments were created by manipulation of the red: far-red light ratio (R: FR), water availability, nitrogen, and micronutrients. Their impacts on plant growth, photosynthetic parameters, and ATR-FTIR spectral profiles, were explored using chemometric techniques, including principal component analysis (PCA), linear discriminant analysis, support vector machines (SVM) and partial least squares regression. Key wavenumbers responsible for spectral differences were identified with PCA loadings, and molecular biomarkers were assigned. Partial least squared regression (PLSR) of spectral absorbance and root water potential (RWP) data was used to create a predictive model for RWP.ResultsSpectra from plants grown in different environments were differentiated using ATR-FTIR spectroscopy coupled with SVM. Biomarkers highlighted through PCA loadings corresponded to several molecules, most commonly cell wall carbohydrates, suggesting that these wavenumbers could be consistent indicators of plant stress across species. R: FR most affected the ATR-FTIR spectra of intact dried leaf material. PLSR prediction of root water potential achieved an R2 of 0.8, supporting the potential use of ATR-FTIR spectrometers as sensors for prediction of plant physiological parameters.ConclusionsJapanese knotweed exhibits environmentally induced phenotypes, indicated by measurable differences in their ATR-FTIR spectra. This high environmental plasticity reflected by key biomolecular changes may contribute to its success as an invasive species. Light quality (R: FR) appears critical in defining the growth and spectral response to environment. Cross-species conservation of biomarkers suggest that they could function as indicators of plant-environment interactions including abiotic stress responses and plant health.

Discovery of bifunctional diterpene cyclases/synthases in bacteria supports a bacterial origin for the plant terpene synthase gene family.

Land plants are well-known producers of terpenoids that play diverse roles in plant-environment interactions. The vast chemical diversity of terpenoids is initiated by terpene synthases. Plants contain a distinct mid-sized terpene synthase gene family termed TPS, which appears to have an ancient origin in a fused bacterial Class I (di)terpene synthase (TS) and Class II diterpene cyclase (DTC), corresponding to the catalytically relevant α-domain and βγ-didomains, respectively. However, while such fused tridomain bifunctional (Class I/II) diterpene cyclases/synthases (DCSs) have been found in plants (and fungi), no examples have been reported from bacteria, leaving the origin of the fusion event initiating the TPS gene family opaque. Here, the discovery of such tridomain bifunctional DCSs in bacteria is reported. Extensive genome mining unearthed five putative bacterial DCSs, with biochemical characterization revealing the expected bifunctional activity for three. The most intriguing was CseDCS from Candidatus sericytochromatia bacterium, which produces ent-kaurene, an intermediate in plant hormone biosynthesis, as this is the hypothesized activity for the ancestral TPS. Unlike the extant functionally equivalent TPSs, it was possible to split CseDCS into separate, independently acting DTC and TS, with the first producing the expected ent-copalyl diphosphate (CPP), serving as a CPP synthase (CPS), while the second converts this to ent-kaurene, serving as a kaurene synthase (KS). Nevertheless, sequence alignment and mutation analysis revealed intriguing similarities between this cyanobacterial fused CPS-KS and functionally equivalent TPSs. Regardless of the exact relationship, the discovery of fused bifunctional DCSs in bacteria supports the hypothesized origin of the plant TPS family from such a bacterial gene.

Bridging the Gap: From Photoperception to the Transcription Control of Genes Related to the Production of Phenolic Compounds.

Phenolic compounds are a group of secondary metabolites responsible for several processes in plants-these compounds are involved in plant-environment interactions (attraction of pollinators, repelling of herbivores, or chemotaxis of microbiota in soil), but also have antioxidative properties and are capable of binding heavy metals or screening ultraviolet radiation. Therefore, the accumulation of these compounds has to be precisely driven, which is ensured on several levels, but the most important aspect seems to be the control of the gene expression. Such transcriptional control requires the presence and activity of transcription factors (TFs) that are driven based on the current requirements of the plant. Two environmental factors mainly affect the accumulation of phenolic compounds-light and temperature. Because it is known that light perception occurs via the specialized sensors (photoreceptors) we decided to combine the biophysical knowledge about light perception in plants with the molecular biology-based knowledge about the transcription control of specific genes to bridge the gap between them. Our review offers insights into the regulation of genes related to phenolic compound production, strengthens understanding of plant responses to environmental cues, and opens avenues for manipulation of the total content and profile of phenolic compounds with potential applications in horticulture and food production.

A data-driven genome annotation approach for cassava.

Genome annotation files play a critical role in dictating the quality of downstream analyses by providing essential predictions for gene positions and structures. These files are pivotal in decoding the complex information encoded within DNA sequences. Here, we generated experimental data resolving RNA 5'- and 3'-ends as well as full-length RNAs for cassava TME12 sticklings in ambient temperature and cold. We used these data to generate genome annotation files using the TranscriptomeReconstructoR (TR) tool. A careful comparison to high-quality genome annotations suggests that our new TR genome annotations identified additional genes, resolved the transcript boundaries more accurately and identified additional RNA isoforms. We enhanced existing cassava genome annotation files with the information from TR that maintained the different transcript models as RNA isoforms. The resultant merged annotation was subsequently utilized for comprehensive analysis. To examine the effects of genome annotation files on gene expression studies, we compared the detection of differentially expressed genes during cold using the same RNA-seq data but alternative genome annotation files. We found that our merged genome annotation that included cold-specific TR gene models identified about twice as many cold-induced genes. These data indicate that environmentally induced genes may be missing in off-the-shelf genome annotation files. In conclusion, TR offers the opportunity to enhance crop genome annotations with implications for the discovery of differentially expressed candidate genes during plant-environment interactions.

Intraspecific Trait Variation Regulates Biodiversity and Community Productivity of Shrublands in Drylands

Intraspecific variation (Intra-V) has played an important role in determining the responses of ecosystem functions to climate change. However, its specific role in the regulation of ecosystem functions during community assembly is less investigated. In this study, we conducted a transect survey in northwest China and determined different plant functional types, namely resource-conservative, medium, and resource-acquisitive strategies, which describe resource-use strategies of plants in multi-functional dimensions. Plant functional traits including canopy, wood density (WD), height, specific leaf area (SLA), and leaf nitrogen (N) and phosphorus (P) concentrations were determined. Ecological filters, including external filtering (assembly processes at the regional scale), internal filtering (assembly processes within a certain community), and functional redundancy, were employed to examine plant environment interactions. We found that with the decrease in environmental pressure, dominant shrub plants changed from conservative to acquisition species in drylands. Specifically, a benign environment (such as stable and adequate precipitation, loose soil, and increased acid deposition) significantly increased plant mean traits, such as SLA and WD of shrubs, especially for conservative strategy plants. In addition, a benign environment mainly reduced the functional redundancy of SLA (FRedSLA) by strengthening internal filtering and, ultimately, increased aboveground biomass but decreased species richness. Our results suggest that conservative strategy plants with stronger adaptability to the external environment may exhibit more competitive advantages and play a more important role in community construction under future climate scenarios of gradual warming and wetting in northwest China. Our results also revealed that trait-based Intra-V may be a more reasonable ecological filter than plant mean traits for predicting the structure and function of dryland ecosystems.

PIF transcription factors-versatile plant epigenome landscapers

Plants are exquisitely responsive to their local light and temperature environment utilizing these environmental cues to modulate their developmental pathways and adjust growth patterns. This responsiveness is primarily achieved by the intricate interplay between the photoreceptor phyB (phytochrome B) and PIF (PHYTOCHROME INTERACTING FACTORs) transcription factors (TFs), forming a pivotal signaling nexus. phyB and PIFs co-associate in photobodies (PBs) and depending on environmental conditions, PIFs can dissociate from PBs to orchestrate gene expression. Until recently, the mechanisms governing epigenome modifications subsequent to PIF binding to target genes remained elusive. This mini review sheds light on the emerging role of PIFs in mediating epigenome reprogramming by recruiting chromatin regulators (CRs). The formation of numerous different PIF-CR complexes enables precise temporal and spatial control over the gene regulatory networks (GRNs) governing plant-environment interactions. We refer to PIFs as epigenome landscapers, as while they do not directly reprogram the epigenome, they act as critical sequence-specific recruitment platforms for CRs. Intriguingly, in the absence of PIFs, the efficacy of epigenome reprogramming is largely compromised in light and temperature-controlled processes. We have thoroughly examined the composition and function of known PIF-CR complexes and will explore also unanswered questions regarding the precise of locations PIF-mediated epigenome reprogramming within genes, nuclei, and plants.