Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions

Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass

BACKGROUND

Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress.

RESULTS

In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls.

CONCLUSION

Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.

Determination of Differential Alternative Splicing Under Stress Conditions

Alternative splicing (AS) is an important mechanism contributing to stress-induced regulation of gene expression and proteome diversity. Massive sequencing technologies allow the identification of transcripts generated via stress-responsive AS, potentially important for adaptation to stress conditions. Several bioinformatics tools have been developed to identify differentially expressed alternative splicing events/transcripts from RNA-sequencing results. This chapter describes a detailed protocol for differential alternative splicing analysis using the rMATS tool. In addition, we provide guidelines for validation of the detected splice variants by qRT-PCR based on the obtained output files.

Multiomics Reveals the Regulatory Mechanisms of Arabidopsis Tissues under Heat Stress

Understanding the mechanisms of responses to high temperatures in Arabidopsis will provide insights into how plants may mitigate heat stress under global climate change. And exploring the interconnections of different modification levels in heat stress response could help us to understand the molecular mechanism of heat stress response in Arabidopsis more comprehensively and precisely. In this paper, we combined multiomics analyses to explore the common heat stress-responsive genes and specific heat-responsive metabolic pathways in Arabidopsis leaf, seedling, and seed tissues. We found that genes such as AT1G54050 play a role in promoting proper protein folding in response to HS (Heat stress). In addition, it was revealed that the binding profile of A1B is altered under elevated temperature conditions. Finally, we also show that two microRNAs, ath-mir156h and ath-mir166b-5p, may be core regulatory molecules in HS. Also elucidated that under HS, plants can regulate specific regulatory mechanisms, such as oxygen levels, by altering the degree of CHH methylation.

Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis

BACKGROUND

Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq.

RESULTS

HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes.

CONCLUSIONS

Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior.

Transcriptome Analysis of Heat Shock Factor C2a Over-Expressing Wheat Roots Reveals Ferroptosis-like Cell Death in Heat Stress Recovery

Wheat (Triticum aestivum L.) growing areas in many regions of the world are subject to heat waves which are predicted to increase in frequency because of climate change. The engineering of crop plants can be a useful strategy to mitigate heat stress-caused yield losses. Previously, we have shown that heat shock factor subclass C (TaHsfC2a-B)-overexpression significantly increased the survival of heat-stressed wheat seedlings. Although previous studies have shown that the overexpression of Hsf genes enhanced the survival of plants under heat stress, the molecular mechanisms are largely unknown. To understand the underlying molecular mechanisms involved in this response, a comparative analysis of the root transcriptomes of untransformed control and TaHsfC2a-overexpressing wheat lines by RNA-sequencing have been performed. The results of RNA-sequencing indicated that the roots of TaHsfC2a-overexpressing wheat seedlings showed lower transcripts of hydrogen peroxide-producing peroxidases, which corresponds to the reduced accumulation of hydrogen peroxide along the roots. In addition, suites of genes from iron transport and nicotianamine-related gene ontology categories showed lower transcript abundance in the roots of TaHsfC2a-overexpressing wheat roots than in the untransformed control line following heat stress, which are in accordance with the reduction in iron accumulation in the roots of transgenic plants under heat stress. Overall, these results suggested the existence of ferroptosis-like cell death under heat stress in wheat roots, and that TaHsfC2a is a key player in this mechanism. To date, this is the first evidence to show that a Hsf gene plays a key role in ferroptosis under heat stress in plants. In future, the role of Hsf genes could be further studied on ferroptosis in plants to identify root-based marker genes to screen for heat-tolerant genotypes.

A long noncoding RNA HILinc1 enhances pear thermotolerance by stabilizing PbHILT1 transcripts through complementary base pairing

As global warming intensifies, heat stress has become a major environmental constraint threatening crop production and quality worldwide. Here, we characterize Heat-induced long intergenic noncoding RNA 1 (HILinc1), a cytoplasm-enriched lincRNA that plays a key role in thermotolerance regulation of pear (Pyrus spp.). HILinc1 Target 1 (PbHILT1) which is the target transcript of HILinc1, was stabilized via complementary base pairing to upregulate its expression. PbHILT1 could bind to Heat shock transcription factor A1b (PbHSFA1b) to enhance its transcriptional activity, leading to the upregulation of a major downstream transcriptional regulator, Multiprotein bridging factor 1c (PbMBF1c), during heat response. Transient overexpressing of either HILinc1 or PbHILT1 increases thermotolerance in pear, while transient silencing of HILinc1 or PbHILT1 makes pear plants more heat sensitive. These findings provide evidences for a new regulatory mechanism by which HILinc1 facilitates PbHSFA1b activity and enhances pear thermotolerance through stabilizing PbHILT1 transcripts.

Heat stress in pear cultivar results in upregulation of long non-coding RNA HILinc1, which binds to and stabilizes PbHILT1 mRNA, which codes for a protein that interacts with heat shock factor A1b, improving thermotolerance.

Diversification of heat shock transcription factors expanded thermal stress responses during early plant evolution

The copy numbers of many plant transcription factor (TF) genes substantially increased during terrestrialization. This allowed TFs to acquire new specificities and thus create gene regulatory networks (GRNs) with new biological functions to help plants adapt to terrestrial environments. Through characterizing heat shock factor (HSF) genes MpHSFA1 and MpHSFB1 in the liverwort Marchantia polymorpha, we explored how heat-responsive GRNs widened their functions in M. polymorpha and Arabidopsis thaliana. An interspecies comparison of heat-induced transcriptomes and the evolutionary rates of HSFs demonstrated the emergence and subsequent rapid evolution of HSFB prior to terrestrialization. Transcriptome and metabolome analyses of M. polymorpha HSF-null mutants revealed that MpHSFA1 controls canonical heat responses such as thermotolerance and metabolic changes. MpHSFB1 also plays essential roles in heat responses, as well as regulating developmental processes including meristem branching and antheridiophore formation. Analysis of cis-regulatory elements revealed development- and stress-related TFs that function directly or indirectly downstream of HSFB. Male gametophytes of M. polymorpha showed higher levels of thermotolerance than female gametophytes, which could be explained by different expression levels of MpHSFA1U and MpHSFA1V on sex chromosome. We propose that the diversification of HSFs is linked to the expansion of HS responses, which enabled coordinated multicellular reactions in land plants.

Mysteries of gene regulation: Promoters are not the sole triggers of gene expression

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TF binding peaks were widely distributed in nonpromoters, especially downstream regions of transcription termination sites.

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Exons of non-coding regions were the prominent regions of TF binding.

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TAD boundaries were colocalized with activating histone marks and TF binding.

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Genes with distinct functions demonstrated substantially different behaviors in cis-regulation and epigenetic signatures.

Cis-regulatory elements of promoters are essential for gene regulation by transcription factors (TFs). However, the regulatory roles of nonpromoter regions, TFs, and epigenetic marks remain poorly understood in plants. In this study, we characterized the cis-regulatory regions of 53 TFs and 19 histone marks in 328 chromatin immunoprecipitation (ChIP-seq) datasets from Arabidopsis. The genome-wide maps indicated that both promoters and regions around the transcription termination sites of protein-coding genes recruit the most TFs. The maps also revealed a diverse of histone combinations. The analysis suggested that exons play critical roles in the regulation of non-coding genes. Additionally, comparative analysis between heat-stress-responsive and nonresponsive genes indicated that the genes with distinct functions also exhibited substantial differences in cis-regulatory regions, histone regulation, and topologically associating domain (TAD) boundary organization. By integrating multiple high-throughput sequencing datasets, this study generated regulatory models for protein-coding genes, non-coding genes, and TAD boundaries to explain the complexity of transcriptional regulation.

Tissue-specific transcriptomic analysis uncovers potential roles of natural antisense transcripts in Arabidopsis heat stress response

Natural antisense transcripts (NATs) are an important class of non-coding ribonucleic acids (RNAs) that have been shown to regulate gene expression. Using strand-specific RNA sequencing, 36,317 NAT pairs were identified, and 5,536 were specifically expressed under heat stress. We found distinct expression patterns between vegetative and reproductive tissues for both coding genes and genes encoding NATs. Genes for heat-responsive NATs are associated with relatively high levels of H3K4me3 and low levels of H3K27me2/3. On the other hand, small RNAs are significantly enriched in sequence overlapping regions of NAT pairs, and a large number of heat-responsive NATs pairs serve as potential precursors of nat-siRNAs. Collectively, our results suggest epigenetic modifications and small RNAs play important roles in the regulation of NAT expression, and highlight the potential significance of heat-inducible NATs.

Unfolding molecular switches in plant heat stress resistance: A comprehensive review

Plant heat stress response is a multi-factorial trait that is precisely regulated by the complex web of transcription factors from various families that modulate heat stress responsive gene expression. Global warming due to climate change affects plant growth and development throughout its life cycle. Adds to this, the frequent occurrence of heat waves is drastically reducing the global crop yield. Molecular plant scientists can help crop breeders by providing genetic markers associated with stress resistance. Plant heat stress response (HSR), however, is a multi-factorial trait and using a single stress resistance trait might not be ideal to develop thermotolerant crops. Transcription factors participate in regulation of plant biological processes and environmental stress responses. Recent studies have revealed that plant HSR is precisely regulated by the complex web of transcription factors from various families. These transcription factors enhance plant heat stress tolerance by regulating the expression level of several stress-responsive genes independently or in cross talk with different other transcription factors. This review explores how signaling pathways triggered by heat stress are regulated by multiple transcription factor families. To our knowledge, we for the first time analyze the role of major transcription factor families in plant HSR along with their regulatory mechanisms. In the end, we will also discuss the potential of emerging technologies to improve thermotolerance in plants.

Analyzing the regulatory role of heat shock transcription factors in plant heat stress tolerance: a brief appraisal

An increase in ambient temperature throughout the twenty-first century has been described as a "worldwide threat" for crop production. Due to their sessile lifestyles, plants have evolved highly sophisticated and complex heat stress response (HSR) mechanisms to respond to higher temperatures. The HSR allows plants to minimize the damages caused by heat stress (HS), thus enabling cellular protection. HSR is crucial for their lifecycle and yield, particularly for plants grown in the field. At the cellular level, HSR involves the production of heat shock proteins (HSPs) and other stress-responsive proteins to counter the negative effects of HS. The expression of most HSPs is transcriptionally regulated by heat shock transcription factors (HSFs). HSFs are a group of evolutionary conserved regulatory proteins present in all eukaryotes and regulate various stress responses and biological processes in plants. In recent years, significant progress has been made in deciphering the complex regulatory network of HSFs, and several HSFs not only from model plants but also from major crops have been functionally characterized. Therefore, this review explores the progress made in this fascinating research area and debates the further potential to breed thermotolerant crop cultivars through the modulation of HSF networks. Furthermore, we discussed the role of HSFs in plant HS tolerance in a class-specific manner and shed light on their functional diversity, which is evident from their mode of action. Additionally, some research gaps have been highlighted concerning class-specific manners.

The Passage of H2O2 from Chloroplasts to Their Associated Nucleus during Retrograde Signalling: Reflections on the Role of the Nuclear Envelope

The response of chloroplasts to adverse environmental cues, principally increases in light intensity, stimulates chloroplast-to-nucleus retrograde signalling, which leads to the induction of immediate protective responses and longer-term acclimation. Hydrogen peroxide (H₂O₂), generated during photosynthesis, is proposed to both initiate and transduce a retrograde signal in response to photoinhibitory light intensities. Signalling specificity achieved by chloroplast-sourced H₂O₂ for signal transduction may be dependent upon the oft-observed close association of a proportion of these organelles with the nucleus. In this review, we consider more precisely the nature of the close association between a chloroplast appressed to the nucleus and the requirement for H₂O₂ to cross both the double membranes of the chloroplast and nuclear envelopes. Of particular relevance is that the endoplasmic reticulum (ER) has close physical contact with chloroplasts and is contiguous with the nuclear envelope. Therefore, the perinuclear space, which transducing H₂O₂ molecules would have to cross, may have an oxidising environment the same as the ER lumen. Based on studies in animal cells, the ER lumen may be a significant source of H₂O₂ in plant cells arising from the oxidative folding of proteins. If this is the case, then there is potential for the ER lumen/perinuclear space to be an important location to modify chloroplast-to-nucleus H₂O₂ signal transduction and thereby introduce modulation of it by additional different environmental cues. These would include for example, heat stress and pathogen infection, which induce the unfolded protein response characterised by an increased H₂O₂ level in the ER lumen.

Heat Stress Resistance Mechanisms of Two Cucumber Varieties from Different Regions

High temperatures affect the yield and quality of vegetable crops. Unlike thermosensitive plants, thermotolerant plants have excellent systems for withstanding heat stress. This study evaluated various heat resistance indexes of the thermotolerant cucumber (TT) and thermosensitive cucumber (TS) plants at the seedling stage. The similarities and differences between the regulatory genes were assessed through transcriptome analysis to understand the mechanisms for heat stress resistance in cucumber. The TT plants exhibited enhanced leaf status, photosystem, root viability, and ROS scavenging under high temperature compared to the TS plants. Additionally, transcriptome analysis showed that the genes involved in photosynthesis, the chlorophyll metabolism, and defense responses were upregulated in TT plants but downregulated in TS plants. Zeatin riboside (ZR), brassinosteroid (BR), and jasmonic acid (JA) levels were higher in TT plants than in TS. The heat stress increased gibberellic acid (GA) and indoleacetic acid (IAA) levels in both plant lines; however, the level of GA was higher in TT. Correlation and interaction analyses revealed that heat cucumber heat resistance is regulated by a few transcription factor family genes and metabolic pathways. Our study revealed different phenotypic and physiological mechanisms of the heat response by the thermotolerant and thermosensitive cucumber plants. The plants were also shown to exhibit different expression profiles and metabolic pathways. The heat resistant pathways and genes of two cucumber varieties were also identified. These results enhance our understanding of the molecular mechanisms of cucumber response to high-temperature stress.

Elongation factor TFIIS is essential for heat stress adaptation in plants

Elongation factor TFIIS (transcription factor IIS) is structurally and biochemically probably the best characterized elongation cofactor of RNA polymerase II. However, little is known about TFIIS regulation or its roles during stress responses. Here, we show that, although TFIIS seems unnecessary under optimal conditions in Arabidopsis, its absence renders plants supersensitive to heat; tfIIs mutants die even when exposed to sublethal high temperature. TFIIS activity is required for thermal adaptation throughout the whole life cycle of plants, ensuring both survival and reproductive success. By employing a transcriptome analysis, we unravel that the absence of TFIIS makes transcriptional reprogramming sluggish, and affects expression and alternative splicing pattern of hundreds of heat-regulated transcripts. Transcriptome changes indirectly cause proteotoxic stress and deterioration of cellular pathways, including photosynthesis, which finally leads to lethality. Contrary to expectations of being constantly present to support transcription, we show that TFIIS is dynamically regulated. TFIIS accumulation during heat occurs in evolutionary distant species, including the unicellular alga Chlamydomonas reinhardtii, dicot Brassica napus and monocot Hordeum vulgare, suggesting that the vital role of TFIIS in stress adaptation of plants is conserved.

Cultivar-biased regulation of HSFA7 and HSFB4a govern high-temperature tolerance in tomato

Cultivar-biased regulation of HSFB4a and HSFA7 mediates heat stress tolerance/sensitivity in tomato. Reduced HSFB4a repressor levels and enhanced HSFA7 activator levels govern thermo-tolerance in tolerant cultivars. Heat shock factors (HSFs) are at the core of heat stress (HS) response in plants. However, the contribution of HSFs governing the inherent thermo-tolerance mechanism in tomato from sub-tropical hot climates is poorly understood. With the above aim, comparative expression profiles of the HSF family in a HS-tolerant (CLN1621L) and -sensitive cultivars (CA4 and Pusa Ruby) of tomato under HS revealed cultivar-biased regulation of an activator (HSFA7) and a repressor (HSFB4a) class HSF. HSFA7 exhibited strong upregulation while HSFB4a showed downregulation in tolerant tomato cultivar upon HS. Functional characterization of HSFA7 and HSFB4a in a tolerant-sensitive cultivar pair by virus-induced gene silencing (VIGS)-based silencing and transient overexpression established them as a positive and a negative regulator of HS tolerance, respectively. Promoter:GUS reporter assays and promoter sequence analyses suggest heat-mediated transcriptional control of both the HSF genes in the contrasting cultivars. Moreover, degradome data highlighted HSFB4a is a probable target of microRNA Sly-miR4200. Transient in-planta Sly-MIR4200-effector:HSFB4a-reporter assays showed miRNA-dependent target down-regulation. Chelation of miRNA by short-tandem-target-mimic of Sly-miR4200 increased target abundance, highlighting a link between Sly-miR4200 and HSFB4a. This miRNA has induced several folds upon HS in the tolerant cultivar where HSFB4a levels are reduced, thus exhibiting the inverse miR:target expression. Thus, we speculate that the alleviation of HSFB4a and increased HSFA7 levels govern thermo-tolerance in the tolerant cultivar by regulating downstream heat stress-responsive genes.

Mechanisms of elevated CO2-induced thermotolerance in plants: the role of phytohormones

Rising atmospheric CO₂ is a key driver of climate change, intensifying drastic changes in meteorological parameters. Plants can sense and respond to changes in environmental parameters including atmospheric CO₂ and temperatures. High temperatures beyond the physiological threshold can significantly affect plant growth and development and thus attenuate crop productivity. However, elevated atmospheric CO₂ can mitigate the deleterious effects of heat stress on plants. Despite a large body of literature supporting the positive impact of elevated CO₂ on thermotolerance, the underlying biological mechanisms and precise molecular pathways that lead to enhanced tolerance to heat stress remain largely unclear. Under heat stress, elevated CO₂-induced expression of respiratory burst oxidase homologs (RBOHs) and reactive oxygen species (ROS) signaling play a critical role in stomatal movement, which optimizes gas exchange to enhance photosynthesis and water use efficiency. Notably, elevated CO₂ also fortifies antioxidant defense and redox homeostasis to alleviate heat-induced oxidative damage. Both hormone-dependent and independent pathways have been shown to mediate high CO₂-induced thermotolerance. The activation of heat-shock factors and subsequent expression of heat-shock proteins are thought to be the essential mechanism downstream of hormone and ROS signaling. Here we review the role of phytohormones in plant response to high atmospheric CO₂ and temperatures. We also discuss the potential mechanisms of elevated CO₂-induced thermotolerance by focusing on several key phytohormones such as ethylene. Finally, we address some limitations of our current understanding and the need for further research to unveil the yet-unknown crosstalk between plant hormones in mediating high CO₂-induced thermotolerance in plants.

Molecular mechanisms of plant tolerance to heat stress: current landscape and future perspectives

We summarize recent studies focusing on the molecular basis of plant heat stress response (HSR), how HSR leads to thermotolerance, and promote plant adaptation to recurring heat stress events. The global crop productivity is facing unprecedented threats due to climate change as high temperature negatively influences plant growth and metabolism. Owing to their sessile nature, plants have developed complex signaling networks which enable them to perceive changes in ambient temperature. This in turn activates a suite of molecular changes that promote plant survival and reproduction under adverse conditions. Deciphering these mechanisms is an important task, as this could facilitate development of molecular markers, which could be ultimately used to breed thermotolerant crop cultivars. In current article, we summarize mechanisms involve in plant heat stress acclimation with special emphasis on advances related to heat stress perception, heat-induced signaling, heat stress-responsive gene expression and thermomemory that promote plant adaptation to short- and long-term-recurring heat-stress events. In the end, we will discuss impact of emerging technologies that could facilitate the development of heat stress-tolerant crop cultivars.

Time-series transcriptomics reveals a BBX32-directed control of acclimation to high light in mature Arabidopsis leaves

The photosynthetic capacity of mature leaves increases after several days' exposure to constant or intermittent episodes of high light (HL) and is manifested primarily as changes in chloroplast physiology. How this chloroplast-level acclimation to HL is initiated and controlled is unknown. From expanded Arabidopsis leaves, we determined HL-dependent changes in transcript abundance of 3844 genes in a 0-6 h time-series transcriptomics experiment. It was hypothesized that among such genes were those that contribute to the initiation of HL acclimation. By focusing on differentially expressed transcription (co-)factor genes and applying dynamic statistical modelling to the temporal transcriptomics data, a regulatory network of 47 predominantly photoreceptor-regulated transcription (co-)factor genes was inferred. The most connected gene in this network was B-BOX DOMAIN CONTAINING PROTEIN32 (BBX32). Plants overexpressing BBX32 were strongly impaired in acclimation to HL and displayed perturbed expression of photosynthesis-associated genes under LL and after exposure to HL. These observations led to demonstrating that as well as regulation of chloroplast-level acclimation by BBX32, CRYPTOCHROME1, LONG HYPOCOTYL5, CONSTITUTIVELY PHOTOMORPHOGENIC1 and SUPPRESSOR OF PHYA-105 are important. In addition, the BBX32-centric gene regulatory network provides a view of the transcriptional control of acclimation in mature leaves distinct from other photoreceptor-regulated processes, such as seedling photomorphogenesis.

Meta-analysis of RNA-Seq studies reveals genes with dominant functions during flower bud endo- to eco-dormancy transition in Prunus species

In deciduous fruit trees, entrance into dormancy occurs in later summer/fall, concomitantly with the shortening of day length and decrease in temperature. Dormancy can be divided into endodormancy, ecodormancy and paradormancy. In Prunus species flower buds, entrance into the dormant stage occurs when the apical meristem is partially differentiated; during dormancy, flower verticils continue their growth and differentiation. Each species and/or cultivar requires exposure to low winter temperature followed by warm temperatures, quantified as chilling and heat requirements, to remove the physiological blocks that inhibit budburst. A comprehensive meta-analysis of transcriptomic studies on flower buds of sweet cherry, apricot and peach was conducted, by investigating the gene expression profiles during bud endo- to ecodormancy transition in genotypes differing in chilling requirements. Conserved and distinctive expression patterns were observed, allowing the identification of gene specifically associated with endodormancy or ecodormancy. In addition to the MADS-box transcription factor family, hormone-related genes, chromatin modifiers, macro- and micro-gametogenesis related genes and environmental integrators, were identified as novel biomarker candidates for flower bud development during winter in stone fruits. In parallel, flower bud differentiation processes were associated to dormancy progression and termination and to environmental factors triggering dormancy phase-specific gene expression.

Genome-wide identification of heat shock factors and heat shock proteins in response to UV and high intensity light stress in lettuce

BACKGROUND

Heat shock factors (Hsfs) and Heat shock proteins (Hsps) belong to an essential group of molecular regulators involved in controlling cellular processes under normal and stress conditions. The role of Hsfs and Hsps is well known in model plant species under diverse stress conditions. While plants Hsfs are vital components of the signal transduction response to maintain cellular homeostasis, Hsps function as chaperones helping to maintain folding of damaged and newly formed proteins during stress conditions. In lettuce (Lactuca sativa), a highly consumed vegetable crop grown in the field and in hydroponic systems, the role of these gene families in response to artificial light is not well characterized.

RESULTS

Using a genome-wide analysis approach, we identified 32 Hsfs and 22 small heat shock proteins (LsHsps) in lettuce, some of which do not have orthologs in Arabidopsis, poplar, and rice. LsHsp60s, LsHsp90s, and LsHsp100s are highly conserved among dicot and monocot species. Surprisingly, LsHsp70s have three times more members than Arabidopsis and two times more than rice. Interestingly, the lettuce genome triplication did not contribute to the increased number of LsHsp70s genes. The large number of LsHsp70s was the result of genome tandem duplication. Chromosomal distribution analysis shows larger tandem repeats of LsHsp70s genes in Chr1, Chr7, Chr8, and Chr9. At the transcriptional level, some genes of the LsHsfs, LsHsps, LsHsp60s, and LsHsp70s families were highly responsive to UV and high intensity light stress, in contrast to LsHsp90s and LsHsp100s which did not respond to a light stimulus.

CONCLUSIONS

Our genome-wide analysis provides a detailed identification of Hsfs and Hsps in lettuce. Chromosomal location and syntenic region analysis together with our transcriptional analysis under different light conditions provide candidate genes for breeding programs aiming to produce lettuce varieties able to grow healthy under hydroponic systems that use artificial light.

The Role of Ribosomal Protein S6 Kinases in Plant Homeostasis

The p70 ribosomal S6 kinase (S6K) family is a group of highly conserved kinases in eukaryotes that regulates cell growth, cell proliferation, and stress response via modulating protein synthesis and ribosomal biogenesis. S6Ks are downstream effectors of the Target of Rapamycin (TOR) pathway, which connects nutrient and energy signaling to growth and homeostasis, under normal and stress conditions. The plant S6K family includes two isoforms, S6K1 and S6K2, which, despite their high level of sequence similarity, have distinct functions and regulation mechanisms. Significant advances on the characterization of human S6Ks have occurred in the past few years, while studies on plant S6Ks are scarce. In this article, we review expression and activation of the two S6K isoforms in plants and we discuss their roles in mediating responses to stresses and developmental cues.

Differential requirement of MED14/17 recruitment for activation of heat inducible genes

The mechanism of heat stress response in plants has been studied, focusing on the function of transcription factors (TFs). Generally, TFs recruit coactivators, such as Mediator, are needed to assemble the transcriptional machinery. However, despite the close relationship with TFs, how coactivators are involved in transcriptional regulation under heat stress conditions is largely unclear. We found a severe thermosensitive phenotype of Arabidopsis mutants of MED14 and MED17. Transcriptomic analysis revealed that a quarter of the heat stress (HS)-inducible genes were commonly downregulated in these mutants. Furthermore, chromatin immunoprecipitation assay showed that the recruitment of Mediator by HsfA1s, the master regulators of heat stress response, is an important step for the expression of HS-inducible genes. There was a differential requirement of Mediator among genes; TF genes have a high requirement whereas heat shock proteins (HSPs) have a low requirement. Furthermore, artificial activation of HsfA1d mimicking perturbation of protein homeostasis induced HSP gene expression without MED14 recruitment but not TF gene expression. Considering the essential role of MED14 in Mediator function, other coactivators may play major roles in HSP activation depending on the cellular conditions. Our findings highlight the importance of differential recruitment of Mediator for the precise control of HS responses in plants.

Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks

Background

Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennials like apple. The aims of this study were to identify quantitative trait loci (QTLs) and to develop genomics-assisted prediction models for salt, alkali, and salt-alkali tolerance in apple rootstock.

Results

A total of 3258 hybrids derived from the apple rootstock cultivars ‘Baleng Crab’ (Malus robusta Rehd., tolerant) × ‘M9’ (M. pumila Mill., sensitive) were used to identify 17, 13, and two QTLs for injury indices of salt, alkali, and salt–alkali stress via bulked segregant analysis. The genotype effects of single nucleotide polymorphism (SNP) markers designed on candidate genes in each QTL interval were estimated. The genomic predicted value of an individual hybrid was calculated by adding the sum of all marker genotype effects to the mean phenotype value of the population. The prediction accuracy was 0.6569, 0.6695, and 0.5834 for injury indices of salt, alkali, and salt–alkali stress, respectively. SNP182G on MdRGLG3, which changes a leucine to an arginine at the vWFA-domain, conferred tolerance to salt, alkali, and salt-alkali stress. SNP761A on MdKCAB, affecting the Kv_beta domain that cooperated with the linked allelic variation SNP11, contributed to salt, alkali, and salt–alkali tolerance in apple rootstock.

Conclusions

The genomics-assisted prediction models can potentially be used in breeding saline, alkaline, and saline-alkaline tolerant apple rootstocks. The QTLs and the functional markers may provide insight for future studies into the genetic variation of plant abiotic stress tolerance.

Genomic analyses of heat stress transcription factors (HSFs) in simulated drought stress response and storage root deterioration after harvest in cassava

Heat shock factors (HSFs) play crucial roles in various plant stress responses. However, the current knowledge about HSFs in cassava, an important crop, is still insufficient. In this research, we identified 32 cassava HSF genes (MeHSFs) and clustered them into three groups (A, B, C) based on phylogenetic analysis and structural characteristics. Conserved motif analyses showed that MeHSFs display domains characteristic to HSF transcription factors. Gene structure analyses suggested that 29 MeHSFs contained only two exons. All identified 32 cassava MeHSFs were distributed on 13 chromosomes. Their expression profiles revealed that the different MeHSFs were expressed differentially in different tissues, most high expression genes belonged to group A. The similar MeHSFs were up-regulated after treatment with both PEG and abscisic acid (ABA), which implied that these MeHSFs may participate in resistance to simulated drought stress associated with the ABA signaling pathway. In addition, several MeHSFs were induced during postharvest physiological deterioration (PPD) in cassava. Our results provided basic but important knowledge for future gene function analysis of MeHSFs toward efforts in improving tolerance to abiotic stress and PPD in cassava.

Patterns of Sequence and Expression Diversification Associate Members of the PADRE Gene Family With Response to Fungal Pathogens

Pathogen infection triggers extensive reprogramming of the plant transcriptome, including numerous genes the function of which is unknown. Due to their wide taxonomic distribution, genes encoding proteins with Domains of Unknown Function (DUFs) activated upon pathogen challenge likely play important roles in disease. In Arabidopsis thaliana, we identified thirteen genes harboring a DUF4228 domain in the top 10% most induced genes after infection by the fungal pathogen Sclerotinia sclerotiorum. Based on functional information collected through homology and contextual searches, we propose to refer to this domain as the pathogen and abiotic stress response, cadmium tolerance, disordered region-containing (PADRE) domain. Genome-wide and phylogenetic analyses indicated that PADRE is specific to plants and diversified into 10 subfamilies early in the evolution of Angiosperms. PADRE typically occurs in small single-domain proteins with a bipartite architecture. PADRE N-terminus harbors conserved sequence motifs, while its C-terminus includes an intrinsically disordered region with multiple phosphorylation sites. A pangenomic survey of PADRE genes expression upon S. sclerotiorum inoculation in Arabidopsis, castor bean, and tomato indicated consistent expression across species within phylogenetic groups. Multi-stress expression profiling and co-expression network analyses associated AtPADRE genes with the induction of anthocyanin biosynthesis and responses to chitin and to hypoxia. Our analyses reveal patterns of sequence and expression diversification consistent with the evolution of a role in disease resistance for an uncharacterized family of plant genes. These findings highlight PADRE genes as prime candidates for the functional dissection of mechanisms underlying plant disease resistance to fungi.

Heat Sensing and Lipid Reprograming as a Signaling Switch for Heat Stress Responses in Wheat

Temperature is an essential physical factor that affects the plant life cycle. Almost all plant species have evolved a robust signal transduction system that enables them to sense changes in the surrounding temperature, relay this message and accordingly adjust their metabolism and cellular functions to avoid heat stress-related damage. Wheat (Triticum aestivum), being a cool-season crop, is very sensitive to heat stress. Any increase in the ambient temperature, especially at the reproductive and grain-filling stages, can cause a drastic loss in wheat yield. Heat stress causes lipid peroxidation due to oxidative stress, resulting in the damage of thylakoid membranes and the disruption of their function, which ultimately decreases photosynthesis and crop yield. The cell membrane/plasma membrane plays prominent roles as an interface system that perceives and translates the changes in environmental signals into intracellular responses. Thus, membrane lipid composition is a critical factor in heat stress tolerance or susceptibility in wheat. In this review, we elucidate the possible involvement of calcium influx as an early heat stress-responsive mechanism in wheat plants. In addition, the physiological implications underlying the changes in lipid metabolism under high-temperature stress in wheat and other plant species will be discussed. In-depth knowledge about wheat lipid reprograming can help develop heat-tolerant wheat varieties and provide approaches to solve the impact of global climate change.

Genome-wide analysis and expression profiling of the heat shock transcription factor gene family in Physic Nut (Jatropha curcas L.)

The heat shock transcription factor (Hsf) family, identified as one of the important gene families, participates in plant development process and some stress response. So far, there have been no reports on the research of the Hsf transcription factors in physic nut. In this study, seventeen putative Hsf genes identified from physic nut genome. Phylogenetic analysis manifested these genes classified into three groups: A, B and C. Chromosomal location showed that they distributed eight out of eleven linkage groups. Expression profiling indicated that fourteen JcHsf genes highly expressed in different tissues except JcHsf1, JcHsf6 and JcHsf13. In addition, induction of six and twelve JcHsf genes noted against salt stress and drought stress, respectively, which demonstrated that the JcHsf genes are involved in abiotic stress responses. Our results contribute to a better understanding of the JcHsf gene family and further study of its function.

Interaction between the Circadian Clock and Regulators of Heat Stress Responses in Plants

The circadian clock is found ubiquitously in nature, and helps organisms coordinate internal biological processes with environmental cues that inform the time of the day or year. Both temperature stress and the clock affect many important biological processes in plants. Specifically, clock-controlled gene regulation and growth are impacted by a compromised clock or heat stress. The interactions linking these two regulatory pathways include several rhythmic transcription factors that are important for coordinating the appropriate response to temperature stress. Here we review the current understanding of clock control of the regulators involved in heat stress responses in plants.

Arabidopsis heat shock transcription factor HSFA7b positively mediates salt stress tolerance by binding to an E-box-like motif to regulate gene expression

Plant heat shock transcription factors (HSFs) are involved in heat and other abiotic stress responses. However, their functions in salt tolerance are little known. In this study, we characterized the function of a HSF from Arabidopsis, AtHSFA7b, in salt tolerance. AtHSFA7b is a nuclear protein with transactivation activity. ChIP-seq combined with an RNA-seq assay indicated that AtHSFA7b preferentially binds to a novel cis-acting element, termed the E-box-like motif, to regulate gene expression; it also binds to the heat shock element motif. Under salt conditions, AtHSFA7b regulates its target genes to mediate serial physiological changes, including maintaining cellular ion homeostasis, reducing water loss rate, decreasing reactive oxygen species accumulation, and adjusting osmotic potential, which ultimately leads to improved salt tolerance. Additionally, most cellulose synthase-like (CSL) and cellulose synthase (CESA) family genes were inhibited by AtHSFA7b; some of them were randomly selected for salt tolerance characterization, and they were mainly found to negatively modulate salt tolerance. By contrast, some transcription factors (TFs) were induced by AtHSFA7b; among them, we randomly identified six TFs that positively regulate salt tolerance. Thus, AtHSFA7b serves as a transactivator that positively mediates salinity tolerance mainly through binding to the E-box-like motif to regulate gene expression.

Male Sterility in Maize after Transient Heat Stress during the Tetrad Stage of Pollen Development

Shifts in the duration and intensity of ambient temperature impair plant development and reproduction, particularly male gametogenesis. Stress exposure causes meiotic defects or premature spore abortion in male reproductive organs, leading to male sterility. However, little is known about the mechanisms underlying stress and male sterility. To elucidate these mechanisms, we imposed a moderate transient heat stress on maize (Zea mays) plants at the tetrad stage of pollen development. After completion of pollen development at optimal conditions, stress responses were assessed in mature pollen. Transient heat stress resulted in reduced starch content, decreased enzymatic activity, and reduced pollen germination, resulting in sterility. A transcriptomic comparison pointed toward misregulation of starch, lipid, and energy biosynthesis-related genes. Metabolomic studies showed an increase of Suc and its monosaccharide components, as well as a reduction in pyruvate. Lipidomic analysis showed increased levels of unsaturated fatty acids and decreased levels of saturated fatty acids. In contrast, the majority of genes involved in developmental processes such as those required for auxin and unfolded protein responses, signaling, and cell wall biosynthesis remained unaltered. It is noteworthy that changes in the regulation of transcriptional and metabolic pathway genes, as well as heat stress proteins, remained altered even though pollen could recover during further development at optimal conditions. In conclusion, our findings demonstrate that a short moderate heat stress during the highly susceptible tetrad stage strongly affects basic metabolic pathways and thus generates germination-defective pollen, ultimately leading to severe yield losses in maize.

The mitogen-activated protein kinase 4-phosphorylated heat shock factor A4A regulates responses to combined salt and heat stresses

Heat shock factors regulate responses to high temperature, salinity, water deprivation, or heavy metals. Their function in combinations of stresses is, however, not known. Arabidopsis HEAT SHOCK FACTOR A4A (HSFA4A) was previously reported to regulate responses to salt and oxidative stresses. Here we show, that the HSFA4A gene is induced by salt, elevated temperature, and a combination of these conditions. Fast translocation of HSFA4A tagged with yellow fluorescent protein from cytosol to nuclei takes place in salt-treated cells. HSFA4A can be phosphorylated not only by mitogen-activated protein (MAP) kinases MPK3 and MPK6 but also by MPK4, and Ser309 is the dominant MAP kinase phosphorylation site. In vivo data suggest that HSFA4A can be the substrate of other kinases as well. Changing Ser309 to Asp or Ala alters intramolecular multimerization. Chromatin immunoprecipitation assays confirmed binding of HSFA4A to promoters of target genes encoding the small heat shock protein HSP17.6A and transcription factors WRKY30 and ZAT12. HSFA4A overexpression enhanced tolerance to individually and simultaneously applied heat and salt stresses through reduction of oxidative damage. Our results suggest that this heat shock factor is a component of a complex stress regulatory pathway, connecting upstream signals mediated by MAP kinases MPK3/6 and MPK4 with transcription regulation of a set of stress-induced target genes.

Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis

Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf-level water-use efficiency (WUE). In Arabidopsis, little is known about the variation of whole-plant water use (PWU) and whole-plant WUE (transpiration efficiency). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large-scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water-use strategies, namely, C24 (low PWU) and Col-0 (high PWU). Subsequent quantitative trait loci mapping and validation through near-isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ13 C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ13 C. and rosette water use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining lifetime PWU but not always leaf-level traits.

Contribution of time of day and the circadian clock to the heat stress responsive transcriptome in Arabidopsis

In Arabidopsis, a large subset of heat responsive genes exhibits diurnal or circadian oscillations. However, to what extent the dimension of time and/or the circadian clock contribute to heat stress responses remains largely unknown. To determine the direct contribution of time of day and/or the clock to differential heat stress responses, we probed wild-type and mutants of the circadian clock genes CCA1, LHY, PRR7, and PRR9 following exposure to heat (37 °C) and moderate cold (10 °C) in the early morning (ZT1) and afternoon (ZT6). Thousands of genes were differentially expressed in response to temperature, time of day, and/or the clock mutation. Approximately 30% more genes were differentially expressed in the afternoon compared to the morning, and heat stress significantly perturbed the transcriptome. Of the DEGs (~3000) specifically responsive to heat stress, ~70% showed time of day (ZT1 or ZT6) occurrence of the transcriptional response. For the DEGs (~1400) that are shared between ZT1 and ZT6, we observed changes to the magnitude of the transcriptional response. In addition, ~2% of all DEGs showed differential responses to temperature stress in the clock mutants. The findings in this study highlight a significant role for time of day in the heat stress responsive transcriptome, and the clock through CCA1 and LHY, appears to have a more profound role than PRR7 and PRR9 in modulating heat stress responses during the day. Our results emphasize the importance of considering the dimension of time in studies on abiotic stress responses in Arabidopsis.

AP2/ERF Transcription Factor Regulatory Networks in Hormone and Abiotic Stress Responses in Arabidopsis

Dynamic environmental changes such as extreme temperature, water scarcity and high salinity affect plant growth, survival, and reproduction. Plants have evolved sophisticated regulatory mechanisms to adapt to these unfavorable conditions, many of which interface with plant hormone signaling pathways. Abiotic stresses alter the production and distribution of phytohormones that in turn mediate stress responses at least in part through hormone- and stress-responsive transcription factors. Among these, the APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) family transcription factors (AP2/ERFs) have emerged as key regulators of various stress responses, in which they also respond to hormones with improved plant survival during stress conditions. Apart from participation in specific stresses, AP2/ERFs are involved in a wide range of stress tolerance, enabling them to form an interconnected stress regulatory network. Additionally, many AP2/ERFs respond to the plant hormones abscisic acid (ABA) and ethylene (ET) to help activate ABA and ET dependent and independent stress-responsive genes. While some AP2/ERFs are implicated in growth and developmental processes mediated by gibberellins (GAs), cytokinins (CTK), and brassinosteroids (BRs). The involvement of AP2/ERFs in hormone signaling adds the complexity of stress regulatory network. In this review, we summarize recent studies on AP2/ERF transcription factors in hormonal and abiotic stress responses with an emphasis on selected family members in Arabidopsis. In addition, we leverage publically available Arabidopsis gene networks and transcriptome data to investigate AP2/ERF regulatory networks, providing context and important clues about the roles of diverse AP2/ERFs in controlling hormone and stress responses.

To defend or to grow: lessons from Arabidopsis C24

The emergence of Arabidopsis as a model species and the availability of genetic and genomic resources have resulted in the identification and detailed characterization of abiotic stress signalling pathways. However, this has led only to limited success in engineering abiotic stress tolerance in crops. This is because there needs to be a deeper understanding of how to combine resistances to a range of stresses with growth and productivity. The natural variation and genomic resources of Arabidopsis thaliana (Arabidopsis) are a great asset to understand the mechanisms of multiple stress tolerances. One natural variant in Arabidopsis is the accession C24, and here we provide an overview of the increasing research interest in this accession. C24 is highlighted as a source of tolerance for multiple abiotic and biotic stresses, and a key accession to understand the basis of basal immunity to infection, high water use efficiency, and water productivity. Multiple biochemical, physiological, and phenological mechanisms have been attributed to these traits in C24, and none of them constrains productivity. Based on the uniqueness of C24, we postulate that the use of variation derived from natural selection in undomesticated species provides opportunities to better understand how complex environmental stress tolerances and resource use efficiency are co-ordinated.