Identification of small non‐coding RNAs responsive to GUN1 and GUN5 related retrograde signals in Arabidopsis thaliana

Habermann, Kristin; Tiwari, Bhavika; Krantz, Marcus; Adler, Stephan O.; Klipp, Edda; Arif, Muhammad; Frank, Wolfgang

doi:10.1111/tpj.14912

Cited by 10 publications

(31 citation statements)

References 84 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recently published work indicates that retrograde signalling modulates nuclear gene expression not only by triggering differential transcript accumulation, but also by altering splicing patterns (Petrillo et al ., 2014), read‐through events (Crisp et al ., 2018) and microRNA biogenesis (Fang et al ., 2019). Accordingly, our consortium has identified specific small RNAs (sRNAs) that respond to GUN signals (Habermann et al ., 2020) or exposure to cold (Tiwari et al ., 2020), and we have constructed a cold‐specific miRNA and transcription factor‐dependent gene regulatory network.…”

Section: Ra3 Signalling: Coordination Of Different Acclimation Respomentioning

confidence: 99%

“…By combining experimental techniques for subcellular fractionation with omics techniques, we will further deepen our understanding of the metabolic pathways, transport processes and signalling cascades that affect the chloroplast and connect it to the cytosol, nucleus and other compartments. Moreover, it will promote the integration into metabolic networks of information emerging from signalling cascades, derived by interaction network mapping (Habermann et al ., 2020). Integrating signalling processes into metabolic reprogramming is of particular interest for chloroplast‐related research due to the significant impact of retrograde signalling on acclimation (Leister, 2019; Marino et al ., 2019) and adaptation (Zhao et al ., 2019).…”

Section: Mathematical Modelling Of Acclimation (Ra4) and Systems Biologymentioning

confidence: 99%

See 1 more Smart Citation

Acclimation in plants – the Green Hub consortium

et al. 2021

Self Cite

View full text Add to dashboard Cite

Summary Acclimation is the capacity to adapt to environmental changes within the lifetime of an individual. This ability allows plants to cope with the continuous variation in ambient conditions to which they are exposed as sessile organisms. Because environmental changes and extremes are becoming even more pronounced due to the current period of climate change, enhancing the efficacy of plant acclimation is a promising strategy for mitigating the consequences of global warming on crop yields. At the cellular level, the chloroplast plays a central role in many acclimation responses, acting both as a sensor of environmental change and as a target of cellular acclimation responses. In this Perspective article, we outline the activities of the Green Hub consortium funded by the German Science Foundation. The main aim of this research collaboration is to understand and strategically modify the cellular networks that mediate plant acclimation to adverse environments, employing Arabidopsis, tobacco (Nicotiana tabacum) and Chlamydomonas as model organisms. These efforts will contribute to ‘smart breeding’ methods designed to create crop plants with improved acclimation properties. To this end, the model oilseed crop Camelina sativa is being used to test modulators of acclimation for their potential to enhance crop yield under adverse environmental conditions. Here we highlight the current state of research on the role of gene expression, metabolism and signalling in acclimation, with a focus on chloroplast‐related processes. In addition, further approaches to uncovering acclimation mechanisms derived from systems and computational biology, as well as adaptive laboratory evolution with photosynthetic microbes, are highlighted.

show abstract

Section: Ra3 Signalling: Coordination Of Different Acclimation Respomentioning

confidence: 99%

Section: Mathematical Modelling Of Acclimation (Ra4) and Systems Biologymentioning

confidence: 99%

Acclimation in plants – the Green Hub consortium

et al. 2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…After each cycle, the EvaGreen signals were measured and melting curves were monitored to confirm primer specificities. The ΔΔCt method was used to calculate the expression levels following normalization against UBI1 housekeeping gene ( Habermann et al, 2020 ; Tiwari et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Identification of Small RNAs During High Light Acclimation in Arabidopsis thaliana

et al. 2021

Self Cite

View full text Add to dashboard Cite

The biological significance of non-coding RNAs (ncRNAs) has been firmly established to be important for the regulation of genes involved in stress acclimation. Light plays an important role for the growth of plants providing the energy for photosynthesis; however, excessive light conditions can also cause substantial defects. Small RNAs (sRNAs) are a class of non-coding RNAs that regulate transcript levels of protein-coding genes and mediate epigenetic silencing. Next generation sequencing facilitates the identification of small non-coding RNA classes such as miRNAs (microRNAs) and small-interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), but changes in the ncRNA transcriptome in response to high light are poorly understood. We subjected Arabidopsis plants to high light conditions and performed a temporal in-depth study of the transcriptome data after 3 h, 6 h, and 2 days of high light treatment. We identified a large number of high light responsive miRNAs and sRNAs derived from NAT gene pairs, lncRNAs and TAS transcripts. We performed target predictions for differentially expressed miRNAs and correlated their expression levels through mRNA sequencing data. GO analysis of the targets revealed an overrepresentation of genes involved in transcriptional regulation. In A. thaliana, sRNA-mediated regulation of gene expression in response to high light treatment is mainly carried out by miRNAs and sRNAs derived from NAT gene pairs, and from lncRNAs. This study provides a deeper understanding of sRNA-dependent regulatory networks in high light acclimation.

show abstract

“…For example, the involvement of the plastid-nucleus located DNA/RNA binding protein WHIRLY1 in miRNA expression regulation during light stress in barley was postulated [ 90 ]. sRNA sequencing combined with mRNA/lncRNA sequencing on Arabidopsis wild-type plants and two retrograde signaling mutants, gun1 and gun5, treated with the herbicide norflurazon shed light on cross-talk between sRNAs (including miRNAs) and retrograde signaling [ 91 ]. Additionally, the functional role of chloroplast-derived signals in miRNA regulation was postulated recently by Fang et al, 2019 [ 92 ], in the context of heat stress.…”

Section: Retrograde 1 O 2 Signa...mentioning

confidence: 99%

Plastid retrograde regulation of miRNA expression in response to light stress

et al. 2022

View full text Add to dashboard Cite

Background MicroRNAs (miRNAs) are a class of endogenous noncoding RNAs that play a pivotal role in the regulation of plant development and responses to the surrounding environment. Despite the efforts made to elucidate their function in the adaptation of plants to many abiotic and biotic stresses, their role in high light (HL) stress is still vague. HL stress often arises upon plant exposure to full sunlight. Subsequent changes in nuclear gene expression are triggered by chloroplast-derived retrograde signals. Results In this study, we show that HL is involved in miRNA-dependent regulation in Arabidopsis thaliana rosettes. Microtranscriptomic screening revealed a limited number of miRNAs reacting to HL. To explain the miRNA regulation mechanisms at the different biogenesis stages, chemical and genetic approaches were applied. First, we tested the possible role of plastoquinone (PQ) redox changes using photosynthetic electron transport chain inhibitors. The results suggest that increased primary transcript abundance (pri-miRNAs) of HL-regulated miRNAs is dependent on signals upstream of PQ. This indicates that such signals may originate from photosystem II, which is the main singlet oxygen (1O2) source. Nevertheless, no changes in pri-miRNA expression upon a dark–light shift in the conditional fluorescent (flu) mutant producing 1O2 were observed when compared to wild-type plants. Thus, we explored the 1O2 signaling pathway, which is initiated independently in HL and is related to β-carotene oxidation and production of volatile derivatives, such as β-cyclocitral (β-CC). Pri-miRNA induction by β-CC, which is a component of this 1O2 pathway, as well as an altered response in the methylene blue sensitivity 1 (mbs1) mutant support the role of 1O2 signaling in miRNA regulation. Conclusions We show that light stress triggers changes in miRNA expression. This stress response may be regulated by reactive oxygen species (ROS)-related signaling. In conclusion, our results link ROS action to miRNA biogenesis, suggesting its contribution to inconsistent pri- and mature miRNA dynamics.

show abstract

Identification of small non‐coding RNAs responsive to GUN1 and GUN5 related retrograde signals in Arabidopsis thaliana

Cited by 10 publications

References 84 publications

Acclimation in plants – the Green Hub consortium

Acclimation in plants – the Green Hub consortium

Identification of Small RNAs During High Light Acclimation in Arabidopsis thaliana

Plastid retrograde regulation of miRNA expression in response to light stress

Contact Info

Product

Resources

About