A negative feedback loop of TOR signaling balances growth and stress-response trade-offs in plants

K, Muhammed Jamsheer; Jindal, Sunita; Sharma, Mohan; Awasthi, Prakhar; Sreejath, S; Sharma, Manvi; Mannully, Chanchal Thomas; Laxmi, Ashverya

doi:10.1016/j.celrep.2022.110631

Cited by 46 publications

(22 citation statements)

References 97 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Through this series of events, WHIRLY1 may act as a plastidial signal-damping ABA-related stress response. Similar negative feedback loops have already been described in ABA signaling [ 56 , 57 ]. Such function as a platform which in response to different environmental conditions dynamically interacts with different regulatory factors could allow balancing major developmental and stress-related pathways in an environment-sensitive manner.…”

Section: Discussionsupporting

confidence: 71%

WHIRLY1 Acts Upstream of ABA-Related Reprogramming of Drought-Induced Gene Expression in Barley and Affects Stress-Related Histone Modifications

Manh

Ost

Peiter

et al. 2023

IJMS

View full text Add to dashboard Cite

WHIRLY1, a small plant-specific ssDNA-binding protein, dually located in chloroplasts and the nucleus, is discussed to act as a retrograde signal transmitting a stress signal from the chloroplast to the nucleus and triggering there a stress-related gene expression. In this work, we investigated the function of WHIRLY1 in the drought stress response of barley, employing two overexpression lines (oeW1-2 and oeW1-15). The overexpression of WHIRLY1 delayed the drought-stress-related onset of senescence in primary leaves. Two abscisic acid (ABA)-dependent marker genes of drought stress, HvNCED1 and HvS40, whose expression in the wild type was induced during drought treatment, were not induced in overexpression lines. In addition, a drought-related increase in ABA concentration in the leaves was suppressed in WHIRLY1 overexpression lines. To analyze the impact of the gain-of-function of WHIRLY1 on the drought-related reprogramming of nuclear gene expression, RNAseq was performed comparing the wild type and an overexpression line. Cluster analyses revealed a set of genes highly up-regulated in response to drought in the wild type but not in the WHIRLY1 overexpression lines. Among these genes were many stress- and abscisic acid (ABA)-related ones. Another cluster comprised genes up-regulated in the oeW1 lines compared to the wild type. These were related to primary metabolism, chloroplast function and growth. Our results indicate that WHIRLY1 acts as a hub, balancing trade-off between stress-related and developmental pathways. To test whether the gain-of-function of WHIRLY1 affects the epigenetic control of stress-related gene expression, we analyzed drought-related histone modifications in different regions of the promoter and at the transcriptional start sites of HvNCED1 and HvS40. Interestingly, the level of euchromatic marks (H3K4me3 and H3K9ac) was clearly decreased in both genes in a WHIRLY1 overexpression line. Our results indicate that WHIRLY1, which is discussed to act as a retrograde signal, affects the ABA-related reprogramming of nuclear gene expression during drought via differential histone modifications.

show abstract

Section: Discussionsupporting

confidence: 71%

WHIRLY1 Acts Upstream of ABA-Related Reprogramming of Drought-Induced Gene Expression in Barley and Affects Stress-Related Histone Modifications

Manh

Ost

Peiter

et al. 2023

IJMS

View full text Add to dashboard Cite

show abstract

“…To determine whether these mutants show any defect in TOR signaling, seedlings were grown in the media containing either 8 mM or 60 mM sucrose, representing low and high energy environments, respectively. As a source of energy, sucrose is known to promote the growth of the seedlings germinated in vitro and this growth is mediated by TOR signaling [ 26 , 27 ]. However, this response is subdued under a low-energy environment.…”

Section: Resultsmentioning

confidence: 99%

Targeting TOR and SnRK1 Genes in Rice with CRISPR/Cas9

Pathak

Maurya

Faria

et al. 2022

Plants

Self Cite

View full text Add to dashboard Cite

Genome targeting with CRISPR/Cas9 is a popular method for introducing mutations and creating knock-out effects. However, limited information is currently available on the mutagenesis of essential genes. This study investigated the efficiency of CRISPR/Cas9 in targeting rice essential genes: the singleton TARGET OF RAPAMYCIN (OsTOR) and the three paralogs of the Sucrose non-fermenting-1 (SNF1)-related kinase 1 (OsSnRK1α), OsSnRK1αA, OsSnRK1αB and OsSnRK1αC. Strong activity of constitutively expressed CRISPR/Cas9 was effective in creating mutations in OsTOR and OsSnRK1α genes, but inducible CRISPR/Cas9 failed to generate detectable mutations. The rate of OsTOR mutagenesis was relatively lower and only the kinase domain of OsTOR could be targeted, while mutations in the HEAT region were unrecoverable. OsSnRK1α paralogs could be targeted at higher rates; however, sterility or early senescence was observed in >50% of the primary mutants. Additionally, OsSnRK1αB and OsSnRK1αC, which bear high sequence homologies, could be targeted simultaneously to generate double-mutants. Further, although limited types of mutations were found in the surviving mutants, the recovered lines displayed loss-of-function or knockdown tor or snrk1 phenotypes. Overall, our data show that mutations in these essential genes can be created by CRISPR/Cas9 to facilitate investigations on their roles in plant development and environmental response in rice.

show abstract

“…Proteins represent the effectors of the plant cell, rendering the lack of time-resolved quantitative proteomic data relating to their salt and osmotic stress responses a critical gap in our understanding. Interestingly, plants are proposed to have three stages of abiotic stress response after stress onset, including: a stop phase, quiescent phase and a recovery phase (68, 69), during which, plants modify their growth rate to allocate resources for stress tolerance (70). For example, 5 d-old Arabidopsis seedlings exposed to salt stress revealed that 4 to 5 h after treatment, growth rates rapidly slowed down (stop phase), remaining steady for an additional 4 h (quiescent phase) before recovering growth 13 to 24 h after stress onset (69).…”

Section: Discussionmentioning

confidence: 99%

Quantitative Time-Course Analysis of Osmotic and Salt Stress inArabidopsis thalianausing Short Gradient Multi-CV FAIMSpro BoxCar DIA

Gallo

Talasila

et al. 2023

Preprint

View full text Add to dashboard Cite

A major limitation when undertaking quantitative proteomic time-course experimentation is the tradeoff between depth-of-analysis and speed-of-analysis. In high complexity and high dynamic range sample types, such as plant extracts, balance between resolution and time is especially apparent. To address this, we evaluate multiple composition voltage (CV) High Field Asymetric Waveform Ion Mobility Spectrometry (FAIMSpro) settings using the latest label-free single-shot Orbitrap-based DIA acquisition workflows for their ability to deeply-quantify the Arabidopsis thaliana seedling proteome. Using a BoxCarDIA acquisition workflow with a -30 -50 -70 CV FAIMSpro setting we are able to consistently quantify >5000 Arabidopsis seedling proteins over a 21-minute gradient, facilitating the analysis of ~42 samples per day. Utilizing this acquisition approach, we then quantified proteome-level changes occurring in Arabidopsis seedling shoots and roots over 24 h of salt and osmotic stress, to identify early and late stress response proteins and reveal stress response overlaps. Here, we successfully quantify >6400 shoot and >8500 root protein groups, respectively, quantifying nearly ~9700 unique protein groups in total across the study. Collectively, we pioneer a short gradient, multi-CV FAIMSpro BoxCarDIA acquisition workflow that represents an exciting new analysis approach for undertaking quantitative proteomic time-course experimentation in plants.

show abstract

A negative feedback loop of TOR signaling balances growth and stress-response trade-offs in plants

Cited by 46 publications

References 97 publications

WHIRLY1 Acts Upstream of ABA-Related Reprogramming of Drought-Induced Gene Expression in Barley and Affects Stress-Related Histone Modifications

WHIRLY1 Acts Upstream of ABA-Related Reprogramming of Drought-Induced Gene Expression in Barley and Affects Stress-Related Histone Modifications

Targeting TOR and SnRK1 Genes in Rice with CRISPR/Cas9

Quantitative Time-Course Analysis of Osmotic and Salt Stress inArabidopsis thalianausing Short Gradient Multi-CV FAIMSpro BoxCar DIA

Contact Info

Product

Resources

About