SWATH-MS quantitative proteomic investigation of nitrogen starvation in Arabidopsis reveals new aspects of plant nitrogen stress responses

2018 ◽  
Vol 187 ◽  
pp. 161-170 ◽  
Author(s):  
Fu-Yuan Zhu ◽  
Mo-Xian Chen ◽  
Wai-Lung Chan ◽  
Feng Yang ◽  
Yuan Tian ◽  
...  
Keyword(s):  
Stress Responses ◽  
Nitrogen Starvation ◽  
Nitrogen Stress ◽  
Plant Nitrogen ◽  
Proteomic Investigation

scholarly journals RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4

2019 ◽  
Author(s):  
Vinay K Nagarajan ◽  
Patrick M Kukulich ◽  
Bryan von Hagel ◽  
Pamela J Green
Keyword(s):  
Stress Responses ◽  
Lateral Root ◽  
Nitrogen Stress ◽  
Degradome Analysis ◽  
Nonsense Mediated Decay ◽  
Whole Plant ◽  
Major Player ◽  
Plant Level ◽  
The Impact ◽  
Dark Stress

Abstract XRN4, the plant cytoplasmic homolog of yeast and metazoan XRN1, catalyzes exoribonucleolytic degradation of uncapped mRNAs from the 5′ end. Most studies of cytoplasmic XRN substrates have focused on polyadenylated transcripts, although many substrates are likely first deadenylated. Here, we report the global investigation of XRN4 substrates in both polyadenylated and nonpolyadenylated RNA to better understand the impact of the enzyme in Arabidopsis. RNA degradome analysis demonstrated that xrn4 mutants overaccumulate many more decapped deadenylated intermediates than those that are polyadenylated. Among these XRN4 substrates that have 5′ ends precisely at cap sites, those associated with photosynthesis, nitrogen responses and auxin responses were enriched. Moreover, xrn4 was found to be defective in the dark stress response and lateral root growth during N resupply, demonstrating that XRN4 is required during both processes. XRN4 also contributes to nonsense-mediated decay (NMD) and xrn4 accumulates 3′ fragments of select NMD targets, despite the lack of the metazoan endoribonuclease SMG6 in plants. Beyond demonstrating that XRN4 is a major player in multiple decay pathways, this study identified intriguing molecular impacts of the enzyme, including those that led to new insights about mRNA decay and discovery of functional contributions at the whole-plant level.

scholarly journals Plant DNA methylation is sensitive to parent seed N content and influences the growth of rice

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaoru Fan ◽  
Laihua Liu ◽  
Kaiyun Qian ◽  
Jingguang Chen ◽  
Yuyue Zhang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Plant Growth ◽  
Nitrogen Content ◽  
Nitrogen Stress ◽  
Wild Type ◽  
High Nitrogen ◽  
N Content ◽  
Plant Nitrogen ◽  
Overexpression Line ◽  
N Deficiency

Abstract Background Nitrogen (N) is an important nutrient for plant growth, development, and agricultural production. Nitrogen stress could induce epigenetic changes in plants. In our research, overexpression of the OsNAR2.1 line was used as a testing target in rice plants with high nitrogen-use efficiency to study the changes of rice methylation and growth in respond of the endogenous and external nitrogen stress. Results Our results showed that external N deficiency could decrease seed N content and plant growth of the overexpression line. During the filial growth, we found that the low parent seed nitrogen (LPSN) in the overexpression line could lead to a decrease in the filial seed nitrogen content, total plant nitrogen content, yield, and OsNAR2.1 expression (28, 35, 23, and 55%, respectively) compared with high parent seed nitrogen (HPSN) in high nitrogen external supply. However, such decreases were not observed in wild type. Furthermore, methylation sequencing results showed that LPSN caused massive gene methylation changes, which enriched in over 20 GO pathways in the filial overexpression line, and the expression of OsNAR2.1 in LPSN filial overexpression plants was significantly reduced compared to HPSN filial plants in high external N, which was not shown in wild type. Conclusions We suggest that the parent seed nitrogen content decreased induced DNA methylation changes at the epigenetic level and significantly decreased the expression of OsNAR2.1, resulting in a heritable phenotype of N deficiency over two generations of the overexpression line.

scholarly journals Global poplar root and leaf transcriptomes reveal links between growth and stress responses under nitrogen starvation and excess

2015 ◽  
Vol 35 (12) ◽  
pp. 1283-1302 ◽  
Author(s):  
Jie Luo ◽  
Jing Zhou ◽  
Hong Li ◽  
Wenguang Shi ◽  
Andrea Polle ◽  
...  
Keyword(s):  
Stress Responses ◽  
Nitrogen Starvation ◽  
Poplar Root

scholarly journals Proteomic and Transcriptomic Analyses of “Candidatus Pelagibacter ubique” Describe the First PII-Independent Response to Nitrogen Limitation in a Free-Living Alphaproteobacterium

mBio ◽  
2013 ◽  
Vol 4 (6) ◽  
Author(s):  
Daniel P. Smith ◽  
J. Cameron Thrash ◽  
Carrie D. Nicora ◽  
Mary S. Lipton ◽  
Kristin E. Burnum-Johnson ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Stress Responses ◽  
Nitrogen Limitation ◽  
Nitrogen Assimilation ◽  
Field Studies ◽  
Nitrogen Stress ◽  
Marine Microorganisms ◽  
Geochemical Cycles ◽  
Major Nutrients ◽  
Microbial Productivity

ABSTRACTNitrogen is one of the major nutrients limiting microbial productivity in the ocean, and as a result, most marine microorganisms have evolved systems for responding to nitrogen stress. The highly abundant alphaproteobacterium “CandidatusPelagibacter ubique,” a cultured member of the orderPelagibacterales(SAR11), lacks the canonical GlnB, GlnD, GlnK, and NtrB/NtrC genes for regulating nitrogen assimilation, raising questions about how these organisms respond to nitrogen limitation. A survey of 266Alphaproteobacteriagenomes found these five regulatory genes nearly universally conserved, absent only in intracellular parasites and members of the orderPelagibacterales, including “Ca. Pelagibacter ubique.” Global differences in mRNA and protein expression between nitrogen-limited and nitrogen-replete cultures were measured to identify nitrogen stress responses in “Ca.Pelagibacter ubique” strain HTCC1062. Transporters for ammonium (AmtB), taurine (TauA), amino acids (YhdW), and opines (OccT) were all elevated in nitrogen-limited cells, indicating that they devote increased resources to the assimilation of nitrogenous organic compounds. Enzymes for assimilating amine into glutamine (GlnA), glutamate (GltBD), and glycine (AspC) were similarly upregulated. Differential regulation of the transcriptional regulator NtrX in the two-component signaling system NtrY/NtrX was also observed, implicating it in control of the nitrogen starvation response. Comparisons of the transcriptome and proteome supported previous observations of uncoupling between transcription and translation in nutrient-deprived “Ca.Pelagibacter ubique” cells. Overall, these data reveal a streamlined, PII-independent response to nitrogen stress in “Ca.Pelagibacter ubique,” and likely otherPelagibacterales, and show that they respond to nitrogen stress by allocating more resources to the assimilation of nitrogen-rich organic compounds.IMPORTANCEPelagibacteralesare extraordinarily abundant and play a pivotal role in marine geochemical cycles, as one of the major recyclers of labile dissolved organic matter. They are also models for understanding how streamlining selection can reshape chemoheterotroph metabolism. Streamlining and its broad importance to environmental microbiology are emerging slowly from studies that reveal the complete genomes of uncultured organisms. Here, we report another remarkable example of streamlined metabolism inPelagibacterales, this time in systems that control nitrogen assimilation.Pelagibacteralesare major contributors to metatranscriptomes and metaproteomes from ocean systems, where patterns of gene expression are used to gain insight into ocean conditions and geochemical cycles. The data presented here supply background that is essential to interpreting data from field studies.

scholarly journals miRNAomic Approach to Plant Nitrogen Starvation

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Peerzada Yasir Yousuf ◽  
Peerzada Arshid Shabir ◽  
Khalid Rehman Hakeem
Keyword(s):  
Nitrogen Starvation ◽  
Regulation Of Gene Expression ◽  
Regulatory Mechanisms ◽  
Nitrogen Use ◽  
Plant Nitrogen ◽  
Environmental Consequences ◽  
Current Review ◽  
N Utilization ◽  
N Metabolism ◽  
Growth Development

Nitrogen (N) is one of the indispensable nutrients required by plants for their growth, development, and survival. Being a limited nutrient, it is mostly supplied exogenously to the plants, to maintain quality and productivity. The increased use of N fertilizers is associated with high-cost inputs and negative environmental consequences, which necessitates the development of nitrogen-use-efficient plants for sustainable agriculture. Understanding the regulatory mechanisms underlying N metabolism in plants under low N is one of the prerequisites for the development of nitrogen-use-efficient plants. One of the important and recently discovered groups of regulatory molecules acting at the posttranscriptional and translational levels are microRNAs (miRNAs). miRNAs are known to play critical roles in the regulation of gene expression in plants under different stress conditions including N stress. Several classes of miRNAs associated with N metabolism have been identified so far. These nitrogen-responsive miRNAs may provide a platform for a better understanding of the regulation of N metabolism and pave a way for the development of genotypes for better N utilization. The current review presents a brief outline of miRNAs and their regulatory role in N metabolism.

scholarly journals A novel single-cell screening platform reveals proteome plasticity during yeast stress responses

2013 ◽  
Vol 200 (6) ◽  
pp. 839-850 ◽  
Author(s):  
Michal Breker ◽  
Melissa Gymrek ◽  
Maya Schuldiner
Keyword(s):  
Single Cell ◽  
Stress Responses ◽  
Nitrogen Starvation ◽  
Bet Hedging ◽  
Transcriptional Responses ◽  
Cellular Physiology ◽  
Protein Levels ◽  
Hedging Strategies ◽  
Screening Platform ◽  
External Stimuli

Uncovering the mechanisms underlying robust responses of cells to stress is crucial for our understanding of cellular physiology. Indeed, vast amounts of data have been collected on transcriptional responses in Saccharomyces cerevisiae. However, only a handful of pioneering studies describe the dynamics of proteins in response to external stimuli, despite the fact that regulation of protein levels and localization is an essential part of such responses. Here we characterized unprecedented proteome plasticity by systematically tracking the localization and abundance of 5,330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H2O2, and nitrogen starvation) using the GFP-tagged yeast library. We uncovered a unique “fingerprint” of changes for each stress and elucidated a new response arsenal for adapting to radical environments. These include bet-hedging strategies, organelle rearrangement, and redistribution of protein localizations. All data are available for download through our online database, LOQATE (localization and quantitation atlas of yeast proteome).

Assessment of plant nitrogen stress in wheat (Triticum aestivum L.) through hyperspectral indices

2012 ◽  
Vol 33 (20) ◽  
pp. 6342-6360 ◽  
Author(s):  
Rajeev Ranjan ◽  
Usha Kiran Chopra ◽  
Rabi N. Sahoo ◽  
Anil Kumar Singh ◽  
Sanatan Pradhan
Keyword(s):  
Triticum Aestivum ◽  
Triticum Aestivum L ◽  
Nitrogen Stress ◽  
Plant Nitrogen

scholarly journals Metatranscriptomic comparison of endophytic and pathogenic Fusarium–Arabidopsis interactions reveals plant transcriptional plasticity

2021 ◽  
Author(s):  
Li Guo ◽  
Houlin Yu ◽  
Bo Wang ◽  
Kathryn Vescio ◽  
Gregory A. DeIulio ◽  
...  
Keyword(s):  
Fusarium Oxysporum ◽  
Stress Responses ◽  
Fungal Endophytes ◽  
Plant Stress ◽  
Fine Tuning ◽  
Post Inoculation ◽  
Molecular Response ◽  
Plant Nitrogen ◽  
Accessory Genes ◽  
Transcriptional Plasticity

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two Fusarium oxysporum strains share a core genome of about 46 Mb, in addition to unique 1,229 and 5,415 accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (~80%) in responding to both fungal inoculums at all time points from 12 to 96 h post inoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses plant growth/development related functions, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest time point sampled and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.

scholarly journals High-throughput profiling and analysis of plant responses over time to abiotic stress

2017 ◽  
Author(s):  
Kira M. Veley ◽  
Jeffrey C. Berry ◽  
Sarah J. Fentress ◽  
Daniel P. Schachtman ◽  
Ivan Baxter ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
High Throughput ◽  
Stress Responses ◽  
Low Cost ◽  
Abiotic Stress Tolerance ◽  
Crop Improvement ◽  
Plant Responses ◽  
Nitrogen Deprivation ◽  
Plant Nitrogen ◽  
Over Time

ABSTRACTSorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass crop prized for abiotic stress tolerance. However, measuring genotype-by-environment (G × E) interactions remains a progress bottleneck. Here we describe strategies for identifying shape, color and ionomic indicators of plant nitrogen use efficiency. We subjected a panel of 30 genetically diverse sorghum genotypes to a spectrum of nitrogen deprivation and measured responses using high-throughput phenotyping technology followed by ionomic profiling. Responses were quantified using shape (16 measurable outputs), color (hue and intensity) and ionome (18 elements). We measured the speed at which specific genotypes respond to environmental conditions, both in terms of biomass and color changes, and identified individual genotypes that perform most favorably. With this analysis we present a novel approach to quantifying color-based stress indicators over time. Additionally, ionomic profiling was conducted as an independent, low cost and high throughput option for characterizing G × E, identifying the elements most affected by either genotype or treatment and suggesting signaling that occurs in response to the environment. This entire dataset and associated scripts are made available through an open access, user-friendly, web-based interface. In summary, this work provides analysis tools for visualizing and quantifying plant abiotic stress responses over time. These methods can be deployed as a time-efficient method of dissecting the genetic mechanisms used by sorghum to respond to the environment to accelerate crop improvement.

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