An advanced protocol for profiling RNA-binding proteins in Arabidopsis using plant phase extraction DOI Creative Commons
Yong Zhang, Ye Xu, Todd H. Skaggs

et al.

Biology Methods and Protocols, Journal Year: 2023, Volume and Issue: 8(1)

Published: Jan. 1, 2023

Abstract RNA-binding proteins (RBPs) are key players in regulating cell fate and essential developmental processes. Systematic profiling of the proteome (RBPome) is thus indispensable for researchers aiming to understand mechanisms post-transcriptional gene regulation. RBPome identification methods developed humans, mice, bacteria have successfully identified RBPomes these organisms. However, biochemical genetic complexities plant tissues greatly hindered effectiveness plants. Moreover, RBPs been predominantly discovered through oligo d(T) based affinity purification (RNA-interactome capture). Since polyadenylated RNA only accounts less than 5% total population eukaryotic cells, there a pressing need develop comprehensive, yet unbiased, method capture full spectrum Here, we describe detailed protocol Plant Phase Extraction (PPE), recently identify Arabidopsis (Zhang Y, Xu Skaggs TH, et al. phase extraction: enhanced discovery its dynamics Cell 2023; 35: 2750–72.) [1]. The PPE enables efficient enrichment both poly(A) non-poly(A) from various quickly reproducibly. Most importantly, allows unveiling dynamic RBP–RNA interactions under abiotic biotic stress conditions during different stages. This provides much broader more accurate understanding RBPs, marking significant advancement molecular biology.

Language: Английский

Insights into plant salt stress signaling and tolerance DOI Creative Commons
Huapeng Zhou,

Haifan Shi,

Yongqing Yang

et al.

Journal of genetics and genomics/Journal of Genetics and Genomics, Journal Year: 2023, Volume and Issue: 51(1), P. 16 - 34

Published: Aug. 29, 2023

Soil salinization is an essential environmental stressor, threatening agricultural yield and ecological security worldwide. Saline soils accumulate excessive soluble salts which are detrimental to most plants by limiting plant growth productivity. It of great necessity for efficiently deal with the adverse effects caused salt stress survival successful reproduction. Multiple determinants tolerance have been identified in plants, cellular physiological mechanisms response adaption intensely characterized. Plants respond signals rapidly initiate signaling pathways re-establish homeostasis adjusted metabolism. This review summarizes advances perception, signaling, plants. A better understanding resistance will contribute improving crop performance under saline conditions using multiple engineering approaches. The rhizosphere microbiome-mediated as well chemical priming enhanced also discussed this review.

Language: Английский

Citations

171
Light regulates nuclear detainment of intron-retained transcripts through COP1-spliceosome to modulate photomorphogenesis DOI Creative Commons
Hua Zhou, Haiyue Zeng, Tingting Yan

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 15, 2024

Abstract Intron retention (IR) is the most common alternative splicing event in Arabidopsis . An increasing number of studies have demonstrated major role IR gene expression regulation. The impacts on plant growth and development response to environments remain underexplored. Here, we found that functions directly regulation a genome-wide scale through detainment intron-retained transcripts (IRTs) nucleus. Nuclear-retained IRTs can be kept away from translation this mechanism. COP1-dependent light modulation signaling genes, such as PIF4 , RVE1 ABA3 contribute seedling morphological changing conditions. Furthermore, light-induced changes are under control spliceosome, part ubiquitination degradation DCS1, plant-specific spliceosomal component. Our data suggest regulates activity spliceosome consequent IRT nucleus modulate photomorphogenesis COP1.

Language: Английский

Citations

7
Plant RNA-binding proteins: Phase separation dynamics and functional mechanisms underlying plant development and stress responses DOI Creative Commons

Sheng Fan,

Yu Zhang,

Shaobo Zhu

et al.

Molecular Plant, Journal Year: 2024, Volume and Issue: 17(4), P. 531 - 551

Published: Feb. 27, 2024

RNA-binding proteins (RBPs) accompany RNA from synthesis to decay, mediating every aspect of metabolism and impacting diverse cellular developmental processes in eukaryotes. Many RBPs undergo phase separation along with their bound form function dynamic membraneless biomolecular condensates for spatiotemporal coordination or regulation metabolism. Increasing evidence suggests that phase-separating domains intrinsically disordered regions play important roles plant development stress adaptation. Here, we summarize the current knowledge about how partitioning into controls enables sensing experimental changes confer growth plasticity under conditions, a focus on dynamics functional mechanisms RBP-rich nuclear cytoplasmic granules We also discuss multiple factors, such as environmental signals, protein modifications, N

Language: Английский

Citations

6
Analysis of the root mRNA interactome from canola and rice: crop species that span the eudicot-monocot boundary DOI

Chris R. Joshna,

Dilini Atugala,

Daniela Espinoza

et al.

Plant Science, Journal Year: 2025, Volume and Issue: unknown, P. 112525 - 112525

Published: April 1, 2025

Language: Английский

Citations

0
Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association DOI Open Access
Julieta L. Mateos, Dorothee Staiger

The Plant Cell, Journal Year: 2022, Volume and Issue: 35(6), P. 1708 - 1726

Published: Dec. 3, 2022

RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in plant's life. RBPs engage an on-off relationship with their RNA partners, accompanying virtually every stage processing function. While the function of plethora plant development stress responses has been described, we are lacking systems-level understanding components RNA-based regulation. Novel techniques substantially enlarged compendium experimental evidence for binding to RNAs cell, proteome. Furthermore, ribonomics methods adapted use plants profile vivo repertoire genome-wide. Here, discuss how recent technological achievements provided novel insights into mode action at genome-wide scale. touch upon two emerging topics, connection phase separation cell extracellular RNAs. Finally, define open questions be addressed move toward integrated RBP

Language: Английский

Citations

16
Progress in genome-wide identification of RBPs and their role in mitigating stresses, and growth in plants DOI
Muhammad Haroon,

Hala Tariq,

Rabail Afzal

et al.

South African Journal of Botany, Journal Year: 2023, Volume and Issue: 160, P. 132 - 146

Published: July 7, 2023

Language: Английский

Citations

6
Protein–RNA interactions: from mass spectrometry to drug discovery DOI Creative Commons

Benjamin Steinmetz,

Izabela Smok,

Maria Bikaki

et al.

Essays in Biochemistry, Journal Year: 2023, Volume and Issue: 67(2), P. 175 - 186

Published: March 1, 2023

Proteins and RNAs are fundamental parts of biological systems, their interactions affect many essential cellular processes. Therefore, it is crucial to understand at a molecular systems level how proteins form complexes mutually functions. In the present mini-review, we will first provide an overview different mass spectrometry (MS)-based methods study RNA-binding proteome (RBPome), most which based on photochemical cross-linking. As show, some these also able higher-resolution information about binding sites, important for structural characterisation protein-RNA interactions. addition, classical biology techniques such as nuclear magnetic resonance (NMR) spectroscopy biophysical electron paramagnetic (EPR) fluorescence-based contribute detailed understanding between two classes biomolecules. We discuss relevance in context formation membrane-less organelles (MLOs) by liquid-liquid phase separation (LLPS) processes emerging importance targets drug discovery.

Language: Английский

Citations

5
B Vitamins: An Update on Their Importance for Plant Homeostasis DOI
Teresa B. Fitzpatrick

Annual Review of Plant Biology, Journal Year: 2024, Volume and Issue: 75(1), P. 67 - 93

Published: March 1, 2024

B vitamins are a source of coenzymes for vast array enzyme reactions, particularly those metabolism. As metabolism is the basis decisions that drive maintenance, growth, and development, vitamin–derived key components facilitate these processes. For over century, we have known about essential compounds elucidated their pathways biosynthesis, repair, salvage, degradation in numerous organisms. Only now beginning to understand importance regulatory processes, which becoming an important topic plants. Here, I highlight discuss emerging evidence on how integrated into vital from energy generation nutrition gene expression, thereby contribute coordination growth developmental programs, concern maintenance stable state, foundational tenet plant homeostasis.

Language: Английский

Citations

1
From genes to traits: Trends in RNA-binding proteins and their role in plant trait development: A review DOI
Shazia Rehman, Saraj Bahadur, Wei Xia

et al.

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: unknown, P. 136753 - 136753

Published: Oct. 1, 2024

Language: Английский

Citations

1
A new phase of identifying RNA-binding proteins: Plant phase extraction DOI Creative Commons
Nora Flynn

The Plant Cell, Journal Year: 2023, Volume and Issue: 35(8), P. 2699 - 2700

Published: May 30, 2023

Language: Английский

Citations

0