Reference genes for quantitative Arabidopsis single molecule RNA fluorescence in situ hybridization

Spatial omics for accelerating plant research and crop improvement

Plant cells communicate information to regulate developmental processes and respond to environmental stresses. This communication spans various 'omics' layers within a cell and operates through intricate regulatory networks. The emergence of spatial omics presents a promising approach to thoroughly analyze cells, allowing the combined analysis of diverse modalities either in parallel or on the same tissue section. Here, we provide an overview of recent advancements in spatial omics and delineate scientific discoveries in plant research enabled by these technologies. We delve into experimental and computational challenges and outline strategies to navigate these challenges for advancing breeding efforts. With ongoing insightful discoveries and improved accessibility, spatial omics stands on the brink of playing a crucial role in designing future crops.

Ribosome stalling-induced NIP5;1 mRNA decay triggers ARGONAUTE1-dependent transcription downregulation

In eukaryotes, messenger RNA (mRNA) accumulation is regulated through the levels of transcription, processing, and degradation. Here, we uncover the multi-level regulatory mechanism governing the expression of NIP5;1, a boron (B) diffusion facilitator in Arabidopsis. B-dependent NIP5;1 mRNA degradation is triggered by ribosome stalling at an AUGUAA sequence in its 5'-untranslated region. We showed that deletion of ATGTAA also abolishes B-dependent transcriptional downregulation, revealing a dual role of this sequence in both mRNA degradation and transcriptional control. Small RNAs (sRNAs) and ARGONAUTE1 (AGO1) are implicated in mRNA-degradation-mediated B-dependent transcriptional downregulation: a 5'-3' exonuclease mutant, xrn4, presents both elevated levels of NIP5;1 mRNA degradation intermediates and transcriptional downregulation; AGO1-associated sRNA-sequencing reveals the presence of sRNAs with sequences upstream of NIP5;1 AUGUAA; and nascent mRNA profiling by global run-on sequencing demonstrates RNA polymerase II pausing at ATGTAA, a phenomenon diminished in the ago1 mutant that lacks B-dependent transcriptional downregulation. These findings point to multi-level coordination of NIP5;1 expression with the AUGUAA sequence at its core: ribosome stalling orchestrates translational inhibition, mRNA degradation and transcriptional downregulation in response to B. The fast response resulting from this synergy suggests that similar mechanisms may exist in other eukaryotic systems for efficient and rapid regulation of gene expression.

AtPRMT3-RPS2B promotes ribosome biogenesis and coordinates growth and cold adaptation trade-off

Translation, a fundamental process regulating cellular growth and proliferation, relies on functional ribosomes. As sessile organisms, plants have evolved adaptive strategies to maintain a delicate balance between growth and stress response. But the underlying mechanisms, particularly on the translational level, remain less understood. In this study, we revealed the mechanisms of AtPRMT3-RPS2B in orchestrating ribosome assembly and managing translational regulation. Through a forward genetic screen, we identified PDCD2-D1 as a suppressor gene restoring abnormal development and ribosome biogenesis in atprmt3-2 mutants. Our findings confirmed that PDCD2 interacts with AtPRMT3-RPS2B, and facilitates pre-ribosome transport through nuclear pore complex, finally ensuring normal ribosome translation in the cytoplasm. Additionally, the dysfunction of AtPRMT3-RPS2B was found to enhance freezing tolerance. Moreover, we revealed that AtPRMT3-RPS2B promotes the translation of housekeeping mRNAs while concurrently repressing stress-related mRNAs. In summary, our study sheds light on the regulatory roles of AtPRMT3-RPS2B in ribosome assembly and translational balance, enabling the trade-off between growth and stress.

Frontiers in plant RNA research in ICAR2023: from lab to innovative agriculture

The recent growth in global warming, soil contamination, and climate instability have widely disturbed ecosystems, and will have a significant negative impact on the growth of plants that produce grains, fruits and woody biomass. To conquer this difficult situation, we need to understand the molecular bias of plant environmental responses and promote development of new technologies for sustainable maintenance of crop production. Accumulated molecular biological data have highlighted the importance of RNA-based mechanisms for plant stress responses. Here, we report the most advanced plant RNA research presented in the 33rd International Conference on Arabidopsis Research (ICAR2023), held as a hybrid event on June 5-9, 2023 in Chiba, Japan, and focused on "Arabidopsis for Sustainable Development Goals". Six workshops/concurrent sessions in ICAR2023 targeted plant RNA biology, and many RNA-related topics could be found in other sessions. In this meeting report, we focus on the workshops/concurrent sessions targeting RNA biology, to share what is happening now at the forefront of plant RNA research.

Single-Cell Genotyping of Single-Nucleotide Mutations Using In Situ Allele-Specific Loop-Mediated Isothermal Amplification

Single-nucleotide mutations (SNMs) in the bacterial genome may cause antibiotic resistance. The visualization of SNMs can indicate antibiotic resistance phenotypes at the single-cell level but remains challenging. Herein, we proposed an in situ allele-specific isothermal amplification proceeded inside cells, allowing us to image bacterial genes with single-nucleotide resolution. The primer for loop-mediated isothermal amplification (LAMP) was designed with artificial mismatch bases to serve as an allele-specific probe, endowing LAMP to specifically amplify genes with SNMs. Due to the high amplification efficiency of LAMP, the method termed AlleLAMP can generate high gain for imaging SNMs and precisely quantify mutated quinolone-resistant Salmonella in bacterial mixture. We utilized AlleLAMP to survey the selection of antibiotic resistance under the preservative stress and found that the mutant quinolone-resistant strain owned a survival advantage over the wild-type quinolone-sensitive strain under the stress of preservatives. AlleLAMP can serve as a single-cell tool for analyzing the relationship between bacterial genotype and phenotype.