Bacterial Infection Disrupts Clock Gene Expression to Attenuate Immune Responses

Dynamic changes in mRNA nucleocytoplasmic localization in the nitrate response of Arabidopsis roots

Nitrate is a nutrient and signal that regulates gene expression. The nitrate response has been extensively characterized at the organism, organ, and cell-type-specific levels, but intracellular mRNA dynamics remain unexplored. To characterize nuclear and cytoplasmic transcriptome dynamics in response to nitrate, we performed a time-course expression analysis after nitrate treatment in isolated nuclei, cytoplasm, and whole roots. We identified 402 differentially localized transcripts (DLTs) in response to nitrate treatment. Induced DLT genes showed rapid and transient recruitment of the RNA polymerase II, together with an increase in the mRNA turnover rates. DLTs code for genes involved in metabolic processes, localization, and response to stimulus indicating DLTs include genes with relevant functions for the nitrate response that have not been previously identified. Using single-molecule RNA FISH, we observed early nuclear accumulation of the NITRATE REDUCTASE 1 (NIA1) transcripts in their transcription sites. We found that transcription of NIA1, a gene showing delayed cytoplasmic accumulation, is rapidly and transiently activated; however, its transcripts become unstable when they reach the cytoplasm. Our study reveals the dynamic localization of mRNAs between the nucleus and cytoplasm as an emerging feature in the temporal control of gene expression in response to nitrate treatment in Arabidopsis roots.

Arginine methylation of SM-LIKE PROTEIN 4 antagonistically affects alternative splicing during Arabidopsis stress responses

Arabidopsis (Arabidopsis thaliana) PROTEIN ARGININE METHYLTRANSFERASE5 (PRMT5) post-translationally modifies RNA-binding proteins by arginine (R) methylation. However, the impact of this modification on the regulation of RNA processing is largely unknown. We used the spliceosome component, SM-LIKE PROTEIN 4 (LSM4), as a paradigm to study the role of R-methylation in RNA processing. We found that LSM4 regulates alternative splicing (AS) of a suite of its in vivo targets identified here. The lsm4 and prmt5 mutants show a considerable overlap of genes with altered AS raising the possibility that splicing of those genes could be regulated by PRMT5-dependent LSM4 methylation. Indeed, LSM4 methylation impacts AS, particularly of genes linked with stress response. Wild-type LSM4 and an unmethylable version complement the lsm4-1 mutant, suggesting that methylation is not critical for growth in normal environments. However, LSM4 methylation increases with abscisic acid and is necessary for plants to grow under abiotic stress. Conversely, bacterial infection reduces LSM4 methylation, and plants that express unmethylable-LSM4 are more resistant to Pseudomonas than those expressing wild-type LSM4. This tolerance correlates with decreased intron retention of immune-response genes upon infection. Taken together, this provides direct evidence that R-methylation adjusts LSM4 function on pre-mRNA splicing in an antagonistic manner in response to biotic and abiotic stress.

The circadian clock and thermal regulation in plants: novel insights into the role of positive circadian clock regulators in temperature responses

The impact of rising global temperatures on crop yields is a serious concern, and the development of heat-resistant crop varieties is crucial for mitigating the effects of climate change on agriculture. To achieve this, a better understanding of the molecular basis of the thermal responses of plants is necessary. The circadian clock plays a central role in modulating plant biology in synchrony with environmental changes, including temperature fluctuations. Recent studies have uncovered the role of transcriptional activators of the core circadian network in plant temperature responses. This expert view highlights key novel findings regarding the role of the RVE and LNK gene families in controlling gene expression patterns and plant growth under different temperature conditions, ranging from regular diurnal oscillations to extreme stress temperatures. These findings reinforce the essential role of the circadian clock in plant adaptation to changing temperatures and provide a basis for future studies on crop improvement.

Plant nuclear envelope as a hub connecting genome organization with regulation of gene expression

Eukaryotic cells organize their genome within the nucleus with a double-layered membrane structure termed the nuclear envelope (NE) as the physical barrier. The NE not only shields the nuclear genome but also spatially separates transcription from translation. Proteins of the NE including nucleoskeleton proteins, inner nuclear membrane proteins, and nuclear pore complexes have been implicated in interacting with underlying genome and chromatin regulators to establish a higher-order chromatin architecture. Here, I summarize recent advances in the knowledge of NE proteins that are involved in chromatin organization, gene regulation, and coordination of transcription and mRNA export. These studies support an emerging view of plant NE as a central hub that contributes to chromatin organization and gene expression in response to various cellular and environmental cues.

COLD REGULATED GENE 27 and 28 Antagonize the Transcriptional Activity of the RVE8/LNK1/LNK2 Circadian Complex

Many molecular and physiological processes in plants occur at a specific time of day. These daily rhythms are coordinated in part by the circadian clock, a timekeeper that uses daylength and temperature to maintain rhythms of approximately 24 hours in various clock-regulated phenotypes. The circadian MYB-like transcription factor REVEILLE 8 (RVE8) interacts with its transcriptional coactivators NIGHT LIGHT INDUCIBLE AND CLOCK REGULATED 1 (LNK1) and LNK2 to promote the expression of evening-phased clock genes and cold tolerance factors. While genetic approaches have commonly been used to discover connections within the clock and between clock elements and other pathways, here we used affinity purification coupled with mass spectrometry to identify time-of-day-specific protein interactors of the RVE8-LNK1/LNK2 complex in Arabidopsis (Arabidopsis thaliana). Among the interactors of RVE8/LNK1/LNK2 were COLD REGULATED GENE 27 (COR27) and COR28, which coprecipitated in an evening-specific manner. In addition to COR27 and COR28, we found an enrichment of temperature-related interactors that led us to establish a previously uncharacterized role for LNK1 and LNK2 in temperature entrainment of the clock. We established that RVE8, LNK1, and either COR27 or COR28 form a tripartite complex in yeast (Saccharomyces cerevisiae) and that the effect of this interaction in planta serves to antagonize transcriptional activation of RVE8 target genes, potentially through mediating RVE8 protein degradation in the evening. Together, these results illustrate how a proteomic approach can be used to identify time-of-day-specific protein interactions. Discovery of the RVE8-LNK-COR protein complex indicates a previously unknown regulatory mechanism for circadian and temperature signaling pathways.

The 5'-3' mRNA Decay Pathway Modulates the Plant Circadian Network in Arabidopsis

Circadian rhythms enable organisms to anticipate and adjust their physiology to periodic environmental changes. These rhythms are controlled by biological clocks that consist of a set of clock genes that regulate each other's expression. Circadian oscillations in messenger RNA (mRNA) levels require the regulation of mRNA production and degradation. While transcription factors controlling clock function have been well characterized from cyanobacteria to humans, the role of factors controlling mRNA decay is largely unknown. Here, we show that mutations in SM-LIKE PROTEIN 1 (LSM1) and exoribonucleases 4 (XRN4), components of the 5'-3' mRNA decay pathway, alter clock function in Arabidopsis. We found that lsm1 and xrn4 mutants display long-period phenotypes for clock gene expression. In xrn4, these circadian defects were associated with changes in circadian phases of expression, but not overall mRNA levels, of several core-clock genes. We then used noninvasive transcriptome-wide mRNA stability analysis to identify genes and pathways regulated by XRN4. Among genes affected in the xrn4 mutant at the transcriptional and posttranscriptional level, we found an enrichment in genes involved in auxin, ethylene and drought recovery. Large effects were not observed for canonical core-clock genes, although the mRNAs of several auxiliary clock genes that control the pace of the clock were stabilized in xrn4 mutants. Our results establish that the 5'-3' mRNA decay pathway constitutes a novel posttranscriptional regulatory layer of the circadian gene network, which probably acts through a combination of small effects on mRNA stability of several auxiliary and some core-clock genes.

Circadian rhythms in infectious diseases and symbiosis

Timing is everything. Many organisms across the tree of life have evolved timekeeping mechanisms that regulate numerous of their cellular functions to optimize timing by anticipating changes in the environment. The specific environmental changes that are sensed depends on the organism. For animals, plants, and free-living microbes, environmental cues include light/dark cycles, daily temperature fluctuations, among others. In contrast, for a microbe that is never free-living, its rhythmic environment is its host's rhythmic biology. Here, we describe recent research on the interactions between hosts and microbes, from the perspective both of symbiosis as well as infections. In addition to describing the biology of the microbes, we focus specifically on how circadian clocks modulate these host-microbe interactions.

Plant circadian clock control of Medicago truncatula nodulation via regulation of nodule cysteine-rich peptides

Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules, we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcription factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of nodule-specific cysteine-rich peptides (NCRs) that have the LHY-bound conserved evening element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.

A glossary of plant cell structures: Current insights and future questions

In this glossary of plant cell structures, we asked experts to summarize a present-day view of plant organelles and structures, including a discussion of outstanding questions. In the following short reviews, the authors discuss the complexities of the plant cell endomembrane system, exciting connections between organelles, novel insights into peroxisome structure and function, dynamics of mitochondria, and the mysteries that need to be unlocked from the plant cell wall. These discussions are focused through a lens of new microscopy techniques. Advanced imaging has uncovered unexpected shapes, dynamics, and intricate membrane formations. With a continued focus in the next decade, these imaging modalities coupled with functional studies are sure to begin to unravel mysteries of the plant cell.

Regulation of Plant Immunity by Nuclear Membrane-Associated Mechanisms

Unlike animals, plants do not have specialized immune cells and lack an adaptive immune system. Instead, plant cells rely on their unique innate immune system to defend against pathogens and coordinate beneficial interactions with commensal and symbiotic microbes. One of the major convergent points for plant immune signaling is the nucleus, where transcriptome reprogramming is initiated to orchestrate defense responses. Mechanisms that regulate selective transport of nuclear signaling cargo and chromatin activity at the nuclear boundary play a pivotal role in immune activation. This review summarizes the current knowledge of how nuclear membrane-associated core protein and protein complexes, including the nuclear pore complex, nuclear transport receptors, and the nucleoskeleton participate in plant innate immune activation and pathogen resistance. We also discuss the role of their functional counterparts in regulating innate immunity in animals and highlight potential common mechanisms that contribute to nuclear membrane-centered immune regulation in higher eukaryotes.

Circadian dynamics of the teleost skin immune-microbiome interface

BACKGROUND

Circadian rhythms of host immune activity and their microbiomes are likely pivotal to health and disease resistance. The integration of chronotherapeutic approaches to disease mitigation in managed animals, however, is yet to be realised. In aquaculture, light manipulation is commonly used to enhance growth and control reproduction but may have unknown negative consequences for animal health. Infectious diseases are a major barrier to sustainable aquaculture and understanding the circadian dynamics of fish immunity and crosstalk with the microbiome is urgently needed.

RESULTS

Here, using rainbow trout (Oncorhynchus mykiss) as a model, we combine 16S rRNA metabarcoding, metagenomic sequencing and direct mRNA quantification methods to simultaneously characterise the circadian dynamics of skin clock and immune gene expression, and daily changes of skin microbiota. We demonstrate daily rhythms in fish skin immune expression and microbiomes, which are modulated by photoperiod and parasitic lice infection. We identify putative associations of host clock and immune gene profiles with microbial composition. Our results suggest circadian perturbation, that shifts the magnitude and timing of immune and microbiota activity, is detrimental to fish health.

CONCLUSIONS

The substantial circadian dynamics and fish host expression-microbiome relationships we find represent a valuable foundation for investigating the utility of chronotherapies in aquaculture, and more broadly contributes to our understanding of the role of microbiomes in circadian health of vertebrates. Video Abstract.

Comparative RNA-Seq Analysis Reveals Potentially Resistance-Related Genes in Response to Bacterial Canker of Tomato

Tomato is one of the most important crops for human consumption. Its production is affected by the actinomycete Clavibacter michiganensis subsp. michiganensis (Cmm), one of the most devastating bacterial pathogens of this crop. Several wild tomato species represent a source of natural resistance to Cmm. Here, we contrasted the transcriptomes of the resistant wild tomato species Solanum arcanum LA2157 and the susceptible species Solanum lycopersicum cv. Ailsa Craig, during the first 24 h of challenge with Cmm. We used three analyses approaches which demonstrated to be complementary: mapping to S. lycopersicum reference genome SL3.0; semi de novo transcriptome assembly; and de novo transcriptome assembly. In a global context, transcriptional changes seem to be similar between both species, although there are some specific genes only upregulated in S. arcanum during Cmm interaction, suggesting that the resistance regulatory mechanism probably diverged during the domestication process. Although S. lycopersicum showed enriched functional groups related to defense, S. arcanum displayed a higher number of induced genes related to bacterial, oomycete, and fungal defense at the first few hours of interaction. This study revealed genes that may contribute to the resistance phenotype in the wild tomato species, such as those that encode for a polyphenol oxidase E, diacyl glycerol kinase, TOM1-like protein 6, and an ankyrin repeat-containing protein, among others. This work will contribute to a better understanding of the defense mechanism against Cmm, and the development of new control methods.

Time Will Tell: Intercellular Communication in the Plant Clock

Multicellular organisms have evolved local and long-distance signaling mechanisms to synchronize development and response to stimuli among a complex network of cells, tissues, and organs. Biological timekeeping is one such activity that is suggested to be coordinated within an organism to anticipate and respond to daily and seasonal patterns in the environment. New research into the plant clock suggests circadian rhythms are communicated between cells and across long distances. However, further clarity is required on the nature of the signaling molecules and the mechanisms underlying signal translocation. Here we summarize the roles and properties of tissue-specific circadian rhythms, discuss the evidence for local and long-distance clock communication, and evaluate the potential signaling molecules and transport mechanisms involved in this system.

Changes in physical activity and sleep habits among adults in Russian Federation during COVID-19: a cross-sectional study

BACKGROUND

The aim of this study was to evaluate the impact of COVID-19 on the levels of physical activity (PA) and sleep and to examine specific COVID-19 factors that may be associated with changes in PA and sleep among adults in Russia.

METHODS

Cross-sectional data were collected during the period of tightest restrictions between 26 April 2020 and 6 June 2020. Eligible participants included all Russian adults aged 18 years and over. Participants reported their sleep patterns and problems, frequency and duration of walking, moderate- and vigorous-intensity PA, and muscle strengthening activities before COVID-19 and during the past 7 days. Access to an outdoor green space and fitness centres, use of online resources, adherence to self-isolation recommendations and other preventive measures from Ministry of Health were self-reported.

RESULTS

The sample included 2432 participants from 62 regions, 83% of who were female. There was a significant decline in the number of days per week participants reported not getting enough sleep (3.21 ± 2.44 to 2.86 ± 2.57; P < 0.001); participants also reported an increase in the number of days per week they had trouble falling asleep (1.70 ± 2.24 to 2.13 ± 2.48; P < 0.001). The proportion of participants who met the WHO Guidelines for PA declined from 68 to 49% (P < 0.001). The proportion who participated in muscle strengthening activities for 2 or more days per week declined from 53 to 45% (P < 0.001).

CONCLUSION

Compared with before COVID-19, PA and sleep hygiene were adversely affected during COVID-19. Awareness of factors associated with these declines will assit policymakers in developing strategies to mitigate the negative lifestyle behaviours that have manifested during the COVID-19 confinement.

Nuclear RNA purification by flow cytometry to study nuclear processes in plants

The nature of plant tissues has continuously hampered understanding of the spatio-temporal and subcellular distribution of RNA-guided processes. Here, we describe a universal protocol based on Arabidopsis to investigate subcellular RNA distribution from virtually any plant species using flow cytometry sorting. This protocol includes all necessary control steps to assess the quality of the nuclear RNA purification. Moreover, it can be easily applied to different plant developmental stages, tissues, cell cycle phases, experimental growth conditions, and specific cell type(s). For complete information on the use and execution of this protocol, please refer to Bologna et al. (2018) and de Leone et al. (2020).

Nucleocytoplasmic Communication in Healthy and Diseased Plant Tissues

The double membrane of the nuclear envelope (NE) constitutes a selective compartment barrier that separates nuclear from cytoplasmic processes. Plant viability and responses to a changing environment depend on the spatial communication between both compartments. This communication is based on the bidirectional exchange of proteins and RNAs and is regulated by a sophisticated transport machinery. Macromolecular traffic across the NE depends on nuclear transport receptors (NTRs) that mediate nuclear import (i.e. importins) or export (i.e. exportins), as well as on nuclear pore complexes (NPCs) that are composed of nucleoporin proteins (NUPs) and span the NE. In this review, we provide an overview of plant NPC- and NTR-directed cargo transport and we consider transport independent functions of NPCs and NE-associated proteins in regulating plant developmental processes and responses to environmental stresses.

Plant Defence Mechanisms Are Modulated by the Circadian System

Simple Summary

The circadian clock is an endogenous time keeping mechanism found in living organisms and their respective pathogens. Numerous studies demonstrate that rhythms generated by this internal biological oscillator regulate and modulate most of the physiological, developmental, and biochemical processes of plants. Importantly, plant defence responses have also been shown to be modulated by the host circadian clock and vice versa. In this review we discuss the current understanding of the interactions between plant immunity and the circadian system. We also describe the possibility of pathogens directly or indirectly influencing plants’ circadian rhythms and suggest that these interactions could help us devise better disease management strategies for plants. Our review raises further research questions and we conclude that experimentation should be completed to unravel the complex mechanisms underlying interactions between plant defence and the circadian system.

Abstract

Plant health is an important aspect of food security, with pathogens, pests, and herbivores all contributing to yield losses in crops. Plants’ defence against pathogens is complex and utilises several metabolic processes, including the circadian system, to coordinate their response. In this review, we examine how plants’ circadian rhythms contribute to defence mechanisms, particularly in response to bacterial pathogen attack. Circadian rhythms contribute to many aspects of the plant–pathogen interaction, although significant gaps in our understanding remain to be explored. We conclude that if these relationships are explored further, better disease management strategies could be revealed.

It's a matter of time: the role of transcriptional regulation in the circadian clock-pathogen crosstalk in plants

Most living organisms possess an internal timekeeping mechanism known as the circadian clock, which enhances fitness by synchronizing the internal timing of biological processes with diurnal and seasonal environmental changes. In plants, the pace of these biological rhythms relies on oscillations in the expression level of hundreds of genes tightly controlled by a group of core clock regulators and co-regulators that engage in transcriptional and translational feedback loops. In the last decade, the role of several core clock genes in the control of defense responses has been addressed, and a growing amount of evidence demonstrates that circadian regulation is relevant for plant immunity. A reciprocal connection between these pathways was also established following the observation that in Arabidopsis thaliana, as well as in crop species like tomato, plant-pathogen interactions trigger a reconfiguration of the circadian transcriptional network. In this review, we summarize the current knowledge regarding the interaction between the circadian clock and biotic stress responses at the transcriptional level, and discuss the relevance of this crosstalk in the plant-pathogen evolutionary arms race. A better understanding of these processes could aid in the development of genetic tools that improve traditional breeding practices, enhancing tolerance to plant diseases that threaten crop yield and food security all around the world.