Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes in Fragaria vesca ecotypes

Plants must adapt with increasing speed to global warming to maintain their fitness.One rapid adaptation mechanism is epigenetic memory,which may provide organisms sufficient time to adapt to climate change.We studied how the perennial Fragaria vesca adapted to warmer temperatures(28◦C vs.18◦C)over three asexual generations.Differences in flowering time,stolon number,and petiole length were induced by warmer temperature in one or more ecotypes after three asexual generations and persisted in a common garden environment.Induced methylome changes differed between the four ecotypes from Norway,Iceland,Italy,and Spain,but shared methylome responses were also identified.Most differentially methylated regions(DMRs)occurred in the CHG context,and most CHG and CHH DMRs were hypermethylated at the warmer temperature.In eight CHG DMR peaks,a highly similar methylation pattern could be observed between ecotypes.On average,13%of the differentially methylated genes between ecotypes also showed a temperature-induced change in gene expression.We observed ecotype-specific methylation and expression patterns for genes related to gibberellin metabolism,flowering time,and epigenetic mechanisms.Furthermore,we observed a negative correlation with gene expression when repetitive elements were found near(±2 kb)or inside genes.In conclusion,lasting phenotypic changes indicative of an epigenetic memory were induced by warmer temperature and were accompanied by changes in DNA methylation patterns.Both shared methylation patterns and transcriptome differences between F.vesca accessions were observed,indicating that DNA methylation may be involved in both general and ecotype-specific phenotypic variation.

Multi-omics:Powerful accelerator for uncovering plant specialized metabolic pathways:The case of leonurine

As sessile organisms,plants employ a unique adaptive strategy to survive harsh terrestrial environments and defend against or interact with coevolving animals and microorganisms.This strategy involves expanding their metabolic systems,resulting in the production of plant specialized metabolites(PSMs)or natural products.Chemically,PSMs constitute a highly diverse group of compounds based on their common core structure,comprising terpenoids,phenylpropanoids,benzenoids,alkaloids and nitrogen-containing compounds,glucosinolates,indoles and sulfur-containing indole compounds,phenolics,and fatty acid derivatives(Garagounis et al.,2021).

6-Phosphogluconate dehydrogenase 2 bridges the OPP and shikimate pathways to enhance aromatic amino acid production in plants

The oxidative pentose phosphate(OPP)pathway provides metabolic intermediates for the shikimate pathway and directs carbon flow to the biosynthesis of aromatic amino acids(AAAs),which serve as basic protein building blocks and precursors of numerous metabolites essential for plant growth.However,genetic evidence linking the two pathways is largely unclear.In this study,we identified 6-phosphogluconate dehydrogenase 2(PGD2),the rate-limiting enzyme of the cytosolic OPP pathway,through suppressor screening of arogenate dehydrogenase 2(adh2)in Arabidopsis.Our data indicated that a single amino acid substitution at position 63(glutamic acid to lysine)of PGD2 enhanced its enzyme activity by facilitating the dissociation of products from the active site of PGD2,thus increasing the accumulation of AAAs and partially restoring the defective phenotype of adh2.Phylogenetic analysis indicated that the point mutation occurred in a well-conserved amino acid residue.Plants with different amino acids at this conserved site of PGDs confer diverse catalytic activities,thus exhibiting distinct AAAs producing capability.These findings uncover the genetic link between the OPP pathway and AAAs biosynthesis through PGD2.The gain-of-function point mutation of PGD2 identified here could be considered as a potential engineering target to alter the metabolic flux for the production of AAAs and downstream compounds.

Do plant histone variants stand idly by while DNA viruses invade the nucleus?

Main text,In the eukaryotic nucleus,the cellular DNA is always wrapped around protein octamers containing two molecules each of histone H2A,H2B,H3,and H4,forming the nucleosome to compact,protect,organize,and control the genome.Linker histone H1 binds to DNA at the entry and exit sites of the core nucleosome.The N-terminal tails of these histones protrude from the nucleosomes and are the sites of various post-translational modifications,such as methylation,acetylation,phosphorylation,and ubiquitination,all of which jointly modulate gene expression,DNA replication,and DNA repair,among other processes(Foroozani et al.2022).

TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants

Protein abundance and localization at the plasma membrane(PM)shapes plant development and mediates adaptation to changing environmental conditions.It is regulated by ubiquitination,a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation.To understand the significance and the variety of roles played by this reversible modification,the function of ubiquitin receptors,which translate the ubiquitin signature into a cellular response,needs to be elucidated.In this study,we show that TOL(TOM1-like)proteins function in plants as multivalent ubiquitin receptors,governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport(ESCRT)pathway.TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains.Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization,abolishing TOL6 ubiquitin receptor activity.Function and localization of TOL6 is itself regulated by ubiquitination,whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes,assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation.Taken together,our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.

The effect of host plants on genotype variability in fitness and honeydew composition of Aphis fabae

Aphid species can be polyphagous, feeding on multiple host plants across genera. As host plant species can have large variation in their phloem composition, this can affect aphid fitness and honeydew composition. Previous research showed significant intraspecific genotype variation in the composition of the honeydew carbohydrates of the black bean aphid Aphis fabae, with the ant attractant trisaccharide melezitose showing especially large variation across different genotypes. In this study, we test if variation in melezitose and carbohydrate composition of aphid honeydew could be linked to the adap- tation of specific aphid genotypes to particular host plants. To this end, 4 high and 5 low melezitose secreting genotypes of the black bean aphid Aphisfabae were reared on 4 com- mon host plants： broad bean, goosefoot, beet, and poppy. The carbohydrate composition, and in particular melezitose secretion, showed important aphid genotype and host plant in- teractions, with some genotypes being high melezitose secreting on 1 host plant but not on another. However, the interaction effects were not paralleled in the fitness measurements, even though there were significant differences in the average fitness across the different host plants. On the whole, this study demonstrates that aphid honeydew composition is influenced by complex herbivore-plant interactions. We discuss the relevance of these findings in the context of ant-aphid mutualisms and adaptive specialization in aphids.

Loss of two families of SPX domain-containing proteins required for vacuolar polyphosphate accumulation coincides with the transition to phosphate storage in green plants

Phosphorus is an essential nutrient for plants.It is stored as inorganic phosphate(Pi)in the vacuoles of land plants but as inorganic polyphosphate(polyP)in chlorophyte algae.Although it is recognized that the SPX-Major Facilitator Superfamily(MFS)and VPE proteins are responsible for Pi influx and efflux,respectively,across the tonoplast in land plants,the mechanisms that underlie polyP homeostasis and the transition of phosphorus storage forms during the evolution of green plants remain unclear.In this study,we showed that CrPTCI,encoding a protein with both SPX and SLC(permease solute carrier 13)domains for Pi transport,and CrVTC4,encoding a protein with both SPX and vacuolar transporter chaperone(VTC)domains for polyP synthesis,are required for vacuolar polyP accumulation in the chlorophyte Chlamydomonas rein-hardtii.Phylogenetic analysis showed that the SPX-SLC,SPX-VTC,and SPX-MFS proteins were present in the common ancestor of green plants(Viridiplantae).The SPX-SLC and SPX-VTC proteins are conserved among species that store phosphorus as vacuolar polyP and absent from genomes of plants that store phosphorus as vacuolar Pi.By contrast,SPX-MFS genes are present in the genomes of streptophytes that store phosphorus as Pi in the vacuoles.These results suggest that loss of SPX-SLC and SPX-VTC genes and functional conservation of SPX-MFS proteins during the evolution of streptophytes accompanied the change from ancestral polyP storage to Pi storage.

The WAK-like protein RFO1 acts as a sensor of the pectin methylation status in Arabidopsis cell walls to modulate root growth and defense

Most organisms adjust their development according to the environmental conditions.For the majority,this implies the sensing of alterations to cell walls caused by different cues.Despite the relevance of this process,few molecular players involved in cell wall sensing are known and characterized.Here,we show that the wall-associated kinase-like protein RESISTANCE TO FUSARIUM OXYSPORUM 1(RFO1)is required for plant growth and early defense against Fusarium oxysporum and functions by sensing changes in the pectin methylation levels in the cell wall.The RFO1 dwell time at the plasma membrane is affected by the pectin methylation status at the cell wall,regulating MITOGEN-ACTIVATED PROTEIN KINASE and gene expression.We show that the extracellular domain of RFO1 binds de-methylated pectin in vitro,whose distribution in the cell wall is altered during F.oxysporum infection.Further analyses also indicate that RFO1 is required for the BR-dependent plant growth alteration in response to inhibition of pectin de-methyl-esterase activity at the cell wall.Collectively,our work demonstrates that RFO1 is a sensor of the pectin methylation status that plays a unique dual role in plant growth and defense against vascular pathogens.

The RdDM Pathway Is Required for Basal Heat Tolerance in Arabidopsis

Heat stress affects epigenetic gene silencing in Arabidopsis. To test for a mechanistic involvement of epige-netic regulation in heat-stress responses, we analyzed the heat tolerance of mutants defective in DNA methylation, his-tone modifications, chromatin-remodeling, or siRNA-based silencing pathways. Plants deficient in NRPD2, the common second-largest subunit of RNA polymerases IV and V, and in the Rpd3-type histone deacetylase HDA6 were hypersensi- tive to heat exposure. Microarray analysis demonstrated that NRPD2 and HDA6 have independent roles in transcriptional reprogramming in response to temperature stress. The misexpression of protein-coding genes in nrpd2 mutants recover-ing from heat correlated with defective epigenetic regulation of adjacent transposon remnants which involved the loss of control of heat-stress-induced read-through transcription. We provide evidence that the transcriptional response to temperature stress, at least partially, relies on the integrity of the RNA-dependent DNA methylation pathway.

Control of Grain Size and Weight by the OsMKKK10-OsM KK4-OsMAPK6 Signaling Pathway in Rice

Grain size is one of the key agronomic traits that determine grain yield in crops. However, the mechanisms underlying grain size control in crops remain elusive. Here we demonstrate that the OsMKKK10-OsMKK4- OsMAPK6 signaling pathway positively regulates grain size and weight in rice. In rice, loss of OsMKKKIO function results in small and light grains, short panicles, and semi-dwarf plants, while overexpression of constitutively active OsMKKK10 （CA-OsMKKK10） results in large and heavy grains, long panicles, and tall plants. OsMKKK10 interacts with and phosphorylates OsMKK4. We identified an OsMKK4 gain-of-func- tion mutant （large11-1D）that produces large and heavy grains. OsMKK4A227T encoded by the large11-1D allele has stronger kinase activity than OsMKK4. Plants overexpressing a constitutively active form of OsMKK4 （OsMKK4oDD） also produce large grains. Further biochemical and genetic analyses revealed that OsMKKK10, OsMKK4, and OsMAPK6 function in a common pathway to control grain size. Taken together, our study establishes an important genetic and molecular framework for OsMKKK10-OsMKK4- OsMAPK6 cascade-mediated control of grain size and weight in rice.

Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice

The utilization of natural genetic variation greatly contributes to improvement of important agronomic traits in crops. Understanding the genetic basis for natural variation of grain size can help breeders develop high- yield rice varieties. In this study, we identify a previously unrecognized gene, named GSE5, in the qSW5/ GW5 locus controlling rice grain size by combining the genome-wide association study with functional analyses. GSE5 encodes a plasma membrane-associated protein with ｜Q domains, which interacts with the rice calmodulin protein, OsCaMl-1. We found that loss of GSE5 function caused wide and heavy grains, while overexpression of GSE5 resulted in narrow grains. We showed that GSE5 regulates grain size predominantly by influencing cell proliferation in spikelet hulls. Three major haplotypes of GSE5 （GSE5, GSE5DELl＋IN1, and GSESDEL~ in cultivated rice were identified based on the deletion/insertion type in its pro- moter region. We demonstrated that a 950-bp deletion （DELl） in indica varieties carrying the GSE5DELl＋IN1 haplotype and a 1212-bp deletion （DEL2） in japonica varieties carrying the GSE5DEL2 haplotype associated with decreased expression of GSE5, resulting in wide grains. Further analyses indicate that wild rice acces- sions contain all three haplotypes of GSE5, suggesting that the GSE5 haplotypes present in cultivated rice are likely to have originated from different wild rice accessions during rice domestication. Taken together, our results indicate that the previously unrecognized GSE5 gene in the qSW5/GW5 locus, which is widely utilized by rice breeders, controls grain size, and reveal that natural variation in the promoter region of GSE5 contributes to grain size diversity in rice.

Transgenerational Inheritance and Resetting of Stress, Induced Loss of Epigenetic Gene Silencing in Arabidopsis

Plants, as sessile organisms, need to sense and adapt to heterogeneous environments and have developed sophisticated responses by changing their cellular physiology, gene regulation, and genome stability. Recent work dem- onstrated heritable stress effects on the control of genome stability in plants--a phenomenon that was suggested to be of epigenetic nature. Here, we show that temperature and UV-B stress cause immediate and heritable changes in the epi- genetic control of a silent reporter gene in Arabidopsis. This stress-mediated release of gene silencing correlated with pronounced alterations in histone occupancy and in histone H3 acetylation but did not involve adjustments in DNA meth- ylation. We observed transmission of stress effects on reporter gene silencing to non-stressed progeny, but this effect was restricted to areas consisting of a small number of cells and limited to a few non-stressed progeny generations. Further- more, stress-induced release of gene silencing was antagonized and reset during seed aging. The transient nature of this phenomenon highlights the ability of plants to restrict stress-induced relaxation of epigenetic control mechanisms, which likely contributes to safeguarding genome integrity.

Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis

Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron-retaining （IR） transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad-range thermal cycles triggered a sharp increase in the long IR CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or Pseudomonas syringae infection induced a similar increase. Thermal stress induced a time delay in accumulation of CCA1 14Rb transcripts, whereas functional mRNA showed steady oscillations. Our data favor a hypothesis that stress-induced instabilities of the central oscillator can be in part compensated through fluctuations in abundance and out-of-phase oscillations of CCA1 IR transcripts. Taken together, our results support a concept that mRNA abundance can be modulated through altering ratios between functional and nonsense/IR transcripts. SR45 protein specifically bound to the retained CCA1 intron in vitro, suggesting that this sp!icing factor could be involved in regulation of intron retention. Transcriptomes of nonsense-mediated mRNA decay （NMD）-impaired and heat-stressed plants shared a set of retained introns associated with stress- and defense-inducible transcripts. Constitutive activation of certain stress response networks in an NMD mutant could be linked to disequilibrium between functional and nonsense mRNAs.

The GW2-WG1-OsbZIP47 pathway controls grain size and weight in rice

Regulation of seed size is a key strategy for improving crop yield and is also a basic biological question.However,the molecular mechanisms by which plants determine their seed size remain elusive.Here,we report that the GW2-WG1-OsbZIP47 regulatory module controls grain width and weight in rice.WG1,which encodes a glutaredoxin protein,promotes grain growth by increasing cell proliferation.Interestingly,WG1 interacts with the transcription factor OsbZIP47 and represses its transcriptional activity by associating with the transcriptional co-repressor ASP1,indicating that WG1 may act as an adaptor protein to recruit the transcriptional co-repressor.In contrary,OsbZIP47 restricts grain growth by decreasing cell proliferation.Further studies reveal that the E3 ubiquitin ligase GW2 ubiquitinates WG1 and targets it for degradation.Genetic analyses confirm that GW2,WG1,and OsbZIP47 function in a comm on pathway to control grain growth.Taken together,ourfindi ngs reveal a genetic and molecular framework for the control of grain size and weight by the GW2-WG1-OsbZIP47 regulatory module,providing new targets for improving seed size and weight in crops.

Coordination of Plastid and Light Signaling Pathways upon Development of Arabidopsis Leaves under Various Photoperiods

Plants synchronize their cellular and physiological functions according to the photoperiod （the length of the light period） in the cycle of 24 h. Photoperiod adjusts several traits in the plant life cycle, including flowering and senes- cence in annuals and seasonal growth cessation in perennials. Photoperiodic development is controlled by the coordinated action of photoreceptors and the circadian clock. During the past 10 years, remarkable progress has been made in under- standing the molecular mechanism of the circadian clock, especially with regard to the transition of Arabidopsis from the vegetative growth to the reproductive phase. Besides flowering photoperiod also modifies plant photosynthetic struc- tures and traits. Light signals controlling biogenesis of chloroplasts and development of leaf photosynthetic structures are perceived both by photoreceptors and in chloroplasts. In this review, we provide evidence suggesting that the photope- riodic development of Arabidopsis leaves mimics the acclimation of plant to various light intensities. Furthermore, the chloroplast-to-nucleus retrograde signals that adjust acclimation to light intensity are proposed to contribute also to the signaling pathways that control photoperiodic acclimation of leaves.

Dissecting Abscisic Acid Signaling Pathways Involved in Cuticle Formation

The cuticle is the outer physical barrier of aerial plant surfaces and an important interaction point between plants and the environment. Many environmental stresses affect cuticle formation, yet the regulatory pathways involved remain undefined. We used a genetics and gene expression analysis in Arabidopsis thaliana to define an abscisic acid （ABA） signaling loop that positively regulates cuticle formation via the core ABA signaling pathway, including the PYR/PYL receptors, PP2C phosphatase, and SNF1-Related Protein Kinase （SnRK） 2.21SnRK2.3/SnRK2.6. Downstream of the SnRK2 kinases, cuticle formation was not regulated by the ABA-responsive element-binding transcription factors but rather by DEWAX, MYB16, MYB94, and MYB96. Additionally, low air humidity increased cuticle formation independent of the core ABA pathway and cell death/reactive oxygen species signaling attenuated expression of cuticle-biosynthesis genes. In Physcornitrella patens, exogenous ABA suppressed expression of cuticle- related genes, whose Arabidopsis orthologs were ABA-induced. Hence, the mechanisms regulating cuticle formation are conserved but sophisticated in land plants. Signaling specifically related to cuticle deficiency was identified to play a major role in the adaptation of ABA signaling pathway mutants to increased humidity and in modulating their immunity to Botrytis cinerea in Arabidopsis. These results define a cuticle-specific downstream branch in the ABA signaling pathway that regulates responses to the external environment.

Ion Channels at the Nucleus： Electrophysiology Meets the Genome

The nuclear envelope is increasingly viewed from an electrophysiological perspective by researchers interested in signal transduction pathways that influence gene transcription and other processes in the nucleus. Here, we describe evidence for ion channels and transporters in the nuclear membranes and for possible ion gating by the nuclear pores. We argue that a systems-level understanding of cellular regulation is likely to require the assimilation of nuclear electrophysiology into molecular and biochemical signaling pathways.

Size matters:G protein signaling is crucial for grain size control in rice

Rice is an important food crop and is consumed by nearly half of the world’s population.Rice grain size is a key yield trait and also affects the quality of grain appearance.Several pathways that control grain size have been identified in rice,such as heterotrimeric guanine nucleotide-binding protein(G protein)signaling,mitogen-activated protein kinase signaling,the ubiquitinproteasome pathway,phytohormone perception and homeostasis,and some transcriptional regulators(Li et al.,2019).

H2A Variants in Arabidopsis: Versatile Regulators of Genome Activity

The eukaryotic nucleosome prevents access to the genome.Convergently evolving histone isoforms,also called histone variants,form diverse families that are enriched over distinct features of plant genomes.Among the diverse families of plant histone variants,H2A.Z exclusively marks genes.Here we review recent research progress on the genome-wide distribution patterns and deposition of H2A.Z in plants as well as its association with histone modifications and roles in plant chromatin regulation.We also discuss some hypotheses that explain the different findings about the roles of H2A.Z in plants.

PGR5-PGRL1-Dependent Cyclic Electron Transport Modulates Linear Electron Transport Rate in Arabidopsis thaliana

Plants need tight regulation of photosynthetic electron transport for survival and growth under environ- mental and metabolic conditions. For this purpose, the linear electron transport （LET） pathway is supple- mented by a number of alternative electron transfer pathways and valves. In Arabidopsis, cyclic electron transport （CET） around photosystem I （PSI）, which recycles electrons from ferrodoxin to plastoquinone, is the most investigated alternative route. However, the interdependence of LET and CET and the relative importance of CET remain unclear, largely due to the difficulties in precise assessment of the contribution of CET in the presence of LET, which dominates electron flow under physiological conditions. We there- fore generated Arabidopsis mutants with a minimal water-splitting activity, and thus a low rate of LET, by combining knockout mutations in Psb01, PsbP2, PsbQ1, PsbQ2, and PsbR loci. The resulting 45 mutant is viable, although mature leaves contain only ~20% of wild-type naturally less abundant Psb02 protein. 45 plants compensate for the reduction in LET by increasing the rate of CET, and inducing a strong non-photochemical quenching （NPQ） response during dark-to-light transitions. To identify the molecular origin of such a high-capacity CET, we constructed three sextuple mutants lacking the qE component of NPQ （45 npq4-1）, NDH-mediated CET （45 crr4-3）, or PGR5-PGRLl-mediated CET （45 pgrS）. Their analysis revealed that PGR5-PGRLl-mediated CET plays a major role in ~pH formation and induction of NPQ in C3 plants. Moreover, while pgr5 dies at the seedling stage under fluctuating light conditions, 45 pgr5 plants are able to survive, which underlines the importance of PGR5 in modulating the intersystem electron transfer.