A molecular framework underlying low-nitrogeninduced early leaf senescence in Arabidopsis thaliana

Nitrogen(N)deficiency causes early leaf senescence,resulting in accelerated whole-plant maturation and severely reduced crop yield.However,the molecular mechanisms underlying N-deficiency-induced early leaf senescence remain unclear,even in the model species Arabidopsis thaliana.In this study,we identified Growth,Development and Splicing 1(GDS1),a previously reported transcription factor,as a new regulator of nitrate(NO3)signaling by a yeast-one-hybrid screen using a NO3enhancer fragment from the promoter of NRT2.1.We showed that GDS1 promotes NO3 signaling,absorption and assimilation by affecting the expression of multiple NO3 regulatory genes,including Nitrate Regulatory Gene2(NRG2).Interestingly,we observedthat gds1mutants show early leaf senescence as well as reduced NO3-contentand Nuptake under N-deficient conditions.Further analyses indicated that GDS1 binds to the promoters of several senescence-related genes,including Phytochrome-lnteracting Transcription Factors 4 and 5(PIF4 and PIF5)and represses their expression.Interestingly,we found that N deficiency decreases GDS1 protein accumulation,and GDS1 could interact with Anaphase Promoting Complex Subunit 10(APC10).Genetic and biochemical experiments demonstrated that Anaphase Promoting Complex or Cyclosome(APC/C)promotes the ubiquitination and degradation of GDS1 under N deficiency,resulting in loss of PIF4 and PiF5 repression and consequent early leaf senescence.Furthermore,we discovered that overexpression of GDS1 could delay leaf senescence and improve seed yield and N-use efficiency(NUE)in Arabidopsis.In summary,our study uncovers a molecular framework illustrating a new mechanism underlying low-N-induced early leaf senescence and provides potential targets for genetic improvement of crop varieties with increased yield and NUE.

Vacuolar phosphate transporters account for variation in phosphate accumulation in Astragalus sinicus cultivars

Astragalus sinicus is a commonly used legume green manure that fixes atmospheric N2 and accumulates mineral nutrients and organic substances that are beneficial to soils and subsequent crops.However,little is known about genotypic variation in,and molecular mechanisms of,Pi(phosphate)uptake and storage in A.sinicus.We recorded the morphological responses of six A.sinicus cultivars from four regions of China to external Pi application and measured their Pi accumulation.We identified full-length transcripts of Pi-signaling and Pi-homeostasis regulators by sequencing and measured the expression level of these genes by qRT-PCR.The major components in Pi signaling and Pi homeostasis were largely conserved between A.sinicus and the model species rice and Arabidopsis.Different A.sinicus varieties responded differently to low-phosphorus(P)stress,and their Pi accumulation was positively correlated with the expression of vacuolar Pi influx gene(SYG1/PHO81/XPR1-MAJOR FACILITATOR SUPERFAMILY(SPX-MFS)-TYPE PROTEIN)AsSPXMFS2 and negatively correlated with the expression of the vacuolar Pi efflux gene(VACUOLAR Pi EFFLUX TRANSPORTER)AsVPE1.We identified key Pi-signaling and Pihomeostasis regulators in A.sinicus.The expression of vacuolar Pi transporter genes could be used as an index to select A.sinicus accessions with high Pi accumulation.

Phosphorus lights up the trade-off between growth and immunity

How plants respond simultaneously to various biotic and abiotic stresses to balance growth and immunity is an old but vibrant topic.Plants need to effectively integrate multiple signaling inputs to make the final decision and,thus,use limited resources efficiently.Typically,plant secondary metabolites,including phytohormones,are the key to modulate investment of resources into immunity or growth.However,the molecular mechanisms underlying this allocation dilemma are far from being understood.

The origin and evolution of salicylic acid signaling and biosynthesis in plants

Salicylic acid(SA)plays a pivotal role in plant response to biotic and abiotic stress.Several core SA signaling regulators and key proteins in SA biosynthesis have been well characterized.However,much remains unknown about the origin,evolution,and early diversification of core elements in plant SA signaling and biosynthesis.In this study,we identified 10 core protein families in SA signaling and biosynthesis across green plant lineages.We found that the key SA signaling receptors,the nonexpresser of pathogenesis-related(NPR)proteins,originated in the most recent common ancestor(MRCA)of land plants and formed divergent groups in the ancestor of seed plants.However,key transcription factors for SA signaling,TGACG motif-binding proteins(TGAs),originated in the MRCA of streptophytes,arguing for the stepwise evolution of core SA signaling in plants.Different from the assembly of the core SA signaling pathway in the ancestor of seed plants,SA exists extensively in green plants,including chlorophytes and streptophyte algae.However,the full isochorismate synthase(ICS)-based SA synthesis pathway was first assembled in the MRCA of land plants.We further revealed that the ancient abnormal inflorescence meristem 1(AIM1)-basedβ-oxidation pathway is crucial for the biosynthesis of SA in chlorophyte algae,and this biosynthesis pathway may have facilitated the adaptation of early-diverging green algae to the high-light-intensity environment on land.Taken together,our findings provide significant insights into the early evolution and diversification of plant SA signaling and biosynthesis pathways,highlighting a crucial role of SA in stress tolerance during plant terrestrialization.

NIGT1 represses plant growth and mitigates phosphate starvation signaling to balance the growth response tradeoff in rice

Inorganic phosphate(Pi)availability is an important factor which affects the growth and yield of crops,thus an appropriate and effective response to Pi fluctuation is critical.However,how crops orchestrate Pi signaling and growth under Pi starvation conditions to optimize the growth defense tradeoff remains unclear.Here we show that a Pi starvationinduced transcription factor NIGT1(NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR 1)controls plant growth and prevents a hyper-response to Pi starvation by directly repressing the expression of growth-related and Pisignaling genes to achieve a balance between growth and response under a varying Pi environment.NIGT1 directly binds to the promoters of Pi starvation signaling marker genes,like IPS1,mi R827,and SPX2,under Pi-deficient conditions to mitigate the Pi-starvation responsive(PSR).It also directly represses the expression of vacuolar Pi efflux transporter genes VPE1/2 to regulate plant Pi homeostasis.We further demonstrate that NIGT1 constrains shoot growth by repressing the expression of growth-related regulatory genes,including brassinolide signal transduction master regulator BZR1,cell division regulator CYCB1;1,and DNA replication regulator PSF3.Our findings reveal the function of NIGT1 in orchestrating plant growth and Pi starvation signaling,and also provide evidence that NIGT1 acts as a safeguard to avoid hyper-response during Pi starvation stress in rice.

The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceaepolyploidizationandits distinct traits

Orychophragmus violaceus,referred to as‘‘eryuelan’’(February orchid)in China,is an early-flowering ornamental plant.The high oil content and abundance of unsaturated fatty acids in O.violaceus seeds make it a potential high-quality oilseed crop.Here,we generated a whole-genome assembly for O.violaceus using Nanopore and Hi-C sequencing technologies.The assembled genome of O.violaceus was~1.3 Gb in size,with 12 pairs of chromosomes.Through investigation of ancestral genome evolution,we determined that the genome of O.violaceus experienced a tetraploidization event from a diploid progenitor with the translocated proto-Calepineae karyotype.Comparisons between the reconstructed subgenomes of O.violaceus identified indicators of subgenome dominance,indicating that subgenomes likely originated via allotetraploidy.O.violaceus was phylogenetically close to the Brassica genus,and tetraploidy in O.violaceus occurred approximately 8.57 million years ago,close in time to the whole-genome triplication of Brassica that likely arose via an intermediate tetraploid lineage.However,the tetraploidization in Orychophragmus was independent of the hexaploidization in Brassica,as evidenced by the results from detailed phylogenetic analyses and comparisons of the break and fusion points of ancestral genomic blocks.Moreover,identification of multi-copy genes regulating the production of high-quality oil highlighted the contributions of both tetraploidization and tandem duplication to functional innovation in O.violaceus.These findings provide novel insights into the polyploidization evolution of plant species and will promote both functional genomic studies and domestication/breeding efforts in O.violaceus.

Two RING-Finger Ubiquitin E3 Ligases Regulate the Degradation of SPX4, An Internal Phosphate Sensor, for Phosphate Homeostasis and Signaling in Rice

SPX-domain-containing proteins (SPXs) play an important role in inorganic phosphate (Pi) sensing,signaling,and transport in eukaryotes.In plants,SPXs are known to integrate cellular Pi status and negatively regulate the activity of Pi central regulators,the PHOSPATE STARVATION RESPONSE proteins (PHRs).The stability of SPXs,such as SPX4,is reduced under Pi-deficient conditions.However,the mechanisms by which SPXs are degraded remain unclear.In this study,using a yeast-twhybrid screen we iden.tified two RING-finger ubiquitin E3 ligases regulating SPX4 degradation,designated SDEL1 and SDEL2,which were post-transcriptionally induced by Pi starvation.We found that both SDELs were located in the nucleus and cytoplasm,had ubiquitin E3 ligase activity,and directly ubiquitinated the K^213 and K^299 lysine residues in SPX4 to regulate its stability.Furthermore,we found that PHR2,a Pi central regulator in rice,could compete with SDELs by interacting with SPX4 under Pi-sufficient conditions,which protected SPX4 from ubiquitination and degradation.Consistent with the biochemical function of SDEL1 and SDEL2,overexpression of SDEL1 or SDEL2 resulted in Pi overaccumulation and induced Pi-starvation signaling even under Pi-sufficient conditions.Conversely,their loss-of-function mutants displayed decreased Pi accumulation and reduced Pi-starvation signaling.Collectively,our study revealed that SDEL1 and SDEL2 facilitate the degradation of SPX4 to modulate PHR2 activity and regulate Pi homeostasis and Pi signaling in response to external Pi availability in rice.

A reciprocal inhibitory module for Pi and iron signaling

Phosphorous(P)and iron(Fe),two essential nutrients for plant growth and development,are highly abundant elements in the earth's crust but often display low availability to plants.Due to the ability to form insoluble complexes,the antagonistic interaction between P and Fe nutrition in plants has been noticed for decades.However,the underlying molecular mechanism modulating the signaling and homeostasis between them re-mains obscure.Here,we show that the possible iron sensors HRZs,the iron deficiency-induced E3 ligases,could interact with the central regulator of phosphate(Pi)signaling,PHR2,and prompt its ubiquitination at lysine residues K319 and K328,leading to its degradation in rice.Consistent with this,the hrzs mutants dis-played a high Pi accumulation phenotype.Furthermore,we found that iron deficiency could attenuate Pi star-vation signaling by inducing the expression of HRZs,which in turn trigger PHR2 protein degradation.Inter-estingly,on the other hand,rice PHRs could negatively regulate the expression of HRZs to modulate iron deficiency responses.Therefore,PHR2 and HRZs form a reciprocal inhibitory module to coordinate Pi and iron signaling and homeostasis in rice.Taken together,our results uncover a molecular link between Pi and iron master regulators,which fine-tunes plant adaptation to Pi and iron availability in rice.

Strategies for improving fertilizer phosphorus use efficiency in Chinese cropping systems

A four-year project,entitled"The mechanisms of fraction transformation and high use efficiency of P fertilizer in Chinese cropping systems"commenced in 2017.The project was established to answer three key questions and looked at 17 cropping systems on ten soils.First,we asked what are the dynamics of transformation,fixation and mobilization of P fertilizers in soil-cropping systems?Second,what are the mechanisms of soil-cropmicrobe interactions by which P fertilizer can be efficiently used?Third,how to manipulate the processes of P use in cropping systems?The targets of this project are(1)to explore the mechanisms of P fixation,the pathways of loss of P availability and the threshold of migration of fertilizer P in the field;(2)to uncover mechanisms by which soil legacy P is mobilized through root physiological and morphological processes and through arbuscular mycorrhizal fungi and P-solubilizing bacteria in rhizosphere and hyphosphere;(3)to estimate the biological potential of crops for high efficiency P absorption and use;(4)to innovate new approaches for improving the efficiency of P fertilizers.The outcomes will provide theoretical support for setting standards for limitation of P fertilizer application rate in the main cropping zones of China.

OsCYCP4s coordinate phosphate starvation signaling with cell cycle progression in rice

Phosphate starvation leads to a strong reduction in shoot growth and yield in crops.The reduced shoot growth is caused by extensive gene expression reprogram-ming triggered by phosphate deficiency,which is not itself a direct consequence of low levels of shoot phosphorus.However,how phosphate starvation inhibits shoot growth in rice is still unclear.In this study,we determined the role of OsCYCP4s in the regulation of shoot growth in response to phosphate starvation in rice.We demonstrate that the ex-pression levels of OsCYCP4s,except OsCYCP4;3,were induced by phosphate starvation.Overexpression of the phosphate starvation induced OsCYCP4s could compete with the other cyclins for the binding with cyclin-dependent kinases,therefore suppressing growth by reducing cell proliferation.The phosphate starvation induced growth inhibition in the loss-of-function mutants cycp4;1,cycp4;2,and cycp4;4 is par-tially compromised.Furthermore,the expression of some phosphate starvation inducible genes is negatively modu-lated by these cyclins,which indicates that these OsCYCP4s may also be involved in phosphate starvation signaling.We conclude that phosphate starvation induced OsCYCP4s might coordinate phosphate starvation signaling and cell cycle progression under phosphate starvation stress.

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.

Unloading phosphate for starch synthesis in cereal grains

The macronutrient phosphorus(P)is essential for plant growth and of vital importance to crop yield.It is taken up from the soil in the form of inorganic orthophosphate[PO_(4)^(3-),HPO_(4)^(2-),H_(2)PO_(4)^(-)(Pi)]by plant roots.As Pi readily forms insoluble complexes and precipitates with organic matter and mineral cations,Pi bioavailability in the soil is usually low and often limits crop growth and final yield.