Identification, biogenesis, function, and mechanism of action of circular RNAs in plants

CircularRNAs(circRNAs)are a class of single-stranded,closedRNAmolecules with unique functions that are ubiquitously expressed in all eukaryotes.The biogenesis of circRNAs is regulated by specific cis-acting elements and trans-acting factors in humans and animals.circRNAs mainly exert their biological functions by acting as microRNA sponges,forming R-loops,interacting with RNA-binding proteins,or being translated into polypeptides or proteins in human and animal cells.Genome-wide identification of circRNAs has been performedin multiple plant species,and the results suggest that circRNAs are abundant and ubiquitously expressed in plants.There is emerging compelling evidence to suggest that circRNAs play essential roles during plant growthanddevelopment as well as inthe responses to bioticandabiotic stress.However,compared with recent advances in human and animal systems,the roles of most circRNAs in plants are unclear at present.Here we review the identification,biogenesis,function,and mechanism of action of plant circRNAs,which will provide a fundamental understanding of the characteristics and complexity of circRNAs in plants.

Gγ subunit AT1/GS3-the“code”of alkaline tolerance in main graminaceous crops

This brief article highlights the results of Zhang et al.(Science 379,eade8416,2023),who recently found that the Gγ subunit AT1/GS3 contributes to alkaline tolerance in several main monocots crops,and revealed the molecular mechanism of AT1/GS3-mediated response to alkaline stress in plants,which involves regulating H_(2)O_(2) levels by inhibiting the phosphorylation of aquaporin PIP2s.

Ca^(2+)-dependent successive phosphorylation of vacuolar transporter MTP8 by CBL2/3-CIPK3/9/26 and CPK5 is critical for manganese homeostasis in Arabidopsis

Manganese(Mn)is an essential micronutrient for all living organisms.However,excess Mn supply that can occur in acid or waterlogged soils has toxic effects on plant physiology and development.Although a variety of Mn transporter families have been characterized,we have only a rudimentary understanding of how these transporters are regulated to uphold and adjust Mn homeostasis in plants.Here,we demonstrate that two calcineurin-B-like proteins,CBL2/3,and their interacting kinases,CIPK3/9/26,are key regulators of plant Mn homeostasis.Arabidopsis mutants lacking CBL2 and 3 or their interacting protein kinases CIPK3/9/26 exhibit remarkably high Mn tolerance.Intriguingly,CIPK3/9/26 interact with and phosphorylate the tonoplast-localized Mn and iron(Fe)transporter MTP8 primarily at Ser35,which is conserved among MTP8 proteins from various species.Mn transport complementation assays in yeast combined with multiple physiological assays indicate that CBL-CIPK-mediated phosphorylation of MTP8 negatively regulates its transport activity from the cytoplasm to the vacuole.Moreover,we show that sequential phosphorylation of MTP8,initially at Ser31/32 by the calcium-dependent protein kinase CPK5 and subsequently at Ser35 by CIPK26,provides an activation/deactivation fine-tuning mechanism for differential regulation of Mn transport.Collectively,our findings define a two-tiered calcium-controlled mechanism for dynamic regulation of Mn homeostasis under conditions of fluctuating Mn supply.

Deciphering the regulatory code of histone modifications in plants

Eukaryotic genomes are compacted into histone-wrapped chromatin,which provides an opportunity to fine-tune the gene expression by dynamically impeding or reinforcing the accessibility of the genome to the transcription factors(TFs)and cofactors.The modification of histones is one of the various mechanisms to regulate DNA exposure by altering the physical properties of nucleosomes(Klemm et al.,2019).In plants,histone modifications play a critical role in establishing the cell identity and responding to environmental cues,including responses to temperature,alterations of flowering time(Liu et al.,2010;He et al.,2021).

Calcium-dependent protein kinases CPK21 and CPK23 phosphorylate and activate the iron-regulated transporter IRT1 to regulate iron deficiency in Arabidopsis

Iron(Fe)is an essential micronutrient for all organisms.Fe availability in the soil is usually much lower than that required for plant growth,and Fe deficiencies seriously restrict crop growth and yield.Calcium(Ca2+)is a second messenger in all eukaryotes;however,it remains largely unknown how Ca2+regulates Fe deficiency.In this study,mutations in CPK21 and CPK23,which are two highly homologous calcium-dependent protein kinases,conferredimpaired growth and rootdevelopment under Fe-deficient conditions,whereas constitutively active CPK21 and CPK23 enhanced plant tolerance to Fe-deficient conditions.Furthermore,we found that CPK21 and CPK23 interacted with and phosphorylated the Fe transporter IRONREGULATED TRANSPORTER1(IRT1)at the Ser149 residue.Biochemical analyses and complementation of Fe transport in yeast and plants indicated that IRT1 Ser149 is critical for IRT1 transport activity.Taken together,these findings suggest that the CPK21/23-IRT1 signaling pathway is critical for Fe homeostasis in plants and provides targets for improving Fe-deficient environments and breeding crops resistant to Fe-deficient conditions.

Balanced nitrogen–iron sufficiency boosts grain yield and nitrogen use efficiency by promoting tillering

Crop yield plays a critical role in global food security.For optimal plant growth and maximal crop yields,nutrients must be balanced.However,the potential significance of balanced nitrogen-iron(N-Fe)for improving crop yield and nitrogen use efficiency(NUE)has not previously been addressed.Here,we show that balanced N-Fe sufficiency significantly increases tiller number and boosts yield and NUE in rice and wheat.NIN-like protein 4(OsNLP4)plays a pivotal role in maintaining the N-Fe balance by coordinately regulating the expression of multiple genes involved in N and Fe metabolism and signaling.OsNLP4 also suppresses OsD3 expression and strigolactone(SL)signaling,thereby promoting tillering.Balanced N-Fe sufficiency promotes the nuclear localization of OsNLP4 by reducing H_(2)O_(2) levels,reinforcing the functions of OsNLP4.Interestingly,we found that OsNLP4 upregulates the expression of a set of H2O2-scavenging genes to promote its own accumulation in the nucleus.Furthermore,we demonstrated that foliar spraying of balanced N-Fe fertilizer at the tillering stage can effectively increase tiller number,yield,and NUE of both rice and wheat in the field.Collectively,these findings reveal the previously unrecognized effects of N-Fe balance on grain yield and NUE as well as the molecular mechanism by which the OsNLP4-OsD3 module integrates N-Fe nutrient signals to downregulate SL signaling and thereby promote rice tillering.Our study sheds light on how N-Fe nutrient signals modulate rice tillering and provide potential innovative approaches that improve crop yield with reduced N fertilizer input for benefitting sustainable agriculture worldwide.

Four plasma membrane-localized MGR transporters mediate xylem Mg^(2+)loading for root-to-shoot Mg^(2+)translocation in Arabidopsis

Magnesium(Mg^(2+)),an essential structural component of chlorophyll,is absorbed from the soil by roots and transported to shoots to support photosynthesis in plants.However,the molecular mechanisms underlying root-to-shoot Mg^(2+)translocation remain largely unknown.We describe here the identification of four plasma membrane(PM)-localized transporters,named Mg^(2+)release transporters(MGRs),that are critical for root-to-shoot Mg transport in Arabidopsis.Functional complementation assays in a Mg^(2+)-uptake-defi-cient bacterial strain confirmed that these MGRs conduct Mg^(2+)transport.PM-localized MGRs(MGR4,MGR5,MGR6,and MGR7)were expressed primarily in root stellar cells and participated in the xylem loading step of the long-distance Mg^(2+)transport process.In particular,MGR4 and MGR6 played a major role in shoot Mg homeostasis,as their loss-of-function mutants were hypersensitive to low Mg^(2+)but tolerant to high Mg^(2+)conditions.Reciprocal grafting analysis further demonstrated that MGR4 functions in the root to determine shoot Mg^(2+)accumulation and physiological phenotypes caused by both low-and high-Mg^(2+)stress.Taken together,our study has identified the long-sought transporters responsible for root-to-shoot Mg^(2+)translocation in plants.

A SPX domain vacuolar transporter links phosphate sensing to homeostasis in Arabidopsis

Excess phosphate(Pi)is stored into the vacuole through Pi transporters so that cytoplasmic Pi levels remain stable in plant cells.We hypothesized that the vacuolar Pi transporters may harbor a Pi-sensing mechanism so that they are activated to deliver Pi into the vacuole only when cytosolic Pi reaches a threshold high level.We tested this hypothesis using Vacuolar Phosphate Transporter 1(VPT1),a SPX domain-containing vacuolar Pi transporter,as a model.Recent studies have defined SPX as a Pi-sensing module that binds inositol polyphosphate signaling molecules(InsPs)produced at high cellular Pi status.We showed here that Pi-deficient conditions or mutation of the SPX domain severely impaired the transport activity of VPT1.We further identified an auto-inhibitory domain in VPT1 that suppresses its transport activity.Taking together the results from detailed structure-function analyses,our study suggests that VPT1 is in the auto-inhibitory state when Pi status is low,whereas at high cellular Pi status InsPs are produced and bind SPX domain to switch on VPT1 activity to deliver Pi into the vacuole.This thus provides an auto-regulatory mechanism for VPT1-mediated Pi sensing and homeostasis in plant cells.