How to make the end of a gene,the simple way

Transcription termination of nearly all protein-coding genes in mammals requires 3’end processing by a multiprotein complex that will cleave and polyadenylate the messenger RNA precursor.Because a variety of enzyme complexes intervene,3’end processing was thought to be fundamentally complex and subject to a multitude of regulatory effects.The possibility to select just one out of several polyadenylation sites,in particular,has caused much questioning and speculation.What appear to be separate mechanisms however can be combined into a defined set of rules,allowing for a relatively simple interpretation of 3’end processing.Ultimately,readiness of the terminal exon splice site determines when a transcript reaches the maturity to select a nearby polyadenylation signal.Transcriptional pausing then acts in concert,extending the timeframe during which the transcription complex is close to polyadenylation sites.Since RNA polymerase pausing is governed by the same type of sequences in bacteria and metazoans,mammalian transcription termination resembles its prokaryote counterpart more than generally thought.

Prophylactic uses of integrin CD18-βA peptide in a murine polymicrobial peritonitis model

AIM:To evaluate the prophylactic properties of integrin CD18-βA peptide in a murine model of abdominal polymicrobial peritonitis and sepsis.METHODS:Bacterial sepsis was induced in Institute of Cancer Research(ICR) mice by cecal ligation and puncture(CLP) surgery.Inflicted mice were then injected with either sterile saline or CD18-βA peptide intraperitoneally at 2 h after surgery,and were sacrificed at 12 and 24 h after surgery.Blood samples were immediately collected,and analyzed for endotoxin activity and tumor necrosis factor(TNF)-α and interleukin(IL)-6.Lungs and liver were studied for CD45+ leukocyte and CD3 mRNA content.Pulmonary expression of intercellular adhesion molecule(ICAM)-1,vascular cell adhesion molecule(VCAM) and E-selectin was also determined.RESULTS:Intraperitoneal injection of CD18-βA peptide significantly suppressed circulating endotoxin activity(P<0.01) at 24 h,as well as serum levels of TNF-α(P<0.05 at 12 and 24 h) and IL-6(P<0.01 at 12 h,P<0.05 at 24 h) in CLP-inflicted mice.CD18-βA peptide also abrogated leukocyte infiltration into liver and lungs as unveiled by reduced CD45+ leukocyte and CD3 mRNA contents.Furthermore,the peptide significantly reduced pulmonary expression of VCAM(P<0.01 at 12 h,P<0.001 at 24 h),E-selectin(P<0.01 at 12 and 24 h),and ICAM-1(P<0.01 at 12 h,P<0.001 at 24 h).These actions of CD18-βA peptide collectively protected septic mice against lethality(P<0.01).CONCLUSION:CD18-βA peptide is a potent endotoxin antagonist that can protect surgical patients against sepsis-associated lethality.

The transcriptional regulator JAZ8 interacts with the C2 protein from geminiviruses and limits the geminiviral infection in Arabidopsis

Jasmonates(JAs) are phytohormones that finely regulate critical biological processes, including plant development and defense. JASMONATE ZIM-DOMAIN(JAZ) proteins are crucial transcriptional regulators that keep JA-responsive genes in a repressed state. In the presence of JA-Ile, JAZ repressors are ubiquitinated and targeted for degradation by the ubiquitin/proteasome system,allowing the activation of downstream transcription factors and, consequently, the induction of JA-responsive genes. A growing body of evidence has shown that JA signaling is crucial in defending against plant viruses and their insect vectors. Here, we describe the interaction of C2proteins from two tomato-infecting geminiviruses from the genus Begomovirus, tomato yellow leaf curl virus(TYLCV) and tomato yellow curl Sardinia virus(TYLCSaV), with the transcriptional repressor JAZ8 from Arabidopsis thaliana and its closest orthologue in tomato, SlJAZ9. Both JAZ and C2proteins colocalize in the nucleus, forming discrete nuclear speckles. Overexpression of JAZ8did not lead to altered responses to TYLCV infection in Arabidopsis;however, knock-down of JAZ8 favors geminiviral infection. Low levels of JAZ8 likely affect the viral infection specifically,since JAZ8-silenced plants neither display obvious developmental phenotypes nor present differences in their interaction with the viral insect vector. In summary, our results show that the geminivirus-encoded C2 interacts with JAZ8 in the nucleus, and suggest that this plant protein exerts an anti-geminiviral effect.

Chemotherapy induces cell plasticity;controlling plasticity increases therapeutic response

Dear Editor,One of the most serious issues in modern oncology is the ineffectiveness of treatments in destroying tumours,which leads to tumour recurrence and,ultimately,patient death.This phenomenon is caused by conventional therapies’fractional killing of tumour cells,which can also cause resistant cells to spread.1 We analysed chemotherapy-resistant cells and discovered that they are smaller than untreated cells(Fig.1a).The fact that this phenomenon occurs in all tested cell types(Hela,A549,Huh7,and MCF7)and regardless of the chemotherapy regimen(TRAIL,Camptothecin,Doxorubicin)suggests that it is a widespread phenomenon(Fig.1a,Supplementary Fig.S1).

Plant adaptation to low phosphorus availability:Core signaling,crosstalks,and applied implications

Phosphorus(P)is an essential nutrient for plant growth and reproduction.Plants preferentially absorb P as orthophosphate(Pi),an ion that displays low solubility and that is readily fixed in the soil,making P limita-tion a condition common to many soils and Pi fertilization an inefficient practice.To cope with Pi limitation,plants have evolved a series of developmental and physiological responses,collectively known as the Pi starvation rescue system(PSR),aimed to improve Pi acquisition and use efficiency(PUE)and protect from Pi-starvation-induced stress.Intensive research has been carried out during the last 20 years to un-ravel the mechanisms underlying the control of the PSR in plants.Here we review the results of this research effort that have led to the identification and characterization of several core Pi starvation signaling components,including sensors,transcription factors,microRNAs(miRNAs)and miRNA inhibitors,kinases,phosphatases,and components of the proteostasis machinery.We also refer to recent results revealing the existence of intricate signaling interplays between Pi and other nutrients and antagonists,N,Fe,Zn,and As,that have changed the initial single-nutrient-centric view to a more integrated view of nutrient homeostasis.Finally,we discuss advances toward improving PUE and future research priorities.

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.

The strigolactone receptor D14 targets SMAX1 for degradation in response to GR24 treatment and osmotic stress

The effects of the phytohormone strigolactone(SL)and smoke-derived karrikins(KARs)on plants are generally distinct,despite the fact that they are perceived through very similar mechanisms.The homologous receptors DWARF14(D14)and KARRIKIN-INSENSITIVE2(KAI2),together with the F-box protein MORE AXILLARY GROWTH2(MAX2),mediate SL and KAR responses,respectively,by targeting different SMAX1-LIKE(SMXL)family proteins for degradation.These mechanisms are putatively well-insulated,with D14-MAX2 targeting SMXL6,SMXL7,and SMXL8 and KAI2-MAX2 targeting SMAX1 and SMXL2 in Arabidopsis thaliana.Recent evidence challenges this model.We investigated whether D14 can target SMAX1 and whether this occurs naturally.Genetic analysis indicates that the SL analog GR24 promotes D14-SMAX1 crosstalk.Although D14 shows weaker interactions with SMAX1 than with SMXL2 or SMXL7,D14 mediates GR24-induced degradation of SMAX1 in plants.Osmotic stress triggers SMAX1 degradation,which is protective,through SL biosynthesis and signaling genes.Thus,D14-SMAX1 crosstalk may be beneficial and not simply a vestige of the evolution of the SL pathway.

Arsenite provides a selective signal that coordinates arsenate uptake and detoxification through the regulation of PHR1 stability in Arabidopsis

In nature,plants acquire nutrients from soils to sustain growth,and at the same time,they need to avoid the uptake of toxic compounds and/or possess tolerance systems to cope with them.This is particularly challenging when the toxic compound and the nutrient are chemically similar,as in the case of phosphate and arsenate.In this study,we demonstrated that regulatory elements of the phosphate starvation response(PSR)coordinate the arsenate detoxification machinery in the cell.We showed that arsenate repression of the phosphate transporter PHT1;1 is associated with the degradation of the PSR master regulator PHR1.Once arsenic is sequestered into the vacuole,PHR1 stability is restored and PHT1;1 expression is recovered.Furthermore,we identified an arsenite responsive SKP1-like protein and a PHR1 interactor F-box(PHIF1)as constituents of the SCF complex responsible for PHR1 degradation.We found that arsenite,the form to which arsenate is reduced for compartmentalization in vacuoles,represses PHT1;1 expression,providing a highly selective signal versus phosphate to control PHT1;1 expression in response to arsenate.Collectively,our results provide molecular insights into a sensing mechanism that regulates arsenate/phosphate uptake depending on the plant’s detoxification capacity.

DET1-mediated COP1 regulation avoids HY5 activity over second-site gene targets to tune plant photomorphogenesis

DE-ETIOLATED 1(DET1)and CONSTITUTIVE PHOTOMORPHOGENESIS 1(COP1)are two essential repressors of Arabidopsis photomorphogenesis.These proteins can associate with CULLIN4 to form independent CRL4-based E3 ubiquitin ligases that mediate the degradation of several photomorphogenic transcription factors,including ELONGATED HYPOCOTYL 5(HY5),thereby controlling multiple gene-regulatory networks.Despite extensive biochemical and genetic analyses of their multi-subunit complexes,the functional links between DET1 and COP1 have long remained elusive.Here,we report that DET1 associates with COP1 in vivo,enhances COP1-HY5 interaction,and promotes COP1 destabilization in a process that dampens HY5 protein abundance.By regulating its accumulation,DET1 avoids HY5 association with hundreds of second-site genomic loci,which are also frequently targeted by the skotomorphogenic transcription factor PHYTOCHROME-INTERACTING FACTOR 3.Accordingly,ectopic HY5 chromatin enrichment favors local gene repression and can trigger fusca-like phenotypes.This study therefore shows that DET1-mediated regulation of COP1 stability tunes down the HY5 cistrome,avoiding hyper-photomorphogenic responses that might compromise plant viability.

Regulation of floral senescence in Arabidopsis by coordinated action of CONSTANS and jasmonate signaling

In Arabidopsis,photoperiodic flowering is controlled by the regulatory hub gene CONSTANS(CO),whereas floral organ senescence is regulated by the jasmonates(JAs).Because these processes are chronologically ordered,it remains unknown whether there are common regulators of both processes.In this study,we discovered that CO protein accumulates in Arabidopsis flowers after floral induction,and it displays a diurnal pattern in floral organs different from that in the leaves.We observed that altered CO expression could affect flower senescence and abscission by interfering with JA response,as shown by petal-specific transcriptomic analysis as well as CO overexpression in JA synthesis and signaling mutants.We found that CO has a ZIM(ZINC-FINGER INFLORESCENCE MERISTEM)like domain that mediates its interaction with the JA response repressor JAZ3(jasmonate ZIM-domain 3).Their interaction inhibits the repressor activity of JAZ3,resulting in activation of downstream transcription factors involved in promoting flower senescence.Furthermore,we showed that CO,JAZ3,and the E3 ubiquitin ligase COI1(Coronatine Insensitive 1)could form a protein complex in planta,which promotes the degradation of both CO and JAZ3 in the presence of JAs.Taken together,our results indicate that CO,a key regulator of photoperiodic flowering,is also involved in promoting flower senescence and abscission by augmenting JA signaling and response.We propose that coordinated recruitment of photoperiodic and JA signaling pathways could be an efficient way for plants to chronologically order floral processes and ensure the success of offspring production.

Roles of Ubiquitination in the Control of Phosphate Starvation Responses in Plants

Throughout evolution, plants have evolved sophisticated adaptive responses that allow them to grow with a limited supply of phos-phate, the preferential form in which the essential macronutrient phosphorus is absorbed by plants. Most of these responses are aimed to increase phosphate availability and acquisition through the roots, to optimize its usage in metabolic processes, and to protect plants from the deleterious effects of phosphate deficiency stress. Regulation of these adaptive responses requires fine percep- tion of the external and internal phosphate levels, and a complex signal transduction pathway that integrates information on the phosphate status at the whole-plant scale. The molecular mecha-nisms that participate in phosphate homeostasis include transcriptional control of gene expression, RNA silencing mediated by microRNAs, regulatory non-coding RNAs of miRNA activity, phosphate transporter trafficking, and post-translational modification of proteins, such as phosphorylation, sumoylation and ubiquitination. Such a varied regulatory repertoire reflects the complexity intrinsic to phosphate surveying and signaling pathways. Here, we describe these regulatory mechanisms, emphasizing the increasing importance of ubiquitination in the control of phosphate starvation responses.

Abscisic Acid Connects Phytohormone Signaling with RNA Metabolic Pathways and Promotes an Antiviral Response that Is Evaded by a Self- Controlled RNA Virus

A complex network of cellular receptors,RNA targeting pathways,and small-molecule signaling provides robust plant immunity and tolerance to viruses.To maximize their fitness,viruses must evolve control mechanisms to balance host immune evasion and plant-damaging effects.The genus Potyvirus comprises plant viruses characterized by RNA genomes that encode large polyproteins led by the P1 protease.A P1 autoinhibitory domain controls polyprotein processing,the release of a downstream functional RNAsilencing suppressor,and viral replication.Here,we show that P1Pro,a plum pox virus clone that lacks the P1 autoinhibitory domain,triggers complex reprogramming of the host transcriptome and high levels of abscisic acid(ABA)accumulation.A meta-analysis highlighted ABA connections with host pathways known to control RNA stability,turnover,maturation,and translation.Transcriptomic changes triggered by P1Pro infection or ABA showed similarities in host RNA abundance and diversity.Genetic and hormone treatment assays showed that ABA promotes plant resistance to potyviral infection.Finally,quantitative mathematical modeling of viral replication in the presence of defense pathways supported self-control of polyprotein processing kinetics as a viral mechanism that attenuates the magnitude of the host antiviral response.Overall,our findings indicate that ABA is an active player in plant antiviral immunity,which is nonetheless evaded by a self-controlled RNA virus.

Reversible acetylation fine-tunes plant hormone signaling and immunity

Plant pests and diseases threaten food security by causing over 10%loss of global crops yield.Plant immunity relies on a complex hormonal signaling network in which jasmonates(JAs)play a central role.JAs are fatty acid–derived hormones ubiquitous in the plant kingdom similar to animal prostaglandins,and are essential phytohormones regulating development,environmental adaptation and defense against necrotrophic pathogens and insects in plants.

p38γand p38δas biomarkers in the interplay of colon cancer and inflammatory bowel diseases

Dear Editor,Colorectal cancer(CRC)is the second leading cause of cancer death according to the World Health Organization.Patients with inflammatory bowel disease(IBD),ulcerative colitis(UC)or Crohn’s disease(CD)are at increased risk of developing colitis-associated CRC(CAC)[1];however,our understanding of the inflammationcancer interplay at the molecular level is still limited.

SARS-CoV-2 interaction with Siglec-1 mediates trans-infection by dendritic cells

Antigen-presenting cells(APCs)may be resistant to SARS-CoV-2 infection but still contribute to viral pathogenesis.Lectins such as sialic acid-binding Ig-like lectin 1(Siglec-1/CD169)mediate the attachment of viruses to APCs.Here,we show that APCs effectively capture SARS-CoV-2 within compartments via recognition of Siglec-1.This receptor interacts with sialylated gangliosides on membranes of SARS-CoV-2 variants.

Propagation of Recombinant Genes through Complex Microbiomes with Synthetic Mini-RP4 Plasmid Vectors

The promiscuous conjugation machinery of the Gram-negative plasmid RP4 has been reassembled in a minimized, highlytransmissible vector for propagating genetically encoded traits through diverse types of naturally occurring microbialcommunities. To this end, the whole of the RP4-encoded transfer determinants (tra, mob genes, and origin of transfer oriT)was excised from their natural context, minimized, and recreated in the form of a streamlined DNA segment borne by anautoselective replicon. The resulting constructs (the pMATING series) could be self-transferred through a variety ofprokaryotic and eukaryotic recipients employing such a rationally designed conjugal delivery device. Insertion of GFP reporterinto pMATING exposed the value of this genetic tool for delivering heterologous genes to both specific mating partners andcomplex consortia (e.g., plant/soil rhizosphere). The results accredited the effective and functional transfer of the recombinantplasmids to a diversity of hosts. Yet the inspection of factors that limit interspecies DNA transfer in such scenarios uncoveredtype VI secretion systems as one of the factual barriers that check otherwise high conjugal frequencies of tested RP4derivatives. We argue that the hereby presented programming of hyperpromiscuous gene transfer can become a phenomenalasset for the propagation of beneficial traits through various scales of the environmental microbiome.